bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human mucosal-associated invariant T (MAIT) cells possess capacity for B cell help
Authors: Bennett Michael S , Trivedi Shubhanshi , Iyer Anita S , Hale J Scott , Leung Daniel T 
Published: August 2017

Abstract
Mucosal-associated invariant T (MAIT) cells are an innate-like T cell subset, restricted by the nonclassic MHC class I-related protein MR1 and enriched at mucosal sites. Human studies have shown an association between MAIT cells and pathogen-specific antibody responses. In this study, we investigate the effect of human MAIT cells on B cells ex vivo. We found that supernatants from microbe- or cytokine-stimulated MAIT cells, when added to purified autologous B cells, increase frequencies of plasmablasts and promote IgA, IgG, and IgM production. We found effects to be mostly MR1-dependent and that the increases in plasmablasts are likely a result of increased differentiation from memory B cells. Furthermore, microbe-activated MAIT cell supernatant contains multiple cytokines known to stimulate B cells, including IL-6, -10, and -21. This study thus provides the first direct evidence of a newly identified role of MAIT cells in providing help to B cells.
Determining geophysical responses from burials in graveyards and cemeteries
Authors: Dick Henry C. , Pringle Jamie K. , Wisniewski Kristopher D. , Goodwin Jon , van der Putten Robert , Evans Gethin T. , Francis James D. , Cassella John P. , Hansen Jamie D. 
Published: August 2017

Graveyards and cemeteries around the world are increasingly designated as full. Therefore, there is a requirement to identify vacant spaces for new burials or to identify existing ones to exhume and then reinter if necessary. Geophysical methods offer a potentially noninvasive target detection solution; however, there has been limited research to identify optimal geophysical detection methods against burial age. We have collected multifrequency (225–900 MHz) ground-penetrating radar (GPR), electrical resistivity, and magnetic susceptibility surface data over known graves with different burial ages and soil types in three UK church graveyards. Results indicate that progressively older burials are more difficult to detect, but this decrease is not linear and is site specific. Medium- to high-frequency GPR and magnetic susceptibility was optimal in clay-rich soils, medium- to high-frequency GPR and electrical resistivity in sandy soils, and electrical resistivity and low-frequency GPR in coarse sand and pebbly soils, respectively. A multigeophysical technique approach should be used by survey practitioners where grave locations are not known to maximize target detection success. Grave soil and grave cuts are important grave position indicators. Grave headstones were not always located where burials were located. We have determined the value of these techniques in grave detection and could potentially date burials from their geophysical responses.
Use of the photoelectric effect as a reservoir quality indicator in the Niobrara Formation, Piceance Basin, northwest Colorado
Authors: Krueger Martin 
Published: August 2017

The late Cretaceous Niobrara Formation and underlying lower Mancos Group have significant petroleum potential in the Piceance Basin of northwest Colorado. Relative to the Denver Basin Niobrara, the Piceance Basin Niobrara has had significantly less drilling activity, and therefore fewer subsurface data are available. There are several key geologic differences pertaining to the Niobrara depositional history in these two basins. First, the overall thickness of the formation increases greatly to the west. Thicknesses of 91.4 m (300 ft), common in the Denver Basin, become thicknesses of as much as 548.6 m (1800 ft) in the Piceance Basin. Second, to date, maximum total organic carbon (TOC) values from the Piceance Basin are approximately 3 wt%, whereas in the Denver Basin, TOC values may be as high as 8 wt%. Several factors may contribute to the lesser TOC, but a significant factor is the dilution of organic material by increasing siliciclastic deposition. Unlike the Denver Basin stratigraphy of organic-rich marls providing the bulk of sourcing to carbonate-rich benches of greater fracture porosity, TOC and carbonate richness are coupled in the Piceance Basin. Core and well-log data suggest that the Piceance Basin Niobrara Formation’s carbonate-rich strata have higher TOC content relative to the interlaying clay-rich strata. This relationship enables the use of the photoelectric effect, the PEF or PE log, to map trends of carbonate richness and classify reservoir quality, where carbonate and organics may be at maximum values. In other unconventional reservoirs that share similar depositional histories and display the positive correlation between carbonate and organic richness, the PEF curve should be used for reservoir quality screening purposes.
Treatment of Patients With Metastatic Cancer Using a Major Histocompatibility Complex Class II–Restricted T-Cell Receptor Targeting the Cancer Germline Antigen MAGE-A3
Authors: Lu Yong-Chen , Parker Linda L. , Lu Tangying , Zheng Zhili , Toomey Mary Ann , White Donald E. , Yao Xin , Li Yong F. , Robbins Paul F. , Feldman Steven A. , van der Bruggen Pierre , Klebanoff Christopher A. , Goff Stephanie L. , Sherry Richard M. , Kammula Udai S. , Yang James C. , Rosenberg Steven A. 
Published: August 2017

