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Background

Childhood acute lymphoblastic leukemia (ALL) is the most common cancer in children, and can now be cured in approximately 80% of patients. Nevertheless, drug resistance is the major cause of treatment failure in children with ALL. The drug methotrexate (MTX), which is widely used to treat many human cancers, is used in essentially all treatment protocols worldwide for newly diagnosed ALL. Although MTX has been extensively studied for many years, relatively little is known about mechanisms of de novo resistance in primary cancer cells, including leukemia cells. This lack of knowledge is due in part to the fact that existing in vitro methods are not sufficiently reliable to permit assessment of MTX resistance in primary ALL cells. Therefore, we measured the in vivo antileukemic effects of MTX and identified genes whose expression differed significantly in patients with a good versus poor response to MTX.

Methods and Findings

We utilized measures of decreased circulating leukemia cells of 293 newly diagnosed children after initial “up-front” in vivo MTX treatment (1 g/m2) to elucidate interpatient differences in the antileukemic effects of MTX. To identify genomic determinants of these effects, we performed a genome-wide assessment of gene expression in primary ALL cells from 161 of these newly diagnosed children (1–18 y). We identified 48 genes and two cDNA clones whose expression was significantly related to the reduction of circulating leukemia cells after initial in vivo treatment with MTX. This finding was validated in an independent cohort of children with ALL. Furthermore, this measure of initial MTX in vivo response and the associated gene expression pattern were predictive of long-term disease-free survival (p < 0.001, p = 0.02).

Conclusions

Together, these data provide new insights into the genomic basis of MTX resistance and interpatient differences in MTX response, pointing to new strategies to overcome MTX resistance in childhood ALL.Trial registrations: Total XV, Therapy for Newly Diagnosed Patients With Acute Lymphoblastic Leukemia, http://www.ClinicalTrials.gov (NCT00137111); Total XIIIBH, Phase III Randomized Study of Antimetabolite-Based Induction plus High-Dose MTX Consolidation for Newly Diagnosed Pediatric Acute Lymphocytic Leukemia at Intermediate or High Risk of Treatment Failure (NCI-T93-0101D); Total XIIIBL, Phase III Randomized Study of Antimetabolite-Based Induction plus High-Dose MTX Consolidation for Newly Diagnosed Pediatric Acute Lymphocytic Leukemia at Lower Risk of Treatment Failure (NCI-T93-0103D).  相似文献   

3.
Background to the debate: Several studies have found disparities in the outcome of medical procedures across different hospitals—better outcomes have been associated with higher procedure volume. An Institute of Medicine workshop found such a “volume–outcome relationship” for two types of cancer surgery: resection of the pancreas and esophagus (http://www.iom.edu/?id=31508). This debate examines whether physicians have an ethical obligation to inform patients of hospital outcome disparities for these cancers.  相似文献   

4.
The introduction of affordable, consumer-oriented 3-D printers is a milestone in the current “maker movement,” which has been heralded as the next industrial revolution. Combined with free and open sharing of detailed design blueprints and accessible development tools, rapid prototypes of complex products can now be assembled in one’s own garage—a game-changer reminiscent of the early days of personal computing. At the same time, 3-D printing has also allowed the scientific and engineering community to build the “little things” that help a lab get up and running much faster and easier than ever before.Applications of 3-D printing technologies (Fig. 1A, Box 1) have become as diverse as the types of materials that can be used for printing. Replacement parts at the International Space Station may be printed in orbit from durable plastics or metals, while back on Earth the food industry is starting to explore the same basic technology to fold strings of chocolate into custom-shaped confectionary. Also, consumer-oriented laser-cutting technology makes it very easy to cut raw materials such as sheets of plywood, acrylic, or aluminum into complex shapes within seconds. The range of possibilities comes to light when those mechanical parts are combined with off-the-shelf electronics, low-cost microcontrollers like Arduino boards [1], and single-board computers such as a Beagleboard [2] or a Raspberry Pi [3]. After an initial investment of typically less than a thousand dollars (e.g., to set-up a 3-D printer), the only other materials needed to build virtually anything include a few hundred grams of plastic (approximately US$30/kg), cables, and basic electronic components [4,5].Open in a separate windowFig 1Examples of open 3-D printed laboratory tools. A 1, Components for laboratory tools, such as the base for a micromanipulator [18] shown here, can be rapidly prototyped using 3-D printing. A 2, The printed parts can be easily combined with an off-the-shelf continuous rotation servo-motor (bottom) to motorize the main axis. B 1, A 3-D printable micropipette [8], designed in OpenSCAD [19], shown in full (left) and cross-section (right). B 2, The pipette consists of the printed parts (blue), two biro fillings with the spring, an off-the-shelf piece of tubing to fit the tip, and one screw used as a spacer. B 3, Assembly is complete with a laboratory glove or balloon spanned between the two main printed parts and sealed with tape to create an airtight bottom chamber continuous with the pipette tip. Accuracy is ±2–10 μl depending on printer precision, and total capacity of the system is easily adjusted using two variables listed in the source code, or accessed via the “Customizer” plugin on the thingiverse link [8]. See also the first table.

Box 1. Glossary

Open source

A collective license that defines terms of free availability and redistribution of published source material. Terms include free and unrestricted distribution, as well as full access to source code/blueprints/circuit board designs and derived works. For details, see http://opensource.org.

Maker movement

Technology-oriented extension of the traditional “Do-it-Yourself (DIY)” movement, typically denoting specific pursuits in electronics, CNC (computer numerical control) tools such as mills and laser cutters, as well as 3-D printing and related technologies.

