bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prospective validation of pathologic complete response models in rectal cancer: Transferability and reproducibility
Authors: van Soest Johan , Meldolesi Elisa , van Stiphout Ruud , Gatta Roberto , Damiani Andrea , Valentini Vincenzo , Lambin Philippe , Dekker Andre 
Published: June 2017

PurposeMultiple models have been developed to predict pathologic complete response (pCR) in locally advanced rectal cancer patients. Unfortunately, validation of these models normally omit the implications of cohort differences on prediction model performance. In this work, we will perform a prospective validation of three pCR models, including information whether this validation will target transferability or reproducibility (cohort differences) of the given models.MethodsWe applied a novel methodology, the cohort differences model, to predict whether a patient belongs to the training or to the validation cohort. If the cohort differences model performs well, it would suggest a large difference in cohort characteristics meaning we would validate the transferability of the model rather than reproducibility. We tested our method in a prospective validation of three existing models for pCR prediction in 154 patients.ResultsOur results showed a large difference between training and validation cohort for one of the three tested models [Area under the Receiver Operating Curve (AUC) cohort differences model: 0.85], signaling the validation leans towards transferability. Two out of three models had a lower AUC for validation (0.66 and 0.58), one model showed a higher AUC in the validation cohort (0.70).DiscussionWe have successfully applied a new methodology in the validation of three prediction models, which allows us to indicate if a validation targeted transferability (large differences between training/validation cohort) or reproducibility (small cohort differences).
High‐resolution 31P echo‐planar spectroscopic imaging in vivo at 7T
Authors: Korzowski Andreas , Bachert Peter 
Published: June 2017

PurposeConventional 31P chemical shift imaging is time‐consuming and yields only limited spatial resolution. The purpose of this study was to demonstrate feasibility of 31P echo‐planar spectroscopic imaging (EPSI) in vivo at 7T.MethodsA 3D 31P EPSI sequence with trapezoidal‐shaped gradient pulses was implemented on a 7T MR scanner. To increase spectral width with reduced demand on gradient performance, a multishot approach was chosen. Acquisition weighting and 31P–{1H} double resonance for nuclear Overhauser signal enhancement were applied to increase sensitivity.Results3D 31P–{1H} EPSI data from model solution and from human calf muscle and brain were obtained from voxels with effective sizes of 4.1 to 16.2 cm3 in measurement times of approximately 10 min. Individual spectra showed well‐resolved resonances of endogenous 31P‐metabolites without artifacts. Volumetric high‐resolution 31P‐metabolite maps in vivo showed metabolic heterogeneity of different tissues.ConclusionIn vivo 31P EPSI at 7T yields high‐quality metabolic images. The proposed multishot EPSI technique reduces the measurement times for acquisition of volumetric high‐resolution maps of 31P‐metabolites or intracellular pH in human studies. Magn Reson Med 79:1251–1259, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
Age at the time of onset of psychosis: A marker of specific needs rather than a determinant of outcome?
Authors: Golay P. , Alameda L. , Mebdouhi N. , Baumann P. , Ferrari C. , Solida A. , Progin P. , Elowe J. , Conus P. 
Published: June 2017

AbstractBackground:While there is suggestion that early onset of psychosis is a determinant of outcome; knowledge regarding correlates of later onset age is more limited. This study explores the characteristics of patients developing psychosis after age 26, towards the end of the usual age range of early intervention programs, in order to identify potential specific needs of such patients.Methods:Two hundred and fifty-six early psychosis patients aged 18–35 were followed-up prospectively over 36 months. Patients with onset after 26 (“later onset”, LO) were compared to the rest of the sample.Results:LO patients (32% of the sample) had shorter DUP, were less likely to be male, had better premorbid functioning and were more likely to have been exposed to trauma. They had greater insight at presentation and less negative symptoms overall. The trajectories for positive and depressive symptoms were similar in both groups. Evolution of functional level was similar in both groups, but while LO patients recovered faster, they were significantly less likely to return to premorbid functional level.Conclusions:Later psychosis onset correlates with better premorbid functioning and higher rate of trauma exposure; the latter should therefore be a treatment focus in such patients. LO patients were less likely to return to premorbid functional level, which suggests that current treatment strategies may not be efficient to help patients maintain employment. The possibility of distinct illness mechanisms according to onset age and the more central role for trauma in patients with onset after age 26 needs to be further explored.
Multitype infinite-allele branching processes in continuous time
Authors: McDonald Thomas O. , Kimmel Marek 
Published: June 2017

