Miracle-dz/UniFAR-FTUs huggingface dataset:
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

An essential prerequisite for any systems-level understanding of cellular functions is to correctly uncover and annotate all functional interactions among proteins in the cell. Toward this goal, remarkable progress has been made in recent years, both in terms of experimental measurements and computational prediction techniques. However, public efforts to collect and present protein interaction information have struggled to keep up with the pace of interaction discovery, partly because protein–protein interaction information can be error-prone and require considerable effort to annotate. Here, we present an update on the online database resource Search Tool for the Retrieval of Interacting Genes (STRING); it provides uniquely comprehensive coverage and ease of access to both experimental as well as predicted interaction information. Interactions in STRING are provided with a confidence score, and accessory information such as protein domains and 3D structures is made available, all within a stable and consistent identifier space. New features in STRING include an interactive network viewer that can cluster networks on demand, updated on-screen previews of structural information including homology models, extensive data updates and strongly improved connectivity and integration with third-party resources. Version 9.0 of STRING covers more than 1100 completely sequenced organisms; the resource can be reached at http://string-db.org.
Safety profiles of adalimumab, etanercept and infliximab: a pharmacovigilance study using a measure of disproportionality in a database of spontaneously reported adverse events

Despite being effective, the biologics approved for treating rheumatoid arthritis have been associated with serious adverse events. This study is aimed at comparing the safety profiles of adalimumab, etanercept and infliximab by analysing the disproportionalities of the associations between the different adverse events and the different biologics in the Portuguese spontaneous reporting database.
Automated Control of an Adaptive Bihormonal, Dual-Sensor Artificial Pancreas and Evaluation During Inpatient Studies

Automated control of blood glucose in patients with type-1 diabetes has not yet been fully implemented. The aim of this study was to design and clinically evaluate a system that integrates a control algorithm with off-the-shelf subcutaneous sensors and pumps to automate the delivery of the hormones glucagon and insulin in response to continuous glucose sensor measurements. The automated component of the system runs an adaptive proportional derivative control algorithm which determines hormone delivery rates based on the sensed glucose measurements and the meal announcements by the patient. We provide details about the system design and the control algorithm, which incorporates both a fading memory proportional derivative controller (FMPD) and an adaptive system for estimating changing sensitivity to insulin based on a glucoregulatory model of insulin action. For an inpatient study carried out in eight subjects using Dexcom SEVEN PLUS sensors, prestudy HbA1c averaged 7.6, which translates to an estimated average glucose of 171 mg/dL. In contrast, during use of the automated system, after initial stabilization, glucose averaged 145 mg/dL and subjects were kept within the euglycemic range (between 70 and 180 mg/dL) for 73.1% of the time, indicating improved glycemic control. A further study on five additional subjects in which we used a newer and more reliable glucose sensor (Dexcom G4 PLATINUM) and made improvements to the insulin and glucagon pump communication system resulted in elimination of hypoglycemic events. For this G4 study, the system was able to maintain subjects' glucose levels within the near-euglycemic range for 71.6% of the study duration and the mean venous glucose level was 151 mg/dL.
Cues for hesitation in speech synthesis

﻿The current study investigates acoustic correlates to perceived hesitation based on previous work showing that pause duration and final lengthening both contribute to the perception of hesitation. It is the total duration increase that is the valid cue rather than the contribution by either factor. The present experiment using speech synthesis was designed to evaluate F0 slope and presence vs. absence of creaky voice before the inserted hesitation in addition to durational cues. The manipulations occurred in two syntactic positions, within a phrase and between two phrases, respectively. The results showed that in addition to durational increase, variation of both F0 slope and creaky voice had perceptual effects, although to a much lesser degree. The results have a bearing on efforts to model spontaneous speech including disfluencies, to be explored, for example, in spoken dialogue systems. ﻿
Common injuries and ailments of the female athlete; pathophysiology, treatment and prevention

