Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential effects of patient symptom subtypes on informal hospice caregiver depression

ABSTRACT Objective: Researchers sought to determine the extent to which burden related to patients' symptom subtypes could predict informal hospice caregiver depression, and to illustrate the differences between caregivers who experience suicidal ideation and those who do not. Method: Informal caregivers recruited from a not-for-profit community-based hospice agency participated in a cross-sectional survey. Self-report questionnaires assessed caregiver burden associated with patient symptomatology (via a modified version of the Memorial Symptom Assessment Scale–Short Form) and caregiver depressive symptoms, including suicidal ideation (measured by the Patient Health Questionnaire–9). Multiple regressions evaluated the unique predictability of patients' symptom subtypes on caregiver depression. Exploratory analyses examined mean differences of study variables between participants who did and did not endorse suicidal ideation. Results: Caregiver burden related to patients' psychological symptoms accounted for significant variance in caregiver depression scores when controlling for burden related to physical symptoms. Among 229 caregivers (M age = 61.4 years), 12 reported suicidal ideation, where 6 of the 12 were male, despite male caregivers comprising less than 20% of the total sample. Significance of results: Burden associated with patients' psychological symptoms uniquely contributed to caregiver depression, further highlighting the clinical utility and necessity for hospice providers to address the emotional needs of patients and their caregivers alike. Developing clinical procedures to identify and respond to such needs would not only behoove hospice agencies, but it would likely enhance the caregiving experience holistically, which might be particularly imperative for male caregivers.
Why are tropical mountain passes ‘low’ for some species? Genetic and stable-isotope tests for differentiation, migration, and expansion in elevational generalist songbirds

Most tropical bird species have narrow elevational ranges, likely reflecting climatic specialization. This is consistent with Janzen’s Rule, the tendency for mountain passes to be effectively ‘higher’ in the tropics. Hence, those few tropical species that occur across broad elevational gradients raise questions. Are they being sundered by diversifying selection along the gradient? Does elevational movement cause them to resist diversification or specialization? Have they recently expanded, suggesting that elevational generalism is short-lived in geological time? Here we tested for differentiation, movement, and expansion in four elevational generalist songbird species on the Andean west slope. We used morphology and mtDNA to test for genetic differentiation between high- and low-elevation populations. Morphology differed for House Wren (Troglodytes aedon) and Hooded Siskin (Spinus magellanicus), but not for Cinereous Conebill (Conirostrum cinereum) and Rufous-collared Sparrow (Zonotrichia capensis), respectively. mtDNA was structured by elevation only in Z. capensis. To test for elevational movements, we measured hydrogen isotope (δ2H) values of metabolically inert feathers and metabolically active liver. δ2H data indicated elevational movements by two tree- and shrub-foraging species with moderate-to-high vagility (C. cinereum and S. magellanicus), and sedentary behavior by two terrestrial-foraging species with low-to-moderate vagility (T. aedon and Z. capensis). In S. magellanicus, elevational movements and lack of mtDNA structure contrast with striking morphological divergence, suggesting strong diversifying selection on body proportions across the ∼50 km gradient. All species except C. cinereum exhibited mtDNA-haplotype variation consistent with recent population expansion across the elevational gradient.In sum,three out of four elevational generalist species underwent genetic divergence despite gene flow, two of four make seasonal elevational movements, and three of four have recently expanded. In different ways, each species defies the tendency for tropical birds to have long-term stable distributions and sedentary habits. We conclude that tropical elevational generalism is rare due to evolutionary instability.
Chloride resistance of concrete containing palm oil fuel ash

