Miracle-dz/UniFAR-FTUs huggingface dataset:
Checkpoint inhibitors in the treatment of urological malignancies

Checkpoint inhibitors are monoclonal antibodies attach to several different receptors on T-cells or tumour cells expressing receptors for cytotoxic T-lymphocyte antigen 4 (CTLA-4), programmed death-1 (PD-1) and their ligand (PD-L1). Since 2010, numerous trials on different tumour types have been conducted, which was resulted in these drugs being approved for the treatment of melanoma, lung cancer, Hodgkin's lymphoma and head and neck cancers. Urological cancers, especially urothelial and renal-cell carcinomas, are immunogenic tumours. Since the late 70s, the bacillus Calmette-Gurin (BCG) vaccine has been used for intravesical instillation in non-muscle invasive bladder cancer from the mid-90s up until the discovery of tyrosine kinase inhibitors (TKIs) in 2007, interleukin-2 (IL-2) and interferon alpha (IFNα), which were the standard of care for metastatic renal-cell cancer. Two checkpoint inhibitors are already approved by the Food and Drug Administration: atezolizumab for metastatic urothelial cancer and nivolumab for metastatic renal-cell carcinoma. There are many drugs are in different phases of clinical development. Here we review the current status of checkpoint inhibitors in the treatment of urological tumours.
MASC: Ultra-low energy multiple-access single-charge TCAM for approximate computing

Memory-based computing using associative memory has emerged as a promising solution to reduce the energy consumption of important classes of streaming applications such as multimedia by avoiding redundant computations. In associative memory, a set of frequent patterns that represent basic functions are pre-stored in ternary content addressable memory (TCAM) and reused. The primary limitation to using associative memory in modern parallel processors is the large search energy required by TCAMs. In TCAMs, all match rows, except hit rows, precharge and discharge in every search operation, resulting in high and undesirable energy consumption. In this paper, we propose a new multiple-access single-charge (MASC) TCAM architecture which is capable of searching TCAM contents multiple times with a single precharging cycle. In contrast to previous designs, the MASC TCAM keeps the match-line voltage of all miss-rows high and uses their charge for the next search operation, while only the hit rows discharge. We use a periodic refresh scheme to guarantee the accuracy of the search. We also implement a new type of approximate associative memory by setting longer refresh times for MASC TCAMs, which yields search results within 1-2 bit Hamming distances of the exact result. Our evaluation on AMD Southern Island GPU shows that using MASC associative memory can improve the average GPGPU energy efficiency by 36.6%, 40.2% and 39.4% for exact matching, selective 1-HD and 2-HD approximations respectively, with acceptable quality of service (PSNR>30dB). These energy savings are 1.8X and 1.6X higher than GPGPU using exact matching TCAM and approximation TCAM that uses voltage overscaling, respectively.
Cooperative requirement of the Gli proteins in neurogenesis

The Gli proteins are critical components of multiple processes in development, homeostasis and disease, including neurogenesis and tumorigenesis. However, it is unclear how the Gli code, the sum of their combinatorial positive and negative functions, dictates cell fate and behavior. Using an antisense approach to knockdown gene function in vivo, we find that each of the three Gli proteins is required for the induction of all primary neurons in the amphibian neural plate and regulates the bHLH/Notch neurogenic cascade. Analyses of endogenous Gli function in Gli-mediated neurogenesis and tumorigenesis, and in animal cap assays, reveal specific requirements that are context specific. Nuclear colocalization and binding studies suggest the formation of complexes, with the first two zinc fingers of the Gli five zinc-finger domain acting as a protein-protein interaction site. The Gli proteins therefore appear to form a dynamic physical network that underlies cooperative function, greatly extending the combinatorial possibilities of the Gli code, which may be further fine-tuned in cell fate specification by co-factor function.
Twin tree hierarchy: a regularized approach to construction of signature matrices for overloaded CDMA