Abstract With increasing numbers of women competing in high school and collegiate athletics, it is important that physicians become familiar with injury patterns and medical conditions unique to the female athlete. Observations and clinical data have elucidated unique biomechanical, anatomic and hormonal factors that predispose skeletally mature female athletes to anterior cruciate ligament (ACL) injuries, patellofemoral disorders and lower extremity stress fractures. Additionally, younger female athletes are particularly at risk of developing components of the “Female Athlete Triad” (more recently included under the syndrome of “Relative Energy Deficiency in Sport” [RED-S]): disordered eating, amenorrhea and osteoporosis. An understanding of the pathophysiology of these conditions has led to the development of programs that can treat their underlying causes, decrease susceptibility to injury, and improve the long-term health of the female athlete. This paper is intended to provide physicians with a review of the sex-specific etiology, prevention and treatment of injuries common to the female athlete.
Fracture analysis of composite co-cured structural joints using decohesion elements

Delamination is one of the predominant forms of failure in laminated composite structures, especially when there is no reinforcement in the thickness direction. To develop composite structures that are more damage tolerant, it is necessary to understand how delamination develops, and how it can affect the residual performance. A number of factors such as residual thermal stresses, matrix-curing shrinkage and manufacturing defects affect how damage will grow in a composite structure. It is important to develop computationally efficient analysis methods that can account for all such factors. The objective of the current work is to apply a newly developed decohesion element to investigate the debond strength of skin-stiffener composite specimens. The process of initiation of delaminations and the propagation of delamination fronts is investigated. The numerical predictions are compared with published experimental results.
The Facilitatory Effect of Referent Gaze on Cognitive Load in Language Processing

This paper considers prediction in language processing by examining the role of the visual context, and specifically, the role of speaker referent gaze on cognitive load. We inspect the anticipatory visual attention during sentence processing together with the cognitive load induced at the points of the gaze cue, and the linguistic referent. Employing a novel measurement of cognitive load the Index of Cognitive Activity (Marshall, 2000) allowed us to simultaneously consider both anticipatory eye-movements and cognitive load. Our results show that the gaze cue is being followed, and considered as a relevant piece of information, which subsequently reduces the cognitive load on the linguistic referent. In addition, we found that considering the gaze cue is in itself not costly, unless it cues an object mismatching with the previous linguistic context.
Diminished Behavioral and Neural Sensitivity to Sound Modulation Is Associated with Moderate Developmental Hearing Loss

The acoustic rearing environment can alter central auditory coding properties, yet altered neural coding is seldom linked with specific deficits to adult perceptual skills. To test whether developmental hearing loss resulted in comparable changes to perception and sensory coding, we examined behavioral and neural detection thresholds for sinusoidally amplitude modulated (sAM) stimuli. Behavioral sAM detection thresholds for slow (5 Hz) modulations were significantly worse for animals reared with bilateral conductive hearing loss (CHL), as compared to controls. This difference could not be attributed to hearing thresholds, proficiency at the task, or proxies for attention. Detection thresholds across the groups did not differ for fast (100 Hz) modulations, a result paralleling that seen in humans. Neural responses to sAM stimuli were recorded in single auditory cortex neurons from separate groups of awake animals. Neurometric analyses indicated equivalent thresholds for the most sensitive neurons, but a significantly poorer detection threshold for slow modulations across the population of CHL neurons as compared to controls. The magnitude of the neural deficit matched that of the behavioral differences, suggesting that a reduction of sensory information can account for limitations to perceptual skills.
Araport: the Arabidopsis Information Portal