Purpose Adoptive transfer of genetically modified T cells is being explored as a treatment for patients with metastatic cancer. Most current strategies use genes that encode major histocompatibility complex (MHC) class I–restricted T-cell receptors (TCRs) or chimeric antigen receptors to genetically modify CD8+ T cells or bulk T cells for treatment. Here, we evaluated the safety and efficacy of an adoptive CD4+ T-cell therapy using an MHC class II–restricted, HLA-DPB1*0401–restricted TCR that recognized the cancer germline antigen, MAGE-A3 (melanoma-associated antigen-A3). Patients and Methods Patients received a lymphodepleting preparative regimen, followed by adoptive transfer of purified CD4+ T cells, retrovirally transduced with MAGE-A3 TCR plus systemic high-dose IL-2. A cell dose escalation was conducted, starting at 107 total cells and escalating at half-log increments to approximately 1011 cells. Nine patients were treated at the highest dose level (0.78 to 1.23 × 1011 cells). Results Seventeen patients were treated. During the cell dose-escalation phase, an objective complete response was observed in a patient with metastatic cervical cancer who received 2.7 × 109 cells (ongoing at ≥ 29 months). Among nine patients who were treated at the highest dose level, objective partial responses were observed in a patient with esophageal cancer (duration, 4 months), a patient with urothelial cancer (ongoing at ≥ 19 months), and a patient with osteosarcoma (duration, 4 months). Most patients experienced transient fevers and the expected hematologic toxicities from lymphodepletion pretreatment. Two patients experienced transient grade 3 and 4 transaminase elevations. There were no treatment-related deaths. Conclusion These results demonstrate the safety and efficacy of administering autologous CD4+ T cells that are genetically engineered to express an MHC class II–restricted antitumor TCR that targets MAGE-A3. This clinical trial extends the reach of TCR gene therapy for patients with metastatic cancer.
Duodenal-Jejunal Flexure GI Stromal Tumor Frequently Heralds Somatic NF1 and Notch Pathway Mutations
Authors: Burgoyne Adam M. , De Siena Martina , Alkhuziem Maha , Tang Chih-Min , Medina Benjamin , Fanta Paul T. , Belinsky Martin G. , von Mehren Margaret , Thorson John A. , Madlensky Lisa , Bowler Timothy , D’Angelo Francesco , Stupack Dwayne G. , Harismendy Olivier , DeMatteo Ronald P. , Sicklick Jason K. 
Published: August 2017

