bluuebunny/crossref_metadata_2025_split huggingface dataset:
Affinity maturation in an HIV broadly neutralizing B-cell lineage through reorientation of variable domains
Authors: Fera Daniela , Schmidt Aaron G. , Haynes Barton F. , Gao Feng , Liao Hua-Xin , Kepler Thomas B. , Harrison Stephen C. 
Published: July 2014

Significance
An HIV vaccine must induce antibodies [broadly neutralizing antibodies (bnAbs)] that neutralize many viral variants. Determining pathways of antibody affinity maturation that have led to specific bnAbs and tracking coevolution in an infected individual of virus and antibody will define characteristics of immunogens that might elicit broad responses. We have followed, in an infected individual, one round of coevolution of viral envelope with antibodies from a single lineage. Insertions into a loop (V5) in gp120 of autologous viruses allowed escape from neutralization by antibodies in this lineage; antibody affinity maturation shifted the relative orientation of the light- and heavy-chain variable domains, allowing binding to envelopes with augmented V5. The results illustrate a mechanism of affinity maturation through mutation outside the antigen combining site.
Material properties of Northeast Pacific zooplankton
Authors: Becker Kaylyn N. , Warren Joseph D. 
Published: July 2014

Abstract
We measured the density and sound speed contrasts relative to seawater of Northeast Pacific zooplankton. The density contrast (g) was measured for euphausiids, decapods (Sergestes similis), amphipods (Primno macropa, Phronima sp., and Hyperiid spp.), siphonophore bracts, chaetognaths, larval fish, crab megalopae, larval squid, and medusae. Morphometric data (length, width, and height) were collected for these taxa. Density contrasts varied within and between zooplankton taxa. The mean and standard deviation (s.d.) for euphausiid density contrast were 1.059 ± 0.009. Relationships between zooplankton density contrast and morphometric measurements, geographic location, and environmental conditions were investigated. Site had a significant effect on euphausiid density contrast. Density contrasts of euphausiids collected in the same geographic area ∼4–10 d apart were significantly higher (p< 0.001). Sound speed contrast (h) was measured for euphausiids and pelagic decapods (S. similis) and it varied between taxa. The mean and s.d. for euphausiid sound speed were 1.019 ± 0.009. Euphausiid mass was calculated from measured density and volume, and a relationship between euphausiid mass and length was produced. We determined that euphausiid volume could be accurately estimated from two-dimensional measurements of animal body shape, and that biomass (or biovolume) could be accurately calculated from digital photographs of animals. Data from this study can improve the accuracy of theoretical acoustic scattering models for these taxa, resulting in more accurate estimates of zooplankton biomass in this region.
Dynamics of T-cell IFN-γ and miR-29a expression during active pulmonary tuberculosis
Authors: Afum-Adjei Awuah Anthony , Ueberberg Bianca , Owusu-Dabo Ellis , Frempong Margaret , Jacobsen Marc 
Published: July 2014

Abstract
IFN-γ is crucial for protection against Mycobacterium tuberculosis. miR-29 was recently shown to non-redundantly inhibit IFN-γ. Here, we investigated IFN-γ and miR-29a expression dynamics of CD4+ T cells from patients during active tuberculosis (TB) (n = 32) and in household contacts who were latently M. tuberculosis infected (n = 19) from Ghana. Whereas M. tuberculosis-specific IFN-γ expression was similar during TB chemotherapy, superantigen stimulation indicated generally impaired IFN-γ expression in TB patients. No interdependency between miR-29a and IFN-γ expression of T cells was observed. However, miR-29a was differentially expressed in T cells during chemotherapy. We concluded that differential miR-29a expression in active TB was not causative for impaired IFN-γ expression.
A fully enzymatic method for site-directed spin labeling of long RNA
Authors: Lebars Isabelle , Vileno Bertrand , Bourbigot Sarah , Turek Philippe , Wolff Philippe , Kieffer Bruno 
Published: July 2014

