bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hysteroscopy after repeated implantation failure of assisted reproductive technology: A meta‐analysis
Authors: Cao Hanyu , You Di , Yuan Mingwei , Xi Mingrong 
Published: January 2018

AbstractWe conducted this meta‐analysis to explore the prognostic value of outpatient (or office) hysteroscopy (OH) preceding in vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI) cycles in women who had experienced repeated implantation failure (RIF), particularly in regard to the conflicting evidence reported by previous studies. Two reviewers independently searched Pubmed, MEDLINE, Web of Science, Cochrane Library and Embase to identify all publications of clinical trials of hysteroscopy with or without endometrial biopsy in RIF patients. The primary outcome measures were clinical pregnancy rate (CPR) and live birth rate (LBR). Pooled relative ratios (RRs) with 95% confidence intervals (CIs) were calculated. Publication bias was detected using funnel plots and Egger's regression tests. Six eligible studies comprising 4143 patients were included. The CPR and LBR were both significantly higher in RIF patients with OH than RIF patients without OH (CPR: RR 1.34, 95% CI 1.14–1.57, P < 0.05; LBR: RR 1.29, 95% CI 1.03–1.62, P < 0.05). Subgroup analysis revealed a significant association between OH and CPR in Asia (CPR: RR 1.49, 95% CI 1.31–1.69; P < 0.05) rather than in Europe (CPR: RR 1.08, 95% CI 0.93–1.26; P = 0.291). However, there was no evidence of a significant difference in either CPR or LBR between the normal and abnormal OH groups (CPR: RR 0.92, 95% CI 0.83–1.02, P = 0.12; LBR: RR 0.76, 95% CI 0.37–1.56, P = 0.450). Hysteroscopy may potentially improve pregnancy outcomes in patients with RIP.
No jab, no record: Catch‐up vaccination of children in immigration detention
Authors: Kiang Karen M , Elia Sonja , Paxton Georgia A 
Published: January 2018

AbstractInternational Health and Medical Services (IHMS) are contracted to provide health services, including catch‐up vaccination, for individuals in immigration detention. Our audit of catch‐up vaccination in asylum seeker children who spent time in held detention demonstrates inadequate and suboptimal vaccine delivery in this setting, and no evidence that IHMS recorded vaccines on the Australian Childhood Immunisation Register at the time. We also found substantial shortfalls in vaccination for these children after they were released from detention. Immunisation in this cohort falls well below Australian community standards, does not demonstrate assurance in IHMS provision of care, and has implications for similar asylum seeker cohorts nationally as well as people in held detention.
From Global Expressivism to Global Pragmatism
Authors: Capps John 
Published: January 2018

AbstractIn the twentieth century, questions of meaning and representation played a central role in the development of pragmatism and analytic philosophy. Present‐day neopragmatism, such as Huw Price's “global expressivism,” is often framed in terms of a nonrepresentationalist theory of meaning. While some neopragmatists, such as Robert Brandom, advocate a more local approach, this article argues for taking Price's global expressivism to its next logical step: global pragmatism. Global pragmatism prioritizes the behavior‐guiding function of language and redefines representation in operational terms. This operational approach (“o‐representation”) stresses the action and conduct‐guiding role of language use, highlights the connection between meaning and action, and addresses issues facing Price's global expressivism.
World‐Pictures and Wittgensteinian Certainty
Authors: Ohtani Hiroshi 
Published: January 2018

AbstractAlthough certainty is a fundamental notion in epistemology, it is less studied in contemporary analytic epistemology than other important notions such as knowledge or justification. This paper focuses on Wittgensteinian certainty, according to which the very basic dimension of our epistemic practices, the elements of our world‐pictures, are objectively certain, in that we cannot legitimately doubt them. The aim of the paper is to offer the best philosophical way to clarify Wittgensteinian certainty, in a way that is consonant with Wittgenstein's fundamental insights. The paper critiques two alternative proposals for clarifying Wittgensteinian certainty that are philosophically unsatisfying: the rule view and the proposition view. Finally, it instead shows how viewing world‐pictures as pictures, in the sense of unclear conceptions, is a more philosophically fruitful approach to understanding world‐pictures.
Modeling Poliovirus Transmission in Pakistan and Afghanistan to Inform Vaccination Strategies in Undervaccinated Subpopulations
Authors: Duintjer Tebbens Radboud J. , Pallansch Mark A. , Cochi Stephen L. , Ehrhardt Derek T. , Farag Noha H. , Hadler Stephen C. , Hampton Lee M. , Martinez Maureen , Wassilak Steve G.F. , Thompson Kimberly M. 
Published: January 2018

