bluuebunny/crossref_metadata_2025_split huggingface dataset:
The yielding transition in amorphous solids under oscillatory shear deformation
Authors: Leishangthem Premkumar , Parmar Anshul D. S. , Sastry Srikanth 
Published: March 2017

AbstractAmorphous solids are ubiquitous among natural and man-made materials. Often used as structural materials for their attractive mechanical properties, their utility depends critically on their response to applied stresses. Processes underlying such mechanical response, and in particular the yielding behaviour of amorphous solids, are not satisfactorily understood. Although studied extensively, observed yielding behaviour can be gradual and depend significantly on conditions of study, making it difficult to convincingly validate existing theoretical descriptions of a sharp yielding transition. Here we employ oscillatory deformation as a reliable probe of the yielding transition. Through extensive computer simulations for a wide range of system sizes, we demonstrate that cyclically deformed model glasses exhibit a sharply defined yielding transition with characteristics that are independent of preparation history. In contrast to prevailing expectations, the statistics of avalanches reveals no signature of the impending transition, but exhibit dramatic, qualitative, changes in character across the transition.
Clonal selection in the human Vδ1 T cell repertoire indicates γδ TCR-dependent adaptive immune surveillance
Authors: Davey Martin S. , Willcox Carrie R. , Joyce Stephen P. , Ladell Kristin , Kasatskaya Sofya A. , McLaren James E. , Hunter Stuart , Salim Mahboob , Mohammed Fiyaz , Price David A. , Chudakov Dmitriy M. , Willcox Benjamin E. 
Published: March 2017

Abstractγδ T cells are considered to be innate-like lymphocytes that respond rapidly to stress without clonal selection and differentiation. Here we use next-generation sequencing to probe how this paradigm relates to human Vδ2negT cells, implicated in responses to viral infection and cancer. The prevalent Vδ1 T cell receptor (TCR) repertoire is private and initially unfocused in cord blood, typically becoming strongly focused on a few high-frequency clonotypes by adulthood. Clonal expansions have differentiated from a naive to effector phenotype associated with CD27 downregulation, retaining proliferative capacity and TCR sensitivity, displaying increased cytotoxic markers and altered homing capabilities, and remaining relatively stable over time. Contrastingly, Vδ2+T cells express semi-invariant TCRs, which are present at birth and shared between individuals. Human Vδ1+T cells have therefore evolved a distinct biology from the Vδ2+subset, involving a central, personalized role for the γδ TCR in directing a highly adaptive yet unconventional form of immune surveillance.
CFTR is involved in the regulation of glucagon secretion in human and rodent alpha cells
Authors: Edlund Anna , Pedersen Morten Gram , Lindqvist Andreas , Wierup Nils , Flodström-Tullberg Malin , Eliasson Lena 
Published: March 2017

AbstractGlucagon is the main counterregulatory hormone in the body. Still, the mechanism involved in the regulation of glucagon secretion from pancreatic alpha cells remains elusive. Dysregulated glucagon secretion is common in patients with Cystic Fibrosis (CF) that develop CF related diabetes (CFRD). CF is caused by a mutation in the Cl− channel Cystic fibrosis transmembrane conductance regulator (CFTR), but whether CFTR is present in human alpha cells and regulate glucagon secretion has not been investigated in detail. Here, both human and mouse alpha cells showed CFTR protein expression, whereas CFTR was absent in somatostatin secreting delta cells. CFTR-current activity induced by cAMP was measured in single alpha cells. Glucagon secretion at different glucose levels and in the presence of forskolin was increased by CFTR-inhibition in human islets, whereas depolarization-induced glucagon secretion was unaffected. CFTR is suggested to mainly regulate the membrane potential through an intrinsic alpha cell effect, as supported by a mathematical model of alpha cell electrophysiology. In conclusion, CFTR channels are present in alpha cells and act as important negative regulators of cAMP-enhanced glucagon secretion through effects on alpha cell membrane potential. Our data support that loss-of-function mutations in CFTR contributes to dysregulated glucagon secretion in CFRD.
YidC and SecYEG form a heterotetrameric protein translocation channel
Authors: Sachelaru Ilie , Winter Lukas , Knyazev Denis G. , Zimmermann Mirjam , Vogt Andreas , Kuttner Roland , Ollinger Nicole , Siligan Christine , Pohl Peter , Koch Hans-Georg 
Published: March 2017

