bluuebunny/crossref_metadata_2025_split huggingface dataset:
Delayed Hypersensitive Process in Subacute Subdural Hematoma
Authors: Tao Zhiqiang , Ding Shenghong , Hu Maotong , Li Jianwei 
Published: July 2015

Abstract
The authors report 2 patients with subacute subdural hematoma (sASDH). An inflammatory process is known to be involved in the development of traumatic subdural effusion (TSE) evolving into chronic subdural hemorrhage (CSDH), but a similar event has not been previously described in acute subdural hematoma (ASDH) evolving into sASDH. In our cases, dexamethasone (DXM) and other conservative treatments were administered to our first patient with dramatic clinical outcome, and a postoperative pathologic examination of the neomembrane of the sASDH in the second patient was done, which showed marked inflammatory process with T-lymphocytes and neutrophils infiltration. The good response to DXM in the first patient and the definite laboratory result of the second patient and their radiologic presentations, as well as a review of relevant literature, suggest that a T-lymphocyte-mediated, delayed hypersensitive reaction triggered by undissolved blood clot may be the driving force of ASDH developing into sASDH, which starts after the seventh day, and peaked by the end of the second week of the clinical course.
Coevolution of male and female reproductive traits drive cascading reinforcement inDrosophila yakuba
Authors: Comeault Aaron A. , Venkat Aarti , Matute Daniel R. 
Published: July 2015

ABSTRACTWhen the ranges of two hybridizing species overlap, individuals may ‘waste’ gametes on inviable or infertile hybrids. In these cases, selection against maladaptive hybridization can lead to the evolution of enhanced reproductive isolation in a process called reinforcement. On the slopes of the African island of São Tomé,Drosophila yakubaand its endemic sister speciesD. santomeahave a well-defined hybrid zone.Drosophila yakubafemales from within this zone show increased postmating-prezygotic isolation towardsD. santomeamales when compared withD. yakubafemales from allopatric populations. To understand why reinforced gametic isolation is confined to areas of secondary contact and has not spread throughout the entireD. yakubageographic range, we studied the costs of reinforcement inD. yakubausing a combination of natural collections and experimental evolution. We found thatD. yakubamales from sympatric populations sire fewer progeny than allopatric males when mated to allopatricD. yakubafemales. Our results suggest that the correlated evolution of male and female reproductive traits in sympatricD. yakubahave associated costs (i.e., reduced male fertility) that prevent the alleles responsible for enhanced isolation from spreading outside the hybrid zone.
Joint estimation of contamination, error and demography for nuclear DNA from ancient humans
Authors: Racimo Fernando , Renaud Gabriel , Slatkin Montgomery 
Published: July 2015

AbstractWhen sequencing an ancient DNA sample from a hominin fossil, DNA from present-day humans involved in excavation and extraction will be sequenced along with the endogenous material. This type of contamination is problematic for downstream analyses as it will introduce a bias towards the population of the contaminating individual(s). Quantifying the extent of contamination is a crucial step as it allows researchers to account for possible biases that may arise in downstream genetic analyses. Here, we present an MCMC algorithm to co-estimate the contamination rate, sequencing error rate and demographic parameters – including drift times and admixture rates – for an ancient nuclear genome obtained from human remains, when the putative contaminating DNA comes from present-day humans. We assume we have a large panel representing the putative contaminant population (e.g. European, East Asian or African). The method is implemented in a C++ program called ’Demographic Inference with Contamination and Error’ (DICE). We applied it to simulations and genome data from ancient Neanderthals and modern humans. With reasonable levels of genome sequence coverage (> 3X), we find we can recover accurate estimates of all these parameters, even when the contamination rate is as high as 50%.
EC-PSI: Associating Enzyme Commission Numbers with Pfam Domains
Authors: Alborzi Seyed Ziaeddin , Devignes Marie-Dominique , Ritchie David W. 
Published: July 2015

