Miracle-dz/UniFAR-FTUs huggingface dataset:
Validation of artificial neural networks as a methodology for donor‐recipient matching for liver transplantation

In 2014, we reported a model for donor‐recipient (D‐R) matching in liver transplantation (LT) based on artificial neural networks (ANNs) from a Spanish multicenter study (Model for Allocation of Donor and Recipient in España [MADR‐E]). The aim is to test the ANN‐based methodology in a different European health care system in order to validate it. An ANN model was designed using a cohort of patients from King's College Hospital (KCH; n = 822). The ANN was trained and tested using KCH pairs for both 3‐ and 12‐month survival models. End points were probability of graft survival (correct classification rate [CCR]) and nonsurvival (minimum sensitivity [MS]). The final model is a rule‐based system for facilitating the decision about the most appropriate D‐R matching. Models designed for KCH had excellent prediction capabilities for both 3 months (CCR–area under the curve [AUC] = 0.94; MS‐AUC = 0.94) and 12 months (CCR‐AUC = 0.78; MS‐AUC = 0.82), almost 15% higher than the best obtained by other known scores such as Model for End‐Stage Liver Disease and balance of risk. Moreover, these results improve the previously reported ones in the multicentric MADR‐E database. In conclusion, the use of ANN for D‐R matching in LT in other health care systems achieved excellent prediction capabilities supporting the validation of these tools. It should be considered as the most advanced, objective, and useful tool to date for the management of waiting lists. Liver Transplantation 24 192–203 2018 AASLD.
Wnt Signaling Genes in Adipose Tissue and Skeletal Muscle of Humans With Different Degrees of Insulin Sensitivity.

CONTEXT The β-catenin-dependent Wnt signaling plays a role in adipogenesis, myogenesis, and glucose homeostasis. OBJECTIVE The aim of this study was to assess adipose tissue and skeletal muscle expression of Wnt/β-catenin signaling genes in a young healthy population according to insulin sensitivity and its regulation by hyperinsulinemia and free fatty acids. DESIGN We examined 117 male volunteers. The participants were divided into subgroups of high-insulin sensitivity (IS) and low-IS on the basis of a 2-hour euglycemic clamp. In 20 subjects, the clamp was prolonged to 6 hours. After 1 week, another 6-hour clamp, with Intralipid/heparin infusion, was performed. Tissue biopsies were performed before each clamp and after 6-hour clamps. Additionally, we collected muscle biopsies from another group of 16 male subjects for cell cultures. Myotubes were treated with insulin separately and in combination with palmitate. RESULTS We found decreased adipose tissue WNT10B, FZD1/8, LRP5, DVL2, CTNN1B, TCF7L2, and AXIN2 and increased muscle WNT10B, FZD1/8, LRP6, DVL1, GSK3B, CTNNB1, TCF7L2, AXIN2, MYC, and CCND1 expression in the low-IS group. Hyperinsulinemia resulted in a decrease in adipose tissue FZD4, LRP5/6, TCF7L2, and AXIN2 and an increase in muscle FZD1/8, DVL1/2/3, TCF7L2, AXIN2, and MYC expression. These changes disappeared after free fatty acid elevation. In myotubes, insulin increased the expression of FZD1, DVL2, CTNNB1, and TCF7L2, whereas palmitate abolished these effects. CONCLUSIONS The association of β-catenin-dependent Wnt signaling with insulin resistance is tissue specific. Observed changes might reflect a compensatory mechanism to increase muscle glucose uptake and to generate new fat cells in insulin-resistant conditions.
Relevant document retrieval using a spoken document

In this paper, we proposed a method of retrieving documents from the World Wide Web using a spoken document as a “key. ” This method can be viewed as a speech version of an ordinary relevant document retrieval, where a text document is used as a query of retrieval. Basically the retrieval is based on an automatic transcription of a spoken document using a speech recognizer. The difficult point of this task is that the automatic transcription contains many recognition errors, therefore we cannot trust keywords extracted from the automatic transcription using conventional method such as tf·idf. To solve this problem, we developed three methods. The first one is to measure relevance of a keyword to the spoken document by using Web documents retrieved using a Web search engine by specifying the keyword as a query. The second one is to compose a query from the selected keywords so that words derive from misrecognitions are excluded and similar words are gathered. The third one is to measure relevance of a downloaded Web document to the spoken document. The experimental results suggest that the proposed methods are promising for retrieving relevant documents of a spoken document.
The effect of ligand efficacy on the formation and stability of a GPCR-G protein complex