Abstract
We introduce extensions to an infinite-allele branching process that allows for multiple types to exist alongside labels. We consider a Markov branching process and general branching process under different assumptions, and show asymptotic results about the growth of the labels as well as the frequency spectrum. These results are motivated by two separate models. The Markov binary splitting results are motivated by a model of clonal evolution in cancer that considers the effect of both driver and passenger mutations on tumor growth. The general process has applications in viral reproduction and dynamics.
Ergodicity of Markov chain Monte Carlo with reversible proposal
Authors: Kamatani K. 
Published: June 2017

AbstractWe describe the ergodic properties of some Metropolis–Hastings algorithms for heavy-tailed target distributions. The results of these algorithms are usually analyzed under a subgeometric ergodic framework, but we prove that the mixed preconditioned Crank–Nicolson (MpCN) algorithm has geometric ergodicity even for heavy-tailed target distributions. This useful property comes from the fact that, under a suitable transformation, the MpCN algorithm becomes a random-walk Metropolis algorithm.
Maternal verbal responsiveness and directiveness: consistency, stability, and relations to child early linguistic development
Authors: PAAVOLA-RUOTSALAINEN LEILA , LEHTOSAARI JAANA , PALOMÄKI JOSEFINA , TERVO IMMI 
Published: June 2017

AbstractMaternal responsive and directive speech to children at ages 0;10 and 2;0 was investigated by applying a procedure first introduced by Flynn and Masur (2007) to a new language community (Finnish). The issues examined were consistency and stability over time, and also the role of responsiveness and directiveness in child linguistic development at 1;0 and 2;6. The measures of maternal speech from each age were used to predict the results of the subsequent linguistic assessment. Negative correlations between responsive and directive utterances were found at both ages. The frequencies of responsive utterances and supportive directives increased over time. Responsiveness was positively, and intrusive directiveness negatively, related to child early comprehensive skills and the use of symbolic actions and communicative gestures. By contrast, no relations were found between responsiveness and directiveness and children's later linguistic capacities.
Poly(4-styrenesulfonate)-induced sulfur vacancy self-healing strategy for monolayer MoS2 homojunction photodiode
Authors: Zhang Xiankun , Liao Qingliang , Liu Shuo , Kang Zhuo , Zhang Zheng , Du Junli , Li Feng , Zhang Shuhao , Xiao Jiankun , Liu Baishan , Ou Yang , Liu Xiaozhi , Gu Lin , Zhang Yue 
Published: June 2017

AbstractWe establish a powerful poly(4-styrenesulfonate) (PSS)-treated strategy for sulfur vacancy healing in monolayer MoS2 to precisely and steadily tune its electronic state. The self-healing mechanism, in which the sulfur vacancies are healed spontaneously by the sulfur adatom clusters on the MoS2 surface through a PSS-induced hydrogenation process, is proposed and demonstrated systematically. The electron concentration of the self-healed MoS2 dramatically decreased by 643 times, leading to a work function enhancement of ∼150 meV. This strategy is employed to fabricate a high performance lateral monolayer MoS2 homojunction which presents a perfect rectifying behaviour, excellent photoresponsivity of ∼308 mA W−1 and outstanding air-stability after two months. Unlike previous chemical doping, the lattice defect-induced local fields are eliminated during the process of the sulfur vacancy self-healing to largely improve the homojunction performance. Our findings demonstrate a promising and facile strategy in 2D material electronic state modulation for the development of next-generation electronics and optoelectronics.
HTLV-1-induced leukotriene B4 secretion by T cells promotes T cell recruitment and virus propagation
Authors: Percher Florent , Curis Céline , Pérès Eléonore , Artesi Maria , Rosewick Nicolas , Jeannin Patricia , Gessain Antoine , Gout Olivier , Mahieux Renaud , Ceccaldi Pierre-Emmanuel , Van den Broeke Anne , Duc Dodon Madeleine , Afonso Philippe V. 
Published: June 2017