AbstractThe heterotrimeric SecYEG complex cooperates with YidC to facilitate membrane protein insertion by an unknown mechanism. Here we show that YidC contacts the interior of the SecY channel resulting in a ligand-activated and voltage-dependent complex with distinct ion channel characteristics. The SecYEG pore diameter decreases from 8 Å to only 5 Å for the YidC-SecYEG pore, indicating a reduction in channel cross-section by YidC intercalation. In the presence of a substrate, YidC relocates to the rim of the pore as indicated by increased pore diameter and loss of YidC crosslinks to the channel interior. Changing the surface charge of the pore by incorporating YidC into the channel wall increases the anion selectivity, and the accompanying change in wall hydrophobicity is liable to alter the partition of helices from the pore into the membrane. This could explain how the exit of transmembrane domains from the SecY channel is facilitated by YidC.
CSF-1 regulates the function of monocytes in Crohn’s disease patients in remission
Authors: Nieto Juan Camilo , Zamora Carlos , Cantó Elisabet , Garcia-Planella Esther , Gordillo Jordi , Ortiz Maria Angels , Juárez Cándido , Vidal Silvia 
Published: March 2017

AbstractDuring the flare-ups of Crohn’s disease (CD) patients, circulating leukocytes actively migrate toward the inflamed sites. During the remission, the lack of symptoms does not necessarily imply immunological remission. To decipher inflammatory mechanisms still operating during CD remission, we compared the expression of chemokine receptors on monocytes from CD and healthy donors (HD), and how these differences could modulate monocyte maturation and cytokine production. Flow cytometry analysis showed a higher expression of CCR5 on monocytes from CD patients than those from HD after 24 h. This CCR5 upregulation was associated with the spontaneous production of CSF-1 and IL-10. The higher expression of CCR5 on CD monocytes increased their migratory pattern in response to CCL5. Signaling through CCR5/CCL5 increased CD163 and HLA-DR expression and diminished TLR4-induced TNF-α and IL-6 secretion during monocyte differentiation. When we analyzed clinical parameters, patients treated with azathioprine had the highest CSF-1 levels and CCR5 expression. Our results suggest that monocytes from CD patients in remission produced high levels of CSF-1 that upregulate CCR5 expression. Consequently, monocytes differentiated in these conditions had a characteristic phenotype and lower production of inflammatory cytokines. The treatment with azathioprine could be responsible for this anti-inflammatory profile of monocytes.
Quantitative chemical exchange saturation transfer (CEST) MRI of glioma using Image Downsampling Expedited Adaptive Least-squares (IDEAL) fitting
Authors: Zhou Iris Yuwen , Wang Enfeng , Cheung Jerry S. , Zhang Xiaoan , Fulci Giulia , Sun Phillip Zhe 
Published: March 2017

AbstractChemical Exchange Saturation Transfer (CEST) MRI is sensitive to dilute metabolites with exchangeable protons, allowing tissue characterization in diseases such as acute stroke and tumor. CEST quantification using multi-pool Lorentzian fitting is challenging due to its strong dependence on image signal-to-noise ratio (SNR), initial values and boundaries. Herein we proposed an Image Downsampling Expedited Adaptive Least-squares (IDEAL) fitting algorithm that quantifies CEST images based on initial values from multi-pool Lorentzian fitting of iteratively less downsampled images until the original resolution. The IDEAL fitting in phantom data with superimposed noise provided smaller coefficient of variation and higher contrast-to-noise ratio at a faster fitting speed compared to conventional fitting. We further applied the IDEAL fitting to quantify CEST MRI in rat gliomas and confirmed its advantage for in vivo CEST quantification. In addition to significant changes in amide proton transfer and semisolid macromolecular magnetization transfer effects, the IDEAL fitting revealed pronounced negative contrasts of tumors in the fitted CEST maps at 2 ppm and −1.6 ppm, likely arising from changes in creatine level and nuclear overhauser effects, which were not found using conventional method. It is anticipated that the proposed method can be generalized to quantify MRI data where SNR is suboptimal.
Female Breast Cancer Mortality Clusters in Shandong Province, China: A Spatial Analysis
Authors: Chu Jie , Zhou Chengchao , Guo Xiaolei , Sun Jiandong , Xue Fuzhong , Zhang Jiyu , Lu Zilong , Fu Zhentao , Xu Aiqiang 
Published: March 2017

