bluuebunny/crossref_metadata_2025_split huggingface dataset:
ProAcePred: prokaryote lysine acetylation sites prediction based on elastic net feature optimization
Authors: Chen Guodong , Cao Man , Luo Kun , Wang Lina , Wen Pingping , Shi Shaoping 
Published: May 2018

AbstractMotivationLysine acetylation exists extensively in prokaryotes, and plays a vital role in function adjustment. Recent progresses in the identification of prokaryote acetylation substrates and sites provide a great opportunity to explore the difference of substrate site specificity between prokaryotic and eukaryotic acetylation. Motif analysis suggests that prokaryotic and eukaryotic acetylation sites have distinct location-specific difference, and it is necessary to develop a prokaryote-specific acetylation sites prediction tool.ResultsTherefore, we collected nine species of prokaryote lysine acetylation data from various databases and literature, and developed a novel online tool named ProAcePred for predicting prokaryote lysine acetylation sites. Optimization of feature vectors via elastic net could considerably improve the prediction performance. Feature analyses demonstrated that evolutionary information played significant roles in prediction model for prokaryote acetylation. Comparison between our method and other tools suggested that our species-specific prediction outperformed other existing works. We expect that the ProAcePred could provide more instructive help for further experimental investigation of prokaryotes acetylation.Availability and implementationhttp://computbiol.ncu.edu.cn/ProAcePredSupplementary informationSupplementary data are available at Bioinformatics online.
Integrability of exponential process and its application to backward stochastic differential equations
Authors: Gashi Bujar , Li Jiajie 
Published: May 2018

Abstract
We consider the integrability problem of an exponential process with unbounded coefficients. The integrability is established under weaker conditions of Kazamaki type, which complements the results of Yong obtained under a Novikov type condition. As applications, we consider the solvability of linear backward stochastic differential equations (BSDEs) and market completeness, the solvability of a Riccati BSDE and optimal investment, all in the setting of unbounded coefficients.
Two decision problems in Contact Logics
Authors: Balbiani Philippe , Gencer Çiğdem , Özdemir Zafer 
Published: May 2018

AbstractContact Logics provide a natural framework for representing and reasoning about regions in several areas of computer science. In this paper, we focus our attention on reasoning methods for Contact Logics and address the satisfiability problem and the unifiability problem. Firstly, we give sound and complete tableaux-based decision procedures in Contact Logics and we obtain new results about the decidability/complexity of the satisfiability problem in these logics. Secondly, we address the computability of the unifiability problem in Contact Logics and we obtain new results about the unification type of the unifiability problem in these logics.
Origin of raptorial feeding in juvenile euarthropods revealed by a Cambrian radiodontan
Authors: Liu Jianni , Lerosey-Aubril Rudy , Steiner Michael , Dunlop Jason A , Shu Degan , Paterson John R 
Published: May 2018

AbstractThe rapid rise of arthropods during the Cambrian quickly established some clades, such as the euarthropod stem-group called Radiodonta, as the dominant and most diverse predators in marine ecosystems. Recent discoveries have shown that the size and dietary ecology of radiodontans are far more diverse than previously thought, but little is known about the feeding habits of juveniles. Here, we document a very small (∼18-mm-long), near-complete specimen of the radiodontan Lyrarapax unguispinus from the early Cambrian Chengjiang Biota of China. This specimen is the smallest radiodontan individual known, representing a juvenile instar. Its adult-like morphology—especially the fully developed spinose frontal appendages and tetraradial oral cone—indicates that L. unguispinus was a well-equipped predator at an early developmental stage, similar to modern raptorial euarthropods, such as mantises, mantis shrimps and arachnids. This evidence, coupled with the basal phylogenetic position of radiodontans, confirms that raptorial feeding habits in juvenile euarthropods appeared early in the evolutionary history of the group.
Anatomical Assessment of the Temporopolar Artery for Revascularization of Deep Recipients
Authors: Tayebi Meybodi Ali , Benet Arnau , Griswold Dylan , Dones Flavia , Preul Mark C , Lawton Michael T 
Published: May 2018

Abstract

BACKGROUND
Intracranial–intracranial and extracranial–intracranial bypass options for revascularization of deep cerebral recipients are limited and technically demanding.

