Miracle-dz/UniFAR-FTUs huggingface dataset:
The Pfam protein families database

Pfam is a widely used database of protein families, currently containing more than 13 000 manually curated protein families as of release 26.0. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/). Here, we report on changes that have occurred since our 2010 NAR paper (release 24.0). Over the last 2 years, we have generated 1840 new families and increased coverage of the UniProt Knowledgebase (UniProtKB) to nearly 80%. Notably, we have taken the step of opening up the annotation of our families to the Wikipedia community, by linking Pfam families to relevant Wikipedia pages and encouraging the Pfam and Wikipedia communities to improve and expand those pages. We continue to improve the Pfam website and add new visualizations, such as the ‘sunburst’ representation of taxonomic distribution of families. In this work we additionally address two topics that will be of particular interest to the Pfam community. First, we explain the definition and use of family-specific, manually curated gathering thresholds. Second, we discuss some of the features of domains of unknown function (also known as DUFs), which constitute a rapidly growing class of families within Pfam.
Population-based cancer screening through community participation: Outcome of a district wide oral cancer screening program from rural Kannur, Kerala, India

Abstract Background: Oral cancer is a major public health challenge, and about one-fifth of all oral cancer cases reported globally are from India. In spite of the potential for early detection by simple visual examination, the majority of patients report in later stages of the disease, especially in low and middle-income countries. We report the results from a district level population-based oral cancer screening program. Methods: A cross-sectional survey was carried out among people aged >15 years in 48 panchayats of Kannur district in Kerala, India. This comprehensive multi-stakeholder district-wide screening was carried out in six stages including planning, sensitization, recruiting of community volunteers and training, survey, organization of specialist camps and referring to cases to cancer center. The descriptive statistical analysis was performed using EpiData analysis software (Version 2.2.2.180). Results: Among the 1,061,088 people in 265,272 houses surveyed, 2507 of them attended the screening camps, and 13 oral cancers and 174 oral precancers were detected. Majority of the oral cancer patients were male (69%), with primary education or illiterate (62%) and low socioeconomic status (61%). Five of the patients diagnosed with early-stage cancer are alive and have good oral health-related quality of life. Conclusion: Detection of precancerous and early-stage cancers should be a priority of oral cancer screening programs. The possible key for addressing cancer screening needs of the rural population is to equip the primary health centers in cancer screening activities with available human resources while adapting to local context.
Peripheral Muscle Function During Repeated Changes of Direction in Basketball.

Purpose: To examine differences between adult male basketball players of different competitive levels (study 1) and changes over a basketball season (study 2) of knee-extensor peripheral muscle function during multistage change-of-direction exercise (MCODE). Methods: In study 1, 111 players from 4 different divisions completed the MCODE during the regular season. In study 2, the MCODE was performed before (T1) and after (T2) the preparation period and during the competitive season (T3) by 32 players from divisions I, II, and III. The MCODE comprised 4 levels of increasing intensity for each player. The twitch peak torque (PT) of knee extensors was measured after each level. PTmax (the highest value of PT) and fatigue were calculated. Results: In study 1, the authors found possibly small differences (effect size [ES] [90% confidence interval] -0.24 [0.39]) in fatigue between divisions I and II. Division I was characterized by likely (ES 0.30-0.65) and very likely to almost certain (ES 0.74-1.41) better PTmax and fatigue levels than divisions III and VI, respectively. In study 2, fatigue was very likely reduced (ES -0.91 to -0.51) among all divisions from T1 to T2, whereas PTmax was likely to very likely reduced (ES -0.51 to -0.39) in divisions II and III. Conclusions: Professional basketball players are characterized by a better peripheral muscle function during MCODE. Most of the seasonal changes in peripheral muscle function occurred after the preparation period. These findings inform practitioners on the development of training programs to enhance the ability to sustain repeated change-of-direction efforts.
Dizziness, Vertigo, and Mental Health Comorbidity in Gulf War Veterans