Abstract
Site-directed spin labeling is emerging as an essential tool to investigate the structural and dynamical features of RNA. We propose here an enzymatic method, which allows the insertion of a paramagnetic center at a specific position in an RNA molecule. The technique is based on a segmental approach using a ligation protocol with T4 RNA ligase 2. One transcribed acceptor RNA is ligated to a donor RNA in which a thio-modified nucleotide is introduced at its 5′-end by in vitro transcription with T7 RNA polymerase. The paramagnetic thiol-specific reagent is subsequently attached to the RNA ligation product. This novel strategy is demonstrated by introducing a paramagnetic probe into the 55 nucleotides long RNA corresponding to K-turn and Specifier Loop domains from the Bacillus subtilis tyrS T-Box leader RNA. The efficiency of the coupling reaction and the quality of the resulting spin-labeled RNA were assessed by Mass Spectrometry, Electron Paramagnetic Resonance (EPR) and Nuclear Magnetic Resonance (NMR). This method enables various combinations of isotopic segmental labeling and spin labeling schemes, a strategy that will be of particular interest to investigate the structural and dynamical properties of large RNA complexes by NMR and EPR spectroscopies.
Locating the Urban In‐between: Tracking the Urban Politics of Infrastructure in Toronto
Authors: Young Douglas , Keil Roger 
Published: July 2014

AbstractIn the urban studies literature, urban politics is usually considered in two distinct locations: the city (often understood in quite conventional centralist ways) and the suburb (understood as spatially peripheral and politically at odds with the central city). At the metropolitan scale, the two types of urban politics are discussed in relation to one another. More recently, the metropolitan scale of urban politics has been expanded to regional dimensions. We pose the question of location of urban politics from a specific deficit in the geography of centre, suburb and metropolis. We argue that in today's regional political socio‐spatiality, politics will have to be found ‘in‐between’ the old lines of demarcation. Following Tom Sieverts' (2003) advice to look at the ‘in‐between’ cities that are neither old downtown nor new suburb but complex urban landscapes of mixed density, use and urbanity, we reveal the political vacuum that is at the heart of the urban region today. Using the politics of infrastructure in Toronto as our empirical example, we will show that vulnerabilities and risks for urban populations in that Canadian metropolis' in‐between city are co‐generated by the failure of conventional political spaces and processes to capture the connectivities threaded through those places that are in‐between the centre and exurbia.
Temperature relations of aerial and aquatic physiological performance in a mid‐intertidal limpetCellana toreuma: Adaptation to rapid changes in thermal stress during emersion
Authors: HUANG Xiongwei , WANG Tifeng , YE Ziwen , HAN Guodong , DONG Yunwei 
Published: July 2014

AbstractThe physiological performance of a mid‐intertidal limpetCellana toreumawas determined to study the physiological adaptation of intertidal animals to rapid changes and extreme temperatures during emersion. The relationship between the Arrhenius breakpoint temperature (ABT) andin situoperative body temperature was studied to predict the possible impact of climate change on the species. The temperature coefficient (Q10) of emersed animals was higher than that of submersed animals and the ratio of aerial: aquatic heart rate rose with increasing temperature. The ABTs of submersed and emersed animals were 30.2 and 34.2°C, respectively. The heart rate and levels of molecular biomarkers (hsps, ampkα, ampkβandsirt1mRNA) were determined in 48 h simulated semi‐diurnal tides. There were no obvious changes of heart rate and gene expression during the transition between emersion and submersion at room temperature, although expressions ofhsp70andhsp90were induced significantly after thermal stress. These results indicate thatC. toreumacan effectively utilize atmospheric oxygen, and the higher Q10and ABT of emersed animals are adaptations to the rapid change and extreme thermal stress during emersion. However, thein situoperative body temperature frequently exceeds the aerial ABT ofC. toreuma, indicating the occurrence of large‐scale mortality ofC. toreumain summer, and this species should be sensitive to increasing temperature in the scenario of climate change.
Large‐scale analysis of frequency modulation in birdsong data bases
Authors: Stowell Dan , Plumbley Mark D. 
Published: July 2014

Summary

Birdsong often contains large amounts of rapid frequency modulation (FM). It is believed that the use or otherwise of FM is adaptive to the acoustic environment and also that there are specific social uses of FM such as trills in aggressive territorial encounters. Yet temporal fine detail of FM is often absent or obscured in standard audio signal analysis methods such as Fourier analysis or linear prediction. Hence, it is important to consider high‐resolution signal processing techniques for analysis of FM in bird vocalizations. If such methods can be applied at big data scales, this offers a further advantage as large data sets become available.

