bluuebunny/crossref_metadata_2025 huggingface dataset:
Requirements for the evaluation of computational speech segregation systems
Authors: May Tobias , Dau Torsten
Published: November 2014

Recent studies on computational speech segregation reported improved speech intelligibility in noise when estimating and applying an ideal binary mask with supervised learning algorithms. However, an important requirement for such systems in technical applications is their robustness to acoustic conditions not considered during training. This study demonstrates that the spectro-temporal noise variations that occur during training and testing determine the achievable segregation performance. In particular, such variations strongly affect the identification of acoustical features in the system associated with perceptual attributes in speech segregation. The results could help establish a framework for a systematic evaluation of future segregation systems.
Cohesion and Performance for Female and Male Sport Teams
Authors: Eys Mark , Evans M. Blair , Martin Luc J. , Ohlert Jeannine , Wolf Svenja A. , Van Bussel Michael , Steins Charlotte
Published: November 2014

A previous meta-analysis examining the relationship between cohesion and performance (Carron, Colman, Wheeler, & Stevens, 2002) revealed that this relationship was significantly stronger for female teams as compared with male teams. The purpose of the current study was to explore perceptions of the cohesion-performance relationship by coaches who have led teams of both genders. Semistructured interviews were employed with Canadian and German coaches with previous experience leading both male and female sport teams. The information obtained through the interviews yielded a number of categories pertaining to potential similarities and differences within female and male sport teams including: (a) the nature of cohesion (e.g., direction of the cohesion-performance relationship), (b) antecedents of cohesion (e.g., approaches to conflict), and (c) the management of cohesion (e.g., developing social cohesion). Overall, the results offer testable propositions regarding gender differences and group involvement in a sport context as well as informing best practices such that teams can attain optimal performance.
Cell cycle–dependent regulation of mitochondrial preprotein translocase
Authors: Harbauer Angelika B. , Opalińska Magdalena , Gerbeth Carolin , Herman Josip S. , Rao Sanjana , Schönfisch Birgit , Guiard Bernard , Schmidt Oliver , Pfanner Nikolaus , Meisinger Chris
Published: November 2014

Mitochondria play central roles in cellular energy conversion, metabolism, and apoptosis. Mitochondria import more than 1000 different proteins from the cytosol. It is unknown if the mitochondrial protein import machinery is connected to the cell division cycle. We found that the cyclin-dependent kinase Cdk1 stimulated assembly of the main mitochondrial entry gate, the translocase of the outer membrane (TOM), in mitosis. The molecular mechanism involved phosphorylation of the cytosolic precursor of Tom6 by cyclin Clb3-activated Cdk1, leading to enhanced import of Tom6 into mitochondria. Tom6 phosphorylation promoted assembly of the protein import channel Tom40 and import of fusion proteins, thus stimulating the respiratory activity of mitochondria in mitosis. Tom6 phosphorylation provides a direct means for regulating mitochondrial biogenesis and activity in a cell cycle-specific manner.
Differentiation of Classical Swine Fever Virus Infection from CP7_E2alf Marker Vaccination by a Multiplex Microsphere Immunoassay
Authors: Xia Hongyan , Harimoorthy Rajiv , Vijayaraghavan Balaje , Blome Sandra , Widén Frederik , Beer Martin , Belák Sándor , Liu Lihong
Published: November 2014

Classical swine fever (CSF) is a highly contagious viral disease of pigs that has a tremendous socioeconomic impact. Vaccines are available for disease control. However, most industrialized countries are implementing stamping-out strategies to eliminate the disease and avoid trade restrictions. These restrictions can be avoided through the use of marker vaccines such as CP7_E2alf. Marker vaccines have to be accompanied by reliable and robust discriminatory assays. In this context, a multiplex microsphere immunoassay for serological differentiation of infected from vaccinated animals (DIVA) was developed to distinguish CSF virus (CSFV)-infected animals from CP7_E2alf-vaccinated animals. To this end, three viral proteins, namely, CSFV E2, CSFV Erns, and bovine viral diarrhea virus (BVDV) E2, were produced in insect cells using a baculovirus expression system; they were used as antigens in a microsphere immunoassay, which was further evaluated by testing a large panel of pig sera and compared to a well-characterized commercial CSFV E2 antibody enzyme-linked immunosorbent assays (ELISAs) and a test version of an improved CSFV Ernsantibody ELISA. Under a cutoff median fluorescence intensity value of 5,522, the multiplex microsphere immunoassay had a sensitivity of 98.5% and a specificity of 98.9% for the detection of antibodies against CSFV E2. The microsphere immunoassay and the CSFV ErnsELISA gave the same results for 155 out of 187 samples (82.8%) for the presence of CSFV Ernsantibodies. This novel multiplex immunoassay is a valuable tool for measuring and differentiating immune responses to vaccination and/or infection in animals.
Draft Genome Sequence of Chromobacterium haemolyticum Causing Human Bacteremia Infection in Japan
Authors: Miki Tsuyoshi , Okada Nobuhiko
Published: November 2014

Chromobacterium haemolyticum
is a Gram-negative bacterium displaying remarkable hemolysis against human and sheep erythrocytes. In addition,
C. haemolyticum
infects humans, in which the infection mechanism remains unknown. We report here the draft genome sequence of
C. haemolyticum
strain T124, isolated from a young patient with sepsis in Japan.
Complete Genome Assembly of Staphylococcus epidermidis AmMS 205
Authors: Davenport K. W. , Daligault H. E. , Minogue T. D. , Bishop-Lilly K. A. , Broomall S. M. , Bruce D. C. , Chain P. S. , Coyne S. R. , Frey K. G. , Gibbons H. S. , Jaissle J. , Redden C. L. , Rosenzweig C. N. , Scholz M. B. , Teshima H. , Johnson S. L.
Published: November 2014

