Miracle-dz/UniFAR-FTUs huggingface dataset:
Sparse signal recovery methods for variant detection in next-generation sequencing data

Recent advances in high-throughput sequencing technologies, have led to the collection of vast quantities of genomic data. , Structural variants (SVs) - rearrangements of the genome, larger than one letter such as inversions, insertions, deletions, and duplications - are an important source of genetic, variation and have been implicated in some genetic diseases. , However, inferring SVs from sequencing data has proven to, be challenging because true SVs are rare and are prone to, low-coverage noise. In this paper, we attempt to mitigate the, deleterious effects of low-coverage sequences by following a, maximum likelihood approach to SV prediction. Specifically, we model the noise using Poisson statistics and constrain, the solution with a sparsity-promoting ℓ1 penalty since SV, instances should be rare. In addition, because offspring SVs, inherit SVs from their parents, we incorporate familial relationships, in the optimization problem formulation to increase, the likelihood of detecting true SV occurrences. Numerical, results are presented to validate our proposed approach.
Maturation of Speech Discrimination in 4- to 7-Yr-Old Children as Indexed by Event-Related Potential Mismatch Responses

Objectives: This study examined maturation of mismatch responses (MMRs) to an English vowel contrast (/I/ versus /&egr;/) in 4- to 7-yr-old children. Design: Event-related potentials were recorded to a standard [&egr;] and deviant [I] vowel presented in trains of 10 stimuli at a rate of 1/650 msecs and with an intertrain interval of 1.5 secs. Each train contained two deviant vowels. Averaged responses were calculated for the infrequent (deviant) and the frequent (standard) trials for each child and compared across age groups. Results: Significantly greater negativity, consistent with the adult mismatch negativity (MMN), was observed to the deviants between 300 and 400 msecs for both younger (4- and 5-yr-old) and older (6- and 7-yr-old) children. This MMN-like negativity shifted earlier in latency by 25 msecs/yr with increasing age. Most of the children younger than 5.5 yrs and some of the older children also showed a positive MMR (p-MMR) peaking between 100 and 300 msecs. The p-MMR diminished in amplitude with increasing age. Conclusions: Maturation of speech discrimination, as indexed by MMN, occurs more rapidly between 4 and 7 yrs of age for vowels than for tones. A p-MMR preceding the MMN also reflects discrimination in younger children and declines in amplitude with age.
The Role of Multiple Neuromodulators in Reinforcement Learning That Is Based on Competition between Eligibility Traces

The ability to maximize reward and avoid punishment is essential for animal survival. Reinforcement learning (RL) refers to the algorithms used by biological or artificial systems to learn how to maximize reward or avoid negative outcomes based on past experiences. While RL is also important in machine learning, the types of mechanistic constraints encountered by biological machinery might be different than those for artificial systems. Two major problems encountered by RL are how to relate a stimulus with a reinforcing signal that is delayed in time (temporal credit assignment), and how to stop learning once the target behaviors are attained (stopping rule). To address the first problem synaptic eligibility traces were introduced, bridging the temporal gap between a stimulus and its reward. Although, these were mere theoretical constructs, recent experiments have provided evidence of their existence. These experiments also reveal that the presence of specific neuromodulators converts the traces into changes in synaptic efficacy. A mechanistic implementation of the stopping rule usually assumes the inhibition of the reward nucleus; however, recent experimental results have shown that learning terminates at the appropriate network state even in setups where the reward nucleus cannot be inhibited. In an effort to describe a learning rule that solves the temporal credit assignment problem and implements a biologically plausible stopping rule, we proposed a model based on two separate synaptic eligibility traces, one for long-term potentiation (LTP) and one for long-term depression (LTD), each obeying different dynamics and having different effective magnitudes. The model has been shown to successfully generate stable learning in recurrent networks. Although, the model assumes the presence of a single neuromodulator, evidence indicates that there are different neuromodulators for expressing the different traces. What could be the role of different neuromodulators for expressing the LTP and LTD traces? Here we expand on our previous model to include several neuromodulators, and illustrate through various examples how different these contribute to learning reward-timing within a wide set of training paradigms and propose further roles that multiple neuromodulators can play in encoding additional information of the rewarding signal.
Transactions on Pattern Analysis and Machine Intelligence 1 Space-time Video Completion Draft Transactions on Pattern Analysis and Machine Intelligence 2