AbstractDue to security, access, and programmatic challenges in areas of Pakistan and Afghanistan, both countries continue to sustain indigenous wild poliovirus (WPV) transmission and threaten the success of global polio eradication and oral poliovirus vaccine (OPV) cessation. We fitted an existing differential‐equation‐based poliovirus transmission and OPV evolution model to Pakistan and Afghanistan using four subpopulations to characterize the well‐vaccinated and undervaccinated subpopulations in each country. We explored retrospective and prospective scenarios for using inactivated poliovirus vaccine (IPV) in routine immunization or supplemental immunization activities (SIAs). The undervaccinated subpopulations sustain the circulation of serotype 1 WPV and serotype 2 circulating vaccine‐derived poliovirus. We find a moderate impact of past IPV use on polio incidence and population immunity to transmission mainly due to (1) the boosting effect of IPV for individuals with preexisting immunity from a live poliovirus infection and (2) the effect of IPV‐only on oropharyngeal transmission for individuals without preexisting immunity from a live poliovirus infection. Future IPV use may similarly yield moderate benefits, particularly if access to undervaccinated subpopulations dramatically improves. However, OPV provides a much greater impact on transmission and the incremental benefit of IPV in addition to OPV remains limited. This study suggests that despite the moderate effect of using IPV in SIAs, using OPV in SIAs remains the most effective means to stop transmission, while limited IPV resources should prioritize IPV use in routine immunization.
Complete Genome Sequences of Three
Bacillus anthracis
Bacteriophages
Authors: Alkalay Sivan , Sternberg Sarit , Coppenhagen-Glazer Shunit , Hazan Ronen 
Published: January 2018

ABSTRACT

The new highly effective
Bacillus anthracis
phages Negev_SA, Carmel_SA, and Tavor_SA were isolated from soil samples, and their complete genomes were sequenced and analyzed. The isolated phages have potential use in future phage therapy treatment against anthrax.
Complete Genome Sequence of Bacteriophage SM9-3Y Infecting
Serratia marcescens
Authors: Hao Yuchong , Shi Hongyan , Li Jinghua , Zhao Chunyan , Huang Honglan , Sun Yanbo 
Published: January 2018

ABSTRACT

Serratia marcescens
is an important opportunistic organism that causes nosocomial infections. Bacteriophage therapy has the potential to control
S. marcescens
infection. We present here the complete genome sequence of a lytic
S. marcescens
bacteriophage, SM9-3Y, which is a linear double-stranded DNA genome of 39,631 bp with 50.7% G+C content.
Complete Genome Sequence of
Escherichia coli
Phage APC_JM3.2 Isolated from a Chicken Cecum
Authors: Mullally Jayne , Stockdale Stephen R. , Smith Muireann K. , Draper Lorraine A. , Ross Paul R. , Hill Colin 
Published: January 2018

ABSTRACT

Avian pathogenic
Escherichia coli
(APEC) bacteria are a significant challenge to the poultry industry. Bacteriophages (phages) have the potential to control APEC strains, increasing animal welfare and economic productivity. Here, we report the isolation of an
E. coli
-infecting phage, APC_JM3.2, isolated from the cecum of a broiler chicken in Ireland.
Two Draft Genome Sequences of
Chromobacterium violaceum
Isolates from the Rio Negro
Authors: da Gama Auricélia Matos , de Almeida Luiz Gustavo , Yamane Tetsuo , Spira Beny 
Published: January 2018

ABSTRACT

The draft genome sequences of two
Chromobacterium violaceum
strains isolated from the Rio Negro are reported here. These bacteria carry most genetic systems associated with the production of bioactive compounds, but unlike other
C. violaceum
strains, they lack a dedicated operon for arsenic resistance.
High-Quality Complete and Draft Genome Sequences for Three
Escherichia
spp. and Three
Shigella
spp. Generated with Pacific Biosciences and Illumina Sequencing and Optical Mapping
Authors: Schroeder Max R. , Juieng Phalasy , Batra Dhwani , Knipe Kristen , Rowe Lori A. , Sheth Mili , Smith Peyton , Garcia-Toledo Lisley , Loparev Vladimir N. , Lindsey Rebecca L. 
Published: January 2018