AbstractThis study aimed to detect the spatial distribution and high-risk clusters of female breast cancer mortality for the years 2011 to 2013 in Shandong Province, China. The urban-rural difference in the spatial distribution and clusters of disease mortality were also examined. Breast cancer mortality data were obtained from the Shandong Death Registration System (SDRS) during 2011 to 2013 and were adjusted for the underreporting rate. The purely spatial scan Statistics method was performed using Discrete Poisson model. Seven significant spatial clusters for high mortality of female breast cancer were detected in Shandong Province at the county level; these clusters were mainly located in the eastern, southern, southwestern, central and northern regions. The spatial distributions differed significantly between urban and rural populations. Population ageing influenced the distribution of breast cancer clusters for the urban eastern residents. This study provided evidence for the presence of clusters of breast cancer mortality in Shandong, China and found urban-rural difference in the clusters, which is helpful for developing effective strategies to control breast cancer in different areas.
Effects of long-term magnesium supplementation on endothelial function and cardiometabolic risk markers: A randomized controlled trial in overweight/obese adults
Authors: Joris Peter J. , Plat Jogchum , Bakker Stephan J. L. , Mensink Ronald P. 
Published: March 2017

AbstractLong-term magnesium supplementation improves arterial stiffness, a cardiovascular disease risk marker. Effects on endothelial function may be another mechanism whereby increased magnesium intakes affect cardiovascular risk. Therefore, a 24-week, randomized, double-blind, placebo-controlled trial was performed to examine effects of magnesium supplementation on endothelial function and cardiometabolic risk markers. Fifty-two overweight and obese subjects (30 men and 22 women, age 62 ± 6 years) were randomized to receive either three times daily magnesium (total dose: 350 mg) or placebo capsules. Endothelial function was assessed at the start and at the end of the study. Cardiometabolic risk markers were measured at baseline, after 12 weeks, and at week 24. Brachial artery flow-mediated vasodilation did not change following long-term magnesium supplementation (0.49 pp; 95% CI: −0.38 to 1.36 pp; P = 0.26). Changes in reactive hyperemia index, retinal microvascular caliber and plasma markers for microvascular endothelial function (sVCAM-1, sICAM-1 and sE-selectin) were also not different. In addition, no effects on serum lipids, plasma glucose, insulin sensitivity, and low-grade systemic inflammation were observed. In conclusion, a daily magnesium supplement of 350 mg for 24 weeks does not improve endothelial function and cardiometabolic risk markers in overweight and obese middle-aged and elderly adults.
Emission optimised control and speed limit for isolated intersections
Authors: Blokpoel Robbin , Hausberger Stefan , Krajzewicz Daniel 
Published: March 2017

Stopping and accelerating at traffic lights is one of the main contributing factors to vehicular emissions in urban environments. The work in this study demonstrates a generic guideline for minimising CO2 emissions at traffic lights. This was done using an adaptive control, which uses a cost function for optimisation, rather than network‐specific control parameters. A new version of the emission model PHEMlight was used, which added of a fuel cut‐off mode during coasting and other improvements compared with the previous version. Using this model, it could be determined that the emission optimal ratio between delay time and stops for the cost function of an adaptive control should be 1:165 at 50 km/h. When the speed limit increases the ratio also increases with 1:296 for 70 km/h. However, it was also found that the optimal free flow travel speed was around 70 km/h. Therefore, with long distances between intersections and a low amount of average stops, the maximum speed should be higher than 50 km/h for emission optimality. Application of the ratio for 50 km/h to the adaptive control algorithm ImFlow resulted in a CO2 emission reduction of 6.3% compared with a vehicle actuated control.
Opportunities to Foster Efficient Communication in Labor and Delivery Using Simulation
Authors: Daniels Kay , Hamilton Colleen , Crowe Susan , Lipman Steven , Halamek Louis , Lee Henry 
Published: March 2017