OBJECTIVE
To assess the anatomical feasibility of using the temporopolar artery (TPA) for revascularization of the anterior cerebral artery (ACA), posterior cerebral artery (PCA), and superior cerebellar arteries (SCA).

METHODS
Orbitozygomatic craniotomy was performed bilaterally on 8 cadaveric heads. The cisternal segment of the TPA was dissected. The TPA was cut at M3-M4 junction with its proximal and distal calibers and the length of the cisternal segment measured. Feasibility of the TPA-A1-ACA, TPA-A2-ACA, TPA-SCA, and TPA-PCA bypasses were assessed.

RESULTS
A total of 17 TPAs were identified in 16 specimens. The average distal TPA caliber was 1.0 ± 0.2 mm, and the average cisternal length was 37.5 ± 9.4 mm. TPA caliber was ≥ 1.0 mm in 12 specimens (70%). The TPA-A1-ACA bypass was feasible in all specimens, whereas the TPA reached the A2-ACA, SCA, and PCA in 94% of specimens (16/17). At the point of anastomosis, the average recipient caliber was 2.5 ± 0.5 mm for A1-ACA, and 2.3 ± 0.7 mm for A2-ACA. The calibers of the SCA and PCA at the anastomosis points were 2.0 ± 0.6 mm, and 2.7 ± 0.8 mm, respectively.

CONCLUSION
The TPA-ACA, TPA-PCA, and TPA-SCA bypasses are anatomically feasible and may be used when the distal caliber of the TPA stump is optimal to provide adequate blood flow. This study lays foundations for clinical use of the TPA for ACA revascularization in well-selected cases.
OAO/MITSuME photometry of dwarf novae. III. CSS130418:174033+414756
Authors: Imada Akira , Isogai Keisuke , Yanagisawa Kenshi , Kawai Nobuyuki 
Published: May 2018

Abstract
We report on multicolor photometry of the short-period dwarf nova CSS130418:174033+414756 during the 2013 superoutburst. The system showed an unusually short superhump period of 0.046346(67) d during stage A, which is one of the shortest periods among dwarf novae below the period minimum. We found that the bluest peaks in g΄ − Ic color variations tended to coincide with the brightness minima of the superhump modulations. We also studied nightly-averaged superhump amplitudes in the g΄, Rc, and Ic bands and found that they have less dependence on wavelength. These properties are likely to be in common with dwarf novae exhibiting superhumps. We successfully obtained g΄ − Rc and Rc − Ic colors during the temporal dip. The color indices were significantly bluer compared with other dips of WZ Sge-type dwarf novae. By using the period of the growing superhumps, we estimated the mass ratio to be q = 0.077(5), which is much larger than the previous study.
Development of a clinical risk score for pain and function following total knee arthroplasty: results from the TRIO study
Authors: Shim Joanna , Mclernon David J , Hamilton David , Simpson Hamish A , Beasley Marcus , Macfarlane Gary J 
Published: May 2018

Abstract

Objectives
The aim was to develop and validate a simple clinical prediction model, based on easily collected preoperative information, to identify patients at high risk of pain and functional disability 6 months after total knee arthroplasty (TKA).

Methods
This was a multicentre cohort study of patients from nine centres across the UK, who were undergoing a primary TKA for OA. Information on sociodemographic, psychosocial, clinical and quality-of-life measures were collected at recruitment. The primary outcome measure for this analysis was the Oxford knee score (OKS), measured 6 months postoperatively by postal questionnaire. Multivariable logistic regression was used to develop the model. Model performance (discrimination and calibration) and internal validity were assessed, and a simple clinical risk score was developed.

Results
Seven hundred and twenty-one participants (mean age 68.3 years; 53% female) provided data for the present analysis, and 14% had a poor outcome at 6 months. Key predictors were poor clinical status, widespread body pain, high expectation of postoperative pain and lack of active coping. The developed model based on these variables demonstrated good discrimination. At the optimal cut-off, the final model had a sensitivity of 83%, specificity of 61% and positive likelihood ratio of 2.11. Excellent agreement was found between observed and predicted outcomes, and there was no evidence of overfitting in the model.