AbstractThe human T-lymphotropic virus type 1 (HTLV-1) is efficiently transmitted through cellular contacts. While the molecular mechanisms of viral cell-to-cell propagation have been extensively studiedin vitro, those facilitating the encounter between infected and target cells remain unknown. In this study, we demonstrate that HTLV-1-infected CD4 T cells secrete a potent chemoattractant, leukotriene B4 (LTB4). LTB4 secretion is dependent on Tax-induced transactivation of thepla2g4cgene, which encodes the cytosolic phospholipase A2 gamma. Inhibition of LTB4 secretion or LTB4 receptor knockdown on target cells reduces T-cell recruitment, cellular contact formation and virus propagationin vitro. Finally, blocking the synthesis of LTB4 in a humanized mouse model of HTLV-1 infection significantly reduces proviral load. This results from a decrease in the number of infected clones while their expansion is not impaired. This study shows the critical role of LTB4 secretion in HTLV-1 transmission bothin vitroandin vivo.
Adaptive and freeze-tolerant heteronetwork organohydrogels with enhanced mechanical stability over a wide temperature range
Authors: Gao Hainan , Zhao Ziguang , Cai Yudong , Zhou Jiajia , Hua Wenda , Chen Lie , Wang Li , Zhang Jianqi , Han Dong , Liu Mingjie , Jiang Lei 
Published: June 2017

AbstractMany biological organisms with exceptional freezing tolerance can resist the damages to cells from extra-/intracellular ice crystals and thus maintain their mechanical stability at subzero temperatures. Inspired by the freezing tolerance mechanisms found in nature, here we report a strategy of combining hydrophilic/oleophilic heteronetworks to produce self-adaptive, freeze-tolerant and mechanically stable organohydrogels. The organohydrogels can simultaneously use water and oil as a dispersion medium, and quickly switch between hydrogel- and organogel-like behaviours in response to the nature of the surrounding phase. Accordingly, their surfaces display unusual adaptive dual superlyophobic in oil/water system (that is, they are superhydrophobic under oil and superoleophobic under water). Moreover, the organogel component can inhibit the ice crystallization of the hydrogel component, thus enhancing the mechanical stability of organohydrogel over a wide temperature range (−78 to 80 °C). The organohydrogels may have promising applications in complex and harsh environments.
Inherited determinants of early recurrent somatic mutations in prostate cancer
Authors: Romanel Alessandro , Garritano Sonia , Stringa Blerta , Blattner Mirjam , Dalfovo Davide , Chakravarty Dimple , Soong David , Cotter Kellie A. , Petris Gianluca , Dhingra Priyanka , Gasperini Paola , Cereseto Anna , Elemento Olivier , Sboner Andrea , Khurana Ekta , Inga Alberto , Rubin Mark A. , Demichelis Francesca 
Published: June 2017

AbstractProstate cancer is a highly heritable molecularly and clinically heterogeneous disease. To discover germline events involved in prostate cancer predisposition, we develop a computational approach to nominate heritable facilitators of somatic genomic events in the context of the androgen receptor signaling. Here, we use a ranking score and benign prostate transcriptomes to identify a non-coding polymorphic regulatory element at 7p14.3 that associates with DNA repair and hormone-regulated transcript levels and with an early recurrent prostate cancer-specific somatic mutation in the Speckle-Type POZ protein (SPOP) gene. The locus shows allele-specific activity that is concomitantly modulated by androgen receptor and by CCAAT/enhancer-binding protein (C/EBP) beta (CEBPB). Deletion of this locus via CRISPR-Cas9 leads to deregulation of the genes predicted to interact with the 7p14.3 locus by Hi-C chromosome conformation capture data. This study suggests that a polymorphism at 7p14.3 may predispose to SPOP mutant prostate cancer subclass through a hormone-dependent DNA damage response.
Macrophage responses to lipopolysaccharide are modulated by a feedback loop involving prostaglandin E2, dual specificity phosphatase 1 and tristetraprolin
Authors: Tang Tina , Scambler Thomas E. , Smallie Tim , Cunliffe Helen E. , Ross Ewan A. , Rosner Dalya R. , O’Neil John D. , Clark Andrew R. 
Published: June 2017