Abstract Background: Gulf War Illness (GWI) is a chronic condition involving symptoms across multiple body systems. Previous research has implicated the vestibular system as a potential underlying factor in the symptoms experienced by veterans with GWI, due in part to exposure to potentially ototoxic chemicals and events. Purpose: To characterize the presence of vertigo and dizziness symptoms in a sample of veterans with GWI using validated self-report instruments, accounting for mental health comorbidities. Research Design: This is a case series, follow-up, prospective interview of clinical veterans; results presented are purely descriptive. Study Sample: Our sample of 50 veterans was a follow-up to a case series of clinical Gulf War veterans evaluated at the War Related Illness and Injury Study Center. Data Collection and Analysis: Veterans participated in a 70-min phone interview where the following questionnaires were administered: Vertigo Symptom Scale (VSS), Patient Health Questionnaire (depression scale), Patient Health Questionnaire (somatization scale), Beck Anxiety Inventory, Posttraumatic Stress Disorder (PTSD) Checklist, Defense and Veterans Brain Injury Center Traumatic Brain Injury Questionnaire, and GWI (Kansas) Questionnaire. We used descriptive (mean/median, standard deviation, interquartile range, and percentage) statistics to describe our sample and illuminate possible relationships between measures. Results: Our primary finding is a substantial report of vertigo symptoms in our sample, according to the VSS. Ninety percent of participants scored above the VSS threshold (>12), suggesting “severe dizziness. ” The most commonly endorsed symptom on the VSS was “headache or pressure in the head. ” Conclusions: We conclude that there is significant burden of vertigo symptoms in veterans with GWI, suggesting a need for objective tests of vestibular function in this population. Furthermore, the relationship between symptoms of vertigo and dizziness, vestibular function, and PTSD warrants further exploration using objective measures.
A Novel Hybrid of a Fading Filter and an Extreme Learning Machine for GPS/INS during GPS Outages

In this paper, a novel algorithm based on the combination of a fading filter (FF) and an extreme learning machine (ELM) is presented for Global Positioning System/Inertial Navigation System (GPS/INS) integrated navigation systems. In order to increase the filtering accuracy of the model, a variable fading factor fading filter based on the fading factor is proposed. It adjusts the fading factor by the ratio of the estimated covariance before and after the moment which proves to have excellent performance in our experiment. An extreme learning machine based on a Fourier orthogonal basis function is introduced that considers the deterioration of the accuracy of the navigation system during GPS outages and has a higher positioning accuracy and faster learning speed than the typical neural network learning algorithm. In the end, a simulation and real road test are performed to verify the effectiveness of this algorithm. The results show that the accuracy of the fading filter based on a variable fading factor is clearly improved, and the proposed improved ELM algorithm can provide position corrections during GPS outages more effectively than the other algorithms (ELM and the traditional radial basis function neural network).
Is Aerobic Exercise Training Beneficial for Adults With Fibromyalgia?: A Cochrane Review Summary with Commentary

The aim of this commentary is to summarize the published Cochrane Review “Aerobic Exercise Training for Adults with Fibromyalgia” by Bidonde et al.,1 (https://www.cochranelibrary.com/cdsr/doi/10.1002/14651858.CD011336/full) which was developed by the Cochrane Musculoskeletal Group. This Cochrane Cor
HIV‐Nef Protein Persists in the Lungs of Aviremic Patients with HIV and Induces Endothelial Cell Death