The Arabidopsis Information Portal (https://www.araport.org) is a new online resource for plant biology research. It houses the Arabidopsis thaliana genome sequence and associated annotation. It was conceived as a framework that allows the research community to develop and release ‘modules’ that integrate, analyze and visualize Arabidopsis data that may reside at remote sites. The current implementation provides an indexed database of core genomic information. These data are made available through feature-rich web applications that provide search, data mining, and genome browser functionality, and also by bulk download and web services. Araport uses software from the InterMine and JBrowse projects to expose curated data from TAIR, GO, BAR, EBI, UniProt, PubMed and EPIC CoGe. The site also hosts ‘science apps,’ developed as prototypes for community modules that use dynamic web pages to present data obtained on-demand from third-party servers via RESTful web services. Designed for sustainability, the Arabidopsis Information Portal strategy exploits existing scientific computing infrastructure, adopts a practical mixture of data integration technologies and encourages collaborative enhancement of the resource by its user community.
Optimal Price Setting with Observation and Menu Costs

We study the price setting problem of a firm in the presence of both observation and menu costs. In this problem the firm optimally decides when to collect costly information on the adequacy of its price, an activity which we refer to as a price “review”. Upon each review, the firm chooses whether to adjust its price, subject to a menu cost, and when to conduct the next price review. This behavior is consistent with recent survey evidence documenting that firms revise prices infrequently and that only a few price revisions yield a price adjustment. The goal of the paper is to study how the firm’s choices map into several observable statistics, depending on the level and relative magnitude of the observation vs the menu cost. The observable statistics are: the frequency of price reviews, the frequency of price adjustments, the size-distribution of price adjustments, and the shape of the hazard rate of price adjustments. We provide an analytical characterization of the firm’s decisions and a mapping from the structural parameters to the observable statistics. We compare these statistics with the ones obtained for the models with only one type of cost. The predictions of the model can, with suitable data, be used to quantify the importance of the menu cost vs. the information cost. We also consider a version of the model where several price adjustment are allowed between observations, a form of price plans or indexation. We find that no indexation is optimal for small inflation rates.
Collagen, agarose, alginate, and Matrigel hydrogels as cell substrates for culture of chondrocytes in vitro: A comparative study

Autologous chondrocyte implantation (ACI) has emerged as a new approach to cartilage repair through the use of harvested chondrocytes. But the expansion of the chondrocytes from the donor tissue in vitro is restricted by limited cell numbers and dedifferentiation of chondrocytes. In this study, we used four types of hydrogels including agarose, alginate, Matrigel, and collagen type I hydrogels to serve as cell substrates and investigated the effect on proliferation and phenotype maintenance of chondrocytes. As a substrate for monolayer culture, collagen facilitated cell expansion and effectively suppressed the dedifferentiation of chondrocytes, as evidenced by fluorescein diacetate/propidium iodide (FDA/PI), hematoxylin‐eosin staining (HE), Safranin O, immunofluorescenceassay, biochemistry analysis, and quantitative real‐time polymerase chain reaction (qRT‐PCR). Compared with that in agarose gels, alginate, and Matrigel, collagen accelerated cell proliferation and enhanced the expression of cartilage specific genes such as ACAN, SOX9, and COLII more markedly. Furthermore, significantly lower expression of COL I (an indicator of dedifferentiation) and COL X (the chondrocyte hypertrophy marker) was present in collagen group than in other groups. This indicated that collagen substrate can better support chondrocyte growth and maintain cell phenotype, due to that it might serve as a cartilage‐like ECM to provide adhesive site for chondrocytes. In summary, collagen hydrogel is a promising cell substrate for chondrocytes culture for ACI.
Referential choice in a second language: evidence for a listener-oriented approach

ABSTRACT One central question in research on spoken language communication concerns how speakers decide how explicit to make a referential expression. In the present paper, we address the debate between a discourse-based approach and a listener-based approach to the choice of referring expressions by testing second language (L2) learners of English on the production of English referential expressions, and comparing their performance to a group of monolingual speakers of English. In two experiments, we found that when native speakers of English use full noun phrases, the L2 speakers tend to choose a pronoun, even when the use of a pronoun leads to ambiguity. Our results show that the pattern observed is not the result of cross-linguistic interference from the L1. Furthermore, a clear dissociation is found between calculating the discourse information and taking the listener's perspective into account, supporting a listener's based approach to the choice of referring expressions.
Chapter 7 Molecular mechanisms involved in the synergistic interaction of the EZH 2 inhibitor 3-deazaneplanocin A ( DZNeP ) with gemcitabine in pancreatic cancer cells