AbstractIn many different cell types, pro-inflammatory agonists induce the expression of cyclooxygenase 2 (COX-2), an enzyme that catalyzes rate-limiting steps in the conversion of arachidonic acid to a variety of lipid signaling molecules, including prostaglandin E2 (PGE2). PGE2 has key roles in many early inflammatory events, such as the changes of vascular function that promote or facilitate leukocyte recruitment to sites of inflammation. Depending on context, it also exerts many important anti-inflammatory effects, for example increasing the expression of the anti-inflammatory cytokine interleukin 10 (IL-10), and decreasing that of the pro-inflammatory cytokine tumor necrosis factor (TNF). The tight control of both biosynthesis of, and cellular responses to, PGE2 are critical for the precise orchestration of the initiation and resolution of inflammatory responses. Here we describe evidence of a negative feedback loop, in which PGE2 augments the expression of dual specificity phosphatase 1, impairs the activity of mitogen-activated protein kinase p38, increases the activity of the mRNA-destabilizing factor tristetraprolin, and thereby inhibits the expression of COX-2. The same feedback mechanism contributes to PGE2-mediated suppression of TNF release. Engagement of the DUSP1-TTP regulatory axis by PGE2 is likely to contribute to the switch between initiation and resolution phases of inflammation.
Determination of Aspergillus pathogens in agricultural products by a specific nanobody-polyclonal antibody sandwich ELISA
Authors: Wang Ting , Li Peiwu , Zhang Qi , Zhang Wen , Zhang Zhaowei , Wang Tong , He Ting 
Published: June 2017

AbstractAspergillus and its poisonous mycotoxins are distributed worldwide throughout the environment and are of particular interest in agriculture and food safety. In order to develop a specific method for rapid detection of Aspergillus flavus to forecast diseases and control aflatoxins, a nanobody, PO8-VHH, highly reactive to A. flavus was isolated from an immunized alpaca nanobody library by phage display. The nanobody was verified to bind to the components of extracellular and intracellular antigen from both A. flavus and A. parasiticus. To construct a sandwich format immunoassay, polyclonal antibodies against Aspergillus were raised with rabbits. Finally, a highly selective nanobody-polyclonal antibody sandwich enzyme-linked immunosorbent assay was optimized and developed. The results revealed that the detection limits of the two fungi were as low as 1 μg mL−1, and that it is able to detect fungal concentrations below to 2 μg mg−1 of peanut and maize grains in both artificially and naturally contaminated samples. Therefore, we here provided a rapid and simple method for monitoring Aspergillus spp. contamination in agricultural products.
Comparative genetic, proteomic and phosphoproteomic analysis of C. elegans embryos with a focus on ham-1/STOX and pig-1/MELK in dopaminergic neuron development
Authors: Offenburger Sarah-Lena , Bensaddek Dalila , Murillo Alejandro Brenes , Lamond Angus I. , Gartner Anton 
Published: June 2017

AbstractAsymmetric cell divisions are required for cellular diversity and defects can lead to altered daughter cell fates and numbers. In a genetic screen for C. elegans mutants with defects in dopaminergic head neuron specification or differentiation, we isolated a new allele of the transcription factor HAM-1 [HSN (Hermaphrodite-Specific Neurons) Abnormal Migration]. Loss of both HAM-1 and its target, the kinase PIG-1 [PAR-1(I)-like Gene], leads to abnormal dopaminergic head neuron numbers. We identified discrete genetic relationships between ham-1, pig-1 and apoptosis pathway genes in dopaminergic head neurons. We used an unbiased, quantitative mass spectrometry-based proteomics approach to characterise direct and indirect protein targets and pathways that mediate the effects of PIG-1 kinase loss in C. elegans embryos. Proteins showing changes in either abundance, or phosphorylation levels, between wild-type and pig-1 mutant embryos are predominantly connected with processes including cell cycle, asymmetric cell division, apoptosis and actomyosin-regulation. Several of these proteins play important roles in C. elegans development. Our data provide an in-depth characterisation of the C. elegans wild-type embryo proteome and phosphoproteome and can be explored via the Encyclopedia of Proteome Dynamics (EPD) – an open access, searchable online database.
Upregulation of arylsulfatase B in carotid atherosclerosis is associated with symptoms of cerebral embolization
Authors: Biros Erik , Moran Corey S. , Maguire Jane , Holliday Elizabeth , Levi Christopher , Golledge Jonathan 
Published: June 2017

