bluuebunny/crossref_metadata_2025_split huggingface dataset:
Capsids and Genomes of Jumbo-Sized Bacteriophages Reveal the Evolutionary Reach of the HK97 Fold
Authors: Hua Jianfei , Huet Alexis , Lopez Carlos A. , Toropova Katerina , Pope Welkin H. , Duda Robert L. , Hendrix Roger W. , Conway James F. 
Published: October 2017

ABSTRACT
Large icosahedral viruses that infect bacteria represent an extreme of the coevolution of capsids and the genomes they accommodate. One subset of these large viruses is the jumbophages, tailed phages with double-stranded DNA genomes of at least 200,000 bp. We explored the mechanism leading to increased capsid and genome sizes by characterizing structures of several jumbophage capsids and the DNA packaged within them. Capsid structures determined for six jumbophages were consistent with the canonical phage HK97 fold, and three had capsid geometries with novel triangulation numbers (T=25, T=28, and T=52). Packaged DNA (chromosome) sizes were larger than the genome sizes, indicating that all jumbophages use a head-full DNA packaging mechanism. For two phages (PAU and G), the sizes appeared very much larger than their genome length. We used two-dimensional DNA gel electrophoresis to show that these two DNAs migrated abnormally due to base modifications and to allow us to calculate their actual chromosome sizes. Our results support a ratchet model of capsid and genome coevolution whereby mutations lead to increased capsid volume and allow the acquisition of additional genes. Once the added genes and larger capsid are established, mutations that restore the smaller size are disfavored.

IMPORTANCE
A large family of viruses share the same fold of the capsid protein as bacteriophage HK97, a virus that infects bacteria. Members of this family use different numbers of the capsid protein to build capsids of different sizes. Here, we examined the structures of extremely large capsids and measured their DNA content relative to the sequenced genome lengths, aiming to understand the process that increases size. We concluded that mutational changes leading to larger capsids become locked in by subsequent changes to the genome organization.
Activation of the
Listeria monocytogenes
Virulence Program by a Reducing Environment
Authors: Portman Jonathan L. , Dubensky Samuel B. , Peterson Bret N. , Whiteley Aaron T. , Portnoy Daniel A. 
Published: October 2017

ABSTRACT

Upon entry into the host cell cytosol, the facultative intracellular pathogen
Listeria monocytogenes
coordinates the expression of numerous essential virulence factors by allosteric binding of glutathione (GSH) to the Crp-Fnr family transcriptional regulator PrfA. Here, we report that robust virulence gene expression can be recapitulated by growing bacteria in a synthetic medium containing GSH or other chemical reducing agents. Bacteria grown under these conditions were 45-fold more virulent in an acute murine infection model and conferred greater immunity to a subsequent lethal challenge than bacteria grown in conventional media. During cultivation
in vitro
, PrfA activation was completely dependent on the intracellular levels of GSH, as a glutathione synthase mutant (Δ
gshF
) was activated by exogenous GSH but not reducing agents. PrfA activation was repressed in a synthetic medium supplemented with oligopeptides, but the repression was relieved by stimulation of the stringent response. These data suggest that cytosolic
L. monocytogenes
interprets a combination of metabolic and redox cues as a signal to initiate robust virulence gene expression
in vivo
.

IMPORTANCE
Intracellular pathogens are responsible for much of the worldwide morbidity and mortality from infectious diseases. These pathogens have evolved various strategies to proliferate within individual cells of the host and avoid the host immune response. Through cellular invasion or the use of specialized secretion machinery, all intracellular pathogens must access the host cell cytosol to establish their replicative niches. Determining how these pathogens sense and respond to the intracellular compartment to establish a successful infection is critical to our basic understanding of the pathogenesis of each organism and for the rational design of therapeutic interventions.
Listeria monocytogenes
is a model intracellular pathogen with robust
in vitro
and
in vivo
infection models. Studies of the host-sensing and downstream signaling mechanisms evolved by
L. monocytogenes
often describe themes of pathogenesis that are broadly applicable to less tractable pathogens. Here, we describe how bacteria use external redox states as a cue to activate virulence.
Tenderness and sensory attributes of 11 muscles from carcasses within the Canadian cull cow grades
Authors: Roberts Jordan C. , Rodas-González Argenis , Juárez Manuel , López-Campos Óscar , Larsen Ivy L. , Aalhus Jennifer L. 
Published: October 2017

