Review of mathematica

Mathematica is an extremely powerful tool designed to perform a multitude of mathematical operations and functions. Stephen Wolfram is the creator of the programming language and has long been a leader in the field of scientific computing. The language is rich in options and the task of learning it may seem daunting at first However, if one proceeds with small steps, first learning the basics and then new functions as becomes necessary, they will be rewarded with learning a robust, powerful language that can be used in virtually any application. Here we discuss examples of Mathematica's utility in risk assessment and review a copy of the newly released version 3. It arrives on a multi‐platform CD (i.e., Windows, Macintosh, UNIX) with a password that allows access on only one of the platforms.

Program: Mathematica, Ver. 3.0

Source: Wolfram Research, Inc., 100 Trade Center Drive, Champaign, IL 61820–7237

System: Windows 95 or Windows NT, Ver. 3.51 or higher with at least 8 MB of RAM, though at least 16 MB of RAM is recommended; many other platforms are available

Cost: Commercial price, $1295 for program, standard add‐on packages, and manual; Educational $895; Regular service $195; Premier service $385     

fingerprint: visual depiction of variation in multiple sequence alignments

There is a lack of programs available that focus on providing an overview of an aligned set of sequences such that the comparison of homologous sites becomes comprehensible and intuitive. Being able to identify similarities, differences, and patterns within a multiple sequence alignment is biologically valuable because it permits visualization of the distribution of a particular feature and inferences about the structure, function, and evolution of the sequences in question. We have therefore created a web server, fingerprint, which combines the characteristics of existing programs that represent identity, variability, charge, hydrophobicity, solvent accessibility, and structure along with new visualizations based on composition, heterogeneity, heterozygosity, d_N/d_S and nucleotide diversity. fingerprint is easy to use and globally accessible through any computer using any major browser. fingerprint is available at http://evol.mcmaster.ca/fingerprint/ .     

An integrated system for high throughput TaqMan based SNP genotyping.

We have developed an integrated laboratory information system that allows the flexible handling of pedigree, phenotype and genotype information. Specifically, it includes client applications for an integrated data import from TaqMan typing files, Mendel checking, data export, handling of pedigree and phenotype information and analysis features. AVAILABILITY: The SQL source code, sources and binaries of the client applications (NT and Windows95/98 platforms) and additional documentation are available at http://www.mucosa.de/.     

EDAS—A database of alternatively spliced human genes

EDAS, an alternatively spliced human gene database, contains data on alignment of proteins, mRNAs, and ESTs. For 8324 human genes, the database contains information on all observed exons and introns and also elementary alternatives formed therefrom. The database allows one to filter the output data by varying the cutoff threshold according to the significance level. The database is available at http://www.genebee.msu.ru/edas/.     

Diagnostic accuracy of MALDI-TOF mass spectrometry for non-small cell lung cancer: a meta-analysis

Objective: To assess the overall accuracy of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in identifying non-small cell lung cancer (NSCLC).

Methods: A comprehensive search of PubMed, EMBASE and CNKI databases as well as the reference lists from relevant articles was performed prior to July 2017. Two authors independently screened articles based on inclusion and exclusion criteria and assessed the quality of each study using the Quality Assessment of Diagnostic Accuracy Studies 2 (QADAS-2) tool. Meta-disc 1.4 and Stata12.0 software programs were used for the statistical analysis.

Results: Eleven eligible articles comprising 16 studies and representing 935 subjects were included in this meta-analysis. The pooled sensitivity and specificity were 0.84 (95% CI: 0.80–0.87) and 0.77 (95% CI: 0.74–0.80), respectively. The overall diagnostic performance as measured by the area under the curve (AUC) for the summary receiver-operating characteristic (SROC) curve was 0.9380.

Conclusions: MALDI-TOF MS has a high diagnostic accuracy for NSCLC.     

CXCR4 as a prognostic biomarker in gastrointestinal cancer: a meta-analysis

Background: CXCR4 is a member of the C-X-C chemokine receptor family, which is associated with multiple types of cancer. Although it has been widely reported, the prognostic value of CXCR4 expression in gastrointestinal (GI) cancer remains controversial.

