bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biotic interactions are an unexpected yet critical control on the complexity of an abiotically driven polar ecosystem
Authors: Lee Charles K. , Laughlin Daniel C. , Bottos Eric M. , Caruso Tancredi , Joy Kurt , Barrett John E. , Brabyn Lars , Nielsen Uffe N. , Adams Byron J. , Wall Diana H. , Hopkins David W. , Pointing Stephen B. , McDonald Ian R. , Cowan Don A. , Banks Jonathan C. , Stichbury Glen A. , Jones Irfon , Zawar-Reza Peyman , Katurji Marwan , Hogg Ian D. , Sparrow Ashley D. , Storey Bryan C. , Allan Green T. G. , Cary S. Craig 
Published: February 2019

AbstractAbiotic and biotic factors control ecosystem biodiversity, but their relative contributions remain unclear. The ultraoligotrophic ecosystem of the Antarctic Dry Valleys, a simple yet highly heterogeneous ecosystem, is a natural laboratory well-suited for resolving the abiotic and biotic controls of community structure. We undertook a multidisciplinary investigation to capture ecologically relevant biotic and abiotic attributes of more than 500 sites in the Dry Valleys, encompassing observed landscape heterogeneities across more than 200 km2. Using richness of autotrophic and heterotrophic taxa as a proxy for functional complexity, we linked measured variables in a parsimonious yet comprehensive structural equation model that explained significant variations in biological complexity and identified landscape-scale and fine-scale abiotic factors as the primary drivers of diversity. However, the inclusion of linkages among functional groups was essential for constructing the best-fitting model. Our findings support the notion that biotic interactions make crucial contributions even in an extremely simple ecosystem.
Oxylipins mediate cell-to-cell communication in Pseudomonas aeruginosa
Authors: Martínez Eriel , Cosnahan Rachael K. , Wu Mousheng , Gadila Shiva. K. , Quick Eric B. , Mobley James A. , Campos-Gómez Javier 
Published: February 2019

AbstractOxygenated unsaturated fatty acids, known as oxylipins, are signaling molecules commonly used for cell-to-cell communication in eukaryotes. However, a role for oxylipins in mediating communication in prokaryotes has not previously been described. Bacteria mainly communicate via quorum sensing, which involves the production and detection of diverse small molecules termed autoinducers. Here we show that oleic acid-derived oxylipins produced by Pseudomonas aeruginosa function as autoinducers of a novel quorum sensing system. We found that this system controls the cell density-dependent expression of a gene subset independently of the quorum sensing systems thus far described in this bacterium. We identified a LysR-type transcriptional regulator as the primary receptor of the oxylipin signal. The discovery of this oxylipin-dependent quorum sensing system reveals that prokaryote-derived oxylipins also mediate cell-to-cell communication in bacteria.
NapM enhances the survival of Mycobacterium tuberculosis under stress and in macrophages
Authors: Liu Yu , Xie Zhiwei , Zhou Xiling , Li Weihui , Zhang Hua , He Zheng-Guo 
Published: February 2019

AbstractHostile environmental cues cause Mycobacterium tuberculosis to enter a state of slow growth for survival. However, the underlying regulatory mechanism remains unclear. DnaA is essential for DNA replication initiation and represents an efficient target for growth regulation in bacteria. Here, we show that the nucleoid-associated protein NapM is a DnaA antagonist, protecting M. tuberculosis from stress-mediated killing. NapM can be induced by diverse stressful signals. It binds to DnaA to inhibit both its DNA replication origin-binding and ATP hydrolysis activity. As a DnaA antagonist, NapM inhibits the mycobacterial DNA synthesis in vitro and in vivo in M. tuberculosis. Furthermore, we show that NapM contributes to the survival of M. tuberculosis under stress and within macrophages during infection. Our findings provide a previously unidentified mechanism of mycobacterial survival under stress and also suggest NapM as a potential drug target for tuberculosis control.
Fully integrated bio‐chip with high sensitivity for electrochemical sensing application
Authors: Chen W.‐H. , Chang C.‐H. , Shih H.‐Y. , Chiu T.‐W. , Kuo C.‐N. 
Published: February 2019