This paper presents a new framework for completion of missing information based on local structures. It poses the task of completion as a global optimization problem with a well-defined objective function and derives a new algorithm to optimize it. Missing values are constrained to form coherent structures with respect to reference examples. We apply this method to space-time completion of large space-time " holes " in video sequences of complex dynamic scenes. The missing portions are filled in by sampling spatio-temporal patches from the available parts of the video, while enforcing global spatio-temporal consistency between all patches in and around the hole. The consistent completion of static scene parts simultaneously with dynamic behaviors leads to realistic looking video sequences and images. Space-time video completion is useful for a variety of tasks, including, but not limited to: (i) Sophisticated video removal (of undesired static or dynamic objects) by completing the appropriate static or dynamic background information, (ii) Correction of missing/corrupted video frames in old movies, (iii) Modifying a visual story by replacing unwanted elements, (iv) Creation of video textures by extending smaller ones, (v) Creation of complete field-of-view stabilized video, and (vi) As images are one-frame videos, we apply the method to this special case as well.
Robust control/scheduling co-design: application to robot control

Control systems running on a computer are subject to timing disturbances coming from implementation constraints. Fortunately closed-loop systems behave robustly w.r. t. modelling errors and disturbances, and the controller design can be performed to explicitly enhance robustness against specific uncertainties. On one hand robustness in process controllers can be used to comply with weakly modelled timing uncertainties. On the other hand the principle of robust closed-loop control can also be applied to the real-time scheduler to provide online adaption of some scheduling parameters, with the objective of controlling the computing resource allocation. The control performance specification may be set according to both control and implementation constraints. The approach is illustrated through several examples using simulation and an experimental feedback scheduler is briefly described.
Single-living is associated with increased risk of long-term mortality among employed patients with acute myocardial infarction

Objective: There is conflicting evidence about the impact of social support on adverse outcome after acute myocardial infarction (MI). We examined the relation between single-living and long-term all-cause mortality after MI. Design: A prospective cohort study of 242 employed patients with MI followed up to 16 years after MI. Results: A total of 106 (43.8%) patients died during the follow-up. Single-living nearly doubled the risk of death; after adjusting for potential confounding factors, single-living was an independent predictor of death, with a hazard ratio of 2.55 (95% confidence interval: 1.52–4.30). Other predictors of death were diabetes mellitus, atrial fibrillation, age, and ejection fraction less than 35%. Conclusion: Single-living is a prognostic determinant of long-term all-cause mortality after MI.
Efficacy of Flipped Classroom and Literature in ESL And EFL: A Revision of a Case Study

We present here a case study that aims to determine to what extent Flipped Classroom is a valid way to introduce difficult and demanding reading texts in the ESL EFL classroom in a university course of English language. In the case of the study, the content objective is the introduction of the reading of passages from Macbeth written by William Shakespeare in a specialized university course for English language students whose linguistic competence is in the region of B2 CFRL. This study revisits some of previously obtained data and crosses these new items with new data gathered during the research described in this paper. We obtain some interesting findings that support the hypothesis that using alternative teaching methods, as Flipped Classroom, can be a valid tool to introduce demanding texts in an environment as the one here described.
Potential Mechanisms Involved in the Anticonvulsant Effect of Recombinant Human VEGF on Maximal Electroshock-induced Seizure

Background: Vascular endothelial growth factor (VEGF) signaling pathway plays an important role in the pathogenesis of seizure. The oxidant/antioxidant factors and miRNA expression in the brain are differentially regulated in seizure. Objectives: We aim to investigate the potential mechanism of action for the recombinant human VEGF (rhVEGF) in mice with maximal electroshock (MES)-induced seizure. Materials & Methods: A total of 40 male mice (weight: 20-25 g) were treated intraperitoneally with normal saline, or rhVEGF (50, 100, and 150 µg/kg, daily for 4 consecutive days). One hour after the last injection, seizures were induced in each animal by MES. The latency for the onset of the first clonus and the duration of hind limb extension (HLE) were recorded. The levels of nitric oxide (NO), total antioxidant capacity (TAC), and micoRNA-142-5p expression were determined in the hippocampus of mice. Blood-brain barrier (BBB) permeability was also estimated by Evans blue dye extravasation method. Results: The administration of rhVEGF at all doses significantly reduced the HLE duration. However, latency for the seizure onset increased after administration of 50 and 150 μg/kg rhVEGF and decreased after administration of 100 μg/kg rhVEGF. In the brain, the NO level decreased, while TAC level and microRNA-142-5p expression increased by rhVEGF treatment in mice with MES-induced seizure. Pretreatment with rhVEGF at doses of 100 and 150 μg/kg reversed the increase in BBB leakage induced by MES-induced seizures. Conclusion: The rhVEGF administration can prevent MES-induced seizures by regulating NO, TAC, and miR-142-5 expression levels in the hippocampus and reducing BBB leakage in mice.
The Symptoms of Advanced Cancer: Identification of Clinical and Research Priorities by Assessment of Prevalence and Severity