Methods: A meta-analysis was conducted to investigate the relationship between CXCR4 and prognosis of patients with GI cancer. Subgroup analysis was also performed according to tumour subtypes and heterogeneity test.

Results: A total of 24 studies including 3637 cases suggested that overexpression of CXCR4 is significantly associated with overall survival (OS) for patients with GI cancer (HR = 1.71, 95% CI = 1.45–2.03, p?=?0.000). Subgroup analysis also indicated that high CXCR4 expression in oesophagus, gastric and colorectal cancer all predicted a worse prognosis (HR = 1.52, 95% CI = 1.26–1.84, p?=?0.001 for oesophagus cancer; HR = 1.59, 95% CI = 1.10–2.30, p?=?0.015 for gastric cancer; HR = 2.21, 95% CI = 1.56–3.14, p?=?0.000 for colorectal cancer).

Conclusions: CXCR4 may serve as a prognostic indicator in GI cancer patients.     

Association between high-sensitivity cardiac troponin T and future cardiovascular incidence in a general Japanese population: results from the Tohoku medical megabank project

Purpose: Elevation of high-sensitivity cardiac troponin T (hs-cTnT) is associated with an increased risk of cardiovascular disease (CVD). This study determined whether hs-cTnT was detectable with N-terminal pro-b-type natriuretic peptide (NT-proBNP) and related to CV risk factors in a general Japanese population.

Materials and methods: The Tohoku Medical Megabank Organization pooled individual participant data for a population-based cohort study in the Iwate prefecture (n?=?30,193, age = 60.2?±?11.5?year).

Results: Hs-cTnT levels were higher in participants with hypertension, diabetes mellitus than in participants without these conditions (all ps < 0.001). Logistic regression analysis demonstrated that NT-proBNP was strongly associated with elevation of hs-cTnT (OR = 3.35, 95% CI = 2.90–3.89, p?<?0.001). The receiver operating characteristic curve analysis showed that hs-cTnT was one of useful biomarker for the differentiation of high risk for CVD (the Suita score ≥ 56) from a general population. Logistic regression analysis demonstrated hs-cTnT levels were related to the CVD high risk group (OR = 2.67, 95% CI = 2.28–3.14, p?<?0.001).

Conclusions: Hs-cTnT levels are associated with elevation of NT-proBNP and high Suita score, which suggests that elevated hs-cTnT is related to subclinical myocardial damage and indicates CV risk.     

Web Watch

Plant biology - with an emphasis on photosynthesis

The Great Plant Escape http://www.urbanext.uiuc.edu/gpe/gpe.html

The Power of Green.http://researchmag.asu.edu/stories/power.html

Photosynthesis http://biology.ck.uc.edu/courses/biol04/photosyn.htm

An Introduction to Photosynthesis and its Applicationhttp://photoscience.la.asu.edu/photosyn/education/photointro.html

Aliens Explorers - Photosynthesis http://www.alienexplorer.com/ecology/topic3.html

The Photosynthesis Processhttp://www.ifmt.nf.ca/mi-net/enviro/photo3.htm     

Online database for mosquito (Diptera,Culicidae) occurrence records in French Guiana

A database providing information on mosquito specimens (Arthropoda: Diptera: Culicidae) collected in French Guiana is presented. Field collections were initiated in 2013 under the auspices of the CEnter for the study of Biodiversity in Amazonia (CEBA: http://www.labexceba.fr/en/). This study is part of an ongoing process aiming to understand the distribution of mosquitoes, including vector species, across French Guiana. Occurrences are recorded after each collecting trip in a database managed by the laboratory Evolution et Diversité Biologique (EDB), Toulouse, France. The dataset is updated monthly and is available online. Voucher specimens and their associated DNA are stored at the laboratory Ecologie des Forêts de Guyane (Ecofog), Kourou, French Guiana. The latest version of the dataset is accessible through EDB’s Integrated Publication Toolkit at http://130.120.204.55:8080/ipt/resource.do?r=mosquitoes_of_french_guiana or through the Global Biodiversity Information Facility data portal at http://www.gbif.org/dataset/5a8aa2ad-261c-4f61-a98e-26dd752fe1c5 It can also be viewed through the Guyanensis platform at http://guyanensis.ups-tlse.fr     