This Letter presents a fully integrated bio‐system with the property of high sensitivity for electrochemical detection, which can intrinsically measure electrochemical characteristics with cyclic voltammetry. In normal circumstances, ultra‐low electrolytes exist in tissue solution, which is difficult to accurately detect the oxidation/reduction signals, limited by the innate circuit and liquid noise. Hence, the conventional topology of the potentiostat circuit is improved and proposed in this Letter to remove the required analogue‐to‐digital converter (ADC). The overall operational mechanism of the potentiostat behaves like a single‐slope ADC, which achieves a compact, easily implemented, and low‐noise design. Additionally, the effective capacitance of potentiostat and liquid resistance make an RC integration to further suppress out‐of‐band noise, thereby enabling the low‐electrolyte detection and improving detecting sensitivity. To simulate the low‐electrolyte environment, only 0.01 M (M = mol/l) phosphate buffered saline background solution is used and required to demonstrate its feasibility of the concept. The measured results show the sensor chip with high sensitivity to sense resistive variation of electrochemical action in low electrolytes.
Biomimetic mineralisation of calcium carbonate using xanthan gum as morphology control agent
Authors: Xu Wei , Liu Huang , Lou Yucui , Jin Weiping , Xue Xiaonan , Liu Xinfang , Yang Ningning 
Published: February 2019

Biomimetic synthesis of calcium carbonate (CaCO3) with various sizes and morphologies using organic matrix has become an interesting hotspot. CaCO3 was synthesised by the reaction of Na2CO3 and CaCl2 in the presence of xanthan gum (XG). The results showed that the fresh mineralised CaCO3/XG were microspheres with large surface area and porosity. The original CaCO3/XG microspheres transformed to brick‐like CaCO3 after ageing 7 days at 4°C. During the morphology transformation, CaCO3 spheres rearranged by attaching to XG molecular, and transformed from a macroscopic view of CaCO3 microspheres to a hexahedral structure related with the XG uncoiled single chains re‐associating into loose several‐fold helix. The study demonstrated that environmental effect coupled XG could be one feasible approach to regulate the structure of CaCO3.
Population genetics of Indian giant river-catfish,Sperata seenghala(Sykes, 1839) using microsatellite markers
Authors: Acharya Aditya P. , Pavan-Kumar Annam , Gireesh-Babu Pathakota , Joshi Chaitanya G. , Chaudhari Aparna , Krishna Gopal 
Published: February 2019

The giant river-catfishSperata seenghalais one of the commercially important freshwater catfishes of India with wide distribution in all major rivers and reservoirs. This fish has huge demand in domestic market due to high nutritional value and low number of intramuscular bones. Conversely, the culture practices for this fish have not yet been standardized and capture fisheries is the only source to meet the demand. This may lead to over exploitation of resources and subsequent population reduction. Knowledge on genetic structure of populations is prerequisite to formulate sustainable management and conservation measures. In the present study, 15 microsatellites were used to characterize population genetics ofS. seenghalacollected from river Brahmaputra, Ganga, Godavari, Mahanadi and Narmada. Locus-wise, the number of alleles varied from 8 to 19 with an average of 12 alleles per locus. The mean observed and expected heterozygosity values varied from 0.622 to 0.699 and 0.733 to 0.774, respectively. Several loci have shown deviation from Hardy–Weinberg equilibrium and no significant linkage disequilibrium between pairs of loci was detected. Pair-wiseFSTvalues between populations ranged from 0.135 (Brahmaputra–Ganga) to 0.173 (Brahmaputra–Narmada) and confirmed the moderate to high genetic differentiation among the populations. AMOVA, Structure and Principal Co-ordinate analyses showed significant genetic differentiation among the sampled populations ofS. seenghala. A total of 65 private alleles were recorded across populations. This study confirmed the distinctiveness of each population ofS. seenghalafrom five major rivers of India. These populations could be treated as distinct management units (MUs) for assessment and management purpose.
Propagation of two independent sources of uncertainty in the electrocardiography imaging inverse solution
Authors: Fikal Najib , Aboulaich Rajae , El Guarmah El Mahdi , Zemzemi Nejib 
Published: February 2019

