bluuebunny/crossref_metadata_2025_split huggingface dataset:
MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data
Authors: Plaza Oñate Florian , Le Chatelier Emmanuelle , Almeida Mathieu , Cervino Alessandra C L , Gauthier Franck , Magoulès Frédéric , Ehrlich S Dusko , Pichaud Matthieu 
Published: September 2018

Abstract

Motivation
Analysis toolkits for shotgun metagenomic data achieve strain-level characterization of complex microbial communities by capturing intra-species gene content variation. Yet, these tools are hampered by the extent of reference genomes that are far from covering all microbial variability, as many species are still not sequenced or have only few strains available. Binning co-abundant genes obtained from de novo assembly is a powerful reference-free technique to discover and reconstitute gene repertoire of microbial species. While current methods accurately identify species core parts, they miss many accessory genes or split them into small gene groups that remain unassociated to core clusters.

Results
We introduce MSPminer, a computationally efficient software tool that reconstitutes Metagenomic Species Pan-genomes (MSPs) by binning co-abundant genes across metagenomic samples. MSPminer relies on a new robust measure of proportionality coupled with an empirical classifier to group and distinguish not only species core genes but accessory genes also. Applied to a large scale metagenomic dataset, MSPminer successfully delineates in a few hours the gene repertoires of 1661 microbial species with similar specificity and higher sensitivity than existing tools. The taxonomic annotation of MSPs reveals microorganisms hitherto unknown and brings coherence in the nomenclature of the species of the human gut microbiota. The provided MSPs can be readily used for taxonomic profiling and biomarkers discovery in human gut metagenomic samples. In addition, MSPminer can be applied on gene count tables from other ecosystems to perform similar analyses.

Availability and implementation
The binary is freely available for non-commercial users at www.enterome.com/downloads.

Supplementary information
Supplementary data are available at Bioinformatics online.
Using electronic health records to characterize prescription patterns: focus on antidepressants in nonpsychiatric outpatient settings
Authors: Deferio Joseph J , Levin Tomer T , Cukor Judith , Banerjee Samprit , Abdulrahman Rozan , Sheth Amit , Mehta Neel , Pathak Jyotishman 
Published: September 2018

Abstract

Objective
To characterize nonpsychiatric prescription patterns of antidepressants according to drug labels and evidence assessments (on-label, evidence-based, and off-label) using structured outpatient electronic health record (EHR) data.

Methods
A retrospective analysis was conducted using deidentified EHR data from an outpatient practice at a New York City-based academic medical center. Structured “medication–diagnosis” pairs for antidepressants from 35 325 patients between January 2010 and December 2015 were compared to the latest drug product labels and evidence assessments.

Results
Of 140 929 antidepressant prescriptions prescribed by primary care providers (PCPs) and nonpsychiatry specialists, 69% were characterized as “on-label/evidence-based uses.” Depression diagnoses were associated with 67 233 (48%) prescriptions in this study, while pain diagnoses were slightly less common (35%). Manual chart review of “off-label use” prescriptions revealed that on-label/evidence-based diagnoses of depression (39%), anxiety (25%), insomnia (13%), mood disorders (7%), and neuropathic pain (5%) were frequently cited as prescription indication despite lacking ICD-9/10 documentation.

Conclusions
The results indicate that antidepressants may be prescribed for off-label uses, by PCPs and nonpsychiatry specialists, less frequently than believed. This study also points to the fact that there are a number of off-label uses that are efficacious and widely accepted by expert clinical opinion but have not been included in drug compendia. Despite the fact that diagnosis codes in the outpatient setting are notoriously inaccurate, our approach demonstrates that the correct codes are often documented in a patient’s recent diagnosis history. Examining both structured and unstructured data will help to further validate findings. Routinely collected clinical data in EHRs can serve as an important resource for future studies in investigating prescribing behaviors in outpatient clinics.
Socioeconomic Differences in Smoking and Cessation Across a Period of Rapid Economic Growth in an Upper-Middle-Income Country
Authors: Mariapun Jeevitha , Hairi Noran N , Ng Chiu-Wan 
Published: September 2018