Lesser Black-backed Gulls Larus fuscus thriving on a non-marine diet

Capsule: Lesser Black-backed Gulls Larus fuscus breeding 30?km from the coast in the Netherlands focussed entirely on terrestrial food sources and reached relatively high breeding success.

Aim: To gain insight in the foraging ecology, habitat use and breeding performance of inland-breeding Lesser Black-backed Gulls.

Methods: We received data from seven birds fitted with global positioning system (GPS) loggers. The colony was frequently visited to collect pellets and boluses and to monitor reproductive success, mortality and growth rate of chicks.

Results: The GPS data revealed that mainly terrestrial habitats were used, 98% of these GPS positions were within 25?km of the colony. Refuse dumps were the most preferred sites, but also agricultural fields and freshwater bodies were often visited. Only two of the 710 recorded trips were directed to the North Sea. The pellet and bolus analyses confirmed the GPS data: no marine food remains were found. Breeding success of birds in the enclosure was relatively high, with 90% of eggs hatched and 51% of chicks fledged (1.6 chicks/pair).

Conclusions: Relying on terrestrial food is feasible when sources are available in the vicinity of the colony. We conclude that Lesser Black-backed Gulls could theoretically shift towards inland breeding after a fishery discards ban.     

C-Phycocyanin elicited antitumor efficacy via cell-cycle arrest,apoptosis induction,and invasion inhibition in esophageal squamous cell carcinoma

Objectives: Mounting evidence has demonstrated that C-Phycocyanin (C-PC) exhibits marked antitumor activity in a wide type of tumors, such as pancreas cancer, breast carcinoma, lung cancer, and colon cancer. The current study aimed to confirm the antitumor efficacy of C-PC in esophageal squamous cell carcinoma (ESCC).

Methods: The efficacy of C-PC was evaluated against the proliferation of ESCC cell lines EC9706 and EC1 by CCK-8 kit and in a mice model of ESCC EC9706. Cell cycle and apoptosis were investigated by flow cytometry, and cell invasion was determined via transwell chamber. Protein expression was examined by Western blots.

Results: We found that C-PC exhibited anti-proliferation ability in a time-dependent manner and a dose-dependent manner in ESCC EC9706 and EC1 cells. Besides, C-PC markedly arrested cell cycle in the G0/G1 phase, induced cell apoptosis and suppressed cell invasion ability in both EC9706 and EC1 cells (p?<?.01). Notably, C-PC evoked the elevations of Bax, PARP, and cleaved-caspase-3 protein, but reduced cyclin D1, CDK4, Bcl-2, MMP-2, and MMP-9 expression levels. Further investigation from in vivo experiment revealed that C-PC displayed significant antitumor efficacy in the xenografted EC9706 model.

Conclusions: Our data presented herein suggest C-PC exerts antitumor efficacy in ESCC.     

sST2 as a novel biomarker for the prediction of in-hospital mortality after coronary artery bypass grafting

Objectives: Soluble suppression of tumorigenicity 2 (sST2) biomarker is an emerging predictor of adverse clinical outcomes, but its prognostic value for in-hospital mortality after coronary artery bypass grafting (CABG) is not well understood. This study measured the association between operative sST2 levels and in-hospital mortality after CABG.

Methods: A prospective cohort of 1560 CABG patients were analyzed from the Northern New England Cardiovascular Disease Study Group Biomarker Study. The primary outcome was in-hospital mortality after CABG surgery (n?=?32).