Abstract It remains a mystery why HIV‐associated end‐organ pathologies persist in the era of combined antiretroviral therapy (ART). One possible mechanism is the continued production of HIV‐encoded proteins in latently HIV‐infected T cells and macrophages. The proapoptotic protein HIV‐Nef persists in the blood of ART‐treated patients within extracellular vesicles (EVs) and peripheral blood mononuclear cells. Here we demonstrate that HIV‐Nef is present in cells and EVs isolated from BAL of patients on ART. We hypothesize that HIV‐Nef persistence in the lung induces endothelial apoptosis leading to endothelial dysfunction and further pulmonary vascular pathologies. The presence of HIV‐Nef in patients with HIV correlates with the surface expression of the proapoptotic endothelial‐monocyte‐activating polypeptide II (EMAPII), which was implicated in progression of pulmonary emphysema via mechanisms involving endothelial cell death. HIV‐Nef protein induces EMAPII surface expression in human embryonic kidney 293T cells, T cells, and human and mouse lung endothelial cells. HIV‐Nef packages itself into EVs and increases the amount of EVs secreted from Nef‐expressing T cells and Nef‐transfected human embryonic kidney 293T cells. EVs from BAL of HIV+ patients and Nef‐transfected cells induce apoptosis in lung microvascular endothelial cells by upregulating EMAPII surface expression in a PAK2‐dependent fashion. Transgenic expression of HIV‐Nef in vascular endothelial‐cadherin+ endothelial cells leads to lung rarefaction, characterized by reduced alveoli and overall increase in lung inspiratory capacity. These changes occur concomitantly with lung endothelial cell apoptosis. Together, these data suggest that HIV‐Nef induces endothelial cell apoptosis via an EMAPII‐dependent mechanism that is sufficient to cause pulmonary vascular pathologies even in the absence of inflammation.
Double dissociation of single-interval and rhythmic temporal prediction in cerebellar degeneration and Parkinson’s disease

Significance The brain uses temporal regularities to anticipate the timing of future events, and adjust attention and action accordingly. We investigated whether subsecond temporal predictions formed in two distinct predictive contexts, when the stream of events is rhythmic or when the specific interval between two events is known, are functionally and neurally distinct. We show that individuals with cerebellar dysfunction were impaired in forming temporal predictions based on single intervals, but not in rhythmic contexts. In contrast, individuals with basal ganglia dysfunction resulting from Parkinson’s disease showed the reverse pattern. This double dissociation constitutes causal evidence in favor of distinct computational and neural mechanisms for interval- and rhythm-based temporal prediction, and highlights the contribution of these subcortical structures to attentional orienting. Predicting the timing of upcoming events is critical for successful interaction in a dynamic world, and is recognized as a key computation for attentional orienting. Temporal predictions can be formed when recent events define a rhythmic structure, as well as in aperiodic streams or even in isolation, when a specified interval is known from previous exposure. However, whether predictions in these two contexts are mediated by a common mechanism, or by distinct, context-dependent mechanisms, is highly controversial. Moreover, although the basal ganglia and cerebellum have been linked to temporal processing, the role of these subcortical structures in temporal orienting of attention is unclear. To address these issues, we tested individuals with cerebellar degeneration or Parkinson’s disease, with the latter serving as a model of basal ganglia dysfunction, on temporal prediction tasks in the subsecond range. The participants performed a visual detection task in which the onset of the target was predictable, based on either a rhythmic stream of stimuli, or a single interval, specified by two events that occurred within an aperiodic stream. Patients with cerebellar degeneration showed no benefit from single-interval cuing but preserved benefit from rhythm cuing, whereas patients with Parkinson’s disease showed no benefit from rhythm cuing but preserved benefit from single-interval cuing. This double dissociation provides causal evidence for functionally nonoverlapping mechanisms of rhythm- and interval-based temporal prediction for attentional orienting, and establishes the separable contributions of the cerebellum and basal ganglia to these functions, suggesting a mechanistic specialization across timing domains.
Puzzling postoperative toxin-induced acute liver failure after nonhepatobiliary surgery

