bluuebunny/crossref_metadata_2025_split huggingface dataset:
Blockage of CD59 Function Restores Activities of Neutralizing and Nonneutralizing Antibodies in Triggering Antibody-Dependent Complement-Mediated Lysis of HIV-1 Virions and Provirus-Activated Latently Infected Cells
Authors: Yang Kai , Lan Jie , Shepherd Nicole , Hu Ningjie , Xing Yanyan , Byrd Daniel , Amet Tohti , Jewell Corlin , Gupta Samir , Kounga Carole , Gao Jimin , Yu Qigui 
Published: July 2015

ABSTRACTBoth HIV-1 virions and infected cells use their surface regulators of complement activation (RCA) to resist antibody-dependent complement-mediated lysis (ADCML). Blockage of the biological function of RCA members, particularly CD59 (a key RCA member that controls formation of the membrane attack complex at the terminal stage of the complement activation cascades via all three activation pathways), has rendered both HIV-1 virions and infected cells sensitive to ADCML mediated by anti-Env antibodies (Abs) or sera/plasma from patients at different stages of viral infection. In the current study, we used the well-characterized anti-HIV-1 neutralizing Abs (nAbs), including 2G12, 2F5, and 4E10, and non-nAbs, including 2.2C, A32, N5-i5, and N12-i15, to investigate whether the enhancement of ADCML by blockage of CD59 function is mediated by nAbs, non-nAbs, or both. We found that all nAbs and two non-nAbs (N5-i5 and A32) strongly reacted to three HIV-1 laboratory strains (R5, X4, and R5/X4), six primary isolates, and provirus-activated ACH-2 cells examined. In contrast, two non-nAbs, 2.2C and N12-i15, reacted weakly and did not react to these targets, respectively. After blockage of CD59 function, the reactive Abs, regardless of their neutralizing activities, significantly enhanced specific ADCML of HIV-1 virions (both laboratory strains and primary isolates) and provirus-activated latently infected cells. The ADMCL efficacy positively correlated with the enzyme-linked immunosorbent assay-reactive intensity of those Abs with their targets. Thus, blockage of RCA function represents a novel approach to restore activities of both nAbs and non-nAbs in triggering ADCML of HIV-1 virions and provirus-activated latently infected cells.IMPORTANCEThere is a renewed interest in the potential role of non-nAbs in the control of HIV-1 infection. Our data, for the first time, demonstrated that blockage of the biological function of RCA members rendered both HIV-1 virions and infected cells sensitive to ADCML mediated by not only nAbs but also non-nAbs. Our results are significant in developing novel immune-based approaches to restore the functions of nAbs and non-nAbs in the circulation of HIV-1-infected individuals to specifically target and clear HIV-1 virions and infected cells. Our data also provide new insights into the mechanisms by which HIV-1 virions and infected cells escape Ab-mediated immunity and could aid in the design and/or development of therapeutic HIV-1 vaccines. In addition, a combination of antiretroviral therapy with RCA blockage, provirus activators, and therapeutic vaccines may represent a novel approach to eliminate HIV-1 reservoirs, i.e., the infected cells harboring replication-competent proviruses and residual viremia.
Impact of Nucleoporin-Mediated Chromatin Localization and Nuclear Architecture on HIV Integration Site Selection
Authors: Wong Richard W. , Mamede João I. , Hope Thomas J. 
Published: July 2015

ABSTRACT
It has been known for a number of years that integration sites of human immunodeficiency virus type 1 (HIV-1) DNA show a preference for actively expressed chromosomal locations. A number of viral and cellular proteins are implicated in this process, but the underlying mechanism is not clear. Two recent breakthrough publications advance our understanding of HIV integration site selection by focusing on the localization of the preferred target genes of integration. These studies reveal that knockdown of certain nucleoporins and components of nucleocytoplasmic trafficking alter integration site preference, not by altering the trafficking of the viral genome but by altering the chromatin subtype localization relative to the structure of the nucleus. Here, we describe the link between the nuclear basket nucleoporins (Tpr and Nup153) and chromatin organization and how altering the host environment by manipulating nuclear structure may have important implications for the preferential integration of HIV into actively transcribed genes, facilitating efficient viral replication.
The Plasmid Mobilome of the Model Plant-SymbiontSinorhizobium meliloti: Coming up with New Questions and Answers
Authors: Lagares Antonio , Sanjuán Juan , Pistorio Mariano 
Published: July 2015