Overloaded code division multiple access being the only means of the capacity extension for conventional code division multiple access accommodates more number of signatures than the spreading gain. Recently, ternary Signature Matrices with Orthogonal Subsets (SMOS) has been proposed, where the capacity maximization is 200%. The proposed multi-user detector using matched filter exploits the twin tree hierarchy of correlation among the subsets to guarantee the errorless recovery. In this paper, we feature the non-ternary version of SMOS (i.e., 2k-ary SMOS) of same capacity, where the binary alphabets in all the k constituent (orthogonal) subsets are unique. Unlike ternary, the tree hierarchy for 2k-ary SMOS is non-uniform. However, the errorless detection of the multi-user detector remains undeviated. For noisy transmission, simulation results show the error performance of the right child for each subset of 2k-ary to be significantly improved over the left. The optimality of the right child of the largest (Hadamard) subset is also discovered. At higher loading, for larger and smaller subsets the superiority is reported for the 2k-ary and ternary, respectively, and the counter-intuitive deviations observed for the lower loading scenarios are logically explained. For the overall capacity maximization being 150%, superiority is featured by the 2k-ary, but beyond, it becomes a conditional entity. Copyright © 2016 John Wiley & Sons, Ltd.
Lipoprotein-associated phospholipase A2, C-reactive protein, and coronary artery disease in individuals with type 1 diabetes and macroalbuminuria

Given the paucity of data in type 1 diabetes concerning lipoprotein-associated phospholipase A 2 (Lp-PLA2), we examined its prospective relationship with coronary artery disease (CAD), as well as the effect of modification by C-reactive protein (CRP) and haptoglobin genotype, in individuals with type 1 diabetes who are at an increased risk for CAD due to also having macroalbuminuria (n=96). Although Lp-PLA2 activity was univariately predictive of CAD (HR=1.54 per SD, p=0.009), this relationship was not significant after covariate adjustment (p=0.59). There was a significant interaction between Lp-PLA2 and CRP (p=0.02), i.e. those with both markers greater than the median level were more likely to have a CAD event than those persons with low levels of both (HR=2.89, p=0.06). When stratified by haptoglobin genotype, Lp-PLA2 was predictive of CAD in persons with the 2/1 (HR=2.40, p=0.05), but not 2/2 (HR=0.66, p=0.27), genotype. The association between Lp-PLA2 activity and CAD differs by CRP and haptoglobin genotype in this group of persons with type 1 diabetes and macroalbuminuria.
Trauma and Addiction Experiences of African American Women

Substance abuse affects African American women at an increasingly alarming rate. The interaction of substance abuse and traumatic events requires exploration. For many African American women, early life trauma plays a critical role in how and when they fall victim to the ravages of substance abuse. This article aboutaphenomenological study ofi SAfrican American women uses intense narratives to disclose experiences of incest, rape, abuse, and other horrors that led to drug and alcohol use to extinguish pain. The themes includefamily history ofsubstance abuse, lack of a caring childhood environment, pain resulting from trauma, and coping and recovery. The womens'stories provide insightsfor nurses in practice and research related to the psychosocial health of women.
Wall Shear Stress Measurement Using Phase Contrast Magnetic Resonance Imaging With Phase Contrast Magnetic Resonance Angiography in Arteriovenous Polytetrafluoroethylene Grafts

Purpose: The purpose of the present article was to determine the changes in luminal vessel area, blood flow, and wall shear stress in both the inflow artery and the venous stenosis of arteriovenous polytetrafluoroethylene (PTFE) grafts. Methods and materials: Polytetrafluoroethylene grafts were placed from the carotid artery to the ipsilateral jugular vein in 8 castrated juvenile male pigs. Contrast-enhanced magnetic resonance angiography (MRA) with cine phase-contrast magnetic resonance imaging (MRI) was performed 2 weeks after graft placement. Results: The mean wall shear stress at the venous stenosis was 4 times higher than the control vein, while the inflow artery was only 2-fold higher. By day 14, venous stenosis had formed, which was characterized by narrowed area and elevated blood flow. Conclusion: By day 14, there is venous stenosis formation in porcine arteriovenous PTFE grafts with increased shear stress with decreased area when compared to control vein.
Face Recognition: A Hybrid Neural Network Approach