AbstractIntroductionHigher smoking rates and lower cessation rates among the poor compared to the rich are evident in high-income countries. In low and middle-income countries (LMICs), many of which are in the early stages of tackling the tobacco epidemic, more knowledge is required of the socioeconomic inequalities in smoking. This is especially the case for upper-middle-income countries, where smoking prevalence is highest. This study examines trends in the socioeconomic gradient in smoking and cessation among adults across a period of rapid economic development in Malaysia, an LMIC with an upper-middle-income economy.MethodsThe socioeconomic trends in smoking were analyzed using data from cross-sectional National Health and Morbidity Surveys for the years 1996, 2006, and 2011. Household per capita income was used as a measure of socioeconomic position. As a measure of inequality, the concentration index that quantified the degree of socioeconomic inequality in a health outcome was computed. Smoking was assessed in current and former smokers. The study population was examined by gender, region, and age group.ResultsThis study found a trend of an increasingly higher smoking prevalence among the poor and higher cessation rates among the rich. With the exception of younger women in Peninsular Malaysia, the socioeconomic gradient in current smoking is concentrated among the poor. For former smokers, especially men, distributions across the years were mostly concentrated among the rich.ConclusionIt is important to ensure that health policies, programs, and interventions consider the potential impact of the socioeconomic patterning in smoking on equity in health.ImplicationsFindings on the socioeconomic gradient in smoking and cessation from Malaysia across a period of rapid economic development will contribute to addressing the paucity of knowledge on the socioeconomic gradient of smoking and cessation in other progressing LMICs. This study provides evidence from an upper-middle-income country, of an increasing trend of smoking among the poor and an increasing trend of cessation rates among the rich, particularly for men. We found opposing trends for younger adult women in the more developed, Peninsular Malaysia. More rich young women were found to have taken up smoking compared to socioeconomically less advantaged young women.
“Electronic Cigarettes” Are Not Cigarettes, and Why That Matters
Authors: Olonoff Matthew , Niaura Raymond , Hitsman Brian 
Published: September 2018

Abstract

As the prevalence rates of cigarette use have declined over the past decade, use of electronic cigarettes (e-cigarettes) continues to increase, and companies are heavily invested in manufacturing new e-cigarette products. Scientists are therefore studying e-cigarette use at a rapid rate, generally by conceptualizing e-cigarettes as similar to traditional cigarettes in their use and effects. Thinking of e-cigarettes as largely comparable with cigarettes, however, fails to capture the unique e-cigarette capabilities, user experiences, and effects on nicotine dependence and even health. Assuming that e-cigarette users puff on their devices as they do cigarettes to attain doses of nicotine comparable in magnitude and asking questions about e-cigarette use modeled after how smoking behavior has been usually assessed (eg, puff number, duration, number of cigarettes per day) may miss important differences. A greater appreciation of the distinct uniqueness of e-cigarettes, as compared with cigarettes, will help to accelerate innovative research on e-cigarettes and other electronic devices, leading to new theoretical models and behavioral measures.

Implications
With research about electronic cigarettes (e-cigarettes) rapidly increasing, this commentary addresses the conceptualization of e-cigarettes as similar to traditional cigarettes. The more we attempt to understand and measure e-cigarettes as equivalent to cigarettes, the more likely research may err in conclusions about these unique devices. Our commentary notes how using unique conceptualizations and measures for e-cigarettes will help accelerate new research.
Israel’s Global Perspective
Authors: Shindler Colin 
Published: September 2018

Abstract
Zionism set out not only to establish a state of the Jews, but also to create a Jewish society, one profoundly different from the ones the immigrants had been born into. The genocide of the Nazis, the abandonment of internationalism by the Soviet Union, and the hostility of Arab nationalism moved Zionism toward a position more concerned with national survival. Israel was forced to abandon a nonaligned status after 1950 and, when diplomatically isolated after the 1973 Yom Kippur War, to cultivate relations with regimes that were considered pariah states, such as South Africa, Chile, and Argentina. The ascendancy of the Israeli Right after 1977 accentuated this approach. The demise of the USSR, the end of the Cold War, and the signing of the Oslo Accords in the 1990s all contributed to the establishment of diplomatic relations with major states such as India and China and Arab neighbors such as Jordan, as well as to unofficial contacts with others such as Cuba. In the twenty-first century many states relegated ideology to a secondary position, assisting Israel’s policy of survivalism.
Perinatal Development of the Medial Nucleus of the Trapezoid Body
Authors: Sivaramakrishnan Shobhana , Brandebura Ashley , Holcomb Paul , Heller Daniel , Kolson Douglas , Jackson Dakota , Mathers Peter H. , Spirou George A. 
Published: September 2018