ABSTRACT

Escherichia
spp., including
E. albertii
and
E. coli
,
Shigella dysenteriae
, and
S. flexneri
are causative agents of foodborne disease. We report here reference-level whole-genome sequences of
E. albertii
(2014C-4356),
E. coli
(2011C-4315 and 2012C-4431),
S. dysenteriae
(BU53M1), and
S. flexneri
(94-3007 and 71-2783).
Near-Complete Genome Sequence of a Fish Nervous Necrosis Virus Isolated from a Clinical Disease Outbreak in Farm-Reared Bream
Sparus aurata
in Spain
Authors: Stathopoulou Panagiota , Rafailidou Nausika , Tzokas Kostas , Batargias Costas , Tsiamis George 
Published: January 2018

ABSTRACT

Sparus aurata
larvae infected by viral nervous necrosis were collected from an aquaculture fish farm. The isolated viral genome, composed of two segments (RNA1 and RNA2), was sequenced and analyzed comparatively. Phylogenetic tree analyses revealed that the isolated strain is a reassortant, exhibiting a red-spotted grouper nervous necrosis virus (RGNNV)-type RNA1 and a striped jack nervous necrosis virus (SJNNV)-type RNA2.
Complete Genome Sequence of
Elizabethkingia miricola
Strain EM798-26 Isolated from the Blood of a Cancer Patient
Authors: Lin Jiun-Nong , Lai Chung-Hsu , Yang Chih-Hui , Huang Yi-Han , Lin Hsi-Hsun 
Published: January 2018

ABSTRACT

Elizabethkingia miricola
EM798-26 was isolated from the blood of a patient with diffuse large B-cell lymphoma in Taiwan. We report here the complete genome sequence of EM798-26, which contains a G+C content of 35.7% and 3,877 candidate protein-coding genes.
Draft Genome Sequence of the Predatory Marine Bacterium
Halobacteriovorax
sp. Strain JY17
Authors: Young Jonathan M. , Skvortsov Timofey , Arkhipova Ksenia , Allen Christopher C. R. 
Published: January 2018

ABSTRACT

A draft genome sequence of
Halobacteriovorax
sp. strain JY17 was assembled from a metagenomic data set. The 3.47-Mbp genome of this unusual predatory bacterium contains 3,263 protein-coding sequences, 33 tRNAs, and 2 copies each of the 16S, 23S, and 5S rRNA genes. This is only the third sequenced representative of this genus.
Evasion of Cytosolic DNA-Stimulated Innate Immune Responses by Herpes Simplex Virus 1
Authors: Zheng Chunfu 
Published: January 2018

ABSTRACT
Recognition of virus-derived nucleic acids by host pattern recognition receptors (PRRs) is crucial for early defense against viral infections. Recent studies revealed that PRRs also include several newly identified DNA sensors, most of which could activate the downstream adaptor stimulator of interferon genes (STING) and lead to the production of host antiviral factors. Herpes simplex virus 1 (HSV-1) is extremely successful in establishing effective infections, due to its capacity to counteract host innate antiviral responses. In this Gem, I summarize the most recent findings on the molecular mechanisms utilized by HSV-1 to target different steps of the cellular DNA-sensor-mediated antiviral signal pathway.
Full-Length Glycosylated Gag of Murine Leukemia Virus Can Associate with the Viral Envelope as a Type I Integral Membrane Protein
Authors: Renner Tyler Milston , Bélanger Kasandra , Lam Cindy , Gerpe María Carla Rosales , McBane Joanne Eileen , Langlois Marc-André 
Published: January 2018

ABSTRACT

The glycosylated Gag protein (gPr80) of murine leukemia viruses (MLVs) has been shown to exhibit multiple roles in facilitating retrovirus release, infection, and resistance to host-encoded retroviral restriction factors, such as APOBEC3, SERINC3, and SERINC5. One way in which gPr80 helps MLVs to escape host innate immune restriction is by increasing capsid stability, a feature that protects viral replication intermediates from being detected by cytosolic DNA sensors. gPr80 also increases the resistance of MLVs to deamination and restriction by mouse APOBEC3 (mA3). How the gPr80 accessory protein, with its three
N
-linked glycosylation sites, contributes to these resistance mechanisms is still not fully understood. Here we further characterized the function of gPr80 and, more specifically, revealed that the asparagines targeted for glycosylation in gPr80 also contribute to capsid stability through their parallel involvement in the Pr65 Gag structural polyprotein. In fact, we demonstrate that sensitivity to deamination by the mA3 and human A3 proteins is directly linked to capsid stability. We also show that full-length gPr80 is detected in purified viruses. However, our results suggest that gPr80 is inserted in the N
exo
C
cyto
orientation of a type I integral membrane protein. Additionally, our experiments have revealed the existence of a large population of Env-deficient virus-like particles (VLPs) harboring gPr80 inserted in the opposite (N
cyto
C
exo
) polarity, which is typical of type II integral membrane proteins. Overall this study provides new insight into the complex nature of the MLV gPr80 accessory protein.