This study investigates the effects of the input parameter uncertainties (organ conductivities, boundary data, etc.) on the electrocardiography (ECG) imaging problem. These inputs are very important for the construction of the torso potential for the forward problem and for the non-invasive electrical potential on the heart surface in the case of the inverse problem.
We propose a new stochastic formulation that allows us to combine both sources of errors. We formulate the forward and inverse stochastic problems by considering the input parameters as random fields and a stochastic optimal control formulation. In order to quantify multiple independent sources of uncertainties on the forward and inverse solutions, we attribute suitable probability density functions for each randomness source and apply stochastic finite elements based on generalized polynomial chaos method. The efficiency of this approach to solve the forward and inverse ECG problems and the usability to quantify the effect of organ conductivity and epicardial boundary data uncertainties in the torso are demonstrated by a number of numerical simulations on a two-dimensional computational mesh of a realistic torso geometry.
Abdominelle Notfallsonografie in der Intensiv- und Akutmedizin
Authors: Schreiber Michael , Greim Clemens-Alexander 
Published: February 2019

ZusammenfassungDie sonografischen Untersuchungstechniken unterstützen die Point-of-Care-Diagnostik (POC-Diagnostik) bei akutmedizinischen Fragestellungen. Für den Intensiv- und Notfallmediziner gilt: Kenntnisse und Fertigkeiten einer fokussierten Sonografie sind unabdingbar. Dieser Artikel beleuchtet die Optionen der abdominellen Notfallsonografie und gibt praktische Hilfestellung.
SPECT-Untersuchungen mit dem 123I-markierten
Dopamintransporter-Liganden FP-CIT (DaTSCANTM)
Authors: Tatsch Klaus , Buchert Ralph , Bartenstein Peter , Barthel Henryk , Boecker Henning , Brust Peter , Drzezga Alexander , la Fougère Christian , Gründer Gerhard , Grünwald Frank , Krause Bernd-J. , Kuwert Torsten , Langen Karl-Josef , Rominger Axel , Sabri Osama , Schreckenberger Mathias , Meyer Philipp T. 
Published: February 2019

ZusammenfassungDie S1-Leitlinie soll bei der Indikationsstellung, Durchführung, Interpretation
und Befundung von SPECT-Untersuchungen des Dopamintransporters (DAT) mit
DaTSCANTM unterstützen. Gegenüber der Vorgängerversion von 2007
berücksichtigt die vorliegende Aktualisierung und Überarbeitung die neuere
wissenschaftliche Literatur, zwischenzeitlich veröffentlichte Guidelines der
europäischen (EANM) und amerikanischen Fachgesellschaften (SNM), sowie die
aktuelle Fassung der S3-Leitlinie „Idiopathisches Parkinson-Syndrom“ der
Deutschen Gesellschaft für Neurologie. Zudem finden neue technische
Möglichkeiten Berücksichtigung.
Assessment of an Orthopaedic Templating Software Package for Cemented Total Hip Arthroplasty
Authors: Newman Michael , Shaw Grant , Kane Timothy 
Published: February 2019

AbstractThe main aim of this article was to assess a large, multisurgeon dataset of cemented total hip arthroplasties that had been templated using software. This assessment compared preoperative templated predictions with what was implanted with regard to (1) femoral prosthesis size, (2) offset, and (3) acetabular cup size. A database of total hip arthroplasties performed by four surgeons between the dates November 7, 2014 and October 31, 2017 was interrogated. The data was refined so that only primary cemented collarless polished tapered stem hip arthroplasties, fully templated on a correctly calibrated pelvic radiograph, were included. This provided 354 cases. The predicted software template was compared with actual implanted component sizes. With regard to the femoral stem, the software was exactly correct in 70.9% and accurate to within one size in 96.89% of cases. With regard to the femoral offset, the software was exactly correct in 87.01% and accurate to within one size in 99.72% of cases. With regard to the acetabular cup size, the software was exactly correct in 61.3% and accurate to within +/− 2 mm in 87.29% of cases. Templating software offers an accurate prediction of the femoral prosthesis size and offset, as well as acetabular cup size. Preoperative insight into likely component sizes and offset provides the operating surgeon with many benefits; templating the pelvic radiograph is a method of cognitive rehearsal, provides insight into potentially challenging aspects of the upcoming surgery, may highlight intraoperative issues where there is a large intraoperative deviation from what is templated, and enables efficient stock keeping for the healthcare institution.
Extreme diversification of floral volatiles within and among species ofLithophragma(Saxifragaceae)
Authors: Friberg Magne , Schwind Christopher , Guimarães Paulo R. , Raguso Robert A. , Thompson John N. 
Published: February 2019