Staphylococcus epidermidis
causes a large number of catheter-related sepsis infections annually in the United States. We present the 2.54-Mbp complete genome assembly of reference strain
S. epidermidis
AmMS 205, including a single 37.7-kbp plasmid. The annotated assembly is available in GenBank under accession numbers CP009046 and CP009047.
Draft Genome Sequence of Non-O1 and Non-O139 Vibrio cholerae Strain VCC19
Authors: de Sá Pablo Caracciolo Gomes , Da Silva Miriam Lopes , Carneiro Adriana Ribeiro , Gomes Jaqueline Conceição Meireles , Dias Larissa Maranhão , Alves Jorianne Thyeska Castro , De Oliveira Veras Adonney Allan , Baraúna Rafael Azevedo , Das Graças Diego Assis , Matté Maria Helena , Sato Maria Ines Zanolli , Hachich Elayse Maria , Matté Glavur Rogério , Ramos Rommel Thiago Jucá , Silva Artur
Published: November 2014

Vibrio cholerae
O1 is the causative agent of cholera and is ubiquitous in the aquatic environment, while
V. cholerae
strains non-O1 and non-O139 are recognized as causative agents of sporadic and localized outbreaks of diarrhea. Here, we report the complete sequence of a non-O1 and non-O139
V. cholerae
strain (VCC19), which was isolated from the environment in Brazil. The sequence includes the integrative conjugative element (ICE). This paper is the first report of the presence of such an element in a
V. cholerae
strain isolated in Brazil.
Complete Genome Sequence of the Quality Control Strain Staphylococcus aureus subsp.
aureus
ATCC 25923
Authors: Treangen Todd J. , Maybank Rosslyn A. , Enke Sana , Friss Mary Beth , Diviak Lynn F. , Karaolis David K. R. , Koren Sergey , Ondov Brian , Phillippy Adam M. , Bergman Nicholas H. , Rosovitz M. J.
Published: November 2014

Staphylococcus aureus
subsp.
aureus
ATCC 25923 is commonly used as a control strain for susceptibility testing to antibiotics and as a quality control strain for commercial products. We present the completed genome sequence for the strain, consisting of the chromosome and a 27.5-kb plasmid.
Draft Genome Sequence of
Sulfitobacter
sp. CB2047, a Member of the
Roseobacter
Clade of Marine Bacteria, Isolated from an
Emiliania huxleyi
Bloom
Authors: Ankrah Nana Y. D. , Lane Thomas , Budinoff Charles R. , Hadden Mary K. , Buchan Alison
Published: November 2014

We announce the draft genome sequence of
Sulfitobacter
sp. strain CB2047, a marine bacterium of the
Roseobacter
clade, isolated from a phytoplankton bloom. The genome encodes pathways for the catabolism of aromatic compounds as well as transformations of carbon monoxide and sulfur species. The strain also encodes a prophage as well as the gene transfer agent (GTA), both of which are prevalent among members of the
Rhodobacterales
order.
Draft Genome Sequence of Bacillus fengqiuensis FJAT-14578, Isolated from a Soil Sample in China
Authors: Liu Guo-Hong , Liu Bo , Tang Jian-Yang , Che Jian-Mei , Zhu Yu-Jing , Su Ming-Xing , Wang Jie-Ping , Chen Qian-Qian
Published: November 2014

Here, we report the first high-quality draft genome sequence of
Bacillus fengqiuensis
FJAT-14578, isolated from a soil sample collected from China. The genome size was 5,569,389 bp, with a 40.93 mol% G+C content. The number of tRNAs was 69 and of rRNAs was 10 (5S, 16S, and 23S).
Whole-Genome Sequences of Five Oligotrophic Bacteria Isolated from Deep within Lechuguilla Cave, New Mexico
Authors: Gan Huan You , Gan Han Ming , Tarasco Alexander Mario , Busairi Nurfatini Idayu , Barton Hazel A. , Hudson André O. , Savka Michael A.
Published: November 2014

Here, we report the whole-genome sequences and annotation of five oligotrophic bacteria from two sites within the Lechuguilla Cave in the Carlsbad Caverns National Park, NM. Three of the five genomes contain an acyl-homoserine lactone signal synthase ortholog (
luxI
) that is involved in cell-to-cell communication via quorum sensing.
Draft Genome Sequence of a Novel SAR11 Clade Species Abundant in a Tibetan Lake
Authors: Oh Seungdae , Zhang Rui , Wu Qinglong L. , Liu Wen-Tso
Published: November 2014

SAR11 clade bacteria are abundant and play a key role in the nutrient cycles of marine and, presumably, inland aquatic environments. We report here the draft genome sequence of a novel species in the SAR11 cluster, reconstructed from a metagenomic data set obtained from a Tibetan lake.
Draft Genome Sequence of Bacillus subtilis Strain NKYL29, an Antimicrobial-Peptide-Producing Strain from Soil
Authors: Jiang Yanbin , Xu Haijin , Li Ying , Liu Hongbin , Yu Lei , Qiao Mingqiang , Liu Gang
Published: November 2014

Bacillus subtilis
strain NKYL29 is an antimicrobial-peptide-producing strain isolated from the soil of Ranzhuang Tunnel in Hebei Province, China. Here, we present the draft genome of this strain, which provides the genetic basis for application of the antimicrobial peptide.
Draft Genome Sequence of the Iron-Oxidizing Acidophile Leptospirillum ferriphilum Type Strain DSM 14647
Authors: Cárdenas Juan Pablo , Lazcano Marcelo , Ossandon Francisco J. , Corbett Melissa , Holmes David S. , Watkin Elizabeth
Published: November 2014