AbstractWith the growing number of protein structures in the protein data bank (PDB), there is a need to annotate these structures at the domain level in order to relate protein structure to protein function. Thanks to the SIFTS database, many PDB chains are now cross-referenced with Pfam domains and enzyme commission (EC) numbers. However, these annotations do not include any explicit relationship between individual Pfam domains and EC numbers. This article presents a novel statistical training-based method called EC-PSI that can automatically infer high confidence associations between EC numbers and Pfam domains directly from EC-chain associations from SIFTS and from EC-sequence associations from the SwissProt, and TrEMBL databases. By collecting and integrating these existing EC-chain/sequence annotations, our approach is able to infer a total of 8,329 direct EC-Pfam associations with an overall F-measure of 0.819 with respect to the manually curated InterPro database, which we treat here as a “gold standard” reference dataset. Thus, compared to the 1,493 EC-Pfam associations in InterPro, our approach provides a way to find over six times as many high quality EC-Pfam associations completely automatically.
Prediction of torsional buckling behaviour of single-walled SiC nanotubes based on molecular mechanics
Authors: Ansari Reza , Mirnezhad Mahdi , Rouhi Hessam , Bazdid-Vahdati Majid 
Published: July 2015

Purpose
– Based on the molecular mechanics approach, the purpose of this paper is to analytically investigate the torsional buckling behavior of single-walled silicon carbide nanotubes (SiCNTs) with different values of diameter and chiral angles.

Design/methodology/approach
– To this end, the mechanical properties and atomic structure of a silicon carbide (SiC) sheet are evaluated based on the density functional theory (DFT) within the framework of the generalized gradient approximation. After that force constants of the total potential energy are theoretically obtained through establishing a linkage between the viewpoints of the quantum mechanics and molecular mechanics. Explicit expressions are presented to obtain the critical buckling shear strain corresponding to different types of chirality. The present model is capable to calculate the torsional buckling behavior of SiCNTs related to various chiral angles. The critical buckling shear strain is obtained for various types of chirality and compared with each other.

Findings
– It is concluded that for all diameters, zigzag nanotubes are more stable than armchair ones. Besides it is found that the minimum critical buckling shear strain is for nanotubes with (n, n/2) chiral vector.

Originality/value
– Investigating the torsional buckling behavior of single-walled SiCNTs with different values of diameter and chiral angle. Obtaining the mechanical properties and atomic structure of the SiC sheet based on the DFT calculations. Establishing a linkage between the molecular mechanics and quantum mechanics and obtaining the force constants of the molecular mechanics. Presenting the closed-form expression to calculate the critical buckling shear strain of single-walled SiCNTs corresponding to various types of chirality.
The golden target: analyzing the tracking performance of leveraged gold ETFs
Authors: Leung Tim , Ward Brian 
Published: July 2015

Purpose
– The purpose of this study is to understand the tracking errors of leveraged exchange-traded funds (LETFs) on gold and demonstrate improved tracking performance by dynamic portfolios of gold futures.

Design/methodology/approach
– The author formulates and solves a constrained quadratic minimization problem to construct static replicating portfolios of both leveraged and unleveraged benchmarks in gold; a dynamic constant leveraged portfolio using gold futures is used to track the path of the leveraged gold benchmark.

Findings
– The results suggest that market-traded LETFs do not track a leveraged position in gold effectively over a long horizon, and the dynamic leveraged futures portfolio achieves lower tracking errors over multiple years.

Research limitations/implications
– The research informs us that investors should consider alternative portfolios with gold futures, rather than holding a leveraged gold exchange-traded funds to achieve a desired leveraged exposure in spot gold.

Originality/value
– The main contribution of the study is the use of gold futures to dynamically replicate a gold benchmark with any given leverage ratio and the detailed comparison of the tracking performance of LETFs versus optimal static and dynamic futures portfolios.
Oral health‐related knowledge, attitudes and self‐efficacy of Australian rural older adults
Authors: Mariño Rodrigo , Hopcraft Matthew , Ghanim Aghareed , Tham Rachel , Khew Chee‐Wah , Stevenson Christine 
Published: July 2015