Purpose GI stromal tumors (GISTs) are commonly associated with somatic mutations in KIT and PDGFRA. However, a subset arises from mutations in NF1, most commonly associated with neurofibromatosis type 1. We define the anatomic distribution of NF1 alterations in GIST. Methods We describe the demographic/clinicopathologic features of 177 patients from two institutions whose GISTs underwent next-generation sequencing of ≥ 315 cancer-related genes. Results We initially identified six (9.7%) of 62 GISTs with NF1 genomic alterations from the first cohort. Of these six patients, five (83.3%) had unifocal tumors at the duodenal-jejunal flexure (DJF). Two additional patients with DJF GISTs had non- NF1 ( KIT and BRAF) genomic alterations. After excluding one DJF GIST with an NF1 single nucleotide polymorphism, four (57.1%) of seven sequenced DJF tumors demonstrated deleterious NF1 alterations, whereas only one (1.8%) of 55 sequenced non-DJF GISTs had a deleterious NF1 somatic mutation ( P < .001). One patient with DJF GIST had a germline NF1 variant that was associated with incomplete penetrance of clinical neurofibromatosis type 1 features along with a somatic NF1 mutation. Of the five DJF GISTs with any NF1 alteration, three (60%) had KIT mutations, and three (60%) had Notch pathway mutations ( NOTCH2, MAML2, CDC73). We validated these findings in a second cohort of 115 GISTs, where two (40%) of five unifocal NF1-mutated GISTs arose at the DJF, and one of these also had a Notch pathway mutation ( EP300). Conclusion Broad genomic profiling of adult GISTs has revealed that NF1 alterations are enriched in DJF GISTs. These tumors also may harbor concurrent activating KIT and/or inactivating Notch pathway mutations. In some cases, germline NF1 genetic testing may be appropriate for patients with DJF GISTs.
Effects of temperature and UVR on organic matter fluxes and the metabolic activity ofAcropora muricata
Authors: Courtial Lucile , Ferrier-Pagès Christine , Jacquet Stéphan , Rodolfo-Metalpa Riccardo , Reynaud Stéphanie , Rottier Cécile , Houlbrèque Fanny 
Published: August 2017

ABSTRACTCoral bleaching events are predicted to occur more frequently in the coming decades with global warming. The susceptibility of corals to bleaching during thermal stress episodes depends on many factors, including the magnitude of thermal stress and irradiance. The interactions among these two factors, and in particular with ultra-violet radiation (UVR), the most harmful component of light, are more complex than assumed, and are not yet well understood. This paper explores the individual and combined effects of temperature and UVR on the metabolism of Acropora muricata, one of the most abundant coral species worldwide. Particulate and dissolved organic matter (POM/DOM) fluxes and organic matter (OM) degradation by the mucus-associated bacteria were also monitored in all conditions. The results show that UVR exposure exacerbated the temperature-induced bleaching, but did not affect OM fluxes, which were only altered by seawater warming. Temperature increase induced a shift from POM release and DOM uptake in healthy corals to POM uptake and DOM release in stressed ones. POM uptake was linked to a significant grazing of pico- and nanoplankton particles during the incubation, to fulfil the energetic requirements of A. muricata in the absence of autotrophy. Finally, OM degradation by mucus-associated bacterial activity was unaffected by UVR exposure, but significantly increased under high temperature. Altogether, our results demonstrate that seawater warming and UVR not only affect coral physiology, but also the way corals interact with the surrounding seawater, with potential consequences for coral reef biogeochemical cycles and food webs.
Myosin II is not required for Drosophila tracheal branch elongation and cell intercalation
Authors: Ochoa-Espinosa Amanda , Harmansa Stefan , Caussinus Emmanuel , Affolter Markus 
Published: August 2017

ABSTRACT
The Drosophila tracheal system consists of an interconnected network of monolayered epithelial tubes that ensures oxygen transport in the larval and adult body. During tracheal dorsal branch (DB) development, individual DBs elongate as a cluster of cells, led by tip cells at the front and trailing cells in the rear. Branch elongation is accompanied by extensive cell intercalation and cell lengthening of the trailing stalk cells. Although cell intercalation is governed by Myosin II (MyoII)-dependent forces during tissue elongation in the Drosophila embryo that lead to germ-band extension, it remained unclear whether MyoII plays a similar active role during tracheal branch elongation and intercalation. Here, we have used a nanobody-based approach to selectively knock down MyoII in tracheal cells. Our data show that, despite the depletion of MyoII function, tip cell migration and stalk cell intercalation (SCI) proceed at a normal rate. This confirms a model in which DB elongation and SCI in the trachea occur as a consequence of tip cell migration, which produces the necessary forces for the branching process.
The wisdom of crowds: regulating cell function through condensed states of living matter
Authors: Alberti Simon 
Published: August 2017