IMPORTANCE
Viruses have evolved numerous strategies to infect, spread in, and persist in their hosts. Here we analyze the details of how the MLV-encoded glycosylated Gag (gPr80) protein protects the virus from being restricted by host innate immune defenses. gPr80 is a variant of the structural Pr65 Gag protein with an 88-amino-acid extended leader sequence that directs the protein for translation and glycosylation in the endoplasmic reticulum. This study dissects the specific contributions of gPr80 glycans and capsid stability in helping the virus to infect cells, spread, and counteract the effects of the host intrinsic restriction factor APOBEC3. Overall this study provides further insight into the elusive role of the gPr80 protein.
Cell-to-Cell Measles Virus Spread between Human Neurons Is Dependent on Hemagglutinin and Hyperfusogenic Fusion Protein
Authors: Sato Yuma , Watanabe Shumpei , Fukuda Yoshinari , Hashiguchi Takao , Yanagi Yusuke , Ohno Shinji 
Published: January 2018

ABSTRACT
Measles virus (MV) usually causes acute infection but in rare cases persists in the brain, resulting in subacute sclerosing panencephalitis (SSPE). Since human neurons, an important target affected in the disease, do not express the known MV receptors (signaling lymphocyte activation molecule [SLAM] and nectin 4), how MV infects neurons and spreads between them is unknown. Recent studies have shown that many virus strains isolated from SSPE patients possess substitutions in the extracellular domain of the fusion (F) protein which confer enhanced fusion activity. Hyperfusogenic viruses with such mutations, unlike the wild-type MV, can induce cell-cell fusion even in SLAM- and nectin 4-negative cells and spread efficiently in human primary neurons and the brains of animal models. We show here that a hyperfusogenic mutant MV, IC323-F(T461I)-EGFP (IC323 with a fusion-enhancing T461I substitution in the F protein and expressing enhanced green fluorescent protein), but not the wild-type MV, spreads in differentiated NT2 cells, a widely used human neuron model. Confocal time-lapse imaging revealed the cell-to-cell spread of IC323-F(T461I)-EGFP between NT2 neurons without syncytium formation. The production of virus particles was strongly suppressed in NT2 neurons, also supporting cell-to-cell viral transmission. The spread of IC323-F(T461I)-EGFP was inhibited by a fusion inhibitor peptide as well as by some but not all of the anti-hemagglutinin antibodies which neutralize SLAM- or nectin-4-dependent MV infection, suggesting the presence of a distinct neuronal receptor. Our results indicate that MV spreads in a cell-to-cell manner between human neurons without causing syncytium formation and that the spread is dependent on the hyperfusogenic F protein, the hemagglutinin, and the putative neuronal receptor for MV.

IMPORTANCE
Measles virus (MV), in rare cases, persists in the human central nervous system (CNS) and causes subacute sclerosing panencephalitis (SSPE) several years after acute infection. This neurological complication is almost always fatal, and there is currently no effective treatment for it. Mechanisms by which MV invades the CNS and causes the disease remain to be elucidated. We have previously shown that fusion-enhancing substitutions in the fusion protein of MVs isolated from SSPE patients contribute to MV spread in neurons. In this study, we demonstrate that MV bearing the hyperfusogenic mutant fusion protein spreads between human neurons in a cell-to-cell manner. Spread of the virus was inhibited by a fusion inhibitor peptide and antibodies against the MV hemagglutinin, indicating that both the hemagglutinin and hyperfusogenic fusion protein play important roles in MV spread between human neurons. The findings help us better understand the disease process of SSPE.
Persistent pulmonary hypertension of the newborn in extremely preterm infants: a Japanese cohort study
Authors: Nakanishi Hidehiko , Suenaga Hideyo , Uchiyama Atsushi , Kusuda Satoshi 
Published: January 2018