3-D printing

Technology to generate three-dimensional objects from raw materials based on computer models. Most consumer-oriented 3-D printers print in plastic by locally melting a strand of raw material at the tip (“hot-end”) and “drawing” a 3-D object in layers. Plastic materials include Acrylnitrile butadiene styrene (ABS) and Polylactic acid (PLA). Many variations of 3-D printers exist, including those based on laser-polymerization or fusion of resins or powdered raw materials (e.g., metal or ceramic printers).

Arduino boards

Inexpensive and consumer-oriented microcontroller boards built around simple processors. These boards offer a variety of interfaces (serial ports, I2C and CAN bus, etc.), μs-timers, and multiple general-purpose input-output (GPIO) pins suitable for running simple, time-precise programs to control custom-built electronics.

Single board computers

Inexpensive single-board computers capable of running a mature operating system with graphical-user interface, such as Linux. Like microcontroller boards, they offer a variety of hardware interfaces and GPIO pins to control custom-built electronics.It therefore comes as no surprise that these technologies are also routinely used by research scientists and, especially, educators aiming to customize existing lab equipment or even build sophisticated lab equipment from scratch for a mere fraction of what commercial alternatives cost [6]. Designs for such “Open Labware” include simple mechanical adaptors [7], micropipettes (Fig. 1B) [8], and an egg-whisk–based centrifuge [9] as well as more sophisticated equipment such as an extracellular amplifier for neurophysiological experiments [10], a thermocycler for PCR [11], or a two-photon microscope [12]. At the same time, conceptually related approaches are also being pursued in chemistry [1315] and material sciences [16,17]. See also
AreaProjectSource
MicroscopySmartphone Microscope http://www.instructables.com/id/10-Smartphone-to-digital-microscope-conversion
iPad Microscope http://www.thingiverse.com/thing:31632
Raspberry Pi Microscope http://www.thingiverse.com/thing:385308
Foldscope http://www.foldscope.com/
Molecular BiologyThermocycler (PCR) http://openpcr.org/
Water bath http://blog.labfab.cc/?p=47
Centrifuge http://www.thingiverse.com/thing:151406
Dremelfuge http://www.thingiverse.com/thing:1483
Colorometer http://www.thingiverse.com/thing:73910
Micropipette http://www.thingiverse.com/thing:255519
Gel Comb http://www.thingiverse.com/thing:352873
Hot Plate http://www.instructables.com/id/Programmable-Temperature-Controller-Hot-Plate/
Magnetic Stirrer http://www.instructables.com/id/How-to-Build-a-Magnetic-Stirrer/
ElectrophysiologyWaveform Generator http://www.instructables.com/id/Arduino-Waveform-Generator/
Open EEG https://www.olimex.com/Products/EEG/OpenEEG/
Mobile ECG http://mobilecg.hu/
Extracellular amplifier https://backyardbrains.com/products/spikerBox
Micromanipulator http://www.thingiverse.com/thing:239105
Open Ephys http://open-ephys.org/
OtherSyringe pump http://www.thingiverse.com/thing:210756
Translational Stage http://www.thingiverse.com/thing:144838
Vacuum pump http://www.instructables.com/id/The-simplest-vacuum-pump-in-the-world/
Skinner Box http://www.kscottz.com/open-skinner-box-pycon-2014/
Open in a separate windowSee also S1 Data.  相似文献   

5.
Sequence Maneuverer: tool for sequence extraction from genomes     
Tayyaba Yasmin  Inayat Ur Rehman  Adnan Ahmad Ansari  Khurrum liaqat  Muhammad Irfan khan 《Bioinformation》2012,8(25):1277-1279
The availability of genomic sequences of many organisms has opened new challenges in many aspects particularly in terms of genome analysis. Sequence extraction is a vital step and many tools have been developed to solve this issue. These tools are available publically but have limitations with reference to the sequence extraction, length of the sequence to be extracted, organism specificity and lack of user friendly interface. We have developed a java based software package having three modules which can be used independently or sequentially. The tool efficiently extracts sequences from large datasets with few simple steps. It can efficiently extract multiple sequences of any desired length from a genome of any organism. The results are crosschecked by published data.

Availability

URL 1: http://ww3.comsats.edu.pk/bio/ResearchProjects.aspxURL 2: http://ww3.comsats.edu.pk/bio/SequenceManeuverer.aspx  相似文献   

6.
Dexamethasone and long-term outcome of tuberculous meningitis in Vietnamese adults and adolescents     
Török ME  Nguyen DB  Tran TH  Nguyen TB  Thwaites GE  Hoang TQ  Nguyen HD  Tran TH  Nguyen TC  Hoang HT  Wolbers M  Farrar JJ 《PloS one》2011,6(12):e27821

Background

Dexamethasone has been shown to reduce mortality in patients with tuberculous meningitis but the long-term outcome of the disease is unknown.

Methods

Vietnamese adults and adolescents with tuberculous meningitis recruited to a randomised, double-blind, placebo-controlled trial of adjunctive dexamethasone were followed-up at five years, to determine the effect of dexamethasone on long-term survival and neurological disability.

Results

545 patients were randomised to receive either dexamethasone (274 patients) or placebo (271 patients). 50 patients (9.2%) were lost to follow-up at five years. In all patients two-year survival, probabilities tended to be higher in the dexamethasone arm (0.63 versus 0.55; p = 0.07) but five-year survival rates were similar (0.54 versus 0.51, p = 0.51) in both groups. In patients with grade 1 TBM, but not with grade 2 or grade 3 TBM, the benefit of dexamethasone treatment tended to persist over time (five-year survival probabilities 0.69 versus 0.55, p = 0.07) but there was no conclusive evidence of treatment effect heterogeneity by TBM grade (p = 0.36). The dexamethasone group had a similar proportion of severely disabled patients among survivors at five years as the placebo group (17/128, 13.2% vs. 17/116, 14.7%) and there was no significant association between dexamethasone treatment and disability status at five years (p = 0.32).