Conclusion
We have developed and validated a clinical prediction model that can be used to identify patients at high risk of a poor outcome after TKA. This clinical risk score may be an aid to shared decision-making between patient and clinician.
Predicting Young Adults Binge Drinking in Nightlife Scenes: An Evaluation of the D-ARIANNA Risk Estimation Model
Authors: Crocamo Cristina , Bartoli Francesco , Montomoli Cristina , Carrà Giuseppe 
Published: May 2018

Objectives:
Binge drinking (BD) among young people has significant public health implications. Thus, there is the need to target users most at risk. We estimated the discriminative accuracy of an innovative model nested in a recently developed e-Health app (Digital-Alcohol RIsk Alertness Notifying Network for Adolescents and young adults [D-ARIANNA]) for BD in young people, examining its performance to predict short-term BD episodes.

Methods:
We consecutively recruited young adults in pubs, discos, or live music events. Participants self-administered the app D-ARIANNA, which incorporates an evidence-based risk estimation model for the dependent variable BD. They were re-evaluated after 2 weeks using a single-item BD behavior as reference. We estimated D-ARIANNA discriminative ability through measures of sensitivity and specificity, and also likelihood ratios. ROC curve analyses were carried out, exploring variability of discriminative ability across subgroups.

Results:
The analyses included 507 subjects, of whom 18% reported at least 1 BD episode at follow-up. The majority of these had been identified as at high/moderate or high risk (65%) at induction. Higher scores from the D-ARIANNA risk estimation model reflected an increase in the likelihood of BD. Additional risk factors such as high pocket money availability and alcohol expectancies influence the predictive ability of the model.

Conclusions:
The D-ARIANNA model showed an appreciable, though modest, predictive ability for subsequent BD episodes. Post-hoc model showed slightly better predictive properties. Using up-to-date technology, D-ARIANNA appears an innovative and promising screening tool for BD among young people. Long-term impact remains to be established, and also the role of additional social and environmental factors.
Nonalcoholic fatty liver disease-associated hepatocellular carcinoma in a hepatitis B virus-endemic area
Authors: Yoon Chang Hwi , Jin Young-Joo , Lee Jin Woo 
Published: May 2018

Background
This study was carried out to evaluate the association between nonalcoholic fatty liver disease (NAFLD) and the development of hepatocellular carcinoma (HCC) between 2005 and 2015 in a hepatitis B virus (HBV)-endemic area.

Patients and methods
The medical records of 1327 patients initially diagnosed with HCC at our institution between January 2005 and December 2015 were analyzed retrospectively. Patients with other malignancies in addition to HCC were excluded. During the study period, changes in the proportion of NAFLD-associated HCC among all HCCs were assessed longitudinally. In addition, the clinical characteristics of NAFLD-associated HCC were evaluated.

Results
Among the 1327 patients, HBV was the most common (65.5%) cause of HCC, and the overall rate of NAFLD-associated HCC was 4.7%. Compared with HBV-associated HCC patients, NAFLD-associated HCC patients were older, had a higher median body mass index, and a larger median tumor size (P<0.05 for all). Liver cirrhosis was less frequent in NAFLD-associated than in HBV-associated HCC patients (P<0.05). The annual proportions of NAFLD-associated HCC patients were 3.4% in 2005, 3.6% in 2006, 3.5% in 2007, 3.2% in 2008, 4.2% in 2009, 4.4% in 2010, 5.6% in 2011, 5.2% in 2012, 5.8% in 2013, 7.0% in 2014, and 6.7% in 2015. From 2008 to 2015, these percentages increased steadily.