We introduce methods from the signal processing literature which can go beyond spectrogram representations to analyse the fine modulations present in a signal at very short time‐scales. Focusing primarily on the genus Phylloscopus, we investigate which of a set of four analysis methods most strongly captures the species signal encoded in birdsong. We evaluate this through a feature selection technique and an automatic classification experiment. In order to find tools useful in practical analysis of large data bases, we also study the computational time taken by the methods, and their robustness to additive noise and MP3 compression.

We find three methods which can robustly represent species‐correlated FM attributes and can be applied to large data sets, and that the simplest method tested also appears to perform the best. We find that features representing the extremes of FM encode species identity supplementary to that captured in frequency features, whereas bandwidth features do not encode additional information.

FM analysis can extract information useful for bioacoustic studies, in addition to measures more commonly used to characterize vocalizations. Further, it can be applied efficiently across very large data sets and archives.
Commentary on the Adding Individual Psychotherapy After Relapse in a Pharmacotherapy Trial: Commentary on the PREDICT Study
Authors: Zweben Allen 
Published: July 2014

BackgroundWith few exceptions there has been a dearth of research evaluating the independent and combined effects of a promising medication and an effective behavioral intervention for alcohol problems. Few studies have incorporated both theory and empirical findings to ascertain how the combination of medication and behavioral intervention interact or work synergistically to produce better outcomes or why a particular combination of pharmacological and behavioral treatment works better than another combination or either of the interventions employed alone.MethodsThe PREDICT Study is one of the few pharmacotherapy trials that has utilized a behavioral intervention to reduce/delay relapse to heavy drinking. The findings in the PREDICT Study were reviewed to gain a better understanding of how the combination of pharmacotherapy and behavioral intervention can be employed to manage the course of recovery for individuals with alcohol use disorders (AUDs).ResultsFindings in the PREDICT Study show that behavioral interventions and pharmacotherapies have complementary functions that can be utilized to address the differential needs, capabilities, and resources associated with AUDs. However, researchers were forced to rely mainly on their own clinical experiences rather than an overarching conceptual model in determining how the approach should be employed with AUD patients, thereby limiting the conclusions that could be drawn from the study findings.ConclusionsDifferent vulnerabilities underlying AUDs should be considered in determining what kinds of behavioral interventions should be paired with particular medications. At the same time, we need to have a better understanding of the clinical course of pharmacobehavioral treatment to deal with the array of problems/situations that arise over the course of combination therapy.
Factors associated with pregnancy outcome in anti‐TNF treated women with inflammatory bowel disease
Authors: Seirafi M. , de Vroey B. , Amiot A. , Seksik P. , Roblin X. , Allez M. , Peyrin‐Biroulet L. , Marteau P. , Cadiot G. , Laharie D. , Boureille A. , De Vos M. , Savoye G. , Rahier J.‐F. , Carbonnel F. , Bonaz B. , Colombel J.‐F. , Bouhnik Y. 
Published: July 2014