The genomic features of the
Leptospirillum ferriphilum
type strain DSM 14647 are described here. An analysis of the predicted genes enriches our knowledge of the molecular basis of iron oxidation, improves our understanding of its role in industrial bioleaching, and suggests how it is adapted to live at extremely low pH.
Genome Sequence of Rickettsia hoogstraalii, a Geographically Widely Distributed Tick-Associated Bacterium
Authors: Sentausa Erwin , El Karkouri Khalid , Nguyen Thi-Tien , Caputo Aurélia , Raoult Didier , Fournier Pierre-Edouard
Published: November 2014

Rickettsia hoogstraalii
is a tick-associated member of the spotted fever group rickettsiae that is geographically widely distributed. We report here the draft genome of
R. hoogstraalii
strain Croatica
T
(=DSM 22243 = UTMB 00003), which was isolated from
Haemaphysalis sulcata
ticks collected in Croatia.
Streamlining HIV Testing for HIV Preexposure Prophylaxis
Authors: Guanira Juan V. , Leigler Teri , Kallas Esper , Schechter Mauro , Sharma Usha , Glidden David , Grant Robert M.
Published: November 2014

HIV-testing algorithms for preexposure prophylaxis (PrEP) should be optimized to minimize the risk of drug resistance, the time off PrEP required to evaluate false-positive screening results, and costs and to expedite the start of therapy for those confirmed to be infected. HIV rapid tests (RTs) for anti-HIV antibodies provide results in less than 1 h and can be conducted by nonlicensed staff at the point of care. In many regions, Western blot (WB) testing is required to confirm reactive RT results. WB testing, however, causes delays in diagnosis and adds expense. The iPrEx study evaluated the safety and efficacy of daily oral emtricitabine-tenofovir disoproxil fumarate among HIV-seronegative men and transgender women who have sex with men: HIV infection was assessed with two RTs plus WB confirmation, followed by HIV-1 plasma viral load testing. During the iPrEx study, there were 51,260 HIV status evaluations among 2,499 volunteers using RTs: 142 (0.28%) had concordant positive results (100% were eventually confirmed) and 19 (0.04%) had discordant results among 14 participants; 11 were eventually determined to be HIV infected. A streamlined approach using only one RT to screen and a second RT to confirm (without WB) would have had nearly the same accuracy. Discrepant RT results are best evaluated with nucleic acid testing, which would also increase sensitivity.
Cognate CD4 T-Cell Licensing of Dendritic Cells Heralds Anti-Cytomegalovirus CD8 T-Cell Immunity after Human Allogeneic Umbilical Cord Blood Transplantation
Authors: Flinsenberg T. W. H. , Spel L. , Jansen M. , Koning D. , de Haar C. , Plantinga M. , Scholman R. , van Loenen M. M. , Nierkens S. , Boon L. , van Baarle D. , Heemskerk M. H. M. , Boelens J. J. , Boes M.
Published: November 2014

Reactivation of human cytomegalovirus (CMV) is hazardous to patients undergoing allogeneic cord blood transplantation (CBT), lowering survival rates by approximately 25%. While antiviral treatment ameliorates viremia, complete viral control requires CD8
+
T-cell-driven immunity. Mouse studies suggest that cognate antigen-specific CD4
+
T-cell licensing of dendritic cells (DCs) is required to generate effective CD8
+
T-cell responses. For humans, this was not fully understood. We here show that CD4
+
T cells are essential for licensing of human DCs to generate effector and memory CD8
+
T-cell immunity against CMV in CBT patients. First, we show in CBT recipients that clonal expansion of CMV-pp65-specific CD4
+
T cells precedes the rise in CMV-pp65-specific CD8
+
T cells. Second, the elicitation of CMV-pp65-specific CD8
+
T cells from rare naive precursors in cord blood requires DC licensing by cognate CMV-pp65-specific CD4
+
T cells. Finally, also CD8
+
T-cell memory responses require CD4
+
T-cell-mediated licensing of DCs in our system, by secretion of gamma interferon (IFN-γ) by pp65-specific CD4
+
T cells. Together, these data show that human DCs require licensing by cognate antigen-specific CD4
+
T cells to elicit effective CD8
+
T-cell-mediated immunity and fight off viral reactivation in CBT patients.

IMPORTANCE
Survival rates after stem cell transplantation are lowered by 25% when patients undergo reactivation of cytomegalovirus (CMV) that they harbor. Immune protection against CMV is mostly executed by white blood cells called killer T cells. We here show that for generation of optimally protective killer T-cell responses that respond to CMV, the early elicitation of help from a second branch of CMV-directed T cells, called helper T cells, is required.
The Influenza Virus Neuraminidase Protein Transmembrane and Head Domains Have Coevolved
Authors: da Silva Diogo V. , Nordholm Johan , Dou Dan , Wang Hao , Rossman Jeremy S. , Daniels Robert
Published: November 2014

Transmembrane domains (TMDs) from single-spanning membrane proteins are commonly viewed as membrane anchors for functional domains. Influenza virus neuraminidase (NA) exemplifies this concept, as it retains enzymatic function upon proteolytic release from the membrane. However, the subtype 1 NA TMDs have become increasingly more polar in human strains since 1918, which suggests that selection pressure exists on this domain. Here, we investigated the N1 TMD-head domain relationship by exchanging a prototypical “old” TMD (1933) with a “recent” (2009), more polar TMD and an engineered hydrophobic TMD. Each exchange altered the TMD association, decreased the NA folding efficiency, and significantly reduced viral budding and replication at 37°C compared to at 33°C, at which NA folds more efficiently. Passaging the chimera viruses at 37°C restored the NA folding efficiency, viral budding, and infectivity by selecting for NA TMD mutations that correspond with their polar or hydrophobic assembly properties. These results demonstrate that single-spanning membrane protein TMDs can influence distal domain folding, as well as membrane-related processes, and suggest the NA TMD in H1N1 viruses has become more polar to maintain compatibility with the evolving enzymatic head domain.