Conclusions

Adjunctive dexamethasone appears to improve the probability of survival in patients with TBM, until at least two years of follow-up. We could not demonstrate a five-year survival benefit of dexamethasone treatment which may be confined to patients with grade 1 TBM.

Trial Registration

ClinicalTrials.gov NCT01317654 NCT01317654?term = tuberculous+meningitis&rank = 3  相似文献   

7.
Safety of postoperative administration of human urinary trypsin inhibitor in lung cancer patients with idiopathic pulmonary fibrosis     
Yamauchi Y  Izumi Y  Inoue M  Sugiura H  Goto T  Anraku M  Ohtsuka T  Kohno M  Soejima K  Nomori H 《PloS one》2011,6(12):e29053

Background

Patients with idiopathic pulmonary fibrosis (IPF) undergoing pulmonary resection for lung cancer carry risks of acute exacerbations of IPF (AE) postoperatively. Currently, agents which may attenuate AE are actively sought. Urinary trypsin inhibitor, ulinastatin, is a synthetic glycoprotein which may potentially inhibit various inflammatory factors associated with the development and progression of IPF. The present study was done to evaluate the effects of administration of high dose ulinastatin in lung cancer patients with IPF immediately following lung resection.

Methods

Patients with IPFs radiologically diagnosed on high resolution CT, and histologically diagnosed resectable lung cancers, were eligible for the study. The effects of escalating doses of ulinastatin 3×105, 6×105, and 9×105 units/body/day, administered postoperatively for 3 days were evaluated. The endpoints were safety and feasibility.

Results

Nine patients were evaluated, in cohorts of 3 patients per dosage. Postoperative follow up ranged from 3 to 12 months (median 9 months). The postoperative courses were uneventful in all patients. No subjective adverse events such as abdominal symptoms or skin rashes, or objective adverse events as per serum laboratory tests, such as liver or kidney dysfunctions potentially attributable to ulinastatin administration were observed. AE was seen in one patient at 3 months after surgery, but since this occurred shortly after administration of chemotherapy, it was considered to be attributable to the chemotherapy rather than surgery.

Discussion

Ulinastatin administration after lung resection in lung cancer patients with IPF was considered to be safe and feasible. Further study is planned at the highest dose of this study to evaluate efficacy.

Trial Registration

UMIN.ac.jp/ctr/UMIN000002410   相似文献   

8.
Sodium stibogluconate (SSG) & paromomycin combination compared to SSG for visceral leishmaniasis in East Africa: a randomised controlled trial     
Musa A  Khalil E  Hailu A  Olobo J  Balasegaram M  Omollo R  Edwards T  Rashid J  Mbui J  Musa B  Abuzaid AA  Ahmed O  Fadlalla A  El-Hassan A  Mueller M  Mucee G  Njoroge S  Manduku V  Mutuma G  Apadet L  Lodenyo H  Mutea D  Kirigi G  Yifru S  Mengistu G  Hurissa Z  Hailu W  Weldegebreal T  Tafes H  Mekonnen Y  Makonnen E  Ndegwa S  Sagaki P  Kimutai R  Kesusu J  Owiti R  Ellis S  Wasunna M 《PLoS neglected tropical diseases》2012,6(6):e1674

Background

Alternative treatments for visceral leishmaniasis (VL) are required in East Africa. Paromomycin sulphate (PM) has been shown to be efficacious for VL treatment in India.

Methods

A multi-centre randomized-controlled trial (RCT) to compare efficacy and safety of PM (20 mg/kg/day for 21 days) and PM plus sodium stibogluconate (SSG) combination (PM, 15 mg/kg/day and SSG, 20 mg/kg/day for 17 days) with SSG (20 mg/kg/day for 30 days) for treatment of VL in East Africa. Patients aged 4–60 years with parasitologically confirmed VL were enrolled, excluding patients with contraindications. Primary and secondary efficacy outcomes were parasite clearance at 6-months follow-up and end of treatment, respectively. Safety was assessed mainly using adverse event (AE) data.

Findings

The PM versus SSG comparison enrolled 205 patients per arm with primary efficacy data available for 198 and 200 patients respectively. The SSG & PM versus SSG comparison enrolled 381 and 386 patients per arm respectively, with primary efficacy data available for 359 patients per arm. In Intention-to-Treat complete-case analyses, the efficacy of PM was significantly lower than SSG (84.3% versus 94.1%, difference = 9.7%, 95% confidence interval, CI: 3.6 to 15.7%, p = 0.002). The efficacy of SSG & PM was comparable to SSG (91.4% versus 93.9%, difference = 2.5%, 95% CI: −1.3 to 6.3%, p = 0.198). End of treatment efficacy results were very similar. There were no apparent differences in the safety profile of the three treatment regimens.

Conclusion

The 17 day SSG & PM combination treatment had a good safety profile and was similar in efficacy to the standard 30 day SSG treatment, suggesting suitability for VL treatment in East Africa.

Clinical Trials Registration

www.clinicaltrials.gov NCT00255567  相似文献   

9.
Nurse-Led,Telephone-Based,Secondary Preventive Follow-Up after Stroke or Transient Ischemic Attack Improves Blood Pressure and LDL Cholesterol: Results from the First 12 Months of the Randomized,Controlled NAILED Stroke Risk Factor Trial     
Anna-Lotta Irewall  Joachim ?gren  Lisa Bergstr?m  Katarina Laurell  Lars S?derstr?m  Thomas Mooe 《PloS one》2015,10(10)

Background

Enhanced secondary preventive follow-up after stroke or transient ischemic attack (TIA) is necessary for improved adherence to recommendations regarding blood pressure (BP) and low-density lipoprotein cholesterol (LDL-C) levels. We investigated whether nurse-led, telephone-based follow-up was more efficient than usual care at improving BP and LDL-C levels at 12 months after hospital discharge.