SignificanceA major challenge in biology is to understand how complex traits important for ecological interactions between species coevolve and diversify across contrasting ecosystems. Floral scents are complex, and are often composed of a diverse array of chemicals important for interactions between plants and pollinators, herbivores, and microbial symbionts. We studied diversification of floral scents among populations of all woodland star species (Lithophragma) across far-western North America. Floral scent variation was structured not only phylogenetically among species and geographically among populations, but some of the divergence was driven by local differences in the presence of coevolvedGreyamoth pollinators. These results highlight the importance of conserving multiple populations of species if we are to maintain the evolutionary potential of coevolving interactions.
Energy Efficiency of Air Conditioners in Developing Countries: A Malaysian Case Study
Authors: Fatihah Salleh Siti , Mohd Isa Aishah , Eqwan Roslan Mohd , Ab Rashid Tuan Abdullah Tuan 
Published: February 2019

Abstract
Growing demand for air conditioner (AC) in developing countries has hit an alarming point. Enforcing higher efficiency standards for cooling appliances is one of the easier initiatives that governments can implement to reduce energy consumption and emissions of potent greenhouse gases. Malaysia has adopted the Minimum Energy Performance Standards (MEPS) in 2013 to regulate the energy performance of five common household appliances including ACs. This work sheds light on the overall improvement of AC’s energy performance after MEPS implementation. A rigorous data collection exercise was conducted to build a comprehensive sales and technical database of MEPS-compliant ACs covering the years 2013-2015. In 2015, the average energy efficiency ratio (EER) of ACs sold in the local market is 3.4, and the cumulative electricity saving and CO2 emission reduction after MEPS implementation are 1,764 GWh and 1,178 ktCO2eq respectively. The results from this study will contribute significantly to the review of the effectiveness of MEPS implementation in developing countries.
A Meta-Analysis of Complication Rates Among Different SMAS Facelift Techniques
Authors: Jacono Andrew A , Alemi A Sean , Russell Joseph L 
Published: February 2019

Abstract

Background
Sub-superficial musculo-aponeurotic system (SMAS) rhytidectomy techniques are considered to have a higher complication profile, especially for facial nerve injury, compared with less invasive SMAS techniques. This results in surgeons avoiding sub-SMAS dissection.

Objectives
The authors sought to aggregate and summarize data on complications among different SMAS facelift techniques.

Methods
A broad systematic search was performed. All included studies: (1) described a SMAS facelifting technique categorized as SMAS plication, SMASectomy/imbrication, SMAS flap, high lateral SMAS flap, deep plane, and composite; and (2) reported the number of postoperative complications in participants. Meta-analysis was performed in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines.

Results
A total 183 studies were included. High lateral SMAS (1.85%) and composite rhytidectomy (1.52%) had the highest rates of temporary nerve injury and were the only techniques to show a statistically significant difference compared with SMAS plication (odds ratio [OR] = 2.71 and 2.22, respectively, P &lt; 0.05). Risk of permanent injury did not differ among techniques. An increase in major hematoma was found for the deep plane (1.22%, OR = 1.67, P &lt; 0.05) and SMAS imbrication (1.92%, OR = 2.65, P &lt; 0.01). Skin necrosis was higher with the SMAS flap (1.57%, OR = 2.29, P &lt; 0.01).

Conclusions
There are statistically significant differences in complication rates between SMAS facelifting techniques for temporary facial nerve injury, hematoma, seroma, necrosis, and infection. Technique should be selected based on quality of results and not the complication profile.

Level of Evidence: 2
Explore, edit and leverage genomic annotations using Python GTF toolkit
Authors: Lopez F , Charbonnier G , Kermezli Y , Belhocine M , Ferré Q , Zweig N , Aribi M , Gonzalez A , Spicuglia S , Puthier D 
Published: February 2019

Abstract

Motivation
While Python has become very popular in bioinformatics, a limited number of libraries exist for fast manipulation of gene coordinates in Ensembl GTF format.