IMPORTANCE
The neuraminidase (NA) protein from influenza A viruses (IAVs) functions to promote viral release and is one of the major surface antigens. The receptor-destroying activity in NA resides in the distal head domain that is linked to the viral membrane by an N-terminal hydrophobic transmembrane domain (TMD). Over the last century, the subtype 1 NA TMDs (N1) in human H1N1 viruses have become increasingly more polar, and the head domains have changed to alter their antigenicity. Here, we provide the first evidence that an “old” N1 head domain from 1933 is incompatible with a “recent” (2009), more polar N1 TMD sequence and that, during viral replication, the head domain drives the selection of TMD mutations. These mutations modify the intrinsic TMD assembly to restore the head domain folding compatibility and the resultant budding deficiency. This likely explains why the N1 TMDs have become more polar and suggests the N1 TMD and head domain have coevolved.
Expression of the Epidermodysplasia Verruciformis-Associated Genes
EVER1
and
EVER2
Is Activated by Exogenous DNA and Inhibited by LMP1 Oncoprotein from Epstein-Barr Virus
Authors: Frecha Cecilia , Chevalier Sébastien A. , van Uden Patrick , Rubio Ivonne , Siouda Maha , Saidj Djamel , Cohen Camille , Lomonte Patrick , Accardi Rosita , Tommasino Massimo
Published: November 2014

EVER1
and
EVER2
are mutated in epidermodysplasia verruciformis patients, who are susceptible to human betapapillomavirus (HPV) infection. It is unknown whether their products control the infection of other viruses. Here, we show that the expression of both genes in B cells is activated immediately after Epstein-Barr virus (EBV) infection, whereas at later stages, it is strongly repressed via activation of the NF-κB signaling pathway by latent membrane protein 1 (LMP1). Ectopic expression of
EVER1
impairs the ability of EBV to infect B cells.
Peri- and Postharvest Factors in the Control of Shiga Toxin-Producing
Escherichia coli
in Beef
Authors: Moxley Rodney A. , Acuff Gary R.
Published: November 2014

Certain Shiga toxin-producing
Escherichia coli
(STEC) strains are important causes of food-borne disease, with hemorrhagic colitis and, in some cases, hemolytic-uremic syndrome as the clinical manifestations of illness. Six serogroups and one serotype of STEC (O26, O45, O103, O111, O121, O145, and O157:H7) are responsible for the vast majority of cases in the United States. Based on recent data for all food commodities combined, 55.3% and 50.0% of the outbreaks of STEC O157 and non-O157 in the United States, respectively, are attributable to beef as a food source. Consequently, the U.S. Department of Agriculture, Food Safety and Inspection Service declared these organisms as adulterants in raw, nonintact beef. In North America, cattle are a major reservoir of STEC strains, with organisms shed in the feces and contaminated hides of the animals being the main vehicle for spread to carcasses at slaughter. A number of peri- and postharvest interventions targeting STEC have been developed, and significant progress has been made in improving the microbiological quality of beef in the past 20 years as a result. However, continued improvements are needed, and accurate assessment of these interventions, especially for non-O157 STEC, would greatly benefit from improvements in detection methods for these organisms.
The Serine Recombinases
Authors: Stark W. Marshall
Published: November 2014

In site-specific recombination, two short DNA sequences (‘sites’) are each cut at specific points in both strands, and the cut ends are rejoined to new partners. The enzymes that mediate recognition of the sites and the subsequent cutting and rejoining steps are called recombinases. Most recombinases fall into one of two families according to similarities of their protein sequences and mechanisms; these families are known as the tyrosine recombinases and the serine recombinases, the names referring to the conserved amino acid residue that attacks the DNA phosphodiester and becomes covalently linked to a DNA strand end during catalysis. This chapter gives an overview of our current understanding of the serine recombinases, their types, biological roles, structures, catalytic mechanisms, mechanisms of regulation, and applications.
Plasmid-Mediated Tolerance Toward Environmental Pollutants
Authors: Segura Ana , Molina Lázaro , Ramos Juan Luis
Published: November 2014

The survival capacity of microorganisms in a contaminated environment is limited by the concentration and/or toxicity of the pollutant. Through evolutionary processes, some bacteria have developed or acquired mechanisms to cope with the deleterious effects of toxic compounds, a phenomenon known as tolerance. Common mechanisms of tolerance include the extrusion of contaminants to the outer media and, when concentrations of pollutants are low, the degradation of the toxic compound. For both of these approaches, plasmids that encode genes for the degradation of contaminants such as toluene, naphthalene, phenol, nitrobenzene, and triazine or are involved in tolerance toward organic solvents and heavy metals, play an important role in the evolution and dissemination of these catabolic pathways and efflux pumps. Environmental plasmids are often conjugative and can transfer their genes between different strains; furthermore, many catabolic or efflux pump genes are often associated with transposable elements, making them one of the major players in bacterial evolution. In this review, we will briefly describe catabolic and tolerance plasmids and advances in the knowledge and biotechnological applications of these plasmids.
Plasmid Biopharmaceuticals
Authors: Prazeres Duarte Miguel F. , Monteiro Gabriel A.
Published: November 2014