Pancreatic ductal adenocarcinoma (PDAC) is characterized by overexpression of Enhancerof Zeste-Homolog-2 (EZH2), which plays a pivotal role in cancer-stem-cell (CSC) selfrenewal through methylation of histone-H3-lysine-27 (H3K27m3). Against this background, EZH2 was identified as an attractive target and we investigated the interaction of the EZH2-inhibitor DZNeP with gemcitabine. EZH2 expression was detected by quantitative-RT-PCR in 15 PDAC cells, including 7 primary cell cultures, showing expression values correlated with their originator tumors (Spearman-R 2 =0.89, P=0.01). EZH2 expression in cancer cells was significantly higher than in normal ductal pancreatic cells and fibroblasts. DZNeP (5 μM, 72-hour-exposure) modulated EZH2 and H3K27m3 protein expression, and synergistically enhanced the antiproliferative activity of gemcitabine, with combination index values of 0.2 (PANC-1), 0.3 (MIA-PaCa-2) and 0.7 (LPC006). The drug combination reduced the percentages of cells in G2/M phase (e.g., from 27 to 19% in PANC-1, P<0.05), and significantly increased apoptosis compared to gemcitabine-alone. Moreover, DZNeP enhanced the mRNA and protein expression of the nucleoside transporters hENT1/hCNT1, possibly because of the significant reduction of deoxynucleotides content (e.g., 25% reduction of deoxycytidine-nucleotides in PANC-1), as detected by LC-MS/MS. DZNeP decreased cell migration, which was additionally reduced by DZNeP/gemcitabine combination (-20% in LPc006, after 8-hour exposure, P<0.05), and associated with increased E-cadherin mRNA and protein expression. Furthermore, DZNeP and DZNeP/gemcitabine combination significantly reduced the volume of PDAC spheroids growing in CSC-selective-medium, and decreased the proportion of CD133+ cells. All these molecular mechanisms underlying the synergism of DZNeP/gemcitabine combination support further studies on this novel therapeutic approach for treatment of PDAC.
Validity of Hydration Non-Invasive Indices during the Weightcutting and Official Weigh-In for Olympic Combat Sports

Background In Olympic combat sports, weight cutting is a common practice aimed to take advantage of competing in weight divisions below the athlete's normal weight. Fluid and food restriction in combination with dehydration (sauna and/or exercise induced profuse sweating) are common weight cut methods. However, the resultant hypohydration could adversely affect health and performance outcomes. Purpose The aim of this study is to determine which of the routinely used non-invasive measures of dehydration best track urine osmolality, the gold standard non-invasive test. Method Immediately prior to the official weigh-in of three National Championships, the hydration status of 345 athletes of Olympic combat sports (i.e., taekwondo, boxing and wrestling) was determined using five separate techniques: i) urine osmolality (UOSM), ii) urine specific gravity (USG), iii) urine color (UCOL), iv) bioelectrical impedance analysis (BIA), and v) thirst perception scale (TPS). All techniques were correlated with UOSM divided into three groups: euhydrated (G1; UOSM 250–700 mOsm·kg H2O−1), dehydrated (G2; UOSM 701–1080 mOsm·kg H2O−1), and severely dehydrated (G3; UOSM 1081–1500 mOsm·kg H2O−1). Results We found a positive high correlation between the UOSM and USG (r = 0.89: p = 0.000), although this relationship lost strength as dehydration increased (G1 r = 0.92; G2 r = 0.73; and G3 r = 0.65; p = 0.000). UCOL showed a moderate although significant correlation when considering the whole sample (r = 0.743: p = 0.000) and G1 (r = 0.702: p = 0.000) but low correlation for the two dehydrated groups (r = 0.498–0.398). TPS and BIA showed very low correlation sizes for all groups assessed. Conclusion In a wide range of pre-competitive hydration status (UOSM 250–1500 mOsm·kg H2O−1), USG is highly associated with UOSM while being a more affordable and easy to use technique. UCOL is a suitable tool when USG is not available. However, BIA or TPS are not sensitive enough to detect hypohydration at official weight-in before an Olympic combat championship.
Limitations of Cytomegalovirus Testing