Methods

We randomized 537 patients to either nurse-led, telephone-based follow-up (intervention) or usual care (control). BP and LDL-C measurements were performed at 1 month (baseline) and 12 months post-discharge. Intervention group patients who did not meet target values at baseline received additional follow-up, including titration of medication and lifestyle counselling, to reach treatment goals (BP < 140/90 mmHg, LDL-C < 2.5 mmol/L).

Results

At 12 months, mean systolic BP, diastolic BP and LDL-C was 3.3 (95% CI 0.3 to 6.3) mmHg, 2.3 mmHg (95% CI 0.5 to 4.2) and 0.3 mmol/L (95% CI 0.1 to 0.4) lower in the intervention group compared to controls. Among participants with values above the treatment goal at baseline, the difference in systolic BP and LDL-C was more pronounced (8.0 mmHg, 95% CI 4.0 to 12.1, and 0.6 mmol/L, 95% CI 0.4 to 0.9). A larger proportion of the intervention group reached the treatment goal for systolic BP (68.5 vs. 56.8%, p = 0.008) and LDL-C (69.7% vs. 50.4%, p < 0.001).

Conclusions

Nurse-led, telephone-based secondary preventive follow-up, including medication adjustment, was significantly more efficient than usual care at improving BP and LDL-C levels by 12 months post-discharge.

Trial Registration

ISRCTN Registry ISRCTN23868518  相似文献   

10.
Beneficial effects on arterial stiffness and pulse-wave reflection of combined enalapril and candesartan in chronic kidney disease - a randomized trial     
M Frimodt-Møller  AL Kamper  S Strandgaard  S Kreiner  AH Nielsen 《PloS one》2012,7(7):e41757

Background

Cardiovascular disease (CVD) is highly prevalent in patients with chronic kidney disease (CKD). Inhibition of the renin-angiotensinsystem (RAS) in hypertension causes differential effects on central and brachial blood pressure (BP), which has been translated into improved outcome. The objective was to examine if a more complete inhibition of RAS by combining an angiotensin converting enzyme inhibitor (ACEI) and an angiotensin receptor antagonist (ARB) compared to monotherapy has an additive effect on central BP and pulse-wave velocity (PWV), which are known markers of CVD.

Methods

Sixty-seven CKD patients (mean GFR 30, range 13–59 ml/min/1.73 m2) participated in an open randomized study of 16 weeks of monotherapy with either enalapril or candesartan followed by 8 weeks of dual blockade aiming at a total dose of 16 mg candesartan and 20 mg enalapril o.d. Pulse-wave measurements were performed at week 0, 8, 16 and 24 by the SphygmoCor device.

Results

Significant additive BP independent reductions were found after dual blockade in aortic PWV (−0.3 m/s, P<0.05) and in augmentation index (−2%, P<0.01) compared to monotherapy. Furthermore pulse pressure amplification was improved (P<0.05) and central systolic BP reduced (−6 mmHg, P<0.01).

Conclusions

Dual blockade of the RAS resulted in an additive BP independent reduction in pulse-wave reflection and arterial stiffness compared to monotherapy in CKD patients.

Trial Registration

Clinical trial.gov NCT00235287 http://www.clinicaltrials.gov/ct2/show/NCT00235287?term=ras+block&rank=1  相似文献   

11.
A Novel Cholinergic Action of Alcohol and the Development of Tolerance to That Effect in Caenorhabditis elegans     
Edward G. Hawkins  Ian Martin  Lindsay M. Kondo  Meredith E. Judy  Victoria E. Brings  Chung-Lung Chan  GinaMari G. Blackwell  Jill C. Bettinger  Andrew G. Davies 《Genetics》2015,199(1):135-149
The Prp43 DExD/H-box protein is required for progression of the biochemically distinct pre-messenger RNA and ribosomal RNA (rRNA) maturation pathways. In Saccharomyces cerevisiae, the Spp382/Ntr1, Sqs1/Pfa1, and Pxr1/Gno1 proteins are implicated as cofactors necessary for Prp43 helicase activation during spliceosome dissociation (Spp382) and rRNA processing (Sqs1 and Pxr1). While otherwise dissimilar in primary sequence, these Prp43-binding proteins each contain a short glycine-rich G-patch motif required for function and thought to act in protein or nucleic acid recognition. Here yeast two-hybrid, domain-swap, and site-directed mutagenesis approaches are used to investigate G-patch domain activity and portability. Our results reveal that the Spp382, Sqs1, and Pxr1 G-patches differ in Prp43 two-hybrid response and in the ability to reconstitute the Spp382 and Pxr1 RNA processing factors. G-patch protein reconstitution did not correlate with the apparent strength of the Prp43 two-hybrid response, suggesting that this domain has function beyond that of a Prp43 tether. Indeed, while critical for Pxr1 activity, the Pxr1 G-patch appears to contribute little to the yeast two-hybrid interaction. Conversely, deletion of the primary Prp43 binding site within Pxr1 (amino acids 102–149) does not impede rRNA processing but affects small nucleolar RNA (snoRNA) biogenesis, resulting in the accumulation of slightly extended forms of select snoRNAs, a phenotype unexpectedly shared by the prp43 loss-of-function mutant. These and related observations reveal differences in how the Spp382, Sqs1, and Pxr1 proteins interact with Prp43 and provide evidence linking G-patch identity with pathway-specific DExD/H-box helicase activity.  相似文献   