Plasmids are currently an indispensable molecular tool in life science research and a central asset for the modern biotechnology industry, supporting its mission to produce pharmaceutical proteins, antibodies, vaccines, industrial enzymes, and molecular diagnostics, to name a few key products. Furthermore, plasmids have gradually stepped up in the past 20 years as useful biopharmaceuticals in the context of gene therapy and DNA vaccination interventions. This review provides a concise coverage of the scientific progress that has been made since the emergence of what are called today plasmid biopharmaceuticals. The most relevant topics are discussed to provide researchers with an updated overview of the field. A brief outline of the initial breakthroughs and innovations is followed by a discussion of the motivation behind the medical uses of plasmids in the context of therapeutic and prophylactic interventions. The molecular characteristics and rationale underlying the design of plasmid vectors as gene transfer agents are described and a description of the most important methods used to deliver plasmid biopharmaceuticalsin vivo(gene gun, electroporation, cationic lipids and polymers, and micro- and nanoparticles) is provided. The major safety issues (integration and autoimmunity) surrounding the use of plasmid biopharmaceuticals is discussed next. Aspects related to the large-scale manufacturing are also covered, and reference is made to the plasmid products that have received marketing authorization as of today.
Fruit and vegetable intake and risk of type 2 diabetes mellitus: meta-analysis of prospective cohort studies
Authors: Li Min , Fan Yingli , Zhang Xiaowei , Hou Wenshang , Tang Zhenyu
Published: November 2014

Objective

To clarify and quantify the potential dose–response association between the intake of fruit and vegetables and risk of type 2 diabetes.

Design

Meta-analysis and systematic review of prospective cohort studies.

Data source

Studies published before February 2014 identified through electronic searches using PubMed and Embase.

Eligibility criteria for selecting studies

Prospective cohort studies with relative risks and 95% CIs for type 2 diabetes according to the intake of fruit, vegetables, or fruit and vegetables.

Results

A total of 10 articles including 13 comparisons with 24 013 cases of type 2 diabetes and 434 342 participants were included in the meta-analysis. Evidence of curve linear associations was seen between fruit and green leafy vegetables consumption and risk of type 2 diabetes (p=0.059 and p=0.036 for non-linearity, respectively). The summary relative risk of type 2 diabetes for an increase of 1 serving fruit consumed/day was 0.93 (95% CI 0.88 to 0.99) without heterogeneity among studies (p=0.477, I2=0%). For vegetables, the combined relative risk of type 2 diabetes for an increase of 1 serving consumed/day was 0.90 (95% CI 0.80 to 1.01) with moderate heterogeneity among studies (p=0.002, I2=66.5%). For green leafy vegetables, the summary relative risk of type 2 diabetes for an increase of 0.2 serving consumed/day was 0.87 (95% CI 0.81 to 0.93) without heterogeneity among studies (p=0.496, I2=0%). The combined estimates showed no significant benefits of increasing the consumption of fruit and vegetables combined.

Conclusions

Higher fruit or green leafy vegetables intake is associated with a significantly reduced risk of type 2 diabetes.
Protocol of the Australasian Malignant Pleural Effusion (AMPLE) trial: a multicentre randomised study comparing indwelling pleural catheter versus talc pleurodesis
Authors: Fysh Edward T H , Thomas Rajesh , Read Catherine A , Lam Ben C H , Yap Elaine , Horwood Fiona C , Lee Pyng , Piccolo Francesco , Shrestha Ranjan , Garske Luke A , Lam David C L , Rosenstengel Andrew , Bint Michael , Murray Kevin , Smith Nicola A , Lee Y C Gary
Published: November 2014

Introduction

Malignant pleural effusion can complicate most cancers. It causes breathlessness and requires hospitalisation for invasive pleural drainages. Malignant effusions often herald advanced cancers and limited prognosis. Minimising time spent in hospital is of high priority to patients and their families. Various treatment strategies exist for the management of malignant effusions, though there is no consensus governing the best choice. Talc pleurodesis is the conventional management but requires hospitalisation (and substantial healthcare resources), can cause significant side effects, and has a suboptimal success rate. Indwelling pleural catheters (IPCs) allow ambulatory fluid drainage without hospitalisation, and are increasingly employed for management of malignant effusions. Previous studies have only investigated the length of hospital care immediately related to IPC insertion. Whether IPC management reduces time spent in hospital in the patients’ remaining lifespan is unknown. A strategy of malignant effusion management that reduces hospital admission days will allow patients to spend more time outside hospital, reduce costs and save healthcare resources.

Methods and analysis

The Australasian Malignant Pleural Effusion (AMPLE) trial is a multicentred, randomised trial designed to compare IPC with talc pleurodesis for the management of malignant pleural effusion. This study will randomise 146 adults with malignant pleural effusions (1:1) to IPC management or talc slurry pleurodesis. The primary end point is the total number of days spent in hospital (for any admissions) from treatment procedure to death or end of study follow-up. Secondary end points include hospital days specific to pleural effusion management, adverse events, self-reported symptom and quality-of-life scores.

Ethics and dissemination

The Sir Charles Gairdner Group Human Research Ethics Committee has approved the study as have the ethics boards of all the participating hospitals. The trial results will be published in peer-reviewed journals and presented at scientific conferences.

Trial registration numbers

Australia New Zealand Clinical Trials Registry—ACTRN12611000567921; National Institutes of Health—NCT02045121.
Diffuse decidual leucocytoclastic necrosis and NK cell aggregates: two distinct features of miscarriage
Authors: Lee Joong Yeup , Kim Eun Na , Hong Joon-Seok , Shim Jae-Yoon , Hwang Doyeong , Kim Ki Chul , Lee JungBok , Kim Chong Jai
Published: November 2014

Aims

Primary histopathology of miscarriage remains undetermined in the majority of cases. This study was conducted to determine histological characteristics pertinent to miscarriage.