Experimental study was conducted to investigate the chloride resistance of concrete containing palm oil fuel ash (POFA). Ground POFA was used to partially replace Portland cement Type I, by 20% by weight of binder in order to prepare POFA concrete. Water cement ratio of 0.28 was used and high water reducing admixture was added to maintain workability. POFA concrete was investigated and tested for compressive strength at ages of 7, 28 and 90 days. Rapid chloride penetration test (ASTM C1202) and salt ponding test (ASTM C1543) were conducted on standard concrete specimens to investigate the chloride resistance of concrete. The results showed that the compressive strength of POFA concrete was improved comparing with plain concrete. The results of chloride penetration tests revealed that significant improvement in terms of chloride resistance could be obtained by using 20 % of ground POFA in concrete mix as cementing replacement material.
Hippocampal and entorhinal cortex volume changes in Alzheimer's disease patients and mild cognitive impairment subjects

Hippocampal and entorhinal cortex as scanned in Magnetic Resonance Imaging (MRI), are two of the most commonly used Regions of Interest (ROIs) for the assessment of Alzheimer's disease (AD). Both structures are used for the classification between Normal Controls (NC), Mild Cognitive Impairment (MCI) and AD subjects and for the disease prognosis. The objective of this study was to evaluate how the volume of these two structures changes between the following groups: NC vs AD, NC vs MCI, MCI vs MCI converters (MCIc — subjects who had converted to AD within 48 months), and AD vs MCIc subjects. Both structures were significantly reduced in volume for MCIc and AD subjects compared to NC. For both MCI and MCIc groups, the atrophy rate was correlated for both structures. In AD subjects, entorhinal cortex was more affected by atrophy. In conclusion, structural MRI and volumetric measurements of the hippocampus and entorhinal cortex can be used as early signs for the assessment of AD, and this is in agreement with previous studies.
Comparative Effectiveness of Mesalamine, Sulfasalazine, Corticosteroids, and Budesonide for the Induction of Remission in Crohn's Disease: A Bayesian Network Meta-analysis

Background: Induction treatment of mild-to-moderate Crohn's disease is controversial. Purpose: To compare the induction of remission between different doses of mesalamine, sulfasalazine, corticosteroids, and budesonide for active Crohn's disease. Data sources: We identified randomized controlled trials from existing Cochrane reviews and an updated literature search in Medline, EMBASE, and CENTRAL to November 2015. Study selection: We included randomized controlled trials (n = 22) in adult patients with Crohn's disease that compared budesonide, sulfasalazine, mesalamine, or corticosteroids with placebo or each other, for the induction of remission (8–17 wks). Mesalamine (above and below 2.4 g/d) and budesonide (above and below 6 mg/d) were stratified into low and high doses. Data extraction: Our primary outcome was remission, defined as a Crohn's Disease Activity Index score <150. A Bayesian random-effects network meta-analysis was performed on the proportion in remission. Data synthesis: Corticosteroids (odds ratio [OR] = 3.80; 95% credible interval [CrI]: 2.48–5.66), high-dose budesonide (OR = 2.96; 95% CrI: 2.06–4.30), and high-dose mesalamine (OR = 2.29; 95% CrI: 1.58–3.33) were superior to placebo. Corticosteroids were similar to high-dose budesonide (OR = 1.21; 95% CrI: 0.84–1.76), but more effective than high-dose mesalamine (OR = 1.83; 95% CrI: 1.16–2.88). Sulfasalazine was not significantly superior to any therapy including placebo. Limitations: Randomized controlled trials that use a strict definition of induction of remission and disease severity at enrollment to assess effectiveness in treating mild-to-moderate Crohn's disease are limited. Conclusions: Corticosteroids and high-dose budesonide were effective treatments for inducing remission in mild-to-moderate Crohn's disease. High-dose mesalamine is an option among patients preferring to avoid steroids.
Achieving Fluency and Coherency in Task-oriented Dialog

