A versatile modelling approach to determine the hydrophobicity of peptides at the atomic level

This study describes a versatile computational method to determine the hydrophobicity of small peptides at the atomic level. Free energies of transfer for individual atoms in peptide structures were derived, utilising two specifically defined parameters: (i) the water-excluding distance to define the dynamic interface between a peptide solute and its surrounding solvent and (ii) the corresponding hydrophobicity index as a relative measure for water occlusion/repulsion. The method was tested on a range of small peptide models (Ac-X-NH₂, G-X-G, Ac-WL-X-LL and Ac-GG-X-GG-NH₂) and several derivatives of these structures, whereby X was any of the 20 most common amino acids that naturally occur in polypeptides or proteins. The advantage of this new method lies in its versatility, ease to implement and capability to provide information on the hydrophobicity characteristics at the atomic level. The approach also encapsulates the impact of factors that influence these properties, but which have hitherto been difficult to accurately quantify, e.g. steric hindrance or proximity effects due to nearby polarised atoms. The method is not conditional on the knowledge of hydrophobicity parameters from the literature and does not require a sophisticated computer software/hardware to enable the atomic solvent-accessible surface areas or other hydrophobicity parameters to be de novo obtained.     

A comparison of optimisation methods and knee joint degrees of freedom on muscle force predictions during single-leg hop landings

The aim of this paper was to compare the effect of different optimisation methods and different knee joint degrees of freedom (DOF) on muscle force predictions during a single legged hop. Nineteen subjects performed single-legged hopping manoeuvres and subject-specific musculoskeletal models were developed to predict muscle forces during the movement. Muscle forces were predicted using static optimisation (SO) and computed muscle control (CMC) methods using either 1 or 3 DOF knee joint models. All sagittal and transverse plane joint angles calculated using inverse kinematics or CMC in a 1 DOF or 3 DOF knee were well-matched (RMS error<3°). Biarticular muscles (hamstrings, rectus femoris and gastrocnemius) showed more differences in muscle force profiles when comparing between the different muscle prediction approaches where these muscles showed larger time delays for many of the comparisons. The muscle force magnitudes of vasti, gluteus maximus and gluteus medius were not greatly influenced by the choice of muscle force prediction method with low normalised root mean squared errors (<48%) observed in most comparisons. We conclude that SO and CMC can be used to predict lower-limb muscle co-contraction during hopping movements. However, care must be taken in interpreting the magnitude of force predicted in the biarticular muscles and the soleus, especially when using a 1 DOF knee. Despite this limitation, given that SO is a more robust and computationally efficient method for predicting muscle forces than CMC, we suggest that SO can be used in conjunction with musculoskeletal models that have a 1 or 3 DOF knee joint to study the relative differences and the role of muscles during hopping activities in future studies.     

Development and implementation of evidence-based guidelines for IV insulin: A statewide collaborative approach

Purpose: Recent studies have shown that the outcomes of hospitalized patients are greatly enhanced when steps are taken to improve control of their blood glucose levels. The Georgia Hospital Association Research and Education Foundation's Partnership for Health Accountability established a Diabetes Special Interest Group (D-SIG) in February 2003. Goals of the D-SIG were to enlighten health care professionals in Georgia hospitals about the benefits of controlling hyperglycemia in hospitalized patients and to develop processes to assist hospitals in the adoption of an IV insulin dosing algorithm, development of an IV insulin standing order set, and implementation of a hyperglycemia management plan.Methods: The D-SIG created an assessment tool titled “Key Elements of IV Insulin Guidelines” and evaluated numerous published IV insulin administration algorithms and protocols. After an extensive literature review, including international protocols and guidelines, user-friendly guidelines for subcutaneous and IV insulin were developed by a multidisciplinary work group, with members representing hospitals and other stakeholders from throughout the state. The group chose a well-researched method that was available in both computerized and hand-calculated formats and developed a Columnar Insulin Dosing Chart to assist with IV insulin infusions. This insulin-infusion table stems from mathematical formulas published by multiple investigators since the 1980s. The D-SIG guidelines and dosing chart were evaluated for ease of use, effectiveness, and safety in 3 settings: a small, rural critical-access hospital (CAH); an intensive care unit (ICU) in the trauma center of a large Georgia teaching hospital; and a surgical ICU in a midsize metropolitan hospital.Results: After implementation of the guidelines, the incidence of hypoglycemia (blood glucose level <60 mg/dL) was 0.9% in the trauma center ICU and 0.6% in the surgical ICU. All hypoglycemic patients in these 2 settings were asymptomatic, remained hypoglycemic only for a short time, and experienced no complications attributable to hypoglycemia. Using a moderate insulin sensitivity level for dosing initiations resulted in a time to target blood glucose level (80–110 mg/dL) of 6.4 hours, whereas using the most conservative approach required 12.8 hours to attain target range. At the CAH, time to reach the target blood glucose level (90–140 mg/dL) was 5.8 hours, and no episodes of hypoglycemia were reported. Although not part of the pilot initiative, the surgical ICU also reported a 5-fold reduction in surgical infection rates. The success of the dosing chart and standing order set paralleled that of the computerized formula when similar initiation doses were used.Conclusions: The Columnar Insulin Dosing Chart and sample clinical guidelines were piloted at 3 different settings and found to be safe and effective. Furthermore, by including the treatment for hypoglycemia in the guidelines, nurses in all patient care areas were able to manage blood glucose levels below the target range in a safe and timely manner. Use of the dosing chart and guidelines reduced blood glucose levels to the target range with no clinically significant hypoglycemia.     