658 Saudi Journal of Anesthesia / Volume 12 / Issue 4 / October‐December 2018 stroke volume variation to guide intraoperative fluid by many authors. [2‐4] It indicates preload and a value of 330–360 ms is usually considered as normal 2 Transesophageal echo has been used to guide GDFT. Of the various parameters used are velocity time integral (VTI) variation, superior vena cava variation, inferior vena cava size, variation and left ventricle size, etc. A VTI variation of more than 12% implies fluid responsiveness 3 Oxygen extraction has also been used to guide intraoperative fluid therapy and has been found to reduce hospital stay and morbidity[5] 4 Even central venous O2 saturation and venous‐to‐arterial CO2 difference as complementary tools for GDFT intraoperatively. [6]
The ADAPT System Description for the IWSLT 2018 Basque to English Translation Task

In this paper we present the ADAPT system built for the Basque to English Low Resource MT Evaluation Campaign. Basque is a low-resourced, morphologically-rich language. This poses a challenge for Neural Machine Translation models which usually achieve better performance when trained with large sets of data. Accordingly, we used synthetic data to improve the translation quality produced by a model built using only authentic data. Our proposal uses back-translated data to: (a) create new sentences, so the system can be trained with more data; and (b) translate sentences that are close to the test set, so the model can be fine-tuned to the document to be translated.
Optimal Scalar Linear Index Codes for Symmetric and Neighboring Side-information Problems

A single unicast index coding problem (SUICP) is called symmetric neighboring and consecutive (SNC) side-information problem if it has $K$ messages and $K$ receivers, the $k$th receiver $R_{k}$ wanting the $k$th message $x_{k}$ and having the side-information $D$ messages immediately after $x_k$ and $U$ ($D\geq U$) messages immediately before $x_k$. Maleki, Cadambe and Jafar obtained the capacity of this SUICP(SNC) and proposed $(U+1)$-dimensional optimal length vector linear index codes by using Vandermonde matrices. However, for a $b$-dimensional vector linear index code, the transmitter needs to wait for $b$ realizations of each message and hence the latency introduced at the transmitter is proportional to $b$. For any given single unicast index coding problem (SUICP) with the side-information graph $G$, MAIS($G$) is used to give a lowerbound on the broadcast rate of the ICP. In this paper, we derive MAIS($G$) of SUICP(SNC) with side-information graph $G$. We construct scalar linear index codes for SUICP(SNC) with length $\left \lceil \frac{K}{U+1} \right \rceil - \left \lfloor \frac{D-U}{U+1} \right \rfloor$. We derive the minrank($G$) of SUICP(SNC) with side-information graph $G$ and show that the constructed scalar linear index codes are of optimal length for SUICP(SNC) with some combinations of $K,D$ and $U$. For SUICP(SNC) with arbitrary $K,D$ and $U$, we show that the length of constructed scalar linear index codes are atmost two index code symbols per message symbol more than the broadcast rate. The given results for SUICP(SNC) are of practical importance due to its relation with topological interference management problem in wireless communication networks.
Disentangling Risk and Uncertainty: When Risk-Taking Measures Are Not About Risk

Many studies claim to measure decision-making under risk by employing the Domain-Specific Risk-Taking (DOSPERT) scale, a self-report measure, or the Balloon Analogue Risk Task (BART), a behavioural task. However, these tasks do not measure decision-making under risk but decision-making under uncertainty, a related but distinct concept. The present commentary discusses both the theoretical and empirical basis of the distinction between uncertainty and risk from the viewpoint of several scientific disciplines and reports how many studies wrongfully employ the DOSPERT scale and BART as risk-taking measures. Importantly, we call for proper distinguishing between (tasks measuring) decision-making under uncertainty and decision-making under risk in psychology, and related fields. We believe this is vital as research has shown that people’s attitudes, behaviour, and brain activity differ between both concepts, indicating that confusing the concepts may lead researchers to erroneous conclusions.
Detecting Rumor and Disinformation by Web Mining