ABSTRACTRhizobia are Gram-negative Alpha- and Betaproteobacteria living in the underground which have the ability to associate with legumes for the establishment of nitrogen-fixing symbioses.Sinorhizobium melilotiin particular—the symbiont ofMedicago,Melilotus, andTrigonellaspp.—has for the past decades served as a model organism for investigating, at the molecular level, the biology, biochemistry, and genetics of a free-living and symbiotic soil bacterium of agricultural relevance. To date, the genomes of seven differentS. melilotistrains have been fully sequenced and annotated, and several other draft genomic sequences are also available. The vast amount of plasmid DNA thatS. melilotifrequently bears (up to 45% of its total genome), the conjugative ability of some of those plasmids, and the extent of the plasmid diversity has provided researchers with an extraordinary system to investigate functional and structural plasmid molecular biology within the evolutionary context surrounding a plant-associated model bacterium. Current evidence indicates that the plasmid mobilome inS. melilotiis composed of replicons varying greatly in size and having diverse conjugative systems and properties along with different evolutionary stabilities and biological roles. While plasmids carrying symbiotic functions (pSyms) are known to have high structural stability (approaching that of chromosomes), the remaining plasmid mobilome (referred to as the non-pSym,functionally cryptic, oraccessorycompartment) has been shown to possess remarkable diversity and to be highly active in conjugation. In light of the modern genomic and current biochemical data on the plasmids ofS. meliloti, the current article revises their main structural components, their transfer and regulatory mechanisms, and their potential as vehicles in shaping the evolution of the rhizobial genome.
The
Agrobacterium
Ti Plasmids
Authors: Gordon Jay E. , Christie Peter J. 
Published: July 2015

ABSTRACT

Agrobacterium tumefaciens
is a plant pathogen with the capacity to deliver a segment of oncogenic DNA carried on a large plasmid called the tumor-inducing or Ti plasmid to susceptible plant cells.
A. tumefaciens
belongs to the class
Alphaproteobacteria
, whose members include other plant pathogens (
Agrobacterium rhizogenes
), plant and insect symbionts (
Rhizobium
spp. and
Wolbachia
spp., respectively), human pathogens (
Brucella
spp.,
Bartonella
spp.,
Rickettsia
spp.), and nonpathogens (
Caulobacter crescentus, Rhodobacter sphaeroides
). Many species of
Alphaproteobacteria
carry large plasmids ranging in size from ∼100 kb to nearly 2 Mb. These large replicons typically code for functions essential for cell physiology, pathogenesis, or symbiosis. Most of these elements rely on a conserved gene cassette termed
repABC
for replication and partitioning, and maintenance at only one or a few copies per cell (
1
). The subject of this review is the ∼200-kb Ti plasmids carried by infectious strains of
A. tumefaciens
. We will summarize the features of this plasmid as a representative of the
repABC
family of megaplasmids. We will also describe novel features of this plasmid that enable
A. tumefaciens
cells to incite tumor formation in plants, sense and respond to an array of plant host and bacterial signal molecules, and maintain and disseminate the plasmid among populations of agrobacteria. At the end of this review, we will describe how this natural genetic engineer has been adapted to spawn an entire industry of plant biotechnology and review its potential for use in future therapeutic applications of plant and nonplant species.
Plasmid-Mediated Antibiotic Resistance and Virulence in Gram-Negatives: the
Klebsiella pneumoniae
Paradigm
Authors: Ramirez Maria S. , Traglia German M. , Lin David L. , Tran Tung , Tolmasky Marcelo E. 
Published: July 2015