12.
VSDK: Virtual screening of small molecules using AutoDock Vina on Windows platform     
Baba N  Akaho E 《Bioinformation》2011,6(10):387-388
Screening of ligand molecules to target proteins using computer-aided docking is a critical step in rational drug discovery. Based on this circumstance, we attempted to develop a virtual screening application system, named VSDK Virtual Screening by Docking, which can function under the Windows platform. This is a user-friendly, flexible, and versatile tool which can be used by users who are familiar with Windows OS. The virtual screening performance was tested for an arbitrarily-selected receptor, FGFR tyrosine kinase (pdb code: 1agw), by using ligands downloaded from ZINC database with its grid size of x,y,z = 30,30,30 and run number of 10. It took 90 minutes for 100 molecules for this virtual screening. VSDK is freely available at the designated URL, and a simplified manual can be downloaded from VSDK home page. This tool will have a more challenging scope and achievement as the computer speed and accuracy are increased and secured in the future.

Availability

The database is available for free at http://www.pharm.kobegakuin.ac.jp/˜akaho/english_top.html  相似文献   

13.
Clinical Effect of Antioxidant Glasses Containing Extracts of Medicinal Plants in Patients with Dry Eye Disease: A Multi-Center,Prospective, Randomized,Double-Blind,Placebo-Controlled Trial     
Won Choi  Jae Chan Kim  Won Soo Kim  Han Jin Oh  Jee Myung Yang  Jee Bum Lee  Kyung Chul Yoon 《PloS one》2015,10(10)

Purpose

To investigate the clinical efficacy and safety of wearable antioxidant glasses containing extracts of medicinal plants in patients with mild dry eye disease (DED).

Methods

Fifty patients with mild DED were randomly assigned to wear either extracts of antioxidant medicinal plants containing (N = 25) or placebo glasses (N = 25). Patients wore the glasses for 15 min three times daily. The ocular surface disease index (OSDI) score, tear film break up time (BUT), and Schirmer’s test were evaluated and compared within the group and between the groups at baseline, 4 weeks, and 8 weeks after treatment.

Results

OSDI score and tear film BUT were significantly improved in the treatment group at 4 and 8 weeks after wearing glasses (all P < 0.001). Compared to the placebo group, the OSDI scores were significantly lower in the treatment group at 8 weeks (P = 0.007). The results of the Schirmer’s test showed significant improvement in the treatment group at 4 weeks (P = 0.035), however there were no significant differences between the other groups or within the groups. No adverse events were reported during the study.

Conclusions

Antioxidant glasses containing extracts of medicinal plants were effective in improving in DED both subjectively and objectively. Wearing antioxidants glasses might be a safe and adjunctive therapeutic option for DED.

Trial Registration

ISRCTN registry 71217488  相似文献   

14.
OrFin: A web tool for detection of putative orthologs     
Mohit Midha  Raja Polavarapu  Potshangbam Angamba Meetei  Hari Krishnan  Krishnaveni Mohareer  Vaibhav Vindal 《Bioinformation》2012,8(15):738-739
Identification of ortholog is one of the important tasks to understand a novel genome. It helps to assign functional annotations, from one organism to another organism. To identify the putative ortholog, Reciprocal Best BLAST hit (RBBH) method is known to be an efficient approach. OrFin makes use of the same approach to identify pair of orthologous proteins for a given set of sequences of two species. It is a user-friendly web tool which works with user defined parameters to search RBBHs. Results are produced in both html and text format.

Availability

This web tool is freely available at http://bifl.uohyd.ac.in/orfin  相似文献   

15.
Biogenesis of RNA Polymerases II and III Requires the Conserved GPN Small GTPases in Saccharomyces cerevisiae     
Sean W. Minaker  Megan C. Filiatrault  Shay Ben-Aroya  Philip Hieter  Peter C. Stirling 《Genetics》2013,193(3):853-864
  相似文献   