In advanced cancer, when cure is impossible, symptoms should be the focus of attention. We report the first prospective, systematic analysis of the severity of 37 symptoms in 1000 patients with advanced cancer, using the Paradox relational database. Pain, easy fatigue, and anorexia were consistently among the 10 most prevalent symptoms associated with cancer at all sites. When pain, anorexia, weakness, anxiety, lack of energy, easy fatigue, early satiety, constipation, and dyspnea were present, 60%-80% of patients rated them as moderate or severe, i.e. of clinical importance. The most common symptoms were also the most severe. In general the same symptoms were clinically important at most primary sites. Clinically important dyspnea, hoarseness, hiccough, and dysphagia were more common in men; anxiety, nausea, vomiting, and early satiety in women. Clinically important dyspepsia, nausea, and vomiting occurred more frequently in gynecological cancers.
Using the Fast Track randomized prevention trial to test the early-starter model of the development of serious conduct problems

The Fast Track prevention trial was used to test hypotheses from the Early-Starter Model of the development of chronic conduct problems. We randomly assigned 891 high-risk first-grade boys and girls (51% African American) to receive the long-term Fast Track prevention or not. After 4 years, outcomes were assessed through teacher ratings, parent ratings, peer nominations, and child self-report. Positive effects of assignment to intervention were evident in teacher and parent ratings of conduct problems, peer social preference scores, and association with deviant peers. Assessments of proximal goals of intervention (e.g., hostile attributional bias, problem-solving skill, harsh parental discipline, aggressive and prosocial behavior at home and school) collected after grade 3 were found to partially mediate these effects. The findings are interpreted as consistent with developmental theory.
Building Height Retrieval From VHR SAR Imagery Based on an Iterative Simulation and Matching Technique

Experimental airborne synthetic aperture radar (SAR) systems achieve spatial resolutions of approximately 10 cm, whereas the new spaceborne very high spatial resolution (VHR) SAR sensors onboard the TerraSAR-X and COSMO-SkyMed satellites achieve spatial resolutions down to 1 m. In VHR SAR data, features from individual urban structures (i.e., buildings) can be identified by their characteristic settings in urban settlement patterns. In this paper, we present a novel concept for the height estimation of generic man-made structures from single detected SAR data. The proposed approach is based on the definition of a hypothesis on the height of the building and on the simulation of a SAR image for testing that hypothesis. A matching procedure is applied between the estimated and the actual SAR image in order to test the height hypothesis. The process is iterated for different height assumptions until the matching function is optimized, and thus, the building height is estimated. The efficiency of the proposed method is demonstrated on a set of 40 flat- and gable-roof buildings using two submeter VHR airborne and two 1-m resolution TerraSAR-X SAR scenes all acquired from the same residential area in Dorsten, Germany. The results show that, in the absence of string disturbing effects, the method is able to estimate the height of flat- and gable-roof buildings in the submeter data to the order of a meter, while the accuracy for the meter resolution spaceborne data is lower but still sufficient to estimate the number of floors of a building.
Levels of self-awareness after acute brain injury: how patients' and rehabilitation specialists' perceptions compare.