The eating quality and shear force of meat from mature beef carcasses graded within the Canadian grading system were compared with youthful carcasses. Eleven muscles were obtained from mature-graded carcasses with >50% ossification (D1, D2, D3, and D4; n = 84) and youthful carcasses with <50% ossification [over 30 mo (OTM); n = 18, and under 30 mo (UTM) of age; n = 18, based on dentition]; muscles were aged 14 d prior to sensory and shear force analysis. Many muscles from mature-graded carcasses were juicier than UTM, however, most were less tender (P < 0.05). Psoas major was tender, particularly in D1 and OTM carcasses where tenderness measures were not significantly different from UTM (P > 0.05). Shear force values from the infraspinatus of D1 and OTM carcasses were not different from UTM. Flavour intensity was higher in several muscles from D1, D2, and D4 carcasses (P < 0.05), whereas flavour intensity was lower in several muscles from D3 (P < 0.05). Changes to eating quality attributes differed among mature grades; therefore, processors could potentially use the information presented here as a guide for utilizing cuts which retain high eating quality and separating those requiring tenderness intervention to reach consumer acceptability.
Low Prevalence of Inappropriate Shocks in Patients With Inherited Arrhythmia Syndromes With the Subcutaneous Implantable Defibrillator Single Center Experience and Long‐Term Follow‐Up
Authors: Rudic Boris , Tülümen Erol , Berlin Veronika , Röger Susanne , Stach Ksenija , Liebe Volker , El‐Battrawy Ibrahim , Dösch Christina , Papavassiliu Theano , Akin Ibrahim , Borggrefe Martin , Kuschyk Jürgen 
Published: October 2017

Background

Up to 40% of patients with transvenous implantable cardioverter‐defibrillator
(ICD)
experience lead‐associated complications and may suffer from high complication rates when lead extraction is indicated. Subcutaneous
ICD
may represent a feasible alternative; however, the efficacy of the subcutaneous
ICD
in the detection and treatment of ventricular arrhythmias in patients with hereditary arrhythmia syndromes has not been fully evaluated.

Methods and Results

Patients with primary hereditary arrhythmia syndromes who fulfilled indication for defibrillator placement were eligible for enrollment. Between 2010 and 2016, 62 consecutive patients with primary hereditary arrhythmia syndromes, without indication for antibradycardia therapy, were enrolled in the study. Mean follow‐up was 31.0±14.2 months. The study cohort comprised of 24 patients with Brugada syndrome, 17 with idiopathic ventricular fibrillation, 6 with long‐
QT
syndrome, 1 with short‐
QT
syndrome, 3 with catecholaminergic polymorphic ventricular tachycardia, 8 with hypertrophic cardiomyopathy, and 3 with arrhythmogenic right ventricular cardiomyopathy. Thirty‐nine patients were implanted for secondary prevention. Twenty‐two patients had a previous transvenous
ICD
implanted, but required revision because of infection or lead defects. A total of 20 spontaneous ventricular tachyarrhythmias requiring shock intervention occurred in 10 patients during follow‐up. All episodes were terminated within the first
ICD
shock delivery with 80 J. Two patients had inappropriate therapies caused by oversensing following an uneventful implantation. No pocket‐site infections and no premature revisions have occurred during follow‐up.

Conclusions

Our study supports the use of the subcutaneous
ICD
for both secondary and primary prevention of sudden cardiac death as a reliable alternative to the conventional transvenous
ICD
.
Cardiac Resynchronization Therapy Using Quadripolar Versus Non‐Quadripolar Left Ventricular Leads Programmed to Biventricular Pacing With Single‐Site Left Ventricular Pacing: Impact on Survival and Heart Failure Hospitalization
Authors: Leyva Francisco , Zegard Abbasin , Qiu Tian , Acquaye Edmund , Ferrante Gaetano , Walton Jamie , Marshall Howard 
Published: October 2017

Background

In cardiac resynchronization therapy (
CRT
), quadripolar (
QUAD
) left ventricular (
LV
) leads are less prone to postoperative complications than non‐
QUAD
leads. Some studies have suggested better clinical outcomes.