16.
Brothers in arms     
Andrea Rinaldi 《EMBO reports》2013,14(10):866-870
The horrific injuries and difficult working conditions faced by military medical personnel have forced the military to fund biomedical research to treat soldiers; those new technologies and techniques contribute significantly to civilian medicine.War is the father of all things, Heraclitus believed. The military''s demand for better weapons and transportation, as well as tools for communication, detection and surveillance has driven technological progress during the past 150 years or so, producing countless civilian applications as a fallout. The military has invested heavily into high-energy physics, materials science, navigation systems and cryptology. Similarly, military-funded biomedical research encompasses the whole range from basic to applied research programmes (Fig 1), and the portion of military-funded research in the biological and medical fields is now considerable.Open in a separate windowFigure 11944 advertisement for Diebold Inc. (Ohio, USA) in support of blood donations for soldiers wounded in the Second World War. The military has traditionally been one of the greatest proponents of active research on synthetic blood production, blood substitutes and oxygen therapeutics for treating battlefield casualties. One recent approach in this direction is The Defense Advanced Research Projects Agency''s (DARPA''s) Blood Pharming programme, which plans to use human haematopoietic stem cells—such as those obtained from umbilical cord blood—as a “starting material to develop an automated, fieldable cell culture and packaging system capable of producing transfusable amounts of universal donor red blood cells” (http://www.darpa.mil/Our_Work/DSO/Programs/Blood_Pharming.aspx).War has always driven medical advances. From ancient Roman to modern times, treating the wounds of war has yielded surgical innovations that have been adopted by mainstream medicine. For example, the terrible effect of modern artillery on soldiers in the First World War was a major impetus for plastic surgery. Similarly, microbiology has benefited from war and military research: from antiseptics to prevent and cure gangrene to the massive production of penicillin during the Second World War, as well as more basic research into a wide range of pathogens, militaries worldwide have long been enthusiastic sponsors of microbiology research. Nowadays, military-funded research on pathogens uses state-of-the-art genotyping methods to study outbreaks and the spread of infection and seeks new ways to combat antibiotic resistance that afflicts both combatants and civilians.…military-funded biomedical research encompasses the whole range from basic to applied research programmes…The US Military Infectious Diseases Research Program (MIDRP) is particularly active in vaccine development to protect soldiers, especially those deployed overseas. Its website notes that: “Since the passing of the 1962 Kefauver–Harris Drug Amendment, which added the FDA requirement for proof of efficacy in addition to proof of safety for human products, there have been 28 innovative vaccines licenced in the US, including 13 vaccines currently designated for paediatric use. These 28 innovative vaccine products targeted new microorganisms, utilized new technology, or consisted of novel combinations of vaccines. Of these 28, the US military played a significant role in the development of seven licenced vaccines” (https://midrp.amedd.army.mil/). These successes include tetravalent meningococcal vaccine and oral typhoid vaccine, while current research is looking into the development of vaccines against malaria, dengue fever and hepatitis E.Similarly, the US Military HIV Research Program (MHRP) is working on the development of a global HIV-1 vaccine (http://www.hivresearch.org). MHRP scientists were behind the RV144 vaccine study in Thailand—the largest ever HIV vaccine study conducted in humans—that demonstrated that the vaccine was capable of eliciting modest and transient protection against the virus [1]. In the wake of the cautious optimism raised by the trial, subsequent research is providing insights into the workings of RV144 and is opening new doors for vaccine designers to strengthen the vaccine. In a recent study, researchers isolated four monoclonal antibodies induced by the RV144 vaccine and directed at a particular region of the HIV virus envelope associated with reduced infection, the variable region 2. They found that these antibodies recognized HIV-1-infected CD4(+) T cells and tagged them for attack by the immune system [2].In response to the medical problems military personnel are suffering in Iraq and Afghanistan, a recent clinical trial funded by the US Department of the Army demonstrated the efficacy of the aminoglycoside antibiotic paromomycin—either with or without gentamicin—for the topical treatment of cutaneous leishmaniasis, the most common form of infection by Leishmania parasites. Cutaneous leishmaniasis—which is endemic in Iraq and Afghanistan and rather frequent among soldiers deployed there—is transmitted to humans through the bite of infected sandflies: it causes skin ulcers and sores and can cause serious disability and social prejudice [3]. Topical treatments would offer advantages over therapies that require the systemic administration of antiparasitic drugs. The study—a phase 3 trial—was conducted in Tunisia and enrolled some 375 patients with one to five ulcerative lesions from cutaneous leishmaniasis. Patients, all aged between 5 and 65, received topical applications of a cream containing either 15% paromomycin with 0.5% gentamicin, 15% paromomycin alone or the control cream, which contained no antibiotic. The combination of paromomycin and gentamicin cured cutaneous leishmaniasis with an efficacy of 81%, compared with 82% for paromomycin alone and just 58% for control—the skin sores of cutaneous leishmaniasis often heal on their own. Researchers reported no adverse reactions to paronomycin-containing creams. Because the combination therapy with gentamicin is probably effective against a larger range of Leishmania parasitic species and strains causing the disease, it could become a first-line treatment for cutaneous leishmaniasis on a global scale the authors concluded [3].…military-funded research on pathogens uses state-of-the-art genotyping methods to study outbreaks and the spread of infectionNot surprisingly, trauma and regenerative and reconstructive medicine are other large areas of research in which military influence is prevalent. The treatment of wounds, shock and the rehabilitation of major trauma patients are the very essence of medical aid on the battlefield (Figs 2, ,3).3). “Our experience of military conflict, in particular the medicine required to deal with severe injuries, has led to significant improvements in trauma medicine. Through advances in the prevention of blood loss and the treatment of coagulopathy for example, patients are now surviving injuries that 5–10 years ago would have been fatal,” said Professor Janet Lord, who leads a team investigating the inflammatory response in injured soldiers at the National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre (NIHR SRMRC) in Birmingham, UK (http://www.srmrc.nihr.ac.uk/).Open in a separate windowFigure 2Medical services in Britain, 1917. Making an artificial leg for a wounded serviceman at Roehampton Hospital in Surrey. This image is from The First World War Poetry Digital Archive, University of Oxford (www.oucs.ox.ac.uk/ww1lit). Copyright: The Imperial War Museum.Open in a separate windowFigure 3US soldiers use the fireman''s carry to move a simulated casualty to safety during a hyper-realistic training environment, known as trauma lanes, as part of the final phase of the Combat Lifesaver Course given by medics from Headquarters Support Company, Headquarters and Headquarters Battalion, 25th Inf. Div., USD-C, at Camp Liberty, Iraq, March 2011. Credit: US Army, photo by Sgt Jennifer Sardam.NIHR SRMRC integrates basic researchers at Birmingham University with clinicians and surgeons at the Royal Centre for Defence Medicine and University Hospital Birmingham to improve the treatment of traumatic injury in both military and civilian patients. As Lord explained, the centre has two trauma-related themes. The first is looking at, “[t]he acute response to injury, which analyses the kinetics and nature of the inflammatory response to tissue damage and is developing novel therapies to ensure the body responds appropriately to injury and does not stay in a hyper-inflamed state. The latter is a particular issue with older patients whose