G protein-coupled receptors (GPCRs) mediate the majority of physiologic responses to hormones and neurotransmitters. However, many GPCRs exhibit varying degrees of agonist-independent G protein activation. This phenomenon is referred to as basal or constitutive activity. For many of these GPCRs, drugs classified as inverse agonists can suppress basal activity. There is a growing body of evidence that basal activity is physiologically relevant, and the ability of a drug to inhibit basal activity may influence its therapeutic properties. However, the molecular mechanism for basal activation and inhibition of basal activity by inverse agonists is poorly understood and difficult to study, because the basally active state is short-lived and represents a minor fraction of receptor conformations. Here, we investigate basal activation of the G protein Gs by the β2 adrenergic receptor (β2AR) by using purified receptor reconstituted into recombinant HDL particles with a stoichiometric excess of Gs. The β2AR is site-specifically labeled with a small, environmentally sensitive fluorophore enabling direct monitoring of agonist- and Gs-induced conformational changes. In the absence of an agonist, the β2AR and Gs can be trapped in a complex by enzymatic depletion of guanine nucleotides. Formation of the complex is enhanced by the agonist isoproterenol, and it rapidly dissociates on exposure to concentrations of GTP and GDP found in the cytoplasm. The inverse agonist ICI prevents formation of the β2AR-Gs complex, but has little effect on preformed complexes. These results provide insights into G protein-induced conformational changes in the β2AR and the structural basis for ligand efficacy.
Closed Form Jitter Analysis of Neuronal Spike Trains

Interval jitter and spike resampling methods are used to analyze the time scale on which temporal correlations occur. They allow the computation of jitter corrected cross correlograms and the performance of an associated statistically robust hypothesis test to decide whether observed correlations at a given time scale are significant. Currently used Monte Carlo methods approximate the probability distribution of coincidences. They require generating $N_{\rm MC}$ simulated spike trains of length $T$ and calculating their correlation with another spike train up to lag $\tau_{\max}$. This is computationally costly $O(N_{\rm MC} \times T \times \tau_{\max})$ and it introduces errors in estimating the $p$ value. Instead, we propose to compute the distribution in closed form, with a complexity of $O(C_{\max} \log(C_{\max}) \tau_{\max})$, where $C_{\max}$ is the maximum possible number of coincidences. All results are then exact rather than approximate, and as a consequence, the $p$-values obtained are the theoretically best possible for the available data and test statistic. In addition, simulations with realistic parameters predict a speed increase over Monte Carlo methods of two orders of magnitude for hypothesis testing, and four orders of magnitude for computing the full jitter-corrected cross correlogram.
Erythropoietin Enhances Hippocampal Response during Memory Retrieval in Humans

Although erythropoietin (Epo) is best known for its effects on erythropoiesis, recent evidence suggests that it also has neurotrophic and neuroprotective properties in animal models of hippocampal function. Such an action in humans would make it an intriguing novel compound for the treatment of neurological and psychiatric disorders. The current study therefore aimed to explore the effects of Epo on neural and behavioral measures of hippocampal function in humans using a functional magnetic resonance imaging paradigm. Volunteers were randomized to receive intravenous injection of Epo (40,000 IU) or saline in a between-subjects, double-blind, randomized design. Neural response during picture encoding and retrieval was tested 1 week later. Epo increased hippocampus response during picture retrieval (n = 11) compared with placebo (n = 12; p = 0.04) independent of changes in hematocrit. This is consistent with upregulation of hippocampal BDNF and neurotrophic actions found in animals and highlights Epo as a promising candidate for treatment of psychiatric disorders.
An efficient algorithm for tree pattern query minimization under broad integrity constraints