Abstract
Bushy cells (BC) of the cochlear nucleus mono-innervate their target neuron, the principal cell of the medial nucleus of the trapezoid body (MNTB), via the calyx of Held (CH) terminal, which is a typically mammalian structure and perhaps the largest nerve terminal in the brain. CH:MNTB innervation has become an attractive model to study neural circuit formation because it forms quickly, passing through stages of competition in mice within 2–4 days. BCs innervate MNTB neurons by E17, but CHs do not begin to grow for another five days (P3). Progress has been made to identify molecular factors for axon guidance, CH growth, and physiological maturation of synaptic partners, but important details remain to be discovered. We summarize key events in CH formation and highlight unresolved issues in molecular and physiological signaling, roles for non-neural cells, and the nature of competition during the first postnatal week.
The History of Clinical Neuropsychology in the Nordic Countries
Authors: Hessen Erik , Hokkanen Laura , Bartfai Aniko , Nyman Håkan , Gade Anders 
Published: September 2018

Abstract
This chapter presents views on the history of clinical neuropsychology in the Nordic countries. These countries have fostered significant contributors to clinical neuropsychology and produced a steady output of respectable clinical research. Nordic Conferences in Neuropsychology have facilitated mutual inspiration and collaboration since 1982 and have influenced training models in clinical neuropsychology. Unlike the training models in the United States and United Kingdom, which require a doctoral degree, those in the Nordic region are comparable to the training of medical specialists, requiring minimum of 9–11 years in psychology and neuropsychology education and practice before obtaining a specialty in clinical neuropsychology. This model produces high-quality specialists who are able to take responsibility in diagnostics, treatment, and rehabilitation. Such specialists have contributed to significant change in diagnostic and rehabilitation practices regarding disorders with cognitive symptoms.
Anterior-Segment Optical Coherence Tomography and Scanning Electron Microscopy to Evaluate Corneal Epithelial Changes in Patients Undergoing Glaucoma Therapy
Authors: Cennamo Gilda , Montorio Daniela , Del Prete Salvatore , Del Prete Antonio , Cennamo Giovanni 
Published: September 2018

Purpose:
To measure corneal epithelial thickness (CET) in patients with glaucoma using anterior-segment optical coherence tomography and to evaluate CET changes in relation to corneal epithelial microvilli analyzed by scanning electron microscopy (SEM).

Methods:
Twenty-two eyes (16 patients) being treated with preservative-containing topical medications and 12 normal eyes underwent anterior-segment optical coherence tomography imaging using RTVue-100. The CET maps generated corresponded to a 6-mm diameter area of cornea that was divided into 17 sectors. We compared the CETs of each sector obtained in the glaucomatous group with those obtained in the control group.

Results:
Glaucomatous eyes were divided into 2 groups based on the number of microvilli on SEM: group 1 (6 eyes) = grades 1 and 2 at SEM (range: 500–3000) and group 2 (10 eyes) = grades 3 and 4 at SEM (range: 0–500). Four CET sectors were significantly thinner in group 1 than in normal eyes: central (P = 0.012), superior (P = 0.005), temporal paracentral (P = 0.003), and temporal midperipheral (P = 0.023). No significant differences were observed between group 2 and normal eyes. CET sectors were significantly thinner in group 1 than in group 2 only in the superior (P = 0.024) and superior-temporal paracentral (P = 0.020) sectors. CET progressively increased in patients with glaucoma as the number of corneal epithelial microvilli decreased.

Conclusions:
CET and corneal epithelial microvilli are new parameters with which to evaluate early stages of corneal epithelial changes during glaucoma therapy. In advanced stages of corneal epithelial damage, SEM evaluation reveals ultrastructural epithelial changes that may not be observed on CET measurements.
Does Same-Day Postoperative Increased Intraocular Pressure Affect Endothelial Cell Density After Descemet Membrane Endothelial Keratoplasty?
Authors: Fajgenbaum Mark A. P. , Hollick Emma J. 
Published: September 2018

Purpose:
High intraocular pressure (IOP) is common in association with intracameral air and gas tamponade after Descemet membrane endothelial keratoplasty (DMEK); yet its influence on endothelial cell survival is unknown. Our aim was to determine the effect of high IOP measured 2 hours after DMEK on 1-month endothelial cell density (ECD). The influence of other potentially relevant factors was also investigated.