chance of recovery from trauma is significantly lower than younger patients,” she said. The second theme is, “[n]eurotrauma and regeneration, which studies traumatic brain injury, trying to develop better ways to detect this early to prevent poor outcomes if it goes undiagnosed,” Lord said.Kevlar helmets and body armour have saved the lives of many soldiers, but they do not protect much the face and eyes, and in general against blasts to the head. Because human retinas and brains show little potential for regeneration, patients with face and eye injuries often suffer from loss of vision and other consequences for the rest of their lives. However, a new stem cell and regenerative approach for the treatment of retinal injury and blindness is on the horizon. “Recent progress in stem cell research has begun to emerge on the possible exploitation of stem cell-based strategies to repair the damaged CNS (central nervous system). In particular, research from our laboratory and others have demonstrated that Müller cells—dormant stem-like cells found throughout the retina—can serve as a source of retinal progenitor cells to regenerate photoreceptors as well as all other types of retinal neurons,” explained Dong Feng Chen at the Schepens Eye Research Institute, Massachusetts Eye and Ear of the Harvard Medical School in Boston (Massachusetts, USA). In collaboration with the US Department of Defence, the Schepens Institute is steering the Military Vision Research Program, “to develop new ways to save the vision of soldiers injured on today''s battlefield and to push the frontier of vision technologies forward” (http://www.schepens.harvard.edu).“My laboratory has shown that adult human and mouse Müller cells can not only regenerate retina-specific neurons, but can also do so following induction by a single small molecule compound, alpha-aminoadipate,” Chen explained. She said that alpha-aminoadipate causes isolated Müller glial cells in culture to loose their glial phenotype, express progenitor cell markers and divide. Injection of alpha-aminoadipate into the subretinal space of adult mice in vivo induces mature Müller glia to de-differentiate and generate new retinal neurons and photoreceptor cells [4]. “Our current effort seeks to further elucidate the molecular pathways underlying the regenerative behaviour of Muller cells and to achieve functional regeneration of the damaged retina with small molecule compounds,” Chen said. “As the retina has long served as a model of the CNS, and Müller cells share commonalities with astroglial lineage cells in the brain and spinal cord, the results of this study can potentially be broadened to future development of treatment strategies for other neurodegenerative diseases, such as brain and spinal cord trauma, or Alzheimer and Parkinson disease.”The treatment of wounds, shock and the rehabilitation of major trauma patients are the very essence of medical aid on the battlefieldBrain injuries account for a large percentage of the wounds sustained by soldiers. The Defense Advanced Research Projects Agency (DARPA), an agency of the US Department of Defense, recently awarded US$6 million to a team of researchers to develop nanotechnology therapies for the treatment of traumatic brain injury and associated infections. The researchers are trying to develop nanoparticles carrying small interfering RNA (siRNA) molecules to reach and treat drug-resistant bacteria and inflammatory cells in the brain. Protecting the siRNA within a nanocomplex covered with specific tissue homing and cell-penetrating peptides will make it possible to deliver the therapeutics to infected cells beyond the blood–brain barrier—which normally makes it difficult to get antibiotics to the brain. The project has been funded within the framework of DARPA''s In Vivo Nanoplatforms programme that “seeks to develop new classes of adaptable nanoparticles for persistent, distributed, unobtrusive physiologic and environmental sensing as well as the treatment of physiologic abnormalities, illness and infectious disease” (www.darpa.mil).“The DARPA funding agency often uses the term ‘DARPA-hard'' to refer to problems that are extremely tough to solve. What makes this a DARPA-hard problem is the fact that it is so difficult to deliver therapeutics to the brain. This is an underserved area of research,” explained team leader Michael Sailor, from the University of California San Diego, in a press release (http://ucsdnews.ucsd.edu/pressrelease/darpa_awards_6_million_to_develop_nanotech_therapies_for_traumatic_brain_in).In the near future, DARPA, whose budget is set for a 1.8% increase to US$2.9 billion next year, will focus on another important project dealing with the CNS. The BRAIN Initiative—short for Brain Research through Advancing Innovative Neurotechnologies—is a new research effort whose proponents intend will “revolutionize our understanding of the human mind and uncover new ways to treat, prevent, and cure brain disorders like Alzheimer''s, schizophrenia, autism, epilepsy and traumatic brain injury” (www.whitehouse.gov). Out of a total US$110 million investment, DARPA will obtain US$50 million to work on understanding the dynamic functions of the brain and demonstrating breakthrough applications based on these insights (Fig 4). In addition to exploring new research areas, this money will be directed towards ongoing projects of typical—although not exclusive—military interest that involve enhancing or recovering brain functions, such as the development of brain-interfaced prosthetics and uncovering the mechanisms underlying neural reorganization and plasticity to accelerate injury recovery.Open in a separate windowFigure 4The BRAIN (Brain Research through Advancing Innovative Neurotechnologies) Initiative infographic. A complete version can be downloaded at http://www.whitehouse.gov/infographics/brain-initiative.“[T]here is this enormous mystery waiting to be unlocked, and the BRAIN Initiative will change that by giving scientists the tools they need to get a dynamic picture of the brain in action and better understand how we think and how we learn and how we remember. And that knowledge could be—will be—transformative,” said US President Obama, presenting the initiative (http://www.whitehouse.gov/the-press-office/2013/04/02/remarks-president-brain-initiative-and-american-innovation).“The President''s initiative reinforces the significance of understanding how the brain records, processes, uses, stores and retrieves vast quantities of information. This kind of knowledge of brain function could inspire the design of a new generation of information processing systems; lead to insights into brain injury and recovery mechanisms; and enable new diagnostics, therapies and devices to repair traumatic injury,” explained DARPA Director Arati Prabhakar in a press release (http://www.darpa.mil/NewsEvents/Releases/2013/04/02.aspx).But BRAIN is also stirring up some controversy. Some scientists fear that this kind of ‘big and bold'' science, with a rigid top-down approach and vaguely defined objectives, will drain resources from smaller projects in fundamental biology [5]. Others ask whether the BRAIN project investment will really generate the huge return hinted at in Obama''s speech during the initiative''s launch, or whether a substantial amount of hype about the potential outcomes was used to sell the project (http://ksj.mit.edu/tracker/2013/04/obamas-brain-initiative-and-alleged-140).As these examples show, the most important player in military-funded biomedical research is the USA, with the UK following at a distance. But other countries with huge defence budgets are gearing up, although with less visibility. In July 2011, for instance, India and Kyrgyzstan opened the joint Mountain Biomedical Research Centre at the Kyrgyz capital Bishkek, to carry out research into the mechanisms of short- and long-term high-altitude adaptation. The institute will use molecular biological approaches to identify markers for screening people for high-altitude resistance and susceptibility to high-altitude sickness, and development of other mountain maladies. On the Indian side, the scientists involved in the new research centre belong to the Defence Institute of Physiology and Applied Sciences, and the money came from India''s defence budget.As mankind seems unlikely to give up on armed conflicts anytime soon, war-torn human bodies will still need to be cured and wounds healed. Whether the original impetus for military-funded biomedical research is noble or not, it nonetheless fuels considerable innovation leading to important medical discoveries that ultimately benefit all.  相似文献   