Purpose – Tree pattern is at the core of XML queries. The tree patterns in XML queries typically contain redundancies, especially when broad integrity constraints (ICs) are present and considered. Apparently, tree pattern minimization has great significance for efficient XML query processing. Although various minimization schemes/algorithms have been proposed, none of them can exploit broad ICs for thoroughly minimizing the tree patterns in XML queries. The purpose of this research is to develop an innovative minimization scheme and provide a novel implementation algorithm.Design/methodology/approach – Query augmentation/expansion was taken as a necessary first‐step by most prior approaches to acquire XML query pattern minimization under the presence of certain ICs. The adopted augmentation/expansion is also the course for the typical O(n4) time‐complexity of the proposed algorithms. This paper presents an innovative approach called allying to effectively circumvent the otherwise necessary augmentation st.
The clinical benefits of perioperative antioxidant vitamin therapy in patients undergoing cardiac surgery: a meta-analysis.

The clinical benefits of perioperative antioxidant vitamin therapy in cardiac patients remain controversial. Here, we conducted a meta-analysis to determine the strength of the evidence supporting the perioperative use of antioxidant vitamins in patients undergoing cardiac surgery. We searched 4 databases (PubMed, EMBASE, Science Citation Index and Cochrane Library) for randomized controlled trials that reported the effects of antioxidant vitamin therapy on patients undergoing cardiac surgery until 6 June 2016. Risk ratio (RR) or mean difference (MD) and its 95% confidence interval (95% CI) served as the summarized results. Heterogeneity among included studies was evaluated using the I2 statistic, which help determine which effect model to apply. We constructed a funnel plot to assess the existence of publication bias. Sensitivity analyses were also conducted to evaluate the robustness of the outcomes. Twelve trials with 1584 cardiac patients were included. Compared with placebo or no antioxidant vitamin therapy, administration of antioxidant vitamin therapy resulted in a reduction in postoperative atrial fibrillation (POAF) (RR 0.55, 95% CI 0.42, 0.73, P < 0.0001), duration of hospital stay (MD -0.68, 95% CI -0.98, -0.39, P < 0.00001), intensive care unit length of stay (MD -0.21, 95% CI -0.30, -0.12, P < 0.00001) and intubation time (MD -2.41, 95% CI -3.83, -0.98, P = 0.001). Our results also showed a trend towards a decrease in postoperative complications (RR 0.72, 95% CI 0.48, 1.08, P = 0.11) and duration of POAF (MD -1.950, 95% CI -3.28, 0.29, P = 0.10). This meta-analysis demonstrated that perioperative antioxidant vitamin therapy in patients undergoing cardiac surgery can reduce the incidence of POAF, duration of hospital stay, intensive care unit length of stay and intubation time.
EXPONENTIAL INEQUALITIES AND FUNCTIONAL ESTIMATIONS FOR WEAK DEPENDENT DATA: APPLICATIONS TO DYNAMICAL SYSTEMS

We estimate density and regression functions for weak dependent data. Using an exponential inequality obtained by Dedecker and Prieur (New dependence coefficients. Examples and applications to statistics, Th. Rel. Fields132 (2005)) and by the author (Exponential inequalities and estimation of conditional probabilities, in Lect. Notes in Stat., Vol. 187 (Springer, 2006)), we control the deviation between the estimator and the function itself. These results are applied to a large class of dynamical systems and lead to estimations of invariant densities and on the mapping itself.
Enhancement of CD8+ T-cell memory by removal of a vaccinia virus nuclear factor-κB inhibitor

Factors influencing T‐cell responses are important for vaccine development but are incompletely understood. Here, vaccinia virus (VACV) protein N1 is shown to impair the development of both effector and memory CD8+ T cells and this correlates with its inhibition of nuclear factor‐κB (NF‐κB) activation. Infection with VACVs that either have the N1L gene deleted (vΔN1) or contain a I6E mutation (vN1.I6E) that abrogates its inhibition of NF‐κB resulted in increased central and memory CD8+ T‐cell populations, increased CD8+ T‐cell cytotoxicity and lower virus titres after challenge. Furthermore, CD8+ memory T‐cell function was increased following infection with vN1.I6E, with more interferon‐γ production and greater protection against VACV infection following passive transfer to naive mice, compared with CD8+ T cells from mice infected with wild‐type virus (vN1.WT). This demonstrates the importance of NF‐κB activation within infected cells for long‐term CD8+ T‐cell memory and vaccine efficacy. Further, it provides a rationale for deleting N1 from VACV vectors to enhance CD8+ T‐cell immunogenicity, while simultaneously reducing virulence to improve vaccine safety.
Sphingolipid‐free Leishmania are defective in membrane trafficking, differentiation and infectivity