Methods and Results

Clinical events were assessed in 847 patients after
CRT
‐pacing or CRT‐defibrillation using either
QUAD
(n=287) or non‐
QUAD
(n=560), programmed to single‐site site
LV
pacing. Over a follow‐up period of 3.2 years (median [interquartile range, 1.90–5.0]),
QUAD
was associated with a lower total mortality (adjusted hazard ratio [
aHR
]: 0.32, 95% confidence interval [
CI
], 0.20–0.52), cardiac mortality (
aHR
: 0.36, 95%
CI
, 0.20–0.65), and heart failure (
HF
) hospitalization (
aHR
: 0.62, 95%
CI
, 0.39–0.99), after adjustment for age, sex, New York Heart Association class,
HF
etiology, device type (
CRT
‐pacing or
CRT
‐defibrillation), comorbidities, atrial rhythm, medication, left ventricular ejection fraction, and creatinine. Death from pump failure was lower with
QUAD
(
aHR
: 0.33; 95%
CI
, 0.18–0.62), but no group differences emerged with respect to sudden cardiac death. There were no differences in implant‐related complications. Re‐interventions for
LV
displacement or phrenic nerve stimulation, which were lower with
QUAD
, predicted total mortality (
aHR
: 1.68, 95%
CI
, 1.11–2.54), cardiac mortality (
aHR
: 2.61, 95%
CI
, 1.66–4.11) and
HF
hospitalization (
aHR
: 2.09, 95% CI, 1.22–3.58).

Conclusions

CRT
using
QUAD
, programmed to biventricular pacing with single‐site
LV
pacing, is associated with a lower total mortality, cardiac mortality, and
HF
hospitalization. These trends were observed for both
CRT
‐defibrillation and
CRT
‐pacing, after adjustment for
HF
cause and other confounders. Re‐intervention for
LV
lead displacement or phrenic nerve stimulation was associated with worse outcomes.
Spiritual Exercises in the Hodayot? 1QHa as Perfective Trajectory
Authors: Leroy Christine 
Published: October 2017

AbstractRecent scholarship has tended to view the Hodayot from the perspective of their liturgical function. Although the Hodayot are texts that participate in the continuities of late Second Temple wisdom traditions the question of the formative features of the psalms deserves greater critical attention. This article explores the possibility of a pedagogical dimension to the psalms and offers a new direction for understanding the dialogical orientation of the compositions. A cursory review of scholarship in favor of the predominantly liturgical function of the Hodayot follows the introduction. The question of a didactic dimension for 1QHa is then taken up by considering a conceptual parallel to a family of practices observed from the Greco-Roman paideutic tradition. A sequence of psalms is examined to illustrate the pedagogy and function of the prayers from within the broader spectrum of embodied ascetic practices and a perfective trajectory of spiritual exercises directed towards ritual transformation.
The Clash of Architects: Impending Developments and Transformations in International Law
Authors: Slawotsky Joel 
Published: October 2017

Abstract
The world stands at the precipice of a transitional moment in the international law writ caused by the reasonable likelihood that new architects will be joining (and eventually supplanting) the present-day architects. Transformative geo-political and economic developments such as obor, the aiib, ndb and the increasing internationalization of the Yuan all herald potentially significant changes to the existing international governance architecture. “Revisionist” states with strong motivations and global ambitions, may will become international law creators as these new architects influence the economic and legal orders. International law is not static and several of the new architects’ customs and norms inherently conflict with current Western ideals. Will international law norms converge? Will Western notions gravitate towards the other spectrum in enlightened self-interest? The impact on international law norms, enforcement, human rights, sustainability, trade and investment treaties and arbitration will be far-reaching. Understanding how this potential re-orientations in power will affect international law is of critical importance.
Informed Consent for Comparative Effectiveness Research Should Not Consider the Risks of the Standard Therapies That Are Being Studied as Risks of the Research
Authors: Lantos John D. 
Published: October 2017