Methods

The study groups were composed of elective abortions (n=29) and miscarriages (n=45) comprised of chromosomally normal (n=15) and abnormal cases (n=30). Immunohistochemistry was done against CD3, CD8, TIA-1 and CD56.

Results

Two histological features—diffuse decidual leucocytoclastic necrosis (DDLN) and decidual natural killer cell aggregates (NKCA)—were relatively common in miscarriages. The frequencies of DDLN and NKCA were different between the groups (p<0.05 and p<0.05, respectively). DDLN was found in 13.8% (4/29) of elective abortions, while it was observed in 60.0% (9/15) and 23.3% (7/30) of chromosomally normal and abnormal miscarriages, respectively. DDLN was more frequent in chromosomally normal miscarriages than in elective abortions (p=0.004). NKCA was present in 13.8% (4/29) of elective abortions, while being found in 33.3% (5/15) and 43.3% (13/30) of chromosomally normal and abnormal miscarriages, respectively. NKCA was more frequent in chromosomally abnormal miscarriages than in elective abortions (p=0.020).

Conclusions

The findings strongly suggest that defective placentation and abnormal maternal immune response are associated with miscarriage. DDLN and NKCA seem to have diagnostic values in the pathological evaluation of miscarriage.
Endotoxin detection in end-stage kidney disease
Authors: Wong Jonathan , Jeraj Hassan , Vilar Enric , Viljoen Adie , Farrington Ken
Published: November 2014

Aims

Endotoxin detection assays are not validated for use in end-stage kidney disease (ESKD). We investigated the accuracy and precision of the kinetic turbidimetric Limulus amoebocyte lysate (LAL) assay to detect endotoxin in plasma from patients with ESKD. Optimisation of endotoxin recovery from plasma using the detergent Tween 80 was also explored.

Methods

Plasma samples from 7 patients with ESKD and 7 healthy subjects were spiked with different concentrations of endotoxin. Repeated measurements for endotoxin at each level of spike were performed to assess the accuracy and precision of spike recovery. Endotoxin recovery in plasma samples diluted in Tween 80 and water was compared.

Results

Mean endotoxin spike recovery was 111.6% and 125.2% in ESKD and healthy subjects, respectively. There was no statistical difference in spike recovery between ESKD and healthy plasma. Precision of the LAL assay in plasma spiked with low (0.05 EU/mL) and high (0.5 EU/mL) concentration of endotoxin spikes was 24.1% and 8.9%, respectively. The use of Tween 80 as a diluent for plasma significantly improved spike recovery in ESKD plasma (100.1% vs 70.4%, p<0.001).

Conclusions

The kinetic LAL turbidimetric assay is a valid tool for the detection of blood endotoxin in patients with ESKD, although in blood specimens with low-level endotoxemia (≤0.05 EU/mL) the assay may be less accurate and precise. Tween 80 can be used as a diluent to optimise recovery of endotoxin in ESKD plasma.
Ion Torrent next-generation sequencing for routine identification of clinically relevant mutations in colorectal cancer patients
Authors: Malapelle Umberto , Vigliar Elena , Sgariglia Roberta , Bellevicine Claudio , Colarossi Lorenzo , Vitale Domenico , Pallante Pierlorenzo , Troncone Giancarlo
Published: November 2014

Aims

To evaluate the accuracy, consumable cost and time around testing (TAT) of a next-generation sequencing (NGS) assay, the Ion Torrent AmpliSeq Colon and Lung Cancer Panel, as an alternative to Sanger sequencing to genotype KRAS, NRAS and BRAF in colorectal cancer patients.

Methods

The Ion Torrent panel was first verified on cell lines and on control samples and then prospectively applied to routine specimens (n=114), with Sanger sequencing as reference.

Results

The Ion Torrent panel detected mutant alleles at the 5% level on cell lines and correctly classified all control tissues. The Ion Torrent assay was successfully carried out on most (95.6%) routine diagnostic samples. Of these, 12 (11%) harboured mutations in the BRAF gene and 47 (43%) in either of the two RAS genes, in two cases with a low abundance of RAS mutant allele which was missed by Sanger sequencing. The mean TAT, from sample receipt to reporting, was 10.4 (Sanger) and 13.0 (Ion Torrent) working days. The consumable cost for genotyping KRAS, NRAS and BRAF was €196 (Sanger) and €187 (Ion Torrent).

Conclusions

Ion Torrent AmpliSeq Colon and Lung Cancer Panel sequencing is as robust as Sanger sequencing in routine diagnostics to select patients for anti-epidermal growth factor receptor (EGFR) therapy for metastatic colorectal cancer.
Myoclonus and hyperalgesia following intended epidural morphine administration in a dog
Authors: Robson Katherine , Alderson Briony
Published: November 2014

A West Highland White Terrier was presented after development of hindlimb myoclonus and hyperalgesia following intended epidural administration of morphine at a referring veterinary practice. MRI was unremarkable, except for the spinal cord extending to the caudal half of the L7 vertebrae. Treatment with systemic analgesia of methadone and sedation/analgesia with medetomidine resolved the clinical signs within 24 hours. The mechanism by which morphine causes adverse neurological side effects has yet to be fully determined; the morphine‐3‐glucuronide (M‐3‐G) metabolite is suspected to be responsible for the adverse effects seen. Hypotheses include action of morphine or the M‐3‐G metabolite on non‐opioid inhibitory (glycine) or excitatory (N‐methyl D‐aspartate) receptors. However, more work is needed to determine the exact pathogenesis. Neuroexcitatory side effects are rarely reported following administration of morphine in dogs and this case demonstrates successful treatment with the use of an alternative opioid, methadone.
Horse impoundments under Control of Horses legislation in the Munster region of Ireland: factors affecting euthanasia
Authors: Cullinane M. , O'Sullivan E. , Collins D. M. , Byrne A. W. , More S. J.
Published: November 2014