A strategic approach to the synthesis of ferrocene appended chalcone linked triazole allied organosilatranes: Antibacterial,antifungal, antiparasitic and antioxidant studies

A series of ferrocene appended chalcone allied triazole coupled organosilatranes (FCTSa 7–FCTSa 12) were synthesised with the aim of amalgamating the pharmacological action of the constituting moieties into a single molecular scaffold. All the synthesised silatranes were well characterized by various spectroscopic techniques like IR, ¹H NMR, ¹³C NMR and elemental analysis. Organosilatranes were then evaluated for their biological alacrity against bacterial and fungal strains compared with the standard drugs Rifampicin and Amphotericin B respectively. The ferrocene conjugates were found to be only moderately effective against the tested microbes. However, the organosilatranes conceded excellent efficacy against parasite G. lamblia with FCTSa 11 arraying the leading results. On the other hand against another parasite T. vaginalis, FCTSa 8 has emerged as an outstanding composite. Further, Total Antioxidant Assay (TAA) with 2,2′-azino-bis-3-(ethylbenzothiazoline-6-sulphonic acid) revealed FCTSa 10 to be the best claimant for radical scavenging activity. Along these lines, introducing some different substituents in the synthesised hybrids may act as a useful strategy for increasing the biological profile of the drugs.     

Quantification of pyrophosphate as a universal approach to determine polymerase activity and assay polymerase inhibitors

The importance of DNA polymerases in biology and biotechnology, and their recognition as potential therapeutic targets, drives development of methods for deriving kinetic characteristics of polymerases and their propensity to perform polynucleotide synthesis over modified DNA templates. Among various polymerases, translesion synthesis (TLS) polymerases enable cells to avoid the cytotoxic stalling of replicative DNA polymerases at chemotherapy-induced DNA lesions, thereby leading to drug resistance. Identification of TLS inhibitors to overcome drug-resistance necessitates the development of appropriate high-throughput assays. Since polymerase-mediated DNA synthesis involves the release of inorganic pyrophosphate (PPi), we established a universal and fast method for monitoring the progress of DNA polymerases based on the quantification of PPi with a fluorescence-based assay that we coupled to in vitro primer extension reactions. The established assay has a nanomolar detection limit in PPi and enables the evaluation of single nucleotide incorporation and DNA synthesis progression kinetics. The results demonstrated that the developed assay is a reliable method for monitoring TLS and identifying nucleoside and nucleotide-based TLS inhibitors.     

A general-purpose framework to simulate musculoskeletal system of human body: using a motion tracking approach*

Computation of muscle force patterns that produce specified movements of muscle-actuated dynamic models is an important and challenging problem. This problem is an undetermined one, and then a proper optimization is required to calculate muscle forces. The purpose of this paper is to develop a general model for calculating all muscle activation and force patterns in an arbitrary human body movement. For this aim, the equations of a multibody system forward dynamics, which is considered for skeletal system of the human body model, is derived using Lagrange–Euler formulation. Next, muscle contraction dynamics is added to this model and forward dynamics of an arbitrary musculoskeletal system is obtained. For optimization purpose, the obtained model is used in computed muscle control algorithm, and a closed-loop system for tracking desired motions is derived. Finally, a popular sport exercise, biceps curl, is simulated by using this algorithm and the validity of the obtained results is evaluated via EMG signals.     