There is a debate at the highest levels of government about how to classify the risks of research studies that evaluate therapies that are in widespread use. Should the risks of those therapies be considered as risks of research that is designed to evaluate those therapies? Or not? The Common Rule states, “In evaluating risks and benefits, the IRB should consider only those risks and benefits that may result from the research (as distinguished from risks and benefits of therapies subjects would receive even if not participating in the research).” (CFR 46.111 (a)(2)). By contrast, the Office of Human Research Protections, in a proposed “guidance” states, “The reasonably foreseeable risks of research include already-identified risks of the standards of care being evaluated as a purpose of the research.” (emphasis added).In this paper, I argue that the Common Rule got it right and OHRP got it wrong. When treatments are in widespread use, the risks of those treatments are ever-present for all patients. By enrolling in formal studies that use rigorous methods to compare one treatment with another and that carefully monitor outcomes and adverse events, patients are protected from the risks of idiosyncratic practice variation. Their risks are decreased, rather than increased.If OHRP's approach becomes the law of the land, patients will be misinformed about the relative risks of treatment and research in ways that undermine autonomy rather than promoting it and that make truly informed consent impossible.
A CD200R-CD28 fusion protein appropriates an inhibitory signal to enhance T-cell function and therapy of murine leukemia
Authors: Oda Shannon K. , Daman Andrew W. , Garcia Nicolas M. , Wagener Felecia , Schmitt Thomas M. , Tan Xiaoxia , Chapuis Aude G. , Greenberg Philip D. 
Published: October 2017

Key PointsIFPs can convert signals from inhibitory ligands into activating signals. Costimulation was most effectively achieved by engineering the IFP to promote the ability to localize in the immunological synapse.
High diving metabolic rate indicated by high-speed transit to depth in negatively buoyant long-finned pilot whales
Authors: Aoki Kagari , Sato Katsufumi , Isojunno Saana , Narazaki Tomoko , Miller Patrick J. O. 
Published: October 2017

ABSTRACTTo maximize foraging duration at depth, diving mammals are expected to use the lowest cost optimal speed during descent and ascent transit and to minimize the cost of transport by achieving neutral buoyancy. Here, we outfitted 18 deep-diving long-finned pilot whales with multi-sensor data loggers and found indications that their diving strategy is associated with higher costs than those of other deep-diving toothed whales. Theoretical models predict that optimal speed is proportional to (basal metabolic rate/drag)1/3 and therefore to body mass0.05. The transit speed of tagged animals (2.7±0.3 m s−1) was substantially higher than the optimal speed predicted from body mass (1.4–1.7 m s−1). According to the theoretical models, this choice of high transit speed, given a similar drag coefficient (median, 0.0035) to that in other cetaceans, indicated greater basal metabolic costs during diving than for other cetaceans. This could explain the comparatively short duration (8.9±1.5 min) of their deep dives (maximum depth, 444±85 m). Hydrodynamic gliding models indicated negative buoyancy of tissue body density (1038.8±1.6 kg m–3, ±95% credible interval, CI) and similar diving gas volume (34.6±0.6 ml kg−1, ±95% CI) to those in other deep-diving toothed whales. High diving metabolic rate and costly negative buoyancy imply a ‘spend more, gain more’ strategy of long-finned pilot whales, differing from that in other deep-diving toothed whales, which limits the costs of locomotion during foraging. We also found that net buoyancy affected the optimal speed: high transit speeds gradually decreased during ascent as the whales approached neutral buoyancy owing to gas expansion.
Life history adjustments to intestinal inflammation in a gut nematode
Authors: Lippens Cédric , Guivier Emmanuel , Ollivier Anthony , Faivre Bruno , Sorci Gabriele 
Published: October 2017

ABSTRACT
Many parasitic nematodes establish chronic infections. This implies a finely tuned interaction with the host immune response in order to avoid infection clearance. Although a number of immune interference mechanisms have been described in nematodes, how parasites adapt to the immune environment provided by their hosts remains largely unexplored. Here, we used the gastrointestinal nematode Heligmosomoides polygyrus to investigate the plasticity of life history traits and immunomodulatory mechanisms in response to intestinal inflammation. We adopted an experimental model of induced colitis and exposed worms to intestinal inflammation at two different developmental stages (larvae and adults). We found that H. polygyrus responded to intestinal inflammation by up-regulating the expression of a candidate gene involved in the interference with the host immune response. Worms infecting mice with colitis also had better infectivity (earlier adult emergence in the intestinal lumen and higher survival) compared with worms infecting control hosts, suggesting that H. polygyrus adjusted its life history schedule in response to intestinal inflammation.
Fatores prognósticos da infeção respiratória aguda baixa grave em crianças menores de 5 anos na Colômbia
Authors: Delgado Romero Andrés Kamilo , Salazar Palechor Yined Marcela , Díaz Rosalba , Solano Victoria Eugenia , Ruiz Beltrán Germán , García Chaves María Andrea , Calvache José Andrés 
Published: October 2017