Results: After risk adjustment, patients in the third tercile of pre-, post- and pre-to-postoperative sST2 values experienced significantly greater odds of in-hospital death compared to patients in the first tercile of sST2 values. The addition of both postoperative and pre-to-postoperative sST2 biomarker significantly improved ability to predict in-hospital mortality status following CABG surgery, compared to using the EuroSCORE II mortality model alone, (c-statistic: 0.83 [95% CI: 0.75, 0.92], p value 0.0213) and (c-statistic: 0.83 [95% CI: 0.75, 0.92], p value 0.0215), respectively.

Conclusion: sST2 values are associated with in-hospital mortality after CABG surgery and postoperative and pre-to-post operative sST2 values improve prediction. Our findings suggest that sST2 can be used as a biomarker to identify adult patients at greatest risk of in-hospital death after CABG surgery.     

Clustal W and Clustal X version 2.0

SUMMARY: The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems. AVAILABILITY: The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/     

Isolation by distance,based on microsatellite data,tested with spatial autocorrelation (spaida) and assignment test (spassign)

spassign and spaida are two small programs useful to detect isolate by distance of microsatellite loci. The programs are written in C and are available for Linux and Windows system at http://www.hi.is/~snaebj/programs.html . spaida calculates two estimates of spatial autocorrelation, Moran's I and Geary's c, first by assuming the infinite allele model, and second by assuming a stepwise mutational model. spassign calculates the assignment probabilities of an individuals genotype to the location where it was sampled and compares probabilities of assignment to other locations. Genetic distances among regions based on the overall differences in likelihoods are calculated.     

Prognostic value of PCT,copeptin, MR-proADM,MR-proANP and CT-proET-1 for severe acute dyspnea in the emergency department: the BIODINER study

Context: Acute dyspnea is a frequent complaint in patients attending the emergency department (ED).

Objective: To evaluate the accuracy of PCT, MR-proANP, MR-proADM, copeptin and CT-proET1 for the risk-stratification of severe acute dyspnea patients presenting to the ED.

Methods: Multicenter prospective study in adult patients with a chief complaint of acute dyspnea. Pro-hormone type biomarkers concentrations were measured on arrival. Combined primary endpoint was a poor outcome.

Results: Three hundred and ninety-four patients were included, 137 (35%) met the primary endpoint. MR-proADM was the only biomarker associated with the primary endpoint (odds ratio 1.43 [95%CI: 1.13–1.82], p?=?0.003) as were the presence of paradoxical abdominal breathing (odds ratio 2.48 [95%CI: 1.31–4.68]) or cyanosis (odds ratio 3.18 [1.46–6.89])

Conclusions: In patients with severe acute dyspnea in the ED, pro-hormone type biomarkers measurements have a low added value to clinical signs for the prediction of poor outcome.     

Utility of nociceptive flexion reflex threshold and bispectral index to predict movement responses under propofol anaesthesia

Introduction: The nociceptive flexion reflex threshold (NFRT) is a promising tool to monitor analgesia during general anaesthesia. Clinical studies have shown that the NFRT allows to predict movement responses to painful stimuli under a combined anaesthetic regime of sedative and opioid agents. Experimental studies indicated that the NFRT is also able to predict such movement responses under an exclusively sedative regime like propofol mono-anaesthesia. Therefore, we performed this study to investigate the ability of the NFRT to predict movement responses to painful stimuli in patients during a clinical propofol mono-anaesthesia.

Methods: We investigated 140 cardiac surgery patients during their postoperative phase under propofol mono-anaesthesia. NFRT and bispectral index (BIS) were determined in each patient right before endotracheal suctioning or painful electrical test stimulation. Prediction probabilities were calculated to quantify how accurate each measure is able to predict movement responses to the stimuli.

Results: The 124 patients included in the analysis received a median propofol dosage of 3.2 (2.5–3.9) [median (IQR)] mg/kg/h. The included patients showed 287 movement responses after a total of 725 investigated stimuli. The prediction probabilities for positive movement responses were 0.63 (95%CI: 0.59–0.67) for the NFRT and 0.69 (95%CI: 0.65–0.73) for the BIS.