Methods:
Retrospective, consecutive series. Inclusions: low-to-moderate risk DMEK surgery alone or combined with phacoemulsification. Exclusions: previous penetrating keratoplasty or glaucoma surgery; grafts with any of the following in the first month: rebubble, rejection, or graft failure.

Results:
Sixty-two grafts met inclusion with 60 having IOP recorded at 2 hours. Thirty-eight percent (23/60) had IOP >30 mm Hg and 22% (13/60) had IOP >40 mm Hg at 2 hours. All grafts with IOP >30 mm Hg had air released and immediate normalization of pressure. One-month ECD (mean ± standard error of mean) was 1872 ± 58 cells/mm2, representing cell loss of 29.8 ± 2.0%. Two-hour IOP was highly insignificant against 1-month ECD when tested as a continuous variable (P = 0.78). Lower 1-month ECD was statistically correlated with lower donor count (P = 0.002) and combined DMEK-phaco surgery (P = 0.01) on univariate and multivariate analysis. Insignificant factors (P > 0.05) against 1-month ECD included patient age, sex and race, surgical indication (Fuchs endothelial dystrophy vs. non-Fuchs endothelial dystrophy), and donor age.

Conclusions:
Increased IOP at 2 hours is common after DMEK, but does not seem to influence early endothelial cell survival. One-month ECD was influenced by donor counts and combined cataract surgery.
Upper Eyelid Approach for the Reconstruction of Isolated Fractures of the Anterior Wall of the Frontal Sinus
Authors: Nguyen David , Hakimi Michael , Sinha Sumedha R. , Martin Mark 
Published: September 2018

Abstract
The management of frontal sinus fractures can vary widely depending on involvement of the anterior wall, the posterior wall, and the frontonasal duct. The main morbidity associated with isolated anterior wall fractures is an aesthetic deformity. Treatment includes coronal, endoscopic, and transcutaneous approaches. However, each has reported limitations and associated risks of iatrogenic injuries. In this paper, the authors discuss a novel approach through the upper eyelid crease and examine 4 cases where it is utilized for anterior frontal sinus wall, superior orbital rim, and orbital roof fracture repair.
Morphometric Analysis of the Facial Profile: Contour of the Side Face and its Variations
Authors: Li Haijun , Wu Xianzhu , Zhang Yidan , Chen Feng 
Published: September 2018

Abstract
Much research has been conducted on the morphological characteristics of the Chinese. However, very few facial measurements have been documented, especially of the side face. This study uses geometirc morphometric method to analyze the contour and variations of the side face in Bai and Yi ethnic minorities from Yunnan province, China. The mark collection proves that for the Bai ethnicity, the variations of the nose are comparatively large, while the forehead variations are small. Variations around the lips and the chin are the largest. For the Yi ethnicity, the forehead also witnesses small variations and the nose again has large variations. The area around the glabella has large variations. Through the comparisons, the area around the glabella tends to extrude more in males both in Bai and Yi. The situation, however, is much more different when it comes to the trichion landmark collection where we see an apparent intrusion in males. For the trichion, Yi people are more intruded than the Bai. Similarities between Bai and Yi are demonstrated by principal component analysis: one can roughly set the males apart from the females using the vertical axis. Profile at the end of horizontal axis suggests that the female facial profile has the following features: the nose is not so prominent as the male, the forehead and the nose are linked by an noticeable arc, the forehead is comparatively steep and is almost in a vertical plane with the lips and the chin. By comparison, the male has a flatter forehead, a more prominent nose, an obvious sellion, and an intruded chin. The common morphologic features of the Chinese face may be reflected through these similarities.
From mechanobiology to developmentally inspired engineering
Authors: Ingber Donald E. 
Published: September 2018