ObjectiveA cross‐sectional study was conducted involving older adults from social clubs within a regional local government area in the state of Victoria, Australia, to identify factors associated with knowledge, and attitudes about oral health, as well as perceived self‐efficacy.MethodsParticipants underwent an oral health interview, followed by a comprehensive oral clinical examination.ResultsA total of 225 older adults participated in this study. The mean age was 70.7 (range: 55–96) years. The majority was females (62.0%) and had incomplete secondary education or less (56.1%); 34.2% were fully edentulous. The mean oral health knowledge score was 24.7 (SD 3.8). None of the socio‐demographic and oral health variables yielded a significant effect on the knowledge score. The attitude score had a mean of 5.0 (SD 1.6). Four variables remained significant in the multivariate analysis [p < 0.0001]. A dentate female, with tertiary education, had better oral health attitudes. Higher oral health knowledge scores were associated with a better attitude. The overall self‐efficacy mean value was 83.1% (SD 10.6). Dental visits and oral health knowledge remained significant in the attitudes multivariate analysis [p < 0.01].ConclusionFindings indicate that there were some misconceptions in oral health among this group of older adults. These are important influences on the success/failure of an oral health programme. Oral health education is needed to increase older adults' oral health knowledge, in particular of oral cancer, and to some extent periodontal disease, and improves attitudes and oral health self‐efficacy. Oral health knowledge, attitudes and self‐efficacy were minimally explained by socio‐demographic and clinical variables.
Participation in online continuing education
Authors: Farrell Barbara , Ward Natalie , Jennings Brad , Jones Caitlin , Jorgenson Derek , Gubbels-Smith Ashley , Dolovich Lisa , Kennie Natalie 
Published: July 2015

Abstract

Objectives
The ADAPT (ADapting pharmacists' skills and Approaches to maximize Patients' drug Therapy effectiveness) e-learning programme requires weekly participation in module activities and facilitated discussion to support skill uptake. In this study, we sought to describe the extent and pattern of, satisfaction with and factors affecting participation in the initial programme offering and reasons for withdrawal.

Methods
Mixed methods – convergent parallel approach. Participation was examined in qualitative data from discussion boards, assignments and action plans. Learner estimations of time commitment and action plan submission rates were calculated. Surveys (Likert scale and open-ended questions) included mid-point and final, exit and participation surveys.

Key findings
Eleven of 86 learners withdrew, most due to time constraints (eight completed an exit survey; seven said they would take ADAPT again). Thirty-five of 75 remaining learners completed a participation survey. Although 50–60% of the remaining 75 learners actively continued participating, only 15/35 respondents felt satisfied with their own participation. Learners spent 3–5 h/week (average) on module activities. Factors challenging participation included difficulty with technology, managing time and group work. Factors facilitating participation included willingness to learn (content of high interest) and supportive work environment. Being informed of programme time scheduling in advance was identified as a way to enhance participation.

Conclusions
This study determined extent of learner participation in an online pharmacist continuing education programme and identified factors influencing participation. Interactions between learners and the online interface, content and with other learners are important considerations for designing online education programmes. Recommendations for programme changes were incorporated following this evaluation to facilitate participation.
Environmental conditions in favour of a hantavirus outbreak in 2015 in Germany?
Authors: Reil D. , Imholt C. , Drewes S. , Ulrich R. G. , Eccard J. A. , Jacob J. 
Published: July 2015

SummaryBank voles can harbour Puumala virus (PUUV) and vole populations usually peak in years after beech mast. A beech mast occurred in 2014 and a predictive model indicates high vole abundance in 2015. This pattern is similar to the years 2009/2011 when beech mast occurred, bank voles multiplied and human PUUV infections increased a year later. Given similar environmental conditions in 2014/2015, increased risk of human PUUV infections in 2015 is likely. Risk management measures are recommended.
Temperature-Dependent Galleria mellonella Mortality as a Result of Yersinia entomophaga Infection
Authors: Hurst Mark R. H. , Beattie Amy K. , Jones Sandra A. , Hsu Pei-Chun , Calder Joanne , van Koten Chikako 
Published: July 2015