Sphingolipids are structural components of the eukaryotic plasma membrane that are involved, together with cholesterol, in the formation of lipid microdomains (rafts). Additionally, sphingolipid metabolites have been shown to modulate a wide variety of cellular events, including differentiation and apoptosis. To investigate the role of de novo sphingolipid biosynthesis in Leishmania, we have focused on serine palmitoyltransferase (SPT), which catalyses the first, rate‐limiting step in the synthetic pathway. Genetic ablation of one SPT subunit, LmLCB2, yields viable null parasites that can no longer synthesize ceramide and sphingolipids de novo. Unexpectedly, LmLCB2 expression (and sphingolipid biosynthesis) is stage regulated in Leishmania, being undetectable in intramacrophage parasites. As expected from this observation, the LmLCB2 null mutants maintain infectivity in vivo. However, they are compromised in their ability to form infective extracellular parasites, correlating with a defect in association of the virulence factor, leishmanolysin or GP63, with lipid rafts during exocytosis and an observed relocalization of a second virulence factor, lipophosphogycan, during differentiation. Thus, de novo sphingolipid biosynthesis is critical for membrane trafficking events in extracellular Leishmania but has at best a minor role in intracellular pathogenesis.
Incidental magnetization transfer contrast by fat saturation preparation pulses in multislice look‐locker echo planar imaging

In this study, it is demonstrated that fat saturation (FS) preparation (prep) pulses generate incidental magnetization transfer contrast (MTC) in multislice Look‐Locker (LL) imaging. It is shown that frequency‐selective FS prep pulses can invoke MTC through the exchange between free and motion‐restricted protons. Simulation reveals that the fractional signal loss by these MTC effects is more severe for smaller flip angles (FAs), shorter repetition times (TRs), and greater number of slices (SN). These incidental MTC effects result in a signal attenuation at a steady state (up to 30%) and a T1 measurement bias (up to 20%) when using inversion recovery (IR) LL echo‐planar imaging (EPI) sequences. Furthermore, it is shown that water‐selective MRI using binomial pulses has the potential to minimize the signal attenuation and provide unbiased T1 measurement without fat artifacts in MR images. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Classifying Facial Gestures in Presence of Head Motion

This paper addresses the problem of automatic facial gestures recognition in an interactive environment. Automatic facial gestures recognition is a difficult problem in computer vision, and most of the work has focused on inferring facial gestures in the context of a static head. In the paper we address the challenging problem of recognizing the facial expressions of a moving head. We present a systematic framework to analyze and classify the facial gestures with the head movement. Our system includes a 3D head pose estimation method to recover the global head motion. After estimating the head pose, the human face is modeled by a collection of face’s regions. These regions represent the face model used for locating and extracting temporal facial features. We propose using a locally affine motion model to represent extracted motion fields. The classification consists of a graphical model for robustly representing the dependencies of the selected facial regions and the support vector machine. Our experiments show that this approach could classify human expressions in interactive environments accurately.
Identification of Secretory Proteins in Mycobacterium tuberculosis Using Pseudo Amino Acid Composition

Tuberculosis is killing millions of lives every year and on the blacklist of the most appalling public health problems. Recent findings suggest that secretory protein of Mycobacterium tuberculosis may serve the purpose of developing specific vaccines and drugs due to their antigenicity. Responding to global infectious disease, we focused on the identification of secretory proteins in Mycobacterium tuberculosis. A novel method called MycoSec was designed by incorporating g-gap dipeptide compositions into pseudo amino acid composition. Analysis of variance-based technique was applied in the process of feature selection and a total of 374 optimal features were obtained and used for constructing the final predicting model. In the jackknife test, MycoSec yielded a good performance with the area under the receiver operating characteristic curve of 0.93, demonstrating that the proposed system is powerful and robust. For user's convenience, the web server MycoSec was established and an obliging manual on how to use it was provided for getting around any trouble unnecessary.
PROGRAMMING PROGRAMMING Pivot Tracing : Dynamic