ABSTRACT

Plasmids harbor genes coding for specific functions including virulence factors and antibiotic resistance that permit bacteria to survive the hostile environment found in the host and resist treatment. Together with other genetic elements such as integrons and transposons, and using a variety of mechanisms, plasmids participate in the dissemination of these traits, resulting in the virtual elimination of barriers among different kinds of bacteria. In this article we review the current information about the physiology of plasmids and their role in virulence and antibiotic resistance from the Gram-negative opportunistic pathogen
Klebsiella pneumoniae
. This bacterium has acquired multidrug resistance and is the causative agent of serious community- and hospital-acquired infections. It is also included in the recently defined ESKAPE group of bacteria that cause most U.S. hospital infections.
Iteron Plasmids
Authors: Konieczny Igor , Bury Katarzyna , Wawrzycka Aleksandra , Wegrzyn Katarzyna 
Published: July 2015

ABSTRACT
Iteron-containing plasmids are model systems for studying the metabolism of extrachromosomal genetic elements in bacterial cells. Here we describe the current knowledge and understanding of the structure of iteron-containing replicons, the structure of the iteron plasmid encoded replication initiation proteins, and the molecular mechanisms for iteron plasmid DNA replication initiation. We also discuss the current understanding of control mechanisms affecting the plasmid copy number and how host chaperone proteins and proteases can affect plasmid maintenance in bacterial cells.
Plasmid Diversity and Adaptation Analyzed by Massive Sequencing of
Escherichia coli
Plasmids
Authors: de Toro María , Garcilláon-Barcia M. Pilar , De La Cruz Fernando 
Published: July 2015

ABSTRACT

Whole-genome sequencing is revolutionizing the analysis of bacterial genomes. It leads to a massive increase in the amount of available data to be analyzed. Bacterial genomes are usually composed of one main chromosome and a number of accessory chromosomes, called plasmids. A recently developed methodology called PLACNET (for
pla
smid
c
onstellation
net
works) allows the reconstruction of the plasmids of a given genome. Thus, it opens an avenue for plasmidome analysis on a global scale. This work reviews our knowledge of the genetic determinants for plasmid propagation (conjugation and related functions), their diversity, and their prevalence in the variety of plasmids found by whole-genome sequencing. It focuses on the results obtained from a collection of 255
Escherichia coli
plasmids reconstructed by PLACNET. The plasmids found in
E. coli
represent a nonaleatory subset of the plasmids found in proteobacteria. Potential reasons for the prevalence of some specific plasmid groups will be discussed and, more importantly, additional questions will be posed.
Clinical use of low haemoglobin density, transferrin saturation, bone marrow morphology, Perl's stain and other plasma markers in the identification of treatable anaemia presenting for cardiac surgery in a prospective cohort study
Authors: Martin-Cabrera Pedro , Hung Matthew , Ortmann Erik , Richards Toby , Ghosh Marcus , Bottrill Fiona , Collier Timothy , Klein Andrew A , Besser Martin W 
Published: July 2015

ObjectivesThe differential diagnosis between iron deficiency anaemia (IDA) and anaemia of chronic disease (ACD) with or without associated iron deficiency can be challenging. We assessed the use of different parameters, both classical like ferritin, transferrin saturation and stainable bone marrow iron stores, and novel markers such as low haemoglobin density (LHD) and hepcidin to help discriminate between the three entities. This would allow the detection of patients with ACD with associated iron deficiency, which could benefit from iron supplementation that would have otherwise remained undetected.Materials and methodsProspective and observational cohort study from 2012 to 2013 where 200 anaemic cardiac surgical patients were recruited and 165 were studied. Detailed blood and bone marrow analyses were performed to establish the aetiology of anaemia.ResultsSeventy-four patients (44.8%) had ACD and 29 (39%) of these had an elevated LHD indicating concomitant iron deficiency. Hepcidin was inappropriately normal or increased in the IDA and ACD group. Mean hepcidin was however lower in the group with IDA (4.8 ng/mL) than in the ACD group (15.0 ng/mL; p=0.002). Median hepcidin was lower in patients with ACD and iron restriction as indicated by LHD >4% (17.5 ng/mL) than on those with no iron restriction (25.9 ng/mL; p=0.045). In patients with ACD there was no concordance between Perl's stain and LHD.ConclusionsLHD was superior to hepcidin and bone marrow iron stores in identifying patients with ACD and associated iron deficiency, which would potentially benefit from parenteral iron therapy.
Plebański–Demiański solution of general relativity and its expressions quadratic and cubic in curvature: Analogies to electromagnetism
Authors: Boos Jens 
Published: July 2015