Conclusion
The annual proportion of NAFLD-associated HCC patients among all HCC patients ranged from 3.2 to 3.5% before 2008, but thereafter, it increased gradually and had doubled to 7.0% by 2014.
Nonesophageal Eosinophilic Gastrointestinal Disorders
Authors: Naramore Sara , Gupta Sandeep K. 
Published: May 2018

ABSTRACTEosinophilic gastrointestinal disorders are a set of conditions with a wide range of clinical manifestations and treatment modalities. The disorders are suspected to result from an abnormal inflammatory response to allergen (s), and individuals may develop a relapsing or chronic disease, if the allergen is not eliminated. Mechanisms of disease pathogenesis, including the humoral immune response, need to be fully elucidated. A variety of therapies are used, although there is a lack of well‐defined randomized, prospective studies. Other therapeutic options are needed as the current treatments have potential concerns; elimination diets may impair a child's quality of life, and corticosteroids have adverse risks with long‐term use. We review what is known about nonesophageal eosinophilic gastrointestinal disorders, and discuss research investigations which need to be conducted to facilitate diagnosis and enhance treatment methods.
Avoiding/inducing dynamic buckling in a thermomechanically coupled plate: a local and global analysis of slow/fast response
Authors: Settimi Valeria , Rega Giuseppe , Saetta Eduardo 
Published: May 2018

The nonlinear response of a reduced model of an orthotropic single-layered plate with thermomechanical coupling is investigated in the presence of thermal excitations, in addition to mechanical ones. Different issues are addressed via accurate and extended local and global analyses. (i) Assessing the possible occurrence, disappearance or modification of mechanical buckling as a result of thermal aspects; (ii) exploiting global dynamics to unveil the effects of coupling; (iii) highlighting the crucial role played by the slow thermal transient evolution in modifying the fast steady mechanical response; (iv) framing the influence of coupling and underlining the need to use a thermomechanical model to grasp the actual plate dynamics; and (v) getting hints of technical interest as to the outcome robustness with respect to variations in the external/internal thermal parameters.
Dissociating cognitive and motoric precursors of human self-initiated action
Authors: Khalighinejad N. , Brann E. , Dorgham A , Haggard P. 
Published: May 2018

AbstractAcross-trial variability of EEG decreases more markedly prior to self-initiated than prior to externally-triggered actions, providing a novel neural precursor for volitional action. However, it remains unclear whether this neural convergence is an early, deliberative stage, or a late, execution-related stage in the chain of cognitive processes that transform intentions to actions. We report two experiments addressing these questions. Self-initiated actions were operationalized as endogenous ‘skip’ responses while waiting for target stimuli in a perceptual decision task. These self-initiated ‘skips’ were compared to blocks where participants were instructed to skip. EEG variability decreased more markedly prior to self-initiated compared to externally-triggered ‘skip’ actions, replicating previous findings.Importantly, this EEG convergence was stronger at fronto-midline electrodes than at either the electrode contralateral or ipsilateral to the hand assigned to the ‘skip’ action in each block (Experiment 1). Further, convergence was stronger when availability of skip responses was ‘rationed’, encouraging deliberate planning before skipping (Experiment 2). This suggests that the initiation of voluntary actions involves a bilaterally-distributed, effector-independent process related to deliberation. A consistent process of volition is detectable during early, deliberative planning, and not only during late, execution-related time windows.
The Human RNA-Binding Proteome and Its Dynamics During Arsenite-Induced Translational Arrest
Authors: Trendel Jakob , Schwarzl Thomas , Prakash Ananth , Bateman Alex , Hentze Matthias W. , Krijgsveld Jeroen 
Published: May 2018

SummaryProteins and RNA functionally and physically intersect in multiple biological processes, however, currently no universal method is available to purify protein-RNA complexes. Here we introduce XRNAX, a method for the generic purification of protein-crosslinked RNA, and demonstrate its versatility to study the composition and dynamics of protein-RNA interactions by various transcriptomic and proteomic approaches. We show that XRNAX captures all RNA biotypes, and use this to characterize the sub-proteomes that interact with coding and non-coding RNAs (ncRNAs), and to identify hundreds of protein-RNA interfaces. Exploiting the quantitative nature of XRNAX, we observe drastic remodeling of the RNA-bound proteome during arsenite-induced stress, distinct from autophagy-induced changes in the total proteome. In addition, we combine XRNAX with CLIP-seq to validate the interaction of ncRNA with Lamin B and EXOSC2. Thus, XRNAX is a resourceful approach to study structural and compositional aspects of protein-RNA interactions to address fundamental questions in RNA-biology.
Face Viewing Behavior Predicts Multisensory Gain During Speech Perception
Authors: Rennig Johannes , Wegner-Clemens Kira , Beauchamp Michael S 
Published: May 2018