Faces represent complex, multidimensional, meaningful visual stimuli and developing a computa- tional model for face recognition is difficult (Turk and Pentland, 1991). We present a hybrid neural network solution which compares favorably with other methods. The system combines local image sam- pling, a self-organizing map neural network, and a convolutional neural network. The self-organizing map provides a quantization of the image samples into a topological space where inputs that are nearby in the original space are also nearby in the output space, thereby providing dimensionality reduction and invariance to minor changes in the image sample, and the convolutional neural network provides for partial invariance to translation, rotation, scale, and deformation. The convolutional network extracts successively larger features in a hierarchical set of layers. We present results using the Karhunen-Loe transform in place of the self-organizing map, and a multilayer perceptron in place of the convolu- tional network. The Karhunen-Lo` eve transform performs almost as well (5.3% error versus 3.8%). The multilayer perceptron performs very poorly (40% error versus 3.8%). The method is capable of rapid classification, requires only fast, approximate normalization and preprocessing, and consistently exhibits better classification performance than the eigenfaces approach (Turk and Pentland, 1991) on the database considered as the number of images per person in the training database is varied from 1 to 5. With 5 images per person the proposed method and eigenfaces result in 3.8% and 10.5% error respectively. The recognizer provides a measure of confidence in its output and classification error approaches zero when rejecting as few as 10% of the examples. We use a database of 400 images of 40 individuals which con- tains quite a high degree of variability in expression, pose, and facial details. We analyze computational complexity and discuss how new classes could be added to the trained recognizer.
Relative Clauses in Heritage Russian: Fossilization or Divergent Grammar?

This paper has two related goals. First, it explores the knowledge of relative clauses in several groups of Russian speakers, children and adults, thus adding new results to the growing body of literature on the processing of relative clauses across languages and populations of speakers. Second, it uses the results from a relative clause study to address the issue of linguistic knowledge in the poorly understood population known as heritage speakers. Heritage speakers are early sequential bilinguals whose first language is a minority language of the society in which they grow up; they learn this language before they acquire the majority language, but the latter then becomes their dominant language. According to a widely accepted definition proposed by Guadelupe Valdes, a heritage speaker of language L is someone who grew up hearing and possibly speaking L in
Particle swarm optimization

A concept for the optimization of nonlinear functions using particle swarm methodology is introduced. The evolution of several paradigms is outlined, and an implementation of one of the paradigms is discussed. Benchmark testing of the paradigm is described, and applications, including nonlinear function optimization and neural network training, are proposed. The relationships between particle swarm optimization and both artificial life and genetic algorithms are described.
A Methodology for Extending Focusing Frameworks

We address the problem of how to develop and assess algorithms for tracking local focus and for proposing referents of pronouns. Previous focusing research has not adequately addressed the processing of complex sentences. We discuss issues involved in processing complex sentences and review a methodology used by other researchers to develop their focusing frameworks. We identify difficulties with that methodology and difficulties with using a corpus analysis to extend focusing frameworks to handle complex sentences. We introduce a new methodology for extending focusing frameworks, which involves two steps. In the first step, a set of systematically constructed texts are used to identify an extension of the focusing framework to handle a particular kind of complex sentence. In the second step, a corpus analysis is used to confirm the extension. We explain how our methodology overcomes the difficulties faced by other approaches.
Application of meta-transcriptomics and -proteomics to analysis of in situ physiological state