Analogies between gravitation and electromagnetism have been known since the 1950s. Here, we examine a fairly general type D solution — the exact seven parameter solution of Plebański–Demiański (PD) — to demonstrate these analogies for a physically meaningful spacetime. The two quadratic curvature invariants B2 - E2 and E⋅B are evaluated analytically. In the asymptotically flat case, the leading terms of E and B can be interpreted as gravitoelectric mass and gravitoelectric current of the PD solution, respectively, if there are no gravitomagnetic monopoles present. Furthermore, the square of the Bel–Robinson tensor reads (B2 + E2)2 for the PD solution, reminiscent of the square of the energy density in electrodynamics. By analogy to the energy–momentum 3-form of the electromagnetic field, we provide an alternative way to derive the recently introduced Bel–Robinson 3-form, from which the Bel–Robinson tensor can be calculated. We also determine the Kummer tensor, a tensor cubic in curvature, for a general type D solution for the first time, and calculate the pieces of its irreducible decomposition. The calculations are carried out in two coordinate systems: In the original polynomial PD coordinates and in a modified Boyer–Lindquist-like version introduced by Griffiths and Podolský (GP) allowing for a more straightforward physical interpretation of the free parameters.
THE CONTAGIOUS POWER OF INNOVATIVENESS: HOW DIFFERENT CORPORATE PARTNERS CONTRIBUTE TO A FIRM'S KNOWLEDGE
Authors: MOOS BERNHARD , WAGNER HEINZ-THEO , BEIMBORN DANIEL , WEITZEL TIM 
Published: July 2015

As innovation is often created in networks, a company's business partners influence its innovative outcome. Although many studies investigate innovation networks as a means to explore and exploit external knowledge, virtually no research has focused on the characteristics of external partners — in particular their innovativeness. This study considers axial and lateral corporate partners and investigates the differential impact of the partners' innovativeness on a company's knowledge stocks (market, technological, organisational, process, and product knowledge).Drawing on the literature on inter-organisational networks and using survey data from the manufacturing industry, the results extend theory by revealing that not only relationships with partners but also their properties — partner innovativeness — are important for a company's knowledge stock. In essence our results suggest that the innovativeness of a firm's axial and lateral partners positively yet diversely influences its various knowledge stocks.
Fc-Receptor Interactions Regulate Both Cytotoxic and Immunomodulatory Therapeutic Antibody Effector Functions
Authors: DiLillo David J. , Ravetch Jeffrey V. 
Published: July 2015

Abstract
Antibodies are now recognized as key therapeutic tools to combat most forms of malignancy. Although the first wave of therapeutic antibodies that emerged over two decades ago directly target tumor cells for killing, a new class of antibody therapies targeting immunoregulatory pathways to boost antitumor immune responses by activating the immune system is poised for clinical success. A notable common characteristic of both classes of therapeutic antibodies is the importance of the IgG Fc domain, which connects the fine specificity of an antibody with immune cells that mediate antibody-triggered effector functions through their engagement of Fc receptor (FcR) family members. It is now clear that multiple variables, including the nature of the target molecules, the local presence of effector cells, and the expression patterns of FcRs, will dictate whether and how an antibody will necessitate interactions with FcRs to mediate optimal therapeutic effects. Thus, through careful in vivo mechanistic analyses of individual therapeutic antibodies, Fc domains engineered for optimal engagement of the appropriate cellular FcRs must be designed to maximize clinical success. Cancer Immunol Res; 3(7); 704–13. ©2015 AACR.
A Comparison of Airborne In Situ Cloud Microphysical Measurement with Ground-Based C-Band Radar Observations in Deep Stratiform Regions of African Squall Lines
Authors: Drigeard E. , Fontaine E. , Wobrock W. , Schwarzenböck A. , Duroure C. , Williams E. R. , Russell B. , Protat A. , Delanoë J. , Cazenave F. , Gosset M. 
Published: July 2015