AbstractDuring face viewing, some individuals prefer to fixate the mouth while others fixate the eyes. Individuals who have a history of mouth fixation might have stronger associations between visual and auditory speech, resulting in improved comprehension. First, we measured eye movements during face-viewing and observed high interindividual variability in mouth fixation time. Next, we measured eye movements and comprehension during perception of noisy auditory speech with or without visual speech. When visual speech was present, participants primarily fixated the mouth, but derived substantial benefit compared to noisy auditory speech with high interindividual variability. The benefit of visual speech was predicted by the eye movements made during the initial face-viewing task, but not by eye movements during the noisy speech task. These findings suggest a link between eye movements during face viewing and audiovisual speech perception and suggest that individual histories of visual exposure shape abilities across cognitive domains.
Neural evidence for age-related differences in representational quality and strategic retrieval processes
Authors: Trelle Alexandra N. , Henson Richard N. , Simons Jon S. 
Published: May 2018

AbstractMounting behavioral evidence suggests that declines in both representational quality and controlled retrieval processes contribute to episodic memory decline with age. The present study sought neural evidence for age-related change in these factors by measuring neural differentiation during encoding of paired associates, and changes in regional BOLD activity and functional connectivity during retrieval conditions that placed low (intact pairs) and high (recombined pairs) demands on controlled retrieval processes. Pattern similarity analysis revealed age-related declines in the differentiation of stimulus representations at encoding, manifesting as both reduced pattern similarity between closely related events, and increased pattern similarity between distinct events. During retrieval, both groups exhibited increased recruitment of areas within the core recollection network, including the hippocampus and angular gyrus, when endorsing studied pairs, whereas younger adults exhibited increased recruitment of, and hippocampal connectivity with, lateral prefrontal regions during correct rejections of recombined pairs. These results provide evidence for age-related changes in representational quality and in the neural mechanisms supporting memory retrieval under conditions of high, but not low, control demand.
Weber’s law is the result of exact temporal accumulation of evidence
Authors: Pardo-Vazquez Jose L. , Castiñeiras Juan , Valente Mafalda , Costa Tiago , Renart Alfonso 
Published: May 2018

AbstractWeber’s law states that the discriminability between two stimulus intensities depends only on their ratio. Despite its status as the cornerstone of psychophysics, the mecha-nisms underlying Weber’s law are still debated, as no principled way exists to choose between its many proposed alternative explanations. We studied this problem training rats to discriminate the lateralization of sounds of different overall level. We found that the rats’ discrimination accuracy in this task is level-invariant, consistent with Weber’s law. Surprisingly, the shape of the reaction time distributions is also level-invariant, implying that the only behavioral effect of changes in the overall level of the sounds is a uniform scaling of time. Furthermore, we demonstrate that Weber’s law breaks down if the stimulus duration is capped at values shorter than the typical reaction time. Together, these facts suggest that Weber’s law is associated to a process of bounded evidence accumulation. Consistent with this hypothesis, we show that, among a broad class of sequential sampling models, the only robust mechanism consistent with reaction time scale-invariance is based on perfect accumulation of evidence up to a constant bound, Poisson-like statistics, and a power-law encoding of stimulus intensity. Fits of a minimal diffusion model with these characteristics describe the rats performance and reaction time distributions with virtually no error. Various manipulations of motivation were unable to alter the rats’ psychometric function, demonstrating the stability of the just-noticeable-difference and suggesting that, at least under some conditions, the bound for evidence accumulation can set a hard limit on discrimination accuracy. Our results establish the mechanistic foundation of the process of intensity discrimination and clarify the factors that limit the precision of sensory systems.