We consider real world task-oriented dialog settings, where agents need to generate both fluent natural language responses and correct external actions like database queries and updates. We demonstrate that, when applied to customer support chat transcripts, Sequence to Sequence (Seq2Seq) models often generate short, incoherent and ungrammatical natural language responses that are dominated by words that occur with high frequency in the training data. These phenomena do not arise in synthetic datasets such as bAbI, where we show Seq2Seq models are nearly perfect. We develop techniques to learn embeddings that succinctly capture relevant information from the dialog history, and demonstrate that nearest neighbor based approaches in this learned neural embedding space generate more fluent responses. However, we see that these methods are not able to accurately predict when to execute an external action. We show how to combine nearest neighbor and Seq2Seq methods in a hybrid model, where nearest neighbor is used to generate fluent responses and Seq2Seq type models ensure dialog coherency and generate accurate external actions. We show that this approach is well suited for customer support scenarios, where agents' responses are typically script-driven, and correct external actions are critically important. The hybrid model on the customer support data achieves a 78% relative improvement in fluency scores, and a 130% improvement in accuracy of external calls.
Fatigue Related to Speech Processing in Children With Hearing Loss: Behavioral, Subjective, and Electrophysiological Measures.

Purpose The purpose of this study was to examine fatigue associated with sustained and effortful speech-processing in children with mild to moderately severe hearing loss. Method We used auditory P300 responses, subjective reports, and behavioral indices (response time, lapses of attention) to measure fatigue resulting from sustained speech-processing demands in 34 children with mild to moderately severe hearing loss (M = 10.03 years, SD = 1.93). Results Compared to baseline values, children with hearing loss showed increased lapses in attention, longer reaction times, reduced P300 amplitudes, and greater reports of fatigue following the completion of the demanding speech-processing tasks. Conclusions Similar to children with normal hearing, children with hearing loss demonstrate reductions in attentional processing of speech in noise following sustained speech-processing tasks-a finding consistent with the development of fatigue.
Kafka interfaces for composable streaming genomics pipelines

Modern sequencing machines produce order of a terabyte of data per day, which need subsequently to go through a complex processing pipeline. The standard workflow begins with a few independent, shared-memory tools, which communicate by means of intermediate files. Given the constant increase of the amount of data produced, this approach is proving more and more unmanageable, due to its lack of robustness and scalability. In this work we propose the adoption of stream computing to simplify the genomic pipeline, boost its performance and improve its fault-tolerance. We decompose the first steps of the genomic processing in two distinct and specialized modules (preprocessing and alignment) and we loosely compose them via communication through Kafka streams, in order to allow for easy composability and integration in the already existing Hadoop-based pipelines. The proposed solution is then experimentally validated on real data and shown to scale almost linearly.
Mobile Application Rating Prediction via Feature-Oriented Matrix Factorization

With the proliferation of mobile application (app) markets (e.g., Google Play, Apple App Store), predicting user preferences on apps becomes a challenging problem. Different from previous work, we assume that a user likes an app because he/she likes certain features of the app (e.g., permission, genre, topic). Based on this assumption, we propose a feature-oriented approach to predict user preferences on apps. Specifically, we transform the original app rating matrix to feature rating data and predict the unknown ratings on the features through a latent factor model, instead of directly predicting ratings on apps. The predicted user ratings on features can be used to generate the ratings on apps. Two integration methods are presented to give different significance for feature preferences. The approach has some obvious advantages: as it integrates feature information to analyze the details of user preference, it can generalize better as the feature rating data is denser, and improve the interpretation of the prediction of app ratings. Experimental results on a real-world dataset demonstrate the effectiveness of the proposed approach.
Convolutional Neural Networks for Phoneme Recognition

This paper presents a novel application of convolutional neural networks to phoneme recognition. The phonetic transcription of the TIMIT speech corpus is used to label spectrogram segments for training the convolutional neural network. A window of a fixed size slides over the spectrogram of the TIMIT utterances and the resulting spectrogram patches are assigned to the appropriate phone class by parsing TIMIT’s phone transcription. The convolutional neural network is the standard GoogLeNet implementation trained with stochastic gradient descent with mini batches. After training, phonetic rescoring is performed in the usual way to map the TIMIT phone set to the smaller standard set. Benchmark results are presented for comparison to other state-of-the-art approaches. Finally, conclusions and future directions with regard to extending the approach are discussed.
MRI With Liver-Specific Contrast for Surveillance of Patients With Cirrhosis at High Risk of Hepatocellular Carcinoma