AbstractThis study addresses clouds with significant ice water content (IWC) in the stratiform regions downwind of the convective cores of African squall lines in the framework of the French–Indian satellite Megha-Tropiques project, observed in August 2010 next to Niamey (13.5°N, 2°E) in the southwestern part of Niger. The objectives included comparing the IWC–Z reflectivity relationship for precipitation radars in deep stratiform anvils, collocating reflectivity observed from ground radar with the calculated reflectivity from in situ microphysics for all aircraft locations inside the radar range, and interpreting the role of large ice crystals in the reflectivity of centimeter radars through analysis of their microphysical characteristics as ice crystals larger than 5 mm frequently occurred. It was found that, in the range of 20–30 dBZ, IWC and C-band reflectivity are not really correlated. Cloud regions with high IWC caused by important crystal number concentrations can lead to the same reflectivity factor as cloud regions with low IWC formed by a few millimeter-sized ice crystals.
Automated Detection of Polarimetric Tornadic Debris Signatures Using a Hydrometeor Classification Algorithm
Authors: Snyder Jeffrey C. , Ryzhkov Alexander V. 
Published: July 2015

AbstractAlthough radial velocity data from Doppler radars can partially resolve some tornadoes, particularly large tornadoes near the radar, most tornadoes are not explicitly resolved by radar owing to inadequate spatiotemporal resolution. In addition, it can be difficult to determine which mesocyclones typically observed on radar are associated with tornadoes. Since debris lofted by tornadoes has scattering characteristics that are distinct from those of hydrometeors, the additional information provided by polarimetric weather radars can aid in identifying debris from tornadoes; the polarimetric tornadic debris signature (TDS) provides what is nearly “ground truth” that a tornado is ongoing (or has recently occurred). This paper outlines a modification to the hydrometeor classification algorithm used with the operational Weather Surveillance Radar-1988 Doppler (WSR-88D) network in the United States to include a TDS category. Examples of automated TDS classification are provided for several recent cases that were observed in the United States.
A Real-Time Convection-Allowing Ensemble Prediction System Initialized by Mesoscale Ensemble Kalman Filter Analyses
Authors: Schwartz Craig S. , Romine Glen S. , Weisman Morris L. , Sobash Ryan A. , Fossell Kathryn R. , Manning Kevin W. , Trier Stanley B. 
Published: July 2015

Abstract
In May and June 2013, the National Center for Atmospheric Research produced real-time 48-h convection-allowing ensemble forecasts at 3-km horizontal grid spacing using the Weather Research and Forecasting (WRF) Model in support of the Mesoscale Predictability Experiment field program. The ensemble forecasts were initialized twice daily at 0000 and 1200 UTC from analysis members of a continuously cycling, limited-area, mesoscale (15 km) ensemble Kalman filter (EnKF) data assimilation system and evaluated with a focus on precipitation and severe weather guidance. Deterministic WRF Model forecasts initialized from GFS analyses were also examined. Subjectively, the ensemble forecasts often produced areas of intense convection over regions where severe weather was observed. Objective statistics confirmed these subjective impressions and indicated that the ensemble was skillful at predicting precipitation and severe weather events. Forecasts initialized at 1200 UTC were more skillful regarding precipitation and severe weather placement than forecasts initialized 12 h earlier at 0000 UTC, and the ensemble forecasts were typically more skillful than GFS-initialized forecasts. At times, 0000 UTC GFS-initialized forecasts had temporal distributions of domain-average rainfall closer to observations than EnKF-initialized forecasts. However, particularly when GFS analyses initialized WRF Model forecasts, 1200 UTC forecasts produced more rainfall during the first diurnal maximum than 0000 UTC forecasts. This behavior was mostly attributed to WRF Model initialization of clouds and moist physical processes. The success of these real-time ensemble forecasts demonstrates the feasibility of using limited-area continuously cycling EnKFs as a method to initialize convection-allowing ensemble forecasts, and future real-time high-resolution ensemble development leveraging EnKFs seems justified.