Analysis of the growth-limiting factor or environmental stressors affecting microbes in situ is of fundamental importance but analytically difficult. Microbes can reduce in situ limiting nutrient concentrations to sub-micromolar levels, and contaminated ecosystems may contain multiple stressors. The patterns of gene or protein expression by microbes in nature can be used to infer growth limitations, because they are regulated in response to environmental conditions. Experimental studies under controlled conditions in the laboratory provide the physiological underpinnings for developing these physiological indicators. Although regulatory networks may differ among specific microbes, there are some broad principles that can be applied, related to limiting nutrient acquisition, resource allocation, and stress responses. As technologies for transcriptomics and proteomics mature, the capacity to apply these approaches to complex microbial communities will accelerate. Global proteomics has the particular advantage that it reflects expressed catalytic activities. Furthermore, the high mass accuracy of some proteomic approaches allows mapping back to specific microbial strains. For example, at the Rifle IFRC field site in Western Colorado, the physiological status of Fe(III)-reducing populations has been tracked over time. Members of a “subsurface clade” within the Geobacter predominated during carbon amendment to the subsurface environment. At the functional level, proteomic identifications produced inferences regarding (i) temporal changes in anabolism and catabolism of acetate, (ii) the onset of N2 fixation when N became limiting, and (iii) expression of phosphate transporters during periods of intense growth. The application of these approaches in situ can lead to discovery of novel physiological adaptations.
Effect of Vacuum Frying on Changes in Quality Attributes of Jackfruit (Artocarpus heterophyllus) Bulb Slices

The effect of frying temperatures and durations on the quality of vacuum fried jackfruit (JF) chips was evaluated. Moisture content and breaking force of JF chips decreased with increase in frying temperature and time during vacuum frying whereas the oil content increased. The frying time for JF chips was found to be 30, 25, and 20 minutes at 80, 90, and 100°C, respectively. JF chips fried at higher temperature resulted in maximum shrinkage (48%). The lightness in terms of hunter L * value decreased significantly (P < 0.05) during frying. Sensory evaluation showed maximum acceptability for JF chips fried at 90°C for 25 min. Frying under vacuum at lower temperatures was found to retain bioactive compounds such as total phenolics, total flavonoids, and total carotenoids in JF chips. Almost 90% of carotenoids were lost from the samples after 30 min of frying at 100°C.
In-hospital mortality after adult living donor liver transplantation : single-center experience

Objectives: To identify the preoperative risk factors associated with in-hospital mortality after living donor liver transplantation (LDLT). Materials and methods: Between November 2001 and May 2015, LDLT were performed in 276 consecutive adult recipients in our hospital. Medical data were collected from the Chinese Liver Transplant Registry. Indications for transplantation and causes of death were analyzed. Potential risk factors for in-hospital mortality after LDLT were analyzed by using univariate and multivariate in this study. Results: From November 2001 to May 2015, 276 consecutive adult recipients underwent LDLT in our hospital. Recipients who received dual grafts or repeat transplant were excluded. A total of 263 LDLT recipients were indentified with an overall in-hospital mortality of 13.7%. The most frequent cause of death was infections (47.2%), which was followed by multiple organ failure (25.0%) and renal failure (8.3%). Associated risk factors included D-MELD more than 600 (P<0.05), preoperative ICU stay (P<0.05) and the Charlson comorbidity index of 1 or higher (P<0.05). Conclusion: Our study indentified that being ICU-bound before LDLT, with a D-MELD score more than 600 and the CCI of 1 or higher were the independent factors that associated with in-hospital mortality after LDLT. These findings could help in patients consulting, donor selection and decision making.
The Role of Autophagy in Kidney Inflammatory Injury via the NF-κB Route Induced by LPS