Importance Current recommendations for patients with cirrhosis are to undergo surveillance for hepatocellular carcinoma (HCC) with ultrasonography (US) every 6 months. However, the sensitivity of US screening to detect early-stage HCC is suboptimal. Magnetic resonance imaging (MRI) with liver-specific contrast may detect additional HCCs missed by US in high-risk patients with cirrhosis. Objective To compare the HCC detection rate of US and MRI in patients with cirrhosis who are at high risk for HCC. Design, Setting, and Participants A prospective surveillance study of 407 patients with cirrhosis and an estimated annual risk of HCC greater than 5% who underwent 1 to 3 biannual screening examinations with paired US and liver-specific contrast-enhanced MRI at a tertiary care hospital between November 2011 and August 2014. All patients were followed-up with dynamic computed tomography (CT) at 6 months after the study. The confirmation of HCC was based on the results of histologic examination and/or typical CT images of HCC. Main Outcomes and Measures HCC detection rates and false-positive findings of US vs MRI. Results A total of 407 eligible patients received 1100 screenings with paired US and MRI. Hepatocellular carcinomas were diagnosed in 43 patients: 1 detected by US only, 26 by MRI only, 11 by both, and 5 were missed by both. The HCC detection rate of MRI was 86.0% (37/43), significantly higher than the 27.9% (12/43) of US (P < .001). Magnetic resonance imaging showed a significantly lower rate of false-positive findings than US (3.0% vs 5.6%; P = .004). Of the 43 patients with HCC, 32 (74.4%) had very early-stage HCC (a single nodule <2 cm), and 29 (67.4%) received curative treatments. The 3-year survival rate of the patients with HCC (86.0%) was not inferior to those without HCC (94.2%; hazard ratio, 2.26; 95% CI, 0.92-5.56; P = .08). Conclusions and Relevance In patients with cirrhosis at high-risk of HCC, screening that used MRI with liver-specific contrast resulted in a higher HCC detection rate and lower false-positive findings compared with US. With MRI screening, most of the cancers detected were at very early stage, which was associated with a high chance of curative treatments and favorable survival of patients. Whether surveillance with MRI would reduce mortality from HCC in high-risk patients requires further investigation. Trial Registration clinicaltrials.gov Identifier: NCT01446666
Effect of Human Learning on Performance of Cloud Applications

End users of cloud applications range from novice to expert depending on how experienced they are in using them. With repeated usage of an application, a user's think time gradually decreases, known as human learning phenomenon. This decrease impacts the system workload thereby affecting the application's transient performance. However, such impact of human learning on system performance has never been accounted for. In this work we propose a closed queueing network model that accounts for human learning in analyzing the transient performance of a tiered cloud application. We solve the model using discrete event simulation. The model results show that the lack of accountability of human learning may lead to incorrectly selecting a virtual machine configuration that fails to meet the system response time requirement.
Nit1 is a metabolite repair enzyme that hydrolyzes deaminated glutathione