Roadmap to determine the point mutations involved in cardiomyopathy disorder: A Bayesian approach

Determining the deleterious non-synonymous single nucleotide polymorphisms (nsSNPs), that might be involved in inducing disease-associated phenomena, is now among the most important field of computational genomic research. The rapid evolution in sequencing technologies has now outranged the limit of available sequence databases and has out-fledged the amount of SNP data that are yet to be characterized. In this article we have performed a comprehensive analysis of deleterious nsSNPs in MyH7 gene associated with cardiomyopathy cases using a set of computational platforms. We implemented a set of computational SNP analysis platforms along with the Bayesian calculations in order to filter the most likely mutation that might be associated with cardiomyopathy associated disorders. The Bayesian calculation depicted 27 fold rises in the likelihood score for causing cardiomyopathy disorder when MyH7 gene mutations were compiled. Furthermore, we reported E466Q mutation in MyH7 motor domain that showed increase in the amyloid propensity of protein, as well as a significant level of pathogenicity was also observed. The prediction roadmap followed in this article has showed a notable range of accuracy and can be used for determining cardiomyopathy associated nsSNPs for other candidate genes.     

A novel and rapid approach to isolating functional ryanodine receptors

Conventional methods of isolating and reconstituting ryanodine receptors (RyRs) from native membranes into proteoliposomes take a minimum of 2 days to complete. We have developed an alternative strategy that can be used to isolate and reconstitute functional RyRs in just 3 h with a similar degree of purification. RyRs isolated by this method display characteristic functional behaviour as assessed by radioligand binding and single channel analyses.     

The Influence of Voice Volume, Pitch, and Speech Rate on Progressive Relaxation Training: Application of Methods from Speech Pathology and Audiology

Vocal characteristics of therapists, including voice volume, pitch and timbre of speech, and rate of speech have been hypothesized to facilitate the therapeutic process, particularly during procedures like progressive relaxation training (PRT). Very little empirical work, however, has examined the relation between vocal characteristics and treatment process or outcome. The purpose of this study was to examine the role of vocal characteristics during a single session of PRT applying technological innovations devised for speech pathology and audiology settings for evaluating therapist's vocal characteristics. Forty-eight high anxious young adult women were randomly assigned to one of four conditions for training: PRT with the recommended therapist voice (RV) that decreased in tone, volume, and rate across the session, PRT with conversational therapist voice during the session (CV), a credible treatment control called systematic self-relaxation (SR), or no treatment control (NT). All subjects participated in a single PRT session during which heart rate, EMG, self-report measures of tension (SRT) and anxiety, and treatment credibility ratings were obtained. Results revealed significant reductions in SRT, self-reported anxiety, and heart rate for participants in all groups. Only the RV group displayed significant reductions in EMG when compared with the other three groups. Participants in the RV group also rated the therapist's voice as “more facilitating” of relaxation when compared to the CV group. These results suggest that methods employed for evaluating the quality of vocal characteristics in speech and audiology clinics may be useful for evaluating the quality of therapist's voice when conducting PRT.     

A general co-expression network-based approach to gene expression analysis: comparison and applications

Background  

Co-expression network-based approaches have become popular in analyzing microarray data, such as for detecting functional gene modules. However, co-expression networks are often constructed by ad hoc methods, and network-based analyses have not been shown to outperform the conventional cluster analyses, partially due to the lack of an unbiased evaluation metric.     

A regio- and stereo-controlled approach to triazoloquinoxalinyl C-nucleosides

The synthesis of a new series of acyclic triazoloquinoxalinyl C-nucleosides and their transformation to their cyclic analogs are described following protection, activation, and deprotection with subsequent intramolecular nucleophilic substitution protocol. The antibacterial potency of the new compounds was determined using an inhibition zone diameter test. The results show that 3a and 2b exhibit good activity against Escherichiacoli and Candidaalbicans. On the other hand, the cyclic mesylated C-nucleoside 13 showed activity against the Gram-positive bacteria (Staphylococcusaureus) and antifungal activity against C. albicans.     