Acute kidney injury (AKI) is a systemic inflammatory response syndrome associated with poor clinical outcomes. No treatments effective for AKI are currently available. Thus, there is an urgent need of development of treatments effective for AKI. Autophagy, an intracellular proteolytic system, is induced in renal cells during AKI. However, whether autophagy is protective or injurious for AKI needs to be clearly clarified. We addressed this question by pharmacological inhibition of autophagy using a mouse model of lipopolysaccharide (LPS) induced-AKI. We found that autophagy was induced in renal cortex of mice during LPS-induced AKI as reflected by a dose-and time-dependent increased accumulation of light chain 3-II (LC3-II), the common marker of autophagy, compared to that of control group; 2) the occurrence of intensive, punctate and increased immunohistochemical staining image of LC3-II in renal cortex; 3) the significant increase in the expression levels of Beclin-1, another key marker of autophagy; 4) the significantly increased levels of plasma urea and serum creatinine and 5) the significant increase in autophagagosome area ratio. We observed that 3-methyladenine (3-MA), a pharmacological inhibitor of autophagy, blocked autophagy flux, alleviated AKI and protected against LPS-induced AKI. LPS triggered kidney inflammation by activation of the canonical NF-κB pathway. This route can be modulated by autophagy. Activation of the canonical NF-κB pathway was reduced in 3-MA+LPS as compared to that in LPS-treated group of mice. Mice pretreated with 3-MA before exposure to LPS showed a reduction in p65 phosphorylation, resulting in the accumulation of ubiquitinated IκB. In conclusion, impairment of autophagy ameliorates LPS-induced inflammation and decreases kidney injury. The accumulation of ubiquitinated IκB may be responsible for this effect.
Comparison of Three Commercially Available Dengue NS1 Antigen Capture Assays for Acute Diagnosis of Dengue in Brazil

Background Dengue is associated with explosive urban epidemics and has become a major public health problem in many tropical developing countries, including Brazil. The laboratory diagnosis of dengue can be carried out using several approaches, however sensitive and specific assays useful to diagnose in the early stage of fever are desirable. The flavivirus non-structural protein NS1, a highly conserved and secreted glycoprotein, is a candidate protein for rapid diagnosis of dengue in endemic countries. Methodology/Principal Findings We aimed to evaluate the potential use of 3 commercial kits in a panel of 450 serum samples for early diagnosis of dengue in Brazil. The PanBio Early ELISA (PanBio Diagnostics) showed a sensitivity of 72.3% (159/220) and a specificity of 100%, while the sensitivity of the Platelia™ NS1 assay (Biorad Laboratories) was 83.6% (184/220). However, the highest sensitivity (89.6%; 197/220) was obtained by using the NS1 Ag Strip (Biorad Laboratories). A lower sensitivity was observed in DENV-3 cases by all 3 kits. Serum positive by virus isolation were more often positive than cases positive by RT-PCR by all three assays and a higher detection rate was observed during the first four days after the onset of the symptoms. The presence or absence of IgM showed no influence in the confirmation by the pan-E Early ELISA (P = 0,6159). However, a higher confirmation by both Platelia™ NS1 (Biorad) and Dengue NS1 Ag Strip (Biorad) in the absence of IgM was statistically significant (P<0,0001 and P = 0,0008, respectively). Only the Platelia™ NS1 test showed a higher sensitivity in confirming primary infections than secondary ones. Conclusions/Significance The results indicate that commercial kits of dengue NS1 antigen are useful for the laboratory diagnosis of acute primary and secondary dengue. It can be used in combination with the MAC-ELISA for case detection and as screening test to complement viral isolation.
Multilinear models of single cell responses in the medial nucleus of the trapezoid body

The representation of acoustic stimuli in the brainstem forms the basis for higher auditory processing. While some characteristics of this representation (e.g. tuning curve) are widely accepted, it remains a challenge to predict the firing rate at high temporal resolution in response to complex stimuli. In this study we explore models for in vivo, single cell responses in the medial nucleus of the trapezoid body (MNTB) under complex sound stimulation. We estimate a family of models, the multilinear models, encompassing the classical spectrotemporal receptive field and allowing arbitrary input-nonlinearities and certain multiplicative interactions between sound energy and its short-term auditory context. We compare these to models of more traditional type, and also evaluate their performance under various stimulus representations. Using the context model, 75% of the explainable variance could be predicted based on a cochlear-like, gamma-tone stimulus representation. The presence of multiplicative contextual interactions strongly reduces certain inhibitory/suppressive regions of the linear kernels, suggesting an underlying nonlinear mechanism, e.g. cochlear or synaptic suppression, as the source of the suppression in MNTB neuronal responses. In conclusion, the context model provides a rich and still interpretable extension over many previous phenomenological models for modeling responses in the auditory brainstem at submillisecond resolution.