The field of mechanobiology emerged based on the recognition of the central role that physical forces play in development and physiology. In this article, which is based on a lecture I presented at the 2018 Royal Society meeting on Mechanics of Development, I review work from my laboratory carried out over the 40 years which helped to birth this field. I will also describe how we are leveraging the fundamental design principles that govern mechanoregulation to develop new experimental tools and organ-engineering approaches as well as novel mechanotherapeutics.This article is part of the Theo Murphy meeting issue ‘Mechanics of development’.
Pathway maps enable straightforward yet customized and semi-automated yet insightful analyses of omics data
Authors: Möller Steffen , Barrantes Israel , Jaster Robert , Henze Larissa , Escobar Hugo Murua , Junghanss Christian , Hakenberg Oliver , Weber Marc-André , Krause Bernd J. , Wolkenhauer Olaf , Ibrahim Saleh , Köhling Rüdiger , Lange Falko , Walter Uwe , Hamed Mohamed , Kowald Axel , Fuellen Georg 
Published: September 2018

AbstractTo explore the molecular processes underlying some biological theme of interest based on public data, gene lists are used herein as input for the construction of annotated pathway maps, employing Cytoscape apps, and then high-throughput (“omics”) gene expression data are overlaid onto these maps. Seeded with a published set of marker genes of the senescence-associated secretory phenotype and the genes of the cellular senescence KEGG pathway, a gene/protein interaction network and annotated clusters (a “pathway map”) of cellular senescence are derived. The map can be amended, by adding some application-specific genes, and overlaid with gene expression data describing cellular senescence of fibroblasts and with disease-related gene expression data associated with prostate and pancreatic cancer, and with ischemic stroke, allowing insights into the role of cellular senescence in disease. Some gene expression data are derived from the “Biomarker Benchmark repository”. The pathway map approach can be followed in principle for any biological theme of interest, fostering much-needed independence from the investigator-biased expert networks usually used for overlaying gene expression data.
Isolation and Characterization of a Novel Alkaline Lipase/Esterase Lip-1420 from a Metagenomic Library
Authors: Lim Hee Kyung , Kim Dal Rye , Woo Min Woo , Hahm Moon-Sun , Hwang In Taek 
Published: September 2018

AbstractA novel lipase gene, Lip-1420, was isolated from a metagenomics library constructed from soil samples from reed marshes and from Mt. Jumbong in Korea consisting of 112,500 recombinant plasmids. A selected recombinant plasmid, Lip-1420, was further analyzed which exhibited the maximum lipolytic activity among 18 recombinant fosmids that showed lipolytic activity. Among them, DNA sequence analysis of a 5,513 bp subclone in pUC119 Lip-1420-sub revealed that 11 ORFs were included in the gene according to the blast search from GenBank. The transformant of Lip-1420-ORF3 exhibited lipolytic activity, and plasmid pET21a(+)-Lipase-6H was constructed and transferred to the expression hostE. coliBL21(DE3). Finally, the lipase Lip1420 was purified from a FPLC system, and the recombinant enzyme was kept in a −70 ºC freezer at a concentration of 1 mg/mL in a buffer solution (50 mM Tris-HCl and 0.15 M NaCl, pH 7.4). The Lip-1420 gene was registered in GenBank (MH628529), and the purified enzyme had an optimal activity at 40 °C and pH 8.0. Kinetic analysis of the Lip-1420 lipase with the substratep-nitrophenyl palmitate was performed at 40°C and pH 8.0, and theKmandVmaxvalues of the protein were determined to be 0.268 mM and 1.821 units, respectively. The purified Lip-1420 exhibited the maximum enzymatic activity towardsp-nitrophenyl palmitate, indicating that it is an esterase.IMPORTANCEThis study provides the knowledge to develop a new lipase from the metagenomics library of rhizosphere in Korea using an activity-based method. In addition, the knowledge gained from this study has allowed us to understand that the natural ecosystems are still an unknown genetic material storage report in relation to industrially useful biocatalysts, which are still rich in biodiversity. Moreover, alkaline lipase has great potential for applications in the detergent industry. Especially in the major part of the global industrial enzyme market with high growth potential. It is used, for example, in detergent additives, biopolymer synthesis, and biodiesel production, synthesis of optically pure compounds and food additives as well as in the paper industry, perfume and fragrance blends, biological purification and waste treatment.