Recently, considerable international attention has been paid to the problem of unwanted horses. In Ireland, stray horses, particularly in urban areas, are a further problem. The Control of Horses Act 1996 was enacted in response to an ongoing problem of uncontrolled horses in public places. As yet, no research work has been conducted focusing on stray horses in Ireland. This paper describes horses impounded under the Act in the Munster region of Ireland during 2005–2012 and the factors influencing decisions regarding their disposal. A logistic regression model was developed to investigate factors influencing the probability that a horse was euthanised during impoundment. In total, 3625 seizure events were recorded, most towards the end of the study period. Predictors for euthanasia during 2010–2012 included seizure location, sex, age, colour, body condition score and year. This study highlights the problem of stray horses in Ireland, particularly in urban areas. There is a need for rigorous enforcement of newly enacted horse identification legislation, allowing a fully integrated traceability system. More is required to manage the long‐established societal problems of stray horses in urban settings, with a uniform approach by all Local Authorities being long overdue.
Feet first into farm animal practice
Authors: Gascoigne Emily
Published: November 2014

The first year in practice is arguably the most challenging, stressful and emotional, says Emily Gascoigne, who qualified in 2012. She has begun her career on a one‐year intern programme with the Royal Veterinary College (RVC) and Synergy Farm Health
Ten‐minute chat
Authors: Middleton Sheldon
Published: November 2014

Sheldon Middleton is happy in his first job five years after qualifying from Cambridge, but his route into the profession was not straightforward.
Sulfur-containing DalPhos ligand variants: synthesis and application in Buchwald−Hartwig amination
Authors: Cook Earl W.F. , Lavery Christopher B. , Wheaton Craig A. , McDonald Robert , Stradiotto Mark
Published: November 2014

We report herein on our synthetic, structural, and catalytic investigations of new P,S-DalPhos ligands featuring pairings of phosphorus and sulfur donor groups as well as new sulfur-containing analogues of the previously reported P,N-ligands Me-DalPhos and Mor-DalPhos, featuring a 2,3-disubstituted thiophenyl backbone. In examining the catalytic performance of these new sulfur-containing ligands in the Buchwald–Hartwig amination of octylamine, aniline, or ammonia with 4-chlorotoluene, noteworthy differences in reactivity behavior relative to Me-DalPhos and Mor-DalPhos were observed.
Nutrient excretion by crustacean zooplankton in the deep chlorophyll layer of Lake Superior
Authors: Oliver Samantha K. , Branstrator Donn K. , Hrabik Thomas R. , Guildford Stephanie J. , Hecky Robert E.
Published: November 2014

We hypothesized that the resident and migrating cold-water zooplankton in Lake Superior concentrate beneath the thermocline and elevate nutrient availability via mineralization in the deep chlorophyll layer (DCL). In August 2010 and 2011, diel vertical net tows and incubation experiments were conducted in the western arm of Lake Superior to measure zooplankton distribution and excretion of dissolved nutrients. Limnocalanus macrurus showed the strongest spatial overlap with the DCL, and the broader crustacean community excreted P at 0.145 μg·mg−1·h−1 and N at 0.617 μg·mg−1·h−1 as soluble reactive phosphorus (SRP) and ammonia, respectively. Mysis diluviana displayed strong diel vertical migration into the DCL and excreted P at 0.013 μg·mg−1·h−1 and N at 0.116 μg·mg−1·h−1 as SRP and ammonia, respectively. Based on primary productivity estimates, the zooplankton community has the potential to meet the daily phosphorus demand by phytoplankton in the DCL during late-season stratification. Our excretion estimates indicate a possible coupling between the cold-water zooplankton community and production in the DCL of Lake Superior.
Efficient Hardware Implementations of Binary-to-BCD Conversion Schemes for Decimal Multiplication
Authors: Al-Khaleel Osama , Al-Qudah Zakaria , Al-Khaleel Mohammad , Bani-Hani Raed , Papachristou Christos , Wolff Francis
Published: November 2014

This paper proposes two high performance binary-to-binary coded decimal (BCD) conversion algorithms for use in BCD multiplication. These algorithms are based on splitting the 7-bit binary partial product of two BCD digits into two groups, computing the contribution of each group to the equivalent BCD partial product, and adding these contributions to compute the final BCD partial product. Designs for the proposed architectures and their implementations targeting both ASIC and FPGA are compared with others. Implementations of BCD array multipliers using both our conversion circuits and existing conversion circuits have been performed. The synthesis results for both ASIC and FPGA show that the proposed designs are faster and occupying less area than the state-of-the-art conversion circuits. Furthermore, the results obtained from comparing BCD multipliers of various sizes show that the enhancement in the area of the conversion circuit grows into a sizable area improvement in the multiplier circuit.
A High-PSRR Low Dropout Regulator for LNB Using the First-Stage Reference-Included Coarse-Filtering Technique
Authors: Li Fanyang , Jiang Hao
Published: November 2014

A high-PSRR low dropout regulator using the first-stage reference-included coarse-filtering technique is presented, for the reduced output ripple of the low noise block (LNB) power supply in the satellite set-top box. Compared with the conventional system, the regulator with the technique is characterized by the two successive negative feedback loops, so as to alleviate the output ripple of the power supply caused by the preceding DC–DC converter's modulation signal. With the technique, the ripple near to the frequency of the LNB supply voltage tuning signal (22 kHz) can be significantly alleviated. To further enhance the PSRR performance without the reference-by-pass capacitor, the bipolar-loop buffer amplifier and the reference-included coarse-filtering regulator are proposed. The circuits are extracted from the LDO layout and simulated with a 0.35 μm BCD process in Cadence. With the typical 16.3 V input supply voltage and loading current 100 mA, the line regulation corresponding to the DC supply voltage is achieved at -72 dB; the PSRR performance of the supply voltage ripple up to the frequency (100 kHz) is better than -70 dB; Moreover, the quiescent current without the loading impedance is less than 153 μA.
Iterated effective embeddings of abelian p-groups
Authors: Downey Rod , Melnikov Alexander G. , Ng Keng Meng
Published: November 2014