Douglas Jabs and coworkers performed a prospective study of 122 patients with cytomegalovirus (CMV) retinitis ([5][1]). They collected blood and urine CMV isolates and performed sensitivity testing of the isolates. The interpretation of laboratory sensitivity testing of CMV strains is, however,
EFFECTS OF INITIAL PASSAGE OF ENDOTOXIN THROUGH THE LIVER ON THE EXTENT OF ACUTE LUNG INJURY IN A RAT MODEL

ABSTRACT We hypothesized that the extent of acute lung injury (ALI) caused by lipopolysaccharide (LPS) is modified with its initial passage through the liver. We tested this hypothesis by administering LPS, 5 mg/kg, or saline to 120 male Wistar rats via the portal vein (PV) or the inferior vena cava (IVC) over 1 h. Four experimental groups of rats were administered saline into the PV, saline into the IVC, LPS into the PV (LPS-PV group), and LPS into the IVC (LPS-IVC group), respectively. At 15 and 30 min after onset of 51Chromium-LPS infusion, the &ggr; counts in the liver were higher in the LPS-PV group than that in the LPS-IVC group. The ratio of 125Iodine-albumin counts in lung tissue to that in plasma per unit of weight (as an assessment of pulmonary microvascular permeability) at 240 min after onset of LPS stimulation, the accumulation of polymorphonuclear cell (assessed by myeloperoxidase activity) and the concentration of tumor necrosis factor &agr; in the lung at 60 and 240 min after onset of LPS infusion, were higher in the LPS-IVC group than in the LPS-PV group. Significant differences in several factors indicative of inflammation and in the extent of LPS-induced ALI were observed after the onset of LPS infusion, depending on whether it was delivered via the PV or the IVC. These observations suggest that the entrapping of LPS during its initial passage through the hepatic circulation may attenuate LPS-induced ALI within 4 h of initiation of LPS stimulation.
Chronolog Admits a Complete Proof Procedure

Chronolog(Z) is a logic programming language based on a linear-time temporal logic with unbounded past and future. It is suitable for applications involving the notion of dynamic change such as modeling periodical changes, non-terminating computations and temporal databases. The declarative semantics of Chronolog(Z) programs are given in terms of temporal Herbrand models and the operational semantics in terms of a resolution-type proof procedure called TiSLD-resolution. TiSLD-resolution is based on the axioms and the rules of inference of the underlying temporal logic. It is shown that TiSLD-resolution is sound and complete. The equivalence of the declarative and the operational semantics of Chronolog(Z) programs is also established.
Robust Non-rigid Motion Tracking and Surface Reconstruction Using L0 Regularization

We present a new motion tracking method to robustly reconstruct non-rigid geometries and motions from single view depth inputs captured by a consumer depth sensor. The idea comes from the observation of the existence of intrinsic articulated subspace in most of non-rigid motions. To take advantage of this characteristic, we propose a novel L0 based motion regularizer with an iterative optimization solver that can implicitly constrain local deformation only on joints with articulated motions, leading to reduced solution space and physical plausible deformations. The L0 strategy is integrated into the available non-rigid motion tracking pipeline, forming the proposed L0-L2 non-rigid motion tracking method that can adaptively stop the tracking error propagation. Extensive experiments over complex human body motions with occlusions, face and hand motions demonstrate that our approach substantially improves tracking robustness and surface reconstruction accuracy.