SummaryBackgroundThe safety of anti‐tumour necrosis factor (TNF) agents during pregnancy is a major concern for child‐bearing women and physicians.AimTo assess the impact of anti‐TNF therapy on adverse pregnancy and foetal outcomes in women with inflammatory bowel disease (IBD).MethodsPregnancies occurring during anti‐TNF treatment or less than 3 months after its cessation in IBD patients followed in GETAID centres were recorded from January 2009 to December 2010. Ninety‐nine pregnancies in women without anti‐TNF treatment were identified from the CESAME registry. We compared pregnancy and neonatal outcomes by a case–control study.ResultsIn the 124 IBD patients followed, 133 pregnancies were reported. At the conception time, 23% of patients had active disease. Eighty‐eight per cent (n = 117) of the 133 pregnancies followed until delivery resulted in 118 liveborns (one twin pregnancy). Complications were observed in 47 (35%) women and 24 (20%) newborns. In multivariate analysis, factors associated with pregnancy complications were: current smoking (P = 0.004), a B2 (stenotic) phenotype in CD women (P = 0.004), occurrence of a flare during pregnancy (P = 0.006) and a past history of complicated pregnancy (P = 0.007). Current smoking was the only factor associated with severe (i.e. potentially lethal) pregnancy complications (P = 0.02). Having IBD for more than 10 years prior to conception was associated with newborn complications (P = 0.007). No difference was found with the control group for any of the pregnancy and neonatal outcomes.ConclusionIn our series, the safety profile of anti‐TNF therapy during pregnancy and the neonatal period appears similar to control group of IBD women not treated with anti‐TNF therapy.
Managing children with chronic myeloid leukaemia (CML)
Authors: de la Fuente Josu , Baruchel André , Biondi Andrea , de Bont Eveline , Dresse Marie‐Françoise , Suttorp Meinolf , Millot Frédéric ,   International BFM Group (iBFM) Study Group Chronic Myeloid Leukaemia Committee
Published: July 2014

SummaryChronic myeloid leukaemia in children and young people is a relatively rare form of leukaemia that shows increased incidence with age and some evidence suggests that the molecular basis differs from that in adults. Significant advances in targeted therapy with the development and use in children of tyrosine kinase inhibitors and the ability to monitor and understand the prognostic significance of minimal residual disease by standardized molecular techniques has shifted the management of this condition from bone marrow transplantation as the main therapeutic modality to individualized treatment for each patient based on achieving specific milestones. The physiological changes occurring during childhood, particularly those affecting growth and development and the long‐term use of treatment, pose specific challenges in this age group, which we are only beginning to understand.
Limited Fine Motor and Grasping Skills in 6‐Month‐Old Infants at High Risk for Autism
Authors: Libertus Klaus , Sheperd Kelly A. , Ross Samuel W. , Landa Rebecca J. 
Published: July 2014

Atypical motor behaviors are common among children with autism spectrum disorders (ASD). However, little is known about onset and functional implications of differences in early motor development among infants later diagnosed with ASD. Two prospective experiments were conducted to investigate motor skills among 6‐month‐olds at increased risk (high risk) for ASD (N1 = 129; N2 = 46). Infants were assessed using the Mullen Scales of Early Learning (MSEL) and during toy play. Across both experiments, high‐risk infants exhibited less mature object manipulation in a highly structured (MSEL) context and reduced grasping activity in an unstructured (free‐play) context than infants with no family history of ASD. Longitudinal assessments suggest that between 6 and 10 months, grasping activity increases in high‐risk infants.
Bet v 1 – a Trojan horse for small ligands boosting allergic sensitization?
Authors: Asam C. , Batista A. L. , Moraes A. H. , de Paula V. S. , Almeida F. C. L. , Aglas L. , Kitzmüller C. , Bohle B. , Ebner C. , Ferreira F. , Wallner M. , Valente A. P. 
Published: July 2014