This paper contributes to the theory of recursively presented (see Higman [Subgroups of finitely presented groups, Proc. R. Soc. Ser. A 262 (1961) 455–475]) infinitely generated abelian groups with solvable word problem. Mal'cev [On recursive Abelian groups, Dokl. Akad. Nauk SSSR 146 (1962) 1009–1012] and independently Rabin [Computable algebra, general theory and theory of computable fields, Trans. Amer. Math. Soc. 95 (1960) 341–360] initiated the study of such groups in the early 1960's. In this paper, we develop a technique that we call iterated effective embeddings. The significance of our new technique is that it extends existing methods from the realm of iterated 0″ arguments to iterated 0‴ ones. This is a new phenomenon in computable algebra. We use this technique to confirm a 30 year-old conjecture of Ash, Knight and Oates [Recursive abelian p-groups of small length, https://dl.dropbox.com/u/4752353/Homepage/AKO.pdf ]. More specifically, Ash, Knight and Oates [Recursive abelian p-groups of small length. https://dl.dropbox.com/u/4752353/Homepage/AKO.pdf ] conjectured that there exists a computable reduced abelian p-group of Ulm type ω such that its effective invariants, defined using limitwise monotonic functions, cannot be found uniformly. We construct a computable reduced abelian p-group of Ulm type ω where its invariants are at the maximum possible level of non-uniformity. The result confirms the conjecture in a strong way, and it provides us with an explanation of why computable reduced p-groups of Ulm type ω seem hard to classify in general. We also use p-basic trees and their iterated embeddings to solve a problem posed in [W. Calvert, D. Cenzer, V. S. Harizanov and A. Morozov, Effective categoricity of abelian p-groups, Ann. Pure Appl. Logic 159(1–2) (2009) 187–197].
Any 11-Colorable knot can be colored with at most six colors
Authors: Cheng Wenfang , Jin Xian'an , Zhao Nana
Published: November 2014

In this paper, we show that any 11-colorable knot has a diagram with a non-trivial 11-coloring such that at most six colors among eleven colors are assigned to arcs of the diagram.
A Decision-Making Model of Social Shopping in Franchising: Assessing Collaboration Strategies
Authors: Lee In , Lee Choong-Kwon , Yoo Sangjin , Choi Moo-Jin
Published: November 2014

Our paper develops a decision-making model of social shopping in franchising to understand impacts of various collaboration strategies on profits of a social intermediary, a franchisor, and a franchisee. Three decision variables are considered to make a daily deal promotion in a manner that results in optimal profits: the social intermediary's advertising expense, the franchisee's service quality expense, and the franchisor's financial assistance to the franchisee. The analysis shows that while system-wide collaboration generates more total profit for all three parties than the profits obtained when they seek to optimize their individual profit functions, the advantage of system-wide collaboration may depend on the parameter values of the profit function and collaboration cost. Since social shopping is just in the early stage of the business model development, most franchises and social intermediaries have not formed concrete collaboration strategies. Our model provides a methodology for different collaborative needs of the franchises and social intermediaries.
An efficient algorithm for pairwise local alignment of protein interaction networks
Authors: Chen Wenbin , Schmidt Matthew , Tian Wenhong , Samatova Nagiza F. , Zhang Shaohong
Published: November 2014

Recently, researchers seeking to understand, modify, and create beneficial traits in organisms have looked for evolutionarily conserved patterns of protein interactions. Their conservation likely means that the proteins of these conserved functional modules are important to the trait's expression.

In this paper, we formulate the problem of identifying these conserved patterns as a graph optimization problem, and develop a fast heuristic algorithm for this problem. We compare the performance of our network alignment algorithm to that of the MaWISh algorithm [Koyutürk M, Kim Y, Topkara U, Subramaniam S, Szpankowski W, Grama A, Pairwise alignment of protein interaction networks, J Comput Biol13(2):182–199, 2006.], which bases its search algorithm on a related decision problem formulation. We find that our algorithm discovers conserved modules with a larger number of proteins in an order of magnitude less time. The protein sets found by our algorithm correspond to known conserved functional modules at comparable precision and recall rates as those produced by the MaWISh algorithm.
Comment on "Cryptanalysis and improvement of the secure quantum sealed-bid auction with post confirmation"
Authors: Zhao Zhangji , Wang Weijia
Published: November 2014

In a recent paper, an improvement of quantum sealed-bid auction protocol is proposed by introducing hash function. However, in this comment, it is shown that the improvement brings in other problems which would not complete the task of a sealed-bid auction fairly.
Cosmological solutions in F(T) gravity with the presence of spinor fields
Authors: Myrzakulov Ratbay , Sáez-Gómez Diego , Tsyba Petr
Published: November 2014

The presence of spinor fields is considered in the framework of some extensions of teleparallel gravity, where the Weitzenböck connection is assumed. Some well-known models as the Chaplygin gas and its generalizations are reconstructed in terms of a spinor field in the framework of teleparallel gravity. In addition, the ΛCDM model is also realized with the presence of a spinor field where a simple self-interacting term is considered and the corresponding action is reconstructed. Other cosmological solutions and the reconstruction of the gravitational action in terms of the scalar torsion are studied.