ABSTRACT
Our understanding of cells has progressed rapidly in recent years, mainly because of technological advances. Modern technology now allows us to observe molecular processes in living cells with high spatial and temporal resolution. At the same time, we are beginning to compile the molecular parts list of cells. However, how all these parts work together to yield complex cellular behavior is still unclear. In addition, the established paradigm of molecular biology, which sees proteins as well-folded enzymes that undergo specific lock-and-key type interactions, is increasingly being challenged. In fact, it is now becoming clear that many proteins do not fold into three-dimensional structures and additionally show highly promiscuous binding behavior. Furthermore, proteins function in collectives and form condensed phases with different material properties, such as liquids, gels, glasses or filaments. Here, I examine emerging evidence that the formation of macromolecular condensates is a fundamental principle in cell biology. I further discuss how different condensed states of living matter regulate cellular functions and decision-making and ensure adaptive behavior and survival in times of cellular crisis.
BAG3-mediated proteostasis at a glance
Authors: Klimek Christina , Kathage Barbara , Wördehoff Judith , Höhfeld Jörg 
Published: August 2017

ABSTRACT
Cellular and organismal survival depend on the ability to maintain the proteome, even under conditions that threaten protein integrity. BCL2-associated athanogene 3 (BAG3) is essential for protein homeostasis (proteostasis) in stressed cells. Owing to its multi-domain structure, it engages in diverse processes that are crucial for proteome maintenance. BAG3 promotes the activity of molecular chaperones, sequesters and concentrates misfolded proteins, initiates autophagic disposal, and balances transcription, translation and degradation. In this Cell Science at a Glance article and the accompanying poster, we discuss the functions of this multi-functional proteostasis tool with a focus on mechanical stress protection and describe the importance of BAG3 for human physiology and pathophysiology.
A pharmacological study of Arabidopsis cell fusion between the persistent synergid and endosperm
Authors: Motomura Kazuki , Kawashima Tomokazu , Berger Frédéric , Kinoshita Tetsu , Higashiyama Tetsuya , Maruyama Daisuke 
Published: August 2017

ABSTRACT
Cell fusion is a pivotal process in fertilization and multinucleate cell formation. A plant cell is ubiquitously surrounded by a hard cell wall, and very few cell fusions have been observed except for gamete fusions. We recently reported that the fertilized central cell (the endosperm) absorbs the persistent synergid, a highly differentiated cell necessary for pollen tube attraction. The synergid–endosperm fusion (SE fusion) appears to eliminate the persistent synergid from fertilized ovule in Arabidopsis thaliana. Here, we analyzed the effects of various inhibitors on SE fusion in an in vitro culture system. Different from other cell fusions, neither disruption of actin polymerization nor protein secretion impaired SE fusion. However, transcriptional and translational inhibitors decreased the SE fusion success rate and also inhibited endosperm division. Failures of SE fusion and endosperm nuclear proliferation were also induced by roscovitine, an inhibitor of cyclin-dependent kinases (CDK). These data indicate unique aspects of SE fusion such as independence of filamentous actin support and the importance of CDK-mediated mitotic control.
Contraceptive Sterilization: Introducing A Couple Perspective to Examine Sociodemographic Differences in Use
Authors: Eeckhaut Mieke C.W. 
Published: August 2017

CONTEXTMost studies of contraceptive use have relied solely on the woman's perspective, but because men's attitudes and preferences are also important, analytic approaches based on couples should also be explored.METHODSData from the 2006–2010 and 2011–2013 rounds of the National Survey of Family Growth yielded a sample of 4,591 men and women who were married or cohabiting with an opposite‐sex partner and who had completed their intended childbearing. Respondents’ reports of both their own and their partners’ characteristics and behaviors were employed in two sets of analyses examining educational and racial and ethnic differences in contraceptive use: an individualistic approach (using multinomial logistic regression) and a couple approach (using multinomial logistic diagonal reference models).RESULTSIn the full model using the individualistic approach, respondents with less than a high school education were less likely than those with at least a college degree to rely on male sterilization (odds ratios, 0.1–0.2) or a reversible method (0.4–0.5), as opposed to female sterilization. Parallel analyses limited to couples in which partners had the same educational levels (i.e., educationally homogamous couples) showed an even greater difference between those with the least and those with the most schooling (0.03 for male sterilization and 0.2 for a reversible method). When race and ethnicity, which had a much higher level of homogamy, were examined, the approaches yielded more similar results.CONCLUSIONSResearch on contraceptive use can benefit from a couple approach, particularly when focusing on partners’ characteristics for which homogamy is relatively low.
CHARGE Syndrome: An Indonesian Case Report
Authors: Pramudita Jessica Juan , Utari Agustini , Winarni Tri Indah , Faradz Sultana MH 
Published: August 2017