Introduction Communication errors are an important contributing factor in adverse outcomes in labor and delivery (L&D) units. The objective of this study was to identify common lapses in verbal communication using simulated obstetrical scenarios and propose alternative formats for communication.
Methods Health care professionals in L&D participated in three simulated clinical scenarios. Scenarios were recorded and reviewed to identify questions repeated within and across scenarios. Questions that were repeated more than once due to ineffective communication were identified. The frequency with which the questions were asked across simulations was identified.
Results Questions were commonly repeated both within and across 27 simulated scenarios. The median number of questions asked was 27 per simulated scenario. Commonly repeated questions focused on three general topics: (1) historical data/information (i.e., estimated gestational age), (2) maternal clinical status (i.e., estimated blood loss), and (3) personnel (i.e., “Has anesthesiologist been called?”).
Conclusion Inefficient verbal communication exists in the process of transferring information during obstetric emergencies. These findings can inform improved training and development of information displays to improve teamwork and communication. A visual display that can report static historical information and specific dynamic clinical data may facilitate optimal human performance.
The effect of physical contact on changes in fatigue markers following rugby union field‐based training
Authors: Roe Gregory , Darrall‐Jones Joshua , Till Kevin , Phibbs Padraic , Read Dale , Weakley Jonathon , Rock Andrew , Jones Ben 
Published: February 2017

AbstractRepeated physical contact in rugby union is thought to contribute to post‐match fatigue; however, no evidence exists on the effect of contact activity during field‐based training on fatigue responses. Therefore, the purpose of this study was to examine the effect of contact during training on fatigue markers in rugby union players. Twenty academy rugby union players participated in the cross‐over study. The magnitude of change in upper‐ and lower‐body neuromuscular function (NMF), whole blood creatine kinase concentration [CK] and perception of well‐being was assessed pre‐training (baseline), immediately and 24 h post‐training following contact and non‐contact, field‐based training. Training load was measured using mean heart rate, session rating of perceived exertion (sRPE) and microtechnology (Catapult Optimeye S5). The inclusion of contact during field‐based training almost certainly increased mean heart rate (9.7; ±3.9%) and sRPE (42; ±29.2%) and resulted in likely and very likely greater decreases in upper‐body NMF (−7.3; ±4.7% versus 2.7; ±5.9%) and perception of well‐being (−8.0; ±4.8% versus −3.4; ±2.2%) 24 h post‐training, respectively, and almost certainly greater elevations in [CK] (88.2; ±40.7% versus 3.7; ±8%). The exclusion of contact from field‐based training almost certainly increased running intensity (19.8; ±5%) and distance (27.5; ±5.3%), resulting in possibly greater decreases in lower‐body NMF (−5.6; ±5.2% versus 2.3; ±2.4%). Practitioners should be aware of the different demands and fatigue responses of contact and non‐contact, field‐based training and can use this information to appropriately schedule such training in the weekly microcycle.
Oncopression: gene expression compendium for cancer with matched normal tissues
Authors: Lee Jungsul , Choi Chulhee 
Published: March 2017

Abstract

Motivation
Expression profile of normal tissue is primary source to find genes showing aberrant expression pattern specific in matched cancer tissue, but sample number of normal control in public gene expression repositories is disproportionally small compared to cancer and scattered in several datasets.

Results
We built oncopression by integrating several datasets into one large dataset for comprehensive analysis about 25 types of human cancers including 20 640 cancer samples and 6801 normal control profiles. Expression profiles in cancers can be directly compared to normal tissue counterparts. Validity of the integration was tested using immunohistochemical staining results and principal component analysis. We have utilized the pre-release version of oncopression to identify cancer-specific genes in several studies.

Availability and Implementation
Free access at http://www.oncopression.com and all expression data are available for download at the site.

Supplementary information
Supplementary data are available at Bioinformatics online.
The effect of spatial dependence on hazard validation
Authors: Iervolino Iunio , Giorgio Massimiliano , Cito Pasquale 
Published: March 2017