Proteasomal activity in skeletal muscle: A matter of assay design, muscle type, and age

The ubiquitin-proteasome system (UPS) is a major degradation system for regulatory and misfolded proteins. UPS function has been implicated to exert a central role in the pathogenesis of various human diseases. Because biochemical analyses are often hampered by the amount of available diseased tissue, we report on the establishment and validation of a luminescence-based proteasomal activity assay applicable to 5-mg quantities of skeletal muscle. We demonstrate that the specific proteasomal activity differs in individual muscle groups and decreases with aging. These findings warrant the use of appropriate controls and a careful interpretation of results in mammalian skeletal muscle pathologies.     

Use of Microneurography to Evaluate Sympathetic Activity in Hypertension: A Brief Review

Muscle sympathetic nerve activity (MSNA) is an important variable in the study of autonomic activity in both normotensive and hypertensive subjects. It is measured directly from the peroneal nerve using microneurography. The technique is complex and difficult to learn, but yields accurate and direct information about sympathetic nerve impulses. MSNA provides not only greater reproducibility than other measures of sympathetic activity, but also a clearer and more consistent reflection of changes in sympathetic activity caused by changes in the subject's status or disease. This technique has been used primarily in basic research settings studying stress and hypertension. It has much potential to enhance our understanding of sympathetic nervous system activity and its role in applied psychophysiology and biofeedback.     

CRISPR technology: A versatile tool to model,screen, and reverse drug resistance in cancer

BackgroundDrug resistance is a serious challenge in cancer treatment that can render chemotherapy a failure. Understanding the mechanisms behind drug resistance and developing novel therapeutic approaches are cardinal steps in overcoming this issue. Clustered regularly interspaced short palindrome repeats (CRISPR) gene-editing technology has proven to be a useful tool to study cancer drug resistance mechanisms and target the responsible genes. In this review, we evaluated original research studies that used the CRISPR tool in three areas related to drug resistance, namely screening resistance-related genes, generating modified models of resistant cells and animals, and removing resistance by genetic manipulation. We reported the targeted genes, study models, and drug groups in these studies. In addition to discussing different applications of CRISPR technology in cancer drug resistance, we analyzed drug resistance mechanisms and provided examples of CRISPR’s role in studying them. Although CRISPR is a powerful tool for examining drug resistance and sensitizing resistant cells to chemotherapy, more studies are required to overcome its disadvantages, such as off-target effects, immunotoxicity, and inefficient delivery of CRISPR/cas9 into the cells.     

DNA extractions from deep subseafloor sediments: novel cryogenic-mill-based procedure and comparison to existing protocols

Extracting DNA from deep subsurface sediments is challenging given the complexity of sediments types, low biomasses, resting structures (spores, cysts) frequently encountered in deep sediments, and the potential presence of enzymatic inhibitors. Promising results for cell lysis efficiency were recently obtained by use of a cryogenic mill (Lipp et al., 2008). These findings encouraged us to devise a DNA extraction protocol using this tool. Thirteen procedures involving a combination of grinding in liquid nitrogen (for various durations and beating rates) with different chemical solutions (phenol, chloroform, SDS, sarkosyl, proteinase, GTC), or with use of DNA recovery kits (MagExtractor®) were compared. Effective DNA extraction was evaluated in terms of cell lysis efficiency, DNA extraction efficiency, DNA yield and determination of prokaryotic diversity. Results were compared to those obtained by standard protocols: the FastDNA®SPIN kit for soil and the Zhou protocol. For most sediment types grinding in a cryogenic mill at a low beating rate in combination with direct phenol-chloroform extraction resulted in much higher DNA yields than those obtained using classical procedures. In general (except for clay-rich sediments), this procedure provided high-quality crude extracts for direct downstream nested-PCR, from cell numbers as low as 1.1 × 10⁶ cells/cm³. This procedure is simple, rapid, low-cost, and could be used with minor modifications for large-scale DNA extractions for a variety of experimental goals.     