AbstractThe aim of this study was to identify genes for which the expression within carotid atherosclerosis was reproducibly associated with the symptoms of cerebral embolization. Two publically available microarray datasets E-MEXP-2257 and GSE21545 were analysed using GeneSpring 11.5. The two datasets utilized a total of 22 and 126 carotid atherosclerosis samples, obtained from patients with and without symptoms of cerebral embolization, respectively. To assess whether the findings were reproducible we analysed carotid atherosclerosis samples from another 8 patients with and 7 patients without symptoms of cerebral embolization using real-time PCR. In vitro studies using VSMC were performed to assess the functional relevance of one of the validated genes. We identified 1624 and 135 differentially expressed genes within carotid atherosclerosis samples of symptomatic compared to asymptomatic patients using the E-MEXP-2257 and GSE21545 datasets, respectively (≥1.15-absolute fold-change, P < 0.05). Only 7 differentially expressed genes or 0.4% (7/1,752) were consistent between the datasets. We validated the differential expression of ARSB which was upregulated 1.15-fold (P = 0.029) in atherosclerosis from symptomatic patients. In vitro incubation of VSMCs with the ARSB inhibitor L-ascorbic acid resulted in marked upregulation of SIRT1 and AMPK. This study suggests that ARSB may represent a novel target to limit carotid embolization.
Free-standing plasmonic metal-dielectric-metal bandpass filter with high transmission efficiency
Authors: Liang Yuzhang , Zhang Si , Cao Xun , Lu Yanqing , Xu Ting 
Published: June 2017

AbstractPlasmonic spectrum filtering devices based on metallic nanostructures have attracted wide attention due to their good reliability, ease of fabrication, and wideband tunability. However, the presence of thick substrate significantly limits the structure’s longitudinal size for further optoelectronic integration and reduces the devices’ performance. Here we propose and demonstrate an ultra-thin plasmonic bandpass filter based on free-standing periodic metal-dielectric-metal stack geometry working in the near-infrared wavelength range. The coupling between free-space electromagnetic waves and spatially confined plasmonic modes in the designed structure is systematically investigated. As demonstrated in the calculation and experiment, the free-standing plasmonic filters have more than 90% transmission efficiency and superior angular tolerance. The experimental results are in good agreement with the theoretical calculations. These artificial nanostructured filtering devices may find potential applications in the extremely compact device architectures.
Long-Term Monitoring of Dolphin Biosonar Activity in Deep Pelagic Waters of the Mediterranean Sea
Authors: Caruso Francesco , Alonge Giuseppe , Bellia Giorgio , De Domenico Emilio , Grammauta Rosario , Larosa Giuseppina , Mazzola Salvatore , Riccobene Giorgio , Pavan Gianni , Papale Elena , Pellegrino Carmelo , Pulvirenti Sara , Sciacca Virginia , Simeone Francesco , Speziale Fabrizio , Viola Salvatore , Buscaino Giuseppa 
Published: June 2017

AbstractDolphins emit short ultrasonic pulses (clicks) to acquire information about the surrounding environment, prey and habitat features. We investigated Delphinidae activity over multiple temporal scales through the detection of their echolocation clicks, using long-term Passive Acoustic Monitoring (PAM). The Istituto Nazionale di Fisica Nucleare operates multidisciplinary seafloor observatories in a deep area of the Central Mediterranean Sea. The Ocean noise Detection Experiment collected data offshore the Gulf of Catania from January 2005 to November 2006, allowing the study of temporal patterns of dolphin activity in this deep pelagic zone for the first time. Nearly 5,500 five-minute recordings acquired over two years were examined using spectrogram analysis and through development and testing of an automatic detection algorithm. Echolocation activity of dolphins was mostly confined to nighttime and crepuscular hours, in contrast with communicative signals (whistles). Seasonal variation, with a peak number of clicks in August, was also evident, but no effect of lunar cycle was observed. Temporal trends in echolocation corresponded to environmental and trophic variability known in the deep pelagic waters of the Ionian Sea. Long-term PAM and the continued development of automatic analysis techniques are essential to advancing the study of pelagic marine mammal distribution and behaviour patterns.