A method for determining whether given text is a rumor or disinformation is proposed, based on web mining and linguistic technology comparing two paragraphs of text. We hypothesize about a family of content generation algorithms which are capable of producing disinformation from a portion of genuine, original text. We then propose a disinformation detection algorithm which finds a candidate source of text on the web and compares it with the given text, applying parse thicket technology. Parse thicket is graph combined from a sequence of parse trees augmented with inter-sentence relations for anaphora and rhetoric structures. We evaluate our algorithm in the domain of customer reviews, considering a product review as an instance of possible disinformation. It is confirmed as a plausible way to detect rumor and disinformation in a web document. Linguistic approach presented here complements social network structure-based described on a corpus of research on disinformation detection.
Hierarchical Factored POMDP for Joint Tasks: Application to Escort Tasks

The number of applications of service robotics in public spaces such as hospitals, museums and malls is a growing trend. Public spaces, however, provide several challenges to the robot, and speciﬁcally with its planning capabilities: they need to cope with a dynamic and uncertain environment and are subject to particular human-robot interaction constraints. A major challenge is the Joint Intention problem. When cooperating with humans, a persistent commitment to achieve a shared goal cannot be always assumed, since they have an unpredictable behavior and may be distracted in environments as dynamic and uncertain as public spaces, and even more so if the human agents are customers, visitors or bystanders. In order to address such issues in a decision-making context, we present a framework based on Hierarchical Factored POMDPs. We describe the general method for ensuring the Joint Intention be-tween human and robot , the hierarchical structure and the Value Decomposition method adopted to build it. We also provide an example application scenario: an Escort Task in a shopping mall for guiding a customer towards a desired point of interest.
Large-scale Interactive Recommendation with Tree-structured Policy Gradient

Reinforcement learning (RL) has recently been introduced to interactive recommender systems (IRS) because of its nature of learning from dynamic interactions and planning for long-run performance. As IRS is always with thousands of items to recommend (i.e., thousands of actions), most existing RL-based methods, however, fail to handle such a large discrete action space problem and thus become inefficient. The existing work that tries to deal with the large discrete action space problem by utilizing the deep deterministic policy gradient framework suffers from the inconsistency between the continuous action representation (the output of the actor network) and the real discrete action. To avoid such inconsistency and achieve high efficiency and recommendation effectiveness, in this paper, we propose a Tree-structured Policy Gradient Recommendation (TPGR) framework, where a balanced hierarchical clustering tree is built over the items and picking an item is formulated as seeking a path from the root to a certain leaf of the tree. Extensive experiments on carefully-designed environments based on two real-world datasets demonstrate that our model provides superior recommendation performance and significant efficiency improvement over state-of-the-art methods.
Red blood cell volume is not decreased in ESA‐naive anemic chronic kidney disease patients

Anemia is defined according to decreased blood hemoglobin concentration ([Hb]), which is considered a marker of low total red blood cell volume (RBCV). Alterations of plasma volume (PV) may also modify [Hb] without concomitant changes in RBCV. Since anemia and fluid retention are frequent complications of chronic kidney disease (CKD), we hypothesized that anemia during CKD may in part be related to expanded PV without a simultaneous decrease in RBCV. We quantified hemoglobin mass, RBCV, PV, and total blood volume (BV) using an automated carbon monoxide device in 40 consecutive stage 3–5 CKD patients not on dialysis and in seven healthy male controls of the same age range. These were compared within and to predicted volumes according to Nadler's formula. Arterial stiffness and NT‐proBNP were measured. RBCV was similar to predicted values range in anemic CKD patients 2073 (1818–2704) versus, 2061 (1725–2473) mL, P > 0.05. In contrast, PV was largely increased in anemic CKD patients (3881 (3212–4352) vs. 2916 (2851–3201)), P = 0.01. Of 26 anemic patients, only six had a >20% decrease in RBCV as the cause for their anemia, whereas 14 had a >20% increase of PV as a cause for their anemia. NT‐pro BNP correlated with eGFR but neither with PV nor BV, whereas arterial stiffness was not correlated to blood volumes. Anemia in CKD as diagnosed by low [Hb] is not necessarily associated to low RBCV but may reflect increased PV. This finding has implications for the treatment of CKD patients and may refrain from normalizing [Hb] levels in all CKD patients.