Muscle-splitting approach to superior and inferior gluteal vessels: versatile source of recipient vessels for free-tissue transfer to sacral, gluteal, and ischial regions

The superior gluteal vessel has been reported as a recipient in free-tissue transfer for the coverage of complex soft-tissue defects in the lumbosacral region, where a suitable recipient vessel is difficult to find. The characteristics of proximity, vessel caliber, and constancy make the superior gluteal vessel preferable to previously reported recipient vessels. However, there are technical difficulties in microsurgery (e.g., short pedicle length and deep location) and muscle injury (transection of the muscle) associated with use of the superior gluteal vessel. The purpose of this article is to present a modification of an approach to the gluteal vessel to alleviate technical difficulties and minimize muscle injury. From August of 1997 to January of 1999, six patients received microvascular transfer of the latissimus dorsi muscle or myocutaneous flap to the sacral (4) and ischial (2) regions. The causes of defects were tumor (1), trauma (1), and pressure sores (4). A muscle-splitting approach was used on the superior gluteal vessel and was later applied to the inferior gluteal vessel. The gluteus maximus muscle was split as needed in the direction of its fibers, and the perforators were dissected down to the superior or inferior gluteal artery and vein deep into the muscle. The follow-up period ranged from 6 to 22 months, and all of the flaps survived with complete recovery of the lesion. The major drawbacks of using the superior and inferior gluteal vessels can be overcome with the muscle-splitting approach, which provides increased accessibility and additional length to the vascular pedicle while causing minimal injury to the muscle itself. It also proves to be an easy, safe, and reliable method of dissection. When free-tissue transfer to sacral, gluteal, and ischial regions is indicated, the muscle-splitting approach to the superior and inferior gluteal vessels is a recommended option in the selection of a recipient vessel.     

Time domain measures of inter-channel EEG correlations: a comparison of linear, nonparametric and nonlinear measures

Correlations between ten-channel EEGs obtained from thirteen healthy adult participants were investigated. Signals were obtained in two behavioral states: eyes open no task and eyes closed no task. Four time domain measures were compared: Pearson product moment correlation, Spearman rank order correlation, Kendall rank order correlation and mutual information. The psychophysiological utility of each measure was assessed by determining its ability to discriminate between conditions. The sensitivity to epoch length was assessed by repeating calculations with 1, 2, 3, …, 8 s epochs. The robustness to noise was assessed by performing calculations with noise corrupted versions of the original signals (SNRs of 0, 5 and 10 dB). Three results were obtained in these calculations. First, mutual information effectively discriminated between states with less data. Pearson, Spearman and Kendall failed to discriminate between states with a 1 s epoch, while a statistically significant separation was obtained with mutual information. Second, at all epoch durations tested, the measure of between-state discrimination was greater for mutual information. Third, discrimination based on mutual information was more robust to noise. The limitations of this study are discussed. Further comparisons should be made with frequency domain measures, with measures constructed with embedded data and with the maximal information coefficient.     

A concise diastereoselective approach to enantioenriched substituted piperidines and their in vitro cytotoxicity evaluation

A library of diversely stereo-oriented, highly substituted 2,6-cis piperidine derivatives were synthesized, and evaluated for their anticancer activity in cancer cells that included A549 (lung cancer, CCL-185), MCF7 (breast cancer (HTB-22), DU145 (prostate cancer (HTB-81), and HeLa (cervical cancer, CCL-2). One stereo-variant emerged as a promising candidate for further design based structure–activity studies.     

A comparison of assay performance measures in screening assays: signal window, Z' factor, and assay variability ratio

In this article, the authors compare the assay performance measures, signal window, Z' factor, and assay variability ratio. They examine their mathematical formulae for similarities and differences, describe their statistical sampling properties using the results of a computer simulation, and illustrate their use with example data. Based on these results, the authors recommend the Z' factor as a preferred measure of assay performance for screening assays and point out that none of these measures are adequate for characterizing concentration-response assays.     

DipoCoup: A versatile program for 3D-structure homology comparison based on residual dipolar couplings and pseudocontact shifts

A program, DipoCoup, is presented that allows to search the protein data bank for proteins which have a three dimensional fold that is at least partially homologous to a protein under investigation. The three dimensional homology search uses secondary structure alignment based on chemical shifts and dipolar couplings or pseudocontact shifts for the three dimensional orientation of secondary structure elements. Moreover, the program offers additional tools for handling and analyzing dipolar couplings.