ABSTRACT

The bacterium
Yersinia entomophaga
is pathogenic to a range of insect species, with death typically occurring within 2 to 5 days of ingestion.
Per os
challenge of larvae of the greater wax moth (
Galleria mellonella
) confirmed that
Y. entomophaga
was virulent when fed to larvae held at 25°C but was avirulent when fed to larvae maintained at 37°C. At 25°C, a dose of ∼4 × 10
7
CFU per larva of a
Y. entomophaga
toxin complex (Yen-TC) deletion derivative, the
Y. entomophaga
ΔTC variant, resulted in 27% mortality. This low level of activity was restored to near-wild-type levels by augmentation of the diet with a sublethal dose of purified Yen-TC. Intrahemocoelic injection of ∼3
Y. entomophaga
or
Y. entomophaga
ΔTC cells per larva gave a 4-day median lethal dose, with similar levels of mortality observed at both 25 and 37°C. Following intrahemocoelic injection of a Yen-TC YenA1 green fluorescent protein fusion strain into larvae maintained at 25°C, the bacteria did not fluoresce until the population density reached 2 × 10
7
CFU ml
−1
of hemolymph. The observed cells also took an irregular form. When the larvae were maintained at 37°C, the cells were small and the observed fluorescence was sporadic and weak, being more consistent at a population density of ∼3 × 10
9
CFU ml
−1
of hemolymph. These findings provide further understanding of the pathobiology of
Y. entomophaga
in insects, showing that the bacterium gains direct access to the hemocoelic cavity, from where it rapidly multiplies to cause disease.
Rerouting Cellular Electron Flux To Increase the Rate of Biological Methane Production
Authors: Catlett Jennie L. , Ortiz Alicia M. , Buan Nicole R. 
Published: July 2015

ABSTRACT

Methanogens are anaerobic archaea that grow by producing methane, a gas that is both an efficient renewable fuel and a potent greenhouse gas. We observed that overexpression of the cytoplasmic heterodisulfide reductase enzyme HdrABC increased the rate of methane production from methanol by 30% without affecting the growth rate relative to the parent strain. Hdr enzymes are essential in all known methane-producing archaea. They function as the terminal oxidases in the methanogen electron transport system by reducing the coenzyme M (2-mercaptoethane sulfonate) and coenzyme B (7-mercaptoheptanoylthreonine sulfonate) heterodisulfide, CoM-S-S-CoB, to regenerate the thiol-coenzymes for reuse. In
Methanosarcina acetivorans
, HdrABC expression caused an increased rate of methanogenesis and a decrease in metabolic efficiency on methylotrophic substrates. When acetate was the sole carbon and energy source, neither deletion nor overexpression of HdrABC had an effect on growth or methane production rates. These results suggest that in cells grown on methylated substrates, the cell compensates for energy losses due to expression of HdrABC with an increased rate of substrate turnover and that HdrABC lacks the appropriate electron donor in acetate-grown cells.
Fundamental Characteristics of Deep-UV Light-Emitting Diodes and Their Application To Control Foodborne Pathogens
Authors: Shin Joo-Yeon , Kim Soo-Ji , Kim Do-Kyun , Kang Dong-Hyun 
Published: July 2015

ABSTRACT

Low-pressure mercury UV (LP-UV) lamps have long been used for bacterial inactivation, but due to certain disadvantages, such as the possibility of mercury leakage, deep-UV-C light-emitting diodes (DUV-LEDs) for disinfection have recently been of great interest as an alternative. Therefore, in this study, we examined the basic spectral properties of DUV-LEDs and the effects of UV-C irradiation for inactivating foodborne pathogens, including
Escherichia coli
O157:H7,
Salmonella enterica
serovar Typhimurium, and
Listeria monocytogenes
, on solid media, as well as in water. As the temperature increased, DUV-LED light intensity decreased slightly, whereas LP-UV lamps showed increasing intensity until they reached a peak at around 30°C. As the irradiation dosage and temperature increased,
E. coli
O157:H7 and
S
. Typhimurium experienced 5- to 6-log-unit reductions.
L. monocytogenes
was reduced by over 5 log units at a dose of 1.67 mJ/cm
2
. At 90% relative humidity (RH), only
E. coli
O157:H7 experienced inactivation significantly greater than at 30 and 60% RH. In a water treatment study involving a continuous system, 6.38-, 5.81-, and 3.47-log-unit reductions were achieved in
E. coli
O157:H7,
S
. Typhimurium, and
L. monocytogenes
, respectively, at 0.5 liter per minute (LPM) and 200 mW output power. The results of this study suggest that the use of DUV-LEDs may compensate for the drawbacks of using LP-UV lamps to inactivate foodborne pathogens.
Attenuation of Colitis by Lactobacillus casei BL23 Is Dependent on the Dairy Delivery Matrix
Authors: Lee Bokyung , Yin Xiaochen , Griffey Stephen M. , Marco Maria L. 
Published: July 2015