Rodrigo Fonseca is an Assistant Professor at Brown University’s Computer Science Department. He holds a PhD from UC Berkeley, and prior to Brown was a visiting researcher at Yahoo! Research. He is broadly interested in networking, distributed systems, and operating systems. His research involves seeking better ways to build, operate, and diagnose distributed systems, including large-scale Internet systems, cloud computing, and mobile computing. He is currently working on dynamic tracing infrastructures for these systems, on new ways to leverage network programmability, and on better ways to manage energy usage in mobile devices. rfonseca@cs.brown. edu Pivot Tracing is a monitoring framework for distributed systems that can seamlessly correlate statistics across applications, components, and machines at runtime without needing to change or redeploy system code. Users can define and install monitoring queries on-the-fly to collect arbitrary statistics from one point in the system while being able to select, filter, and group by events meaningful at other points in the system. Pivot Tracing does not correlate cross-component events using expensive global aggregations, nor does it perform offline analysis. Instead, Pivot Tracing directly correlates events as they happen by piggybacking metadata alongside requests as they execute—even across component and machine boundaries. This gives Pivot Tracing a very low runtime overhead—less than 1% for many cross-component monitoring queries.
11β-Hydroxysteroid Dehydrogenase Type 1 Expression Is Increased in the Aged Mouse Hippocampus and Parietal Cortex and Causes Memory Impairments

Increased neuronal glucocorticoid exposure may underlie interindividual variation in cognitive function with aging in rodents and humans. 11β-Hydroxysteroid dehydrogenase type 1 (11β-HSD1) catalyzes the regeneration of active glucocorticoids within cells (in brain and other tissues), thus amplifying steroid action. We examined whether 11β-HSD1 plays a role in the pathogenesis of cognitive deficits associated with aging in male C57BL/6J mice. We show that 11β-HSD1 levels increase with age in CA3 hippocampus and parietal cortex, correlating with impaired cognitive performance in the water maze. In contrast, neither circulating corticosterone levels nor tissue corticosteroid receptor expression correlates with cognition. 11β-HSD1 elevation appears causal, since aging (18 months) male transgenic mice with forebrain-specific 11β-HSD1 overexpression (∼50% in hippocampus) exhibit premature age-associated cognitive decline in the absence of altered circulating glucocorticoid levels or other behavioral (affective) deficits. Thus, excess 11β-HSD1 in forebrain is a cause of as well as a therapeutic target in memory impairments with aging.
The Software Design Process as a Series of Rotating Subject Pairs

In this paper, we focus on two videos of professional software designers working at the whiteboard on a provided design prompt. We present two related approaches: for the first, we perform a protocol analysis of the sessions, describing which subjects the designers discussed at each point in their design process. For the second, we closely track the ideas that the designers generated, how those ideas related to one another, and which high-level subjects they pertained to. Based on the data gathered, we provide insight into the subconscious strategies that drive the software design process. In particular, we observe that the software designers we studied tended to consider two highlevel subjects at a time, and that they regularly rotated through a mental list of known subjects in an effort to appropriately balance the tradeoffs between them.
Revisiting Priorities: Improving MIR Evaluation Practices

While there is a consensus that evaluation practices in music informatics (MIR) must be improved, there is no consensus about what should be prioritised in order to do so. Priorities include: 1) improving data; 2) improving ﬁgures of merit; 3) employing formal statistical testing; 4) employing cross-validation; and/or 5) implementing transparent, central and immediate evaluation. In this position paper, I argue how these priorities treat only the symptoms of the problem and not its cause: MIR lacks a formal evaluation framework relevant to its aims. I argue that the principal priority is to adapt and integrate the formal de-sign of experiments (DOE) into the MIR research pipeline. Since the aim of DOE is to help one produce the most reliable evidence at the least cost, it stands to reason that DOE will make a signiﬁcant contribution to MIR. Accom-plishing this, however, will not be easy, and will require far more effort than is currently being devoted to it.