17.
Smartphone-Supported versus Full Behavioural Activation for Depression: A Randomised Controlled Trial     
Kien Hoa Ly  Naira Topooco  Hanna Cederlund  Anna Wallin  Jan Bergstr?m  Olof Molander  Per Carlbring  Gerhard Andersson 《PloS one》2015,10(5)

Background

There is need for more cost and time effective treatments for depression. This is the first randomised controlled trial in which a blended treatment - including four face-to-face sessions and a smartphone application - was compared against a full behavioural treatment. Hence, the aim of the current paper was to examine whether a blended smartphone treatment was non-inferior to a full behavioural activation treatment for depression.

Methods

This was a randomised controlled non-inferiority trial (NCT01819025) comparing a blended treatment (n=46) against a full ten-session treatment (n=47) for people suffering from major depression. Primary outcome measure was the BDI-II, that was administered at pre- and post-treatment, as well as six months after the treatment.

Results

Results showed significant improvements in both groups across time on the primary outcome measure (within-group Cohen’s d=1.35; CI [−0.82, 3.52] to d=1.47; CI [−0.41, 3.35]; between group d=−0.13 CI [−2.37, 2.09] and d=−0.10 CI [−2.53, 2.33]). At the same time, the blended treatment reduced the therapist time with an average of 47%.

Conclusions

We could not establish whether the blended treatment was non-inferior to a full BA treatment. Nevertheless, this study points to that the blended treatment approach could possibly treat nearly twice as many patients suffering from depression by using a smartphone applica¬tion as add-on. More studies are needed before we can suggest that the blended treatment method is a promising cost-effective alternative to regular face-to-face treatment for depression.

Trial Registration

Cognitive Behavioral Therapy Treatment of Depression With Smartphone Support NCT01819025  相似文献   

18.
Randomized clinical trial on ivermectin versus thiabendazole for the treatment of strongyloidiasis     
Bisoffi Z  Buonfrate D  Angheben A  Boscolo M  Anselmi M  Marocco S  Monteiro G  Gobbo M  Bisoffi G  Gobbi F 《PLoS neglected tropical diseases》2011,5(7):e1254

Background

Strongyloidiasis may cause a life-threatening disease in immunosuppressed patients. This can only be prevented by effective cure of chronic infections. Direct parasitologic exams are not sensitive enough to prove cure if negative. We used an indirect immune fluorescent antibody test (IFAT) along with direct methods for patient inclusion and efficacy assessment.

Methodology/Principal Findings

Prospective, randomized, open label, phase III trial conducted at the Centre for Tropical Diseases (Verona, Italy) to compare efficacy and safety of ivermectin (single dose, 200 µg/kg) and thiabendazole (two daily doses of 25 mg/Kg for two days) to cure strongyloidiasis. The first patient was recruited on 6th December, 2004. Follow-up visit of the last patient was on 11th January, 2007. Consenting patients responding to inclusion criteria were randomly assigned to one of the treatment arms. Primary outcome was: negative direct and indirect (IFAT) tests at follow-up (4 to 6 months after treatment) or subjects with negative direct test and drop of two or more IFAT titers. Considering 198 patients who concluded follow-up, efficacy was 56.6% for ivermectin and 52.2% for thiabendazole (p = 0.53). If the analysis is restricted to 92 patients with IFAT titer 80 or more before treatment (virtually 100% specific), efficacy would be 68.1% for ivermectin and 68.9% for thiabendazole (p = 0.93). Considering direct parasitological diagnosis only, efficacy would be 85.7% for ivermectin and 94.6% for thiabendazole (p = 0.21). In ivermectin arm, mild to moderate side effects were observed in 24/115 patients (20.9%), versus 79/108 (73.1%) in thiabendazole arm (p = 0.00).

Conclusion

No significant difference in efficacy was observed, while side effects were far more frequent in thiabendazole arm. Ivermectin is the drug of choice, but efficacy of single dose is suboptimal. Different dose schedules should be assessed by future, larger studies.

Trial Registration

Portal of Clinical Research with Medicines in Italy 2004–004693–87  相似文献   

19.
MultiMiTar: a novel multi objective optimization based miRNA-target prediction method     
Mitra R  Bandyopadhyay S 《PloS one》2011,6(9):e24583
  相似文献   

20.
dPORE-miRNA: polymorphic regulation of microRNA genes     
Schmeier S  Schaefer U  MacPherson CR  Bajic VB 《PloS one》2011,6(2):e16657
  相似文献   

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