ABSTRACTThe role of the food delivery matrix in probiotic performance in the intestine is not well understood. Because probiotics are often provided to consumers in dairy products, we investigated the contributions of milk to the health-benefiting performance ofLactobacillus caseiBL23 in a dextran sulfate sodium (DSS)-induced murine model of ulcerative colitis.L. caseiBL23 protected against the development of colitis when ingested in milk but not in a nutrient-free buffer simulating consumption as a nutritional supplement. Consumption of (acidified) milk alone also provided some protection against weight loss and intestinal inflammation but was not as effective asL. caseiand milk in combination. In contrast,L. caseimutants deficient in DltD (lipoteichoic acidd-alanine transfer protein) or RecA (recombinase A) were unable to protect against DSS-induced colitis, even when consumed in the presence of milk. Mice fed eitherL. caseior milk contained reduced quantities of colonic proinflammatory cytokines, indicating that theL. caseiDltD−and RecA−mutants as well asL. caseiBL23 in nutrient-free buffer were effective at modulating immune responses. However, there was not a direct correlation between colitis and quantities of these cytokines at the time of sacrifice. Identification of the cecal microbiota by 16S rRNA gene sequencing showed thatL. caseiin milk enriched forComamonadaceaeandBifidobacteriaceae; however, the consumption of neitherL. caseinor milk resulted in the restoration of the microbiota to resemble that of healthy animals. These findings strongly indicate that probiotic strain efficacy can be influenced by the food/supplement delivery matrix.
Host Avian Beta-Defensin and Toll-Like Receptor Responses of Pigeons following Infection with Pigeon Paramyxovirus Type 1
Authors: Li Yanyan , Xu Qianqian , Zhang Tingting , Gao Mengying , Wang Qiuling , Han Zongxi , Shao Yuhao , Ma Deying , Liu Shengwang 
Published: July 2015

ABSTRACT

The high morbidity and mortality in pigeons caused by pigeon paramyxovirus type 1 (PPMV-1) highlights the need for new insights into the host immune response and novel treatment approaches. Host defense peptides (HDPs) are key components of the innate immune system. In this study, three novel avian β-defensins (AvBDs 2, 7, and 10) were characterized in pigeons and shown to possess direct antiviral activity against PPMV-1
in vitro
. In addition, we evaluated the mRNA expression of these AvBDs and other immune-related genes in tissues of 2-month-old infected pigeons at 3 and 7 days postinfection. We observed that the expression of AvBD2 in the cecal tonsil, lungs, and proventriculus, as well as the expression of AvBD10 in the spleen, lungs, proventriculus, and kidneys, was upregulated in infected pigeons. Similarly, the expression of both Toll-like receptor 3 (TLR3) and TLR7 was increased in the spleen, trachea, and proventriculus, while TLR15 expression was increased only in the lungs of infected pigeons. In addition, inducible nitric oxide synthase (iNOS) expression was upregulated in the spleen, the bursa of Fabricius, the trachea, and the proventriculus of infected pigeons. Furthermore, we observed a high correlation between the expression of AvBD2 and the expression of either TLR7 or TLR15, as well as between AvBD10 expression and either TLR3 or TLR7 expression in respective tissues. The results suggest that PPMV-1 infection can induce innate host responses characterized by the activation of TLRs, particularly TLR3 and TLR7, AvBDs (2 and 10), and iNOS in pigeons.