SummaryBackgroundBirch pollen allergy represents the main cause of winter and spring pollinosis in the temperate climate zone of the northern hemisphere and sensitization towards Bet v 1, the major birch pollen allergen, affects over 100 million allergic patients. The major birch pollen allergen Bet v 1 has been described as promiscuous acceptor for a wide variety of hydrophobic ligands.ObjectiveIn search of intrinsic properties of Bet v 1, which account responsible for the high allergenic potential of the protein, we thought to investigate the effects of ligand‐binding on immunogenic as well as allergenic properties.MethodsAs surrogate ligand of Bet v 1 sodium deoxycholate (DOC) was selected. Recombinant and natural Bet v 1 were characterised physico‐chemically as well as immunologically in the presence or absence of DOC, and an animal model of allergic sensitization was established. Moreover, human IgE binding to Bet v 1 was analysed by nuclear magnetic resonance (NMR) spectroscopy.ResultsLigand‐binding had an overall stabilizing effect on Bet v 1. This translated in a Th2 skewing of the immune response in a mouse model. Analyses of human IgE binding on Bet v 1 in mediator release assays revealed that ligand‐bound allergen‐induced degranulation at lower concentrations; however, in basophil activation tests with human basophils ligand‐binding did not show this effect. For the first time, human IgE epitopes on Bet v 1 were determined using antibodies isolated from patients' sera. The IgE epitope mapping of Bet v 1 demonstrated the presence of multiple binding regions.Conclusions and clinical relevanceDeoxycholate binding stabilizes conformational IgE epitopes on Bet v 1; however, the epitopes themselves remain unaltered. Therefore, we speculate that humans are exposed to both ligand‐bound and free Bet v 1 during sensitization, disclosing the ligand‐binding cavity of the allergen as key structural element.
Factors affecting peri‐implant bone loss: a post‐five‐year retrospective study
Authors: Vázquez Álvarez Rocío , Pérez Sayáns Mario , Gayoso Diz Pilar , García García Abel 
Published: July 2014

AbstractIntroductionAlthough peri‐implant bone loss is one of the parameters included in the criteria for determining implant success, its prevention is of vital importance. The goal of this article is to assess the factors that affect peri‐implant bone loss.Material and methodsAn observational, longitudinal, retrospective study was conducted in 148 partially edentulous patients rehabilitated with implants and with a follow‐up period of 5 years or more. A total of 585 implants were included in the study. Radiographic peri‐implant bone loss was compared with radiographic periodontal bone loss, and other characteristics such as prosthesis design, hygiene, and implant size were studied as potential peri‐implant bone loss modification factors.ResultsIn the univariate analysis, a statistically significant relationship between peri‐implant bone loss and gender (P < 0.05), implant system (P < 0.01), reason for extraction (P < 0.05), splinting (P < 0.0001), and distance between the implant platform and the horizontal component of the prosthesis (P < 0.0001) were observed. In multivariate analysis, the relationship between this peri‐implant loss and gender (P < 0.05), implant system (P < 0.05), splinting (P < 0.001), and the aforementioned distance (P < 0.01) remains.ConclusionsThe distance implant platform‐horizontal component of the prosthesis has the greatest effect on peri‐implant bone loss This distance must be >3.3 mm and <6 mm, above this range, it no longer influences in peri‐implant bone loss and favors the appearance of embrasures and the buildup of bacterial plaque.
Learning a Generative Probabilistic Grammar of Experience: A Process‐Level Model of Language Acquisition
Authors: Kolodny Oren , Lotem Arnon , Edelman Shimon 
Published: July 2014

AbstractWe introduce a set of biologically and computationally motivated design choices for modeling the learning of language, or of other types of sequential, hierarchically structured experience and behavior, and describe an implemented system that conforms to these choices and is capable of unsupervised learning from raw natural‐language corpora. Given a stream of linguistic input, our model incrementally learns a grammar that captures its statistical patterns, which can then be used to parse or generate new data. The grammar constructed in this manner takes the form of a directed weighted graph, whose nodes are recursively (hierarchically) defined patterns over the elements of the input stream. We evaluated the model in seventeen experiments, grouped into five studies, which examined, respectively, (a) the generative ability of grammar learned from a corpus of natural language, (b) the characteristics of the learned representation, (c) sequence segmentation and chunking, (d) artificial grammar learning, and (e) certain types of structure dependence. The model's performance largely vindicates our design choices, suggesting that progress in modeling language acquisition can be made on a broad front—ranging from issues of generativity to the replication of human experimental findings—by bringing biological and computational considerations, as well as lessons from prior efforts, to bear on the modeling approach.