Significance The genomes of the vast majority of eukaryotes encode a protein [named nitrilase-like protein 1 (Nit1) in humans and mice] whose enzymatic function has long been unknown. We show here that the mammalian Nit1 and the corresponding yeast protein efficiently hydrolyze the deaminated form of the common intracellular antioxidant glutathione. In turn, deaminated glutathione can be produced by a side activity of numerous transaminases. Thus, Nit1 repairs an undesired product, arising from the slow (and erroneous) transformation of an important metabolite by some abundant intracellular enzymes. The importance of this Nit1 function is underscored by the finding that enzymes with the same activity occur in Escherichia coli and in other glutathione-producing bacteria. The mammalian gene Nit1 (nitrilase-like protein 1) encodes a protein that is highly conserved in eukaryotes and is thought to act as a tumor suppressor. Despite being ∼35% sequence identical to ω-amidase (Nit2), the Nit1 protein does not hydrolyze efficiently α-ketoglutaramate (a known physiological substrate of Nit2), and its actual enzymatic function has so far remained a puzzle. In the present study, we demonstrate that both the mammalian Nit1 and its yeast ortholog are amidases highly active toward deaminated glutathione (dGSH; i.e., a form of glutathione in which the free amino group has been replaced by a carbonyl group). We further show that Nit1-KO mutants of both human and yeast cells accumulate dGSH and the same compound is excreted in large amounts in the urine of Nit1-KO mice. Finally, we show that several mammalian aminotransferases (transaminases), both cytosolic and mitochondrial, can form dGSH via a common (if slow) side-reaction and provide indirect evidence that transaminases are mainly responsible for dGSH formation in cultured mammalian cells. Altogether, these findings delineate a typical instance of metabolite repair, whereby the promiscuous activity of some abundant enzymes of primary metabolism leads to the formation of a useless and potentially harmful compound, which needs a suitable “repair enzyme” to be destroyed or reconverted into a useful metabolite. The need for a dGSH repair reaction does not appear to be limited to eukaryotes: We demonstrate that Nit1 homologs acting as excellent dGSH amidases also occur in Escherichia coli and other glutathione-producing bacteria.
Ultrafiltration and Microarray for Detection of Microbial Source Tracking Marker and Pathogen Genes in Riverine and Marine Systems

ABSTRACT Pathogen identification and microbial source tracking (MST) to identify sources of fecal pollution improve evaluation of water quality. They contribute to improved assessment of human health risks and remediation of pollution sources. An MST microarray was used to simultaneously detect genes for multiple pathogens and indicators of fecal pollution in freshwater, marine water, sewage-contaminated freshwater and marine water, and treated wastewater. Dead-end ultrafiltration (DEUF) was used to concentrate organisms from water samples, yielding a recovery efficiency of >95% for Escherichia coli and human polyomavirus. Whole-genome amplification (WGA) increased gene copies from ultrafiltered samples and increased the sensitivity of the microarray. Viruses (adenovirus, bocavirus, hepatitis A virus, and human polyomaviruses) were detected in sewage-contaminated samples. Pathogens such as Legionella pneumophila, Shigella flexneri, and Campylobacter fetus were detected along with genes conferring resistance to aminoglycosides, beta-lactams, and tetracycline. Nonmetric dimensional analysis of MST marker genes grouped sewage-spiked freshwater and marine samples with sewage and apart from other fecal sources. The sensitivity (percent true positives) of the microarray probes for gene targets anticipated in sewage was 51 to 57% and was lower than the specificity (percent true negatives; 79 to 81%). A linear relationship between gene copies determined by quantitative PCR and microarray fluorescence was found, indicating the semiquantitative nature of the MST microarray. These results indicate that ultrafiltration coupled with WGA provides sufficient nucleic acids for detection of viruses, bacteria, protozoa, and antibiotic resistance genes by the microarray in applications ranging from beach monitoring to risk assessment.
Fact or fiction: reducing the proportion and impact of false positives

Abstract False positive findings in science are inevitable, but are they particularly common in psychology and psychiatry? The evidence that we review suggests that while not restricted to our field, the problem is acute. We describe the concept of researcher ‘degrees-of-freedom’ to explain how many false-positive findings arise, and how the various strategies of registration, pre-specification, and reporting standards that are being adopted both reduce and make these visible. We review possible benefits and harms of proposed statistical solutions, from tougher requirements for significance, to Bayesian and machine learning approaches to analysis. Finally we consider the organisation and methods for replication and systematic review in psychology and psychiatry.