Conclusions: The NFRT allows the prediction of movement responses under propofol mono-anaesthesia, which confirms its utility as a monitor to predict movement responses under general anaesthesia. The BIS allows an even more accurate prediction, although it does not reflect the physiological structures of movement suppression, but correlates closely with the dose of propofol.

Trial registration: German clinical trial register (DRKS00003062, Deutsches Register Klinischer Studien).     

Inter-regional hybrids of native and non-native Centaurea sulphurea inherit increased competitive ability from the non-natives

Background: Exotic species can rapidly develop adaptations to their non-native regions, such as increased size and competitive ability. Although these traits are believed to be responsible for invasive success, some non-invasive exotic species display them too. This suggests that increased size and competitive ability might be necessary but not sufficient to turn an exotic into a successful invader.

Aim: To assess size and competitive ability of the exotic non-invasive weed Centaurea sulphurea, and of inter-regional hybrids between native and non-native populations.

Methods: We experimentally produced a cohort of C. sulphurea individuals from the native range of the species in Spain, from its non-native range in California, as well as hybrids between the two regions. We grew these plants in pots in competition with the grass Bromus hordeaceus, or alone in control pots.

Results: Individuals from California were larger and better competitors than individuals from Spain. Furthermore, inter-regional hybrids showed competitive responses similar to that of individuals from California.

Conclusions: Our results confirm that increased competitive ability might be more frequent than previously thought among introduced species, since it can be detected in at least some exotic non-invasive species. They also illustrate the importance of maternal effects, how locally adapted traits are conserved and spread in the non-native ranges of exotic species, and suggest that plant size and competitive ability are not directly associated in this species.     

Elevated homocysteine level and prognosis in patients with acute coronary syndrome: a meta-analysis

Objective: Controversial results exist with respect to the association between elevated homocysteine level and adverse prognosis in acute coronary syndrome (ACS) patients. We performed a meta-analysis to evaluate the prognostic value of homocysteine level on ACS patients.

Materials and methods: A comprehensive literature search of PubMed and Embase databases was conducted prior to August 2018. Prospective observational studies reporting the association of baseline homocysteine level with major adverse cardiovascular events (MACE), cardiovascular or all-cause mortality in ACS patients were selected. Pooled risk ratio (RR) and corresponding 95% confidence intervals (CI) were calculated for the highest versus the lowest homocysteine level.

Results: Ten studies including 4120 ACS patients were identified. ACS patients with the highest homocysteine level had an increased risk of MACE (RR 2.01; 95% CI 1.53–2.64) and all-cause mortality (RR 2.05; 95% CI 1.50–2.79) after controlling confounding factors. However, the association between elevated homocysteine level and cardiovascular mortality (RR 1.08; 95% CI 0.83–1.39) was not statistically significant.

Conclusions: Elevated homocysteine level was associated with an increased risk of MACE and all-cause mortality among ACS patients. However, the association of elevated homocysteine level with cardiovascular mortality in ACS patients should be further confirmed in future studies.     

Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis

Introduction: The study of microbial communities based on the combined analysis of genomic and proteomic data – called metaproteogenomics – has gained increased research attention in recent years. This relatively young field aims to elucidate the functional and taxonomic interplay of proteins in microbiomes and its implications on human health and the environment.

Areas covered: This article reviews bioinformatics methods and software tools dedicated to the analysis of data from metaproteomics and metaproteogenomics experiments. In particular, it focuses on the creation of tailored protein sequence databases, on the optimal use of database search algorithms including methods of error rate estimation, and finally on taxonomic and functional annotation of peptide and protein identifications.

Expert opinion: Recently, various promising strategies and software tools have been proposed for handling typical data analysis issues in metaproteomics. However, severe challenges remain that are highlighted and discussed in this article; these include: (i) robust false-positive assessment of peptide and protein identifications, (ii) complex protein inference against a background of highly redundant data, (iii) taxonomic and functional post-processing of identification data, and finally, (iv) the assessment and provision of metrics and tools for quantitative analysis.