Introdução: a infeção respiratória aguda baixa (IRAB) é um dos principais problemas de saúde pública em crianças menores de 5 anos em países em desenvolvimento. O objetivo deste estudo foi descrever a incidência, mortalidade e fatores prognósticos em pacientes menores de 5 anos com diagnóstico de IRAB grave em 2 hospitais de referência de Popayán, Colômbia. Materiais e métodos: estudo de coorte. Incluíramse crianças entre 2 meses e 5 anos com diagnóstico de IRAB grave (pneumonia adquirida em comunidade e/ou bronquite). Coletaramse dados sociodemográficos, paraclínicos e de prognóstico. Os desenlaces de interesse foram a incidência de morte, de ingresso a UCI e o tempo de estadia hospitalar. Se realizou uma análise multivariada para avaliar o efeito de fatores prognósticos. Resultados: incluíramse 121 casos. A incidência de irab grave durante seis meses de seguimento foi 4% IC95% [3,3-4,7]. A mortalidade estimada durante o seguimento foi 0,8% IC95% [0,1-4,4] (1 paciente). O 33% de crianças requereu ingresso a ucip. A mediana de hospitalização global foi 5 dias e de estadia na ucip 4 dias. O antecedente de nascimento prétermo associouse de forma independente com o ingresso à UCIP (or=5,1 ic95% [1,3-20] p=0,019). Discussão: a incidência de IRAB grave foi de 4%. A mortalidade associada foi baixa e o tempo de estadia hospitalar curto. Os fatores relacionados à apresentação de IRAB são consistentes com os documentados na literatura nacional e internacional e o único fator prognóstico de importância para ingresso à ucip foi a história de prematuridade.
Automatically Determining the Segmentation Lines between Images of Adherent Rice Grains
Authors: Chen Yongming , Lin Ping 
Published: October 2017

Abstract. A new strategy for accurately and automatically determining the segmentation lines between images of adherent rice grains was explored based on the characteristics of contour and the techniques of image analysis. The images were captured by using an optical scanner. The original images of touching rice particles were preprocessed by the techniques of image analysis including de-noise, segmentation, and contour extraction. The extracted contours were smoothed by convoluting with Gaussian kernel. The first-derivative of the smoothed vectors was computed to look for the local peaks which corresponded to the segmentation nodes. A radiate triangle region was proposed to determine the confidence region for the potential matching nodes. The direction of radiate region was determined in terms of the axis tilted from the normal through the curvature center. The nodes which fell into the triangle region might become the candidate matching nodes. The splitting line linking between the matching nodes with the shortest distance was considered as the correct splitting path. The results demonstrated that the proposed method could be successfully used to split the images of touching rice particles. Keywords: Confidence region, Image analysis, Matching, Rice particles, Segmentation.
Economic Analysis of Agricultural Tractors in South Korea: Classified Based on Energy Efficiency Grades
Authors: Shin C S , Kim K U , Kwon Patrick 
Published: October 2017

Abstract. This study involved performing an economic analysis on agricultural tractors classified based on energy efficiency grades using the energy efficiency index. Specifically, 131 models of agricultural tractors commonly used between 2006 and 2010 in South Korea were classified into five categories. The relationship between energy efficiency and economic value was evaluated by a numerical method, and a method of predicting cost and fuel savings based on energy efficiency was developed. Grades of energy efficiency labeled from 1–5 were assumed in order to calculate annual fuel and cost savings. The results indicated that the use of the proposed method resulted in fuel and cost savings given an upgrade from the 5th level of energy efficiency to the 1st level and indicated subsequent improvements with each grade level. This method was applied to data from the year 2008, and total fuel and cost savings were obtained. This indicated that fuel and cost savings in an arbitrary year could be predicted using the proposed method and assuming data from an arbitrary year. Keywords: Agricultural tractors, Economic analysis, Energy efficiency classification grade, Energy efficiency index.