Results
We have developed the GTF toolkit Python package (pygtftk), which aims at providing easy and powerful manipulation of gene coordinates in GTF format. For optimal performances, the core engine of pygtftk is a C dynamic library (libgtftk) while the Python API provides usability and readability for developing scripts. Based on this Python package, we have developed the gtftk command line interface that contains 57 sub-commands (v0.9.10) to ease handling of GTF files. These commands may be used to (i) perform basic tasks (e.g. selections, insertions, updates or deletions of features/keys), (ii) select genes/transcripts based on various criteria (e.g. size, exon number, transcription start site location, intron length, GO terms) or (iii) carry out more advanced operations such as coverage analyses of genomic features using bigWig files to create faceted read-coverage diagrams. In conclusion, the pygtftk package greatly simplifies the annotation of GTF files with external information while providing advance tools to perform gene analyses.

Availability and implementation
pygtftk and gtftk have been tested on Linux and MacOSX and are available from https://github.com/dputhier/pygtftk under the MIT license. The libgtftk dynamic library written in C is available from https://github.com/dputhier/libgtftk.
3DBIONOTES v3.0: crossing molecular and structural biology data with genomic variations
Authors: Segura Joan , Sanchez-Garcia Ruben , Sorzano C O S , Carazo J M 
Published: February 2019

Abstract

Motivation
Many diseases are associated to single nucleotide polymorphisms that affect critical regions of proteins as binding sites or post translational modifications. Therefore, analysing genomic variants with structural and molecular biology data is a powerful framework in order to elucidate the potential causes of such diseases.

Results
A new version of our web framework 3DBIONOTES is presented. This version offers new tools to analyse and visualize protein annotations and genomic variants, including a contingency analysis of variants and amino acid features by means of a Fisher exact test, the integration of a gene annotation viewer to highlight protein features on gene sequences and a protein–protein interaction viewer to display protein annotations at network level.

Availability and implementation
The web server is available at https://3dbionotes.cnb.csic.es

Supplementary information
Supplementary data are available at Bioinformatics online.

Contact
Spanish National Institute for Bioinformatics (INB ELIXIR-ES) and Biocomputing Unit, National Centre of Biotechnology (CSIC)/Instruct Image Processing Centre, C/ Darwin nº 3, Campus of Cantoblanco, 28049 Madrid, Spain.
Trichomonas vaginalis Virus Among Women With Trichomoniasis and Associations With Demographics, Clinical Outcomes, and Metronidazole Resistance
Authors: Graves Keonte J , Ghosh Arindam P , Schmidt Norine , Augostini Peter , Secor W Evan , Schwebke Jane R , Martin David H , Kissinger Patricia J , Muzny Christina A 
Published: February 2019

AbstractBackgroundTrichomonas vaginalis virus (TVV) is a non-segmented, 4.5–5.5 kilo-base pair (kbp), double-stranded RNA virus infecting T. vaginalis. The objectives of this study were to examine the TVV prevalence in US Trichomonas vaginalis isolates and TVV’s associations with patient demographics, clinical outcomes, and metronidazole resistance.MethodsArchived T. vaginalis isolates from the enrollment visits of 355 women participating in a T. vaginalis treatment trial in Birmingham, Alabama, were thawed and grown in culture. Their total RNA was extracted using a Trizol reagent. Contaminating, single-stranded RNA was precipitated using 4.0 M Lithium Chloride and centrifugation. The samples were analyzed by gel electrophoresis to visualize a 4.5 kbp band representative of TVV. In vitro testing for metronidazole resistance was also performed on 25/47 isolates obtained from the women’s test of cure visits.ResultsTVV was detected in 142/355 (40%) isolates at the enrollment visit. Women with TVV-positive (TVV+) isolates were significantly older (P = .01), more likely to smoke (P = .04), and less likely to report a history of gonorrhea (P = .04). There was no association between the presence of clinical symptoms or repeat T. vaginalis infections with TVV+ isolates (P = .14 and P = .44, respectively). Of 25 test of cure isolates tested for metronidazole resistance, 0/10 TVV+ isolates demonstrated resistance, while 2/15 TVV-negative isolates demonstrated mild to moderate resistance (P = .23).ConclusionsOf 355 T. vaginalis isolates tested for TVV, T. vaginalis isolates tested for TVV, the prevalence was 40%. However, there was no association of TVV+ isolates with clinical symptoms, repeat infections, or metronidazole resistance. These results suggest that TVV may be commensal to T. vaginalis.