ObjectiveTo investigate the characteristics of persistent pulmonary hypertension of the newborn (PPHN) in extremely preterm infants and its impact on neurodevelopmental outcomes at 3 years of age.DesignA retrospective multicentre cohort study.Settings202 tertiary perinatal centres registered in the Neonatal Research Network of Japan (NRNJ).PatientsInfants born at <28 weeks of gestational age (GA), between 2003 and 2012, were extracted from tertiary perinatal centres participating in NRNJ.Main outcome measuresDemographic characteristics, morbidity, interventions and mortality were compared for infants with and without PPHN. Multivariable logistic analysis was performed to evaluate the impact of PPHN on long-term neurodevelopmental outcomes (the prevalence rate of cerebral palsy, need for home oxygen therapy, and visual, hearing and cognitive impairment) at 3 years of age.ResultsThe prevalence of PPHN among the 12 954 extremely preterm infants enrolled was 8.1% (95% CI 7.7% to 8.6%), with the trend increasing annually, and a higher proportion as GA decreased: 18.5% (range, 15.2% to 22.4%) for infants born at 22 weeks compared with 4.4% (range, 3.8% to 5.2%) for those born at 27 weeks. Clinical chorioamnionitis and premature rupture of membranes were associated with PPHN. On multivariate analysis of the data from 5923 infants followed up for 3 years, PPHN was a significant independent risk factor for visual impairment (adjusted OR, 1.42, 95% CI 1.03 to 1.97).ConclusionsThe prevalence of PPHN in extremely preterm infants has been increasing over the past decade in Japan. Clinicians should be aware of visual impairments as a neurodevelopmental abnormality among infants with PPHN.
High-Dimensional Profiling of Tumor-Specific Immune Responses: Asking T Cells about What They “See” in Cancer
Authors: Newell Evan W. , Becht Etienne 
Published: January 2018

Abstract
The foundations of basic T-cell immunology and an understanding of the roles for T cells in controlling cancer have led to the remarkable yet inconsistent success of cancer immunotherapy. Because of these advances in cancer treatment, the need is urgent for biomarkers that can predict the efficacy of these treatments and for new therapeutic strategies for cases where currently available approaches are ineffective. Although our ability to profile heterogeneous cell populations in human blood or tissue samples has vastly improved in the past decade, identifying the cell subsets relevant to diseases, and to cancer particularly, remains a challenge. Given strong evidence for the implication of T cells specific for tumor-expressed antigens in various forms of effective immunotherapy, here, we focus on the utility, challenges, and techniques for the identification and profiling of these important cells. We review recent techniques that allow identifying and profiling of tumor-specific T cells. As these methods improve, we can expect more rapid progress in the rational design of novel cancer biomarkers and therapies based on antigen-specific T cells. Cancer Immunol Res; 6(1); 2–9. ©2018 AACR.
Nonuniqueness of Attribution in Piecewise Potential Vorticity Inversion
Authors: Egger Joseph , Spengler Thomas 
Published: January 2018

Abstract
Piecewise potential vorticity inversion (PPVI) seeks to determine the impact of observed potential vorticity (PV) anomalies on the surrounding flow. This widely used technique is based on dividing a flow domain D into subdomains D1 and D2 = D − D1. The influence of PV in D1 on the flow in D2 is assessed by removing all PV anomalies in D2 and then inverting the modified PV in D. The resulting flow with streamfunction ψ1 is attributed to the PV anomalies in D1. The relation of PV in D1 to ψ1 in D2 is not unique, because there are many PV distributions in D1 that induce the same ψ1. There is, however, a unique solution if the ageostrophic circulation is included in the inversion procedure.
The superposition principle requires that the sum of inverted flows with PV = 0 in D2 and the complementary ones with PV = 0 in D1 equal the inverted flow for the complete observed PV in D. It is demonstrated, using two isolated PV balls as a paradigmatic example, that the superposition principle is violated if the ageostrophic circulation is included in PPVI, because the ageostrophic circulation cannot be associated with only one of the anomalies.
Inversions of Ertel’s PV are carried out using Charney’s balance condition. PPVI is not unique in that case, because many different PV fields can be specified in D1, which all lead to the same inverted flow in D2. The balance condition assumes vanishing vertical velocity w so that uniqueness cannot be established by including w in the inversion, as was possible in the quasigeostrophic case.