Background: CHARGE syndrome is an autosomal dominant congenital and rare genetic disease.The prevalence of CHARGE syndrome approximately 1:12,000 births.In the previous study, the CHD7 gene mutation is responsible in about 2/3 cases of CHARGE syndrome. The syn­drome associations consist of C-coloboma of the eyes, H-heart disease, A-atresia of the choanae, R-retarded growth and development, G-genital hypoplasia/genitourinary anomalies and E-ear anomalies and/or hearing loss. All defects are not seen in every case and a different spectrum of associations is seen in most of the cases.Method: Case was undergone physical examination by experience pediatricians, pedigree construction, and other diagnostic procedure (X-ray, echo­cardiography, and multi slice computer tomography (MSCT) scan).Results: A boy aged 2 years 9 months with clinical features with match major and minor criterias of CHARGE syndrome.
A hybrid active force control of a lower limb exoskeleton for gait rehabilitation
Authors: Taha Zahari , Abdul Majeed Anwar P.P. , Zainal Abidin Amar Faiz , Hashem Ali Mohammed A. , Khairuddin Ismail Mohd , Deboucha Abdelhakim , Wong Paul Tze Mohd Yashim 
Published: August 2017

Abstract
Owing to the increasing demand for rehabilitation services, robotics have been engaged in addressing the drawbacks of conventional rehabilitation therapy. This paper focuses on the modelling and control of a three-link lower limb exoskeleton for gait rehabilitation that is restricted to the sagittal plane. The exoskeleton that is modelled together with a human lower limb model is subjected to a number of excitations at its joints while performing a joint space trajectory tracking, to investigate the effectiveness of the proposed controller in compensating disturbances. A particle swarm optimised active force control strategy is proposed to facilitate disturbance rejection of a conventional proportional-derivative (PD) control algorithm. The simulation study provides considerable insight into the robustness of the proposed method in attenuating the disturbance effect as compared to the conventional PD counterpart without compromising its tracking performance. The findings from the study further suggest its potential employment on a lower limb exoskeleton.
Association of obesity and health related quality of life in Iranian children and adolescents: the Weight Disorders Survey of the CASPIAN-IV study
Authors: Hovsepian Silva , Qorbani Mostafa , Motlagh Mohammad Esmaeil , Madady Aryan , Mansourian Morteza , Gorabi Armita Mahdavi , Kelishadi Roya 
Published: August 2017

AbstractBackground:Considering the role of different ethnical, cultural and geographical factors in health related quality of life (HRQOL) as well as the perception of different populations regarding various weight disorders, we aimed to evaluate the association between body mass index (BMI) and HRQOL in Iranian children and adolescents.Methods:This cross-sectional study was part of the Weight Disorders Survey of the CASPIAN-IV study. During this study, students aged 6–18 years from urban and rural areas of 30 provinces of Iran were selected. HRQOL of the students was evaluated by using the Persian version of the Pediatric Quality of Life inventory (PedsQL™ 4.0™ 4.0) Generic Core Scales. The mean of total HRQOL and its subscales were compared in underweight, normal weight, overweight and obese students.Results:The mean of total HRQOL, physical functioning and psychological functioning scores in the total population were 83.31, 84.25 and 82.79, respectively. The mean of the total HRQOL score and the psychosocial score were significantly lower in underweight students aged 6–12 years than in other groups (p<0.05). The mean of the total HRQOL score and psychosocial score were significantly lower in obese students aged 13–18 years than in other groups (p<0.05). Overweight and obesity was negatively associated with total HRQOL, psychosocial and school functioning subscales (p<0.05). There was a significant negative association between emotional functioning and obesity (p<0.05).Conclusions:The findings or this study support the importance of personal perception and cultural norm roles in HRQOL. Given the association between weight disorders and psychosocial health, it is suggested that social and cultural factors have a more crucial role in the HRQOL of children and adolescents.