SummaryIn countries where best-practice probabilistic hazard studies and seismic monitoring networks are available, there is increasing interest in direct validation of hazard maps. It usually means trying to quantitatively understand whether probabilities estimated via hazard analysis are consistent with observed frequencies of exceedance of ground motion intensity thresholds. Because the exceedance events of interest are typically rare with respect to the time span covered by data from seismic networks, a common approach underlying these studies is to pool observations from different sites. The main reason for this is to collect a sample large enough to convincingly perform a statistical analysis. However, this requires accounting for the dependence among the stochastic processes counting exceedances of ground motion intensity measures thresholds at different sites. Neglecting this dependence may lead to potentially fallacious conclusions about inadequateness of probabilistic seismic hazard. This study addresses this issue revisiting a hazard validation exercise for Italy, showing that accounting for this kind of spatial dependence can change the results of formal testing.
Staged Growing Rods With Preimplantation of Spinal Anchors for Complex Early Onset Scoliosis
Authors: Gomez Jaime A. , Grzywna Alexandra , Hanstein Regina , Emans John B. , Hresko M.Timothy , Hedequist Daniel , Karlin Lawrence I. , Glotzbecker Michael P. 
Published: March 2017

Background:
Treatment of early onset scoliosis (EOS) with growing rods (GR) can be challenging in patients with significant deformity, hyperkyphosis, or poor bone quality, due to risks of neurological deficit and hardware pull-out. The objective of this study is to report a series of EOS patients managed with a 2-stage GR technique used to minimize these complications.

Methods:
Two-stage GR technique was performed in 8 patients at mean age of 5.4 (range, 3.4 to 7.9) years. At stage 1, proximal and distal anchors were implanted with local fusion. At stage 2, the distraction rods were inserted. There were at least 3 months between stages 1 and 2, and halo-gravity traction was used before stage 2 unless contraindicated. Demographic, clinical, and surgical data were retrospectively reviewed with mean 4.9 (range, 2.0 to 9.4) years of follow-up. Radiographic measurements including Cobb and kyphosis angles were evaluated before stage 1, after halo-gravity traction, after stage 2, and at last follow-up. Indications for staging, anchor healing time, and complications were collected and analyzed.

Results:
Indications for 2-stage surgery were poor bone quality in 5 patients and neurological changes during initial attempt at GR placement in 3 patients. The mean time between stage 1 and 2 was 23 (15 to 45) weeks. Patients have undergone mean 7 (3 to 16) lengthenings. Three patients have been converted to magnetically controlled GR. The major coronal Cobb angle improved from mean 81 degrees (range, 61 to 97) preoperatively to 40 degrees (24 to 50) after stage 2 and remained at 40 degrees (27 to 53) at last follow-up. Kyphosis remained controlled from 45 degrees (10 to 76) preoperatively to 38 degrees (9 to 61) after stage 2 to 41 degrees (17 to 65) at last follow-up. Complications included superficial wound problems (4 patients), broken rods (2 patients), proximal migration (2 patients), and implant prominence (1 patient). At minimum 2-year follow-up, no patients had lingering neurological complications or instrumentation-bone failure of the GR construct.

Conclusions:
Two-stage GR technique can effectively be utilized in EOS patients with poor bone quality or in the event of intraoperative neurological changes. Satisfactory deformity correction can be obtained and routine serial lengthenings can take place with minimal complications.

Level of Evidence:
Level IV— case series.
The role of transoral robotic surgery in the management of oropharyngeal cancer
Authors: Dias Fernando L. , Walder Fernando , Leonhardt Fernando Danelon 
Published: March 2017

Purpose of review
The rising incidence of oropharyngeal squamous cell carcinoma (OPSCC), in large part as a result of the human papillomavirus (HPV), has driven a movement for the change in the management strategies. Renewed interest in minimally invasive approaches of endoscopic head and neck surgery led to introduction of transoral surgery, including transoral robotic surgery (TORS).

Recent findings
Several recent studies, based on large multi-institutional studies and systematic reviews of the literature, have shown excellent oncologic and functional outcomes with TORS for OPSCC. Also, a growing amount of clinical evidence supports the use of TORS in the management of carcinoma of unknown primary site and in selected patients with recurrent OPSCC with acceptable oncologic and better functional outcomes in comparison with traditional surgical approaches. Comparative studies with other therapeutic modalities (conventional surgical and nonsurgical) showed that TORS can be used to treat OPSCC, reducing morbidity and treatment costs, while providing equivalent oncologic results.

Summary
Large and robust data available in the literature supports the role of TORS within the multidisciplinary treatment paradigm for the management of OPSCC. Information from ongoing randomized clinical trials comparing TORS with and without dose-reduced radiotherapy or with and without intensified adjuvant treatment for high-risk OPSCC patients is necessary to determine the role of de-escalation of therapy in the era of HPV and OPSCC.