OBJECTIVE To examine self-awareness regarding performance on 4 daily living tasks and to test theoretical predictions for a model of self-awareness in persons with acquired brain injury. DESIGN A comparative design examining the level of self-awareness recorded by patients and actual patient performance as judged by rehabilitation clinicians. SETTING A community-based residential center providing comprehensive rehabilitation services to persons with acquired brain injury. PARTICIPANTS Fifty-five persons with acquired brain injury and the identified potential to return to independent function in the community. Ten subjects without brain injury provided comparison data. INTERVENTION Information was collected by using patient self-report, clinician rating of patient performance, patient rating of non-brain-injured subjects, and clinician rating of non-brain-injured subjects. MAIN OUTCOME MEASURES Three self-awareness criteria were examined: intellectual, emergent, and anticipatory. Self-awareness was rated for 3 tasks: dressing, meal planning, and money management. RESULTS Statistically significant differences (p <.05) were found for all levels of self-awareness across the 3 tasks. Persons with brain injury judged their abilities higher than clinician ratings of actual performance. No statistical support was found for a hierarchy among intellectual, emergent, and anticipatory self-awareness. CONCLUSIONS No evidence was found supporting a hierarchy among levels of self-awareness as defined and measured in the present study. New methods for operationally defining intellectual, emergent, and anticipatory self-awareness are necessary to examine the relationship between self-awareness and performance.
The stability of longest-queue-first scheduling with variable packet sizes

It is well known that the MaxWeight scheduling algorithm is throughput-optimal in wireless networks. However, its complexity is exponential in the number of links in an ad hoc network. In this work, we consider a greedy variant of the MaxWeight algorithm, called Longest Queue First (LQF). A synchronous version of LQF is known to be throughput-optimal under a topological condition called local pooling. Here we study an asynchronous version of LQF which is suitable for implementation in networks with variable packet sizes. We show that asynchronous LQF is also throughput-optimal under the local pooling condition.
Treatment Outcomes of New Tuberculosis Patients Hospitalized in Kampala, Uganda: A Prospective Cohort Study

Background In most resource limited settings, new tuberculosis (TB) patients are usually treated as outpatients. We sought to investigate the reasons for hospitalisation and the predictors of poor treatment outcomes and mortality in a cohort of hospitalized new TB patients in Kampala, Uganda Methods and findings Ninety-six new TB patients hospitalised between 2003 and 2006 were enrolled and followed for two years. Thirty two were HIV-uninfected and 64 were HIV-infected. Among the HIV-uninfected, the commonest reasons for hospitalization were low Karnofsky score (47%) and need for diagnostic evaluation (25%). HIV-infected patients were commonly hospitalized due to low Karnofsky score (72%), concurrent illness (16%) and diagnostic evaluation (14%). Eleven HIV uninfected patients died (mortality rate 19.7 per 100 person-years) while 41 deaths occurred among the HIV-infected patients (mortality rate 46.9 per 100 person years). In all patients an unsuccessful treatment outcome (treatment failure, death during the treatment period or an unknown outcome) was associated with duration of TB symptoms, with the odds of an unsuccessful outcome decreasing with increasing duration. Among HIV-infected patients, an unsuccessful treatment outcome was also associated with male sex (P = 0.004) and age (P = 0.034). Low Karnofsky score (aHR = 8.93, 95% CI 1.88 – 42.40, P = 0.001) was the only factor significantly associated with mortality among the HIV-uninfected. Mortality among the HIV-infected was associated with the composite variable of CD4 and ART use, with patients with baseline CD4 below 200 cells/µL who were not on ART at a greater risk of death than those who were on ART, and low Karnofsky score (aHR = 2.02, 95% CI 1.02 – 4.01, P = 0.045). Conclusion Poor health status is a common cause of hospitalisation for new TB patients. Mortality in this study was very high and associated with advanced HIV Disease and no use of ART.
A green fluorescent protein fused to rice prolamin forms protein body-like structures in transgenic rice

Prolamins, a group of rice (Oryza sativa) seed storage proteins, are synthesized on the rough endoplasmic reticulum (ER) and deposited in ER-derived type I protein bodies (PB-Is) in rice endosperm cells. The accumulation mechanism of prolamins, which do not possess the well-known ER retention signal, remains unclear. In order to elucidate whether the accumulation of prolamin in the ER requires seed-specific factors, the subcellular localization of the constitutively expressed green fluorescent protein fused to prolamin (prolamin–GFP) was examined in seeds, leaves, and roots of transgenic rice plants. The prolamin–GFP fusion proteins accumulated not only in the seeds but also in the leaves and roots. Microscopic observation of GFP fluorescence and immunocytochemical analysis revealed that prolamin–GFP fusion proteins specifically accumulated in PB-Is in the endosperm, whereas they were deposited in the electron-dense structures in the leaves and roots. The ER chaperone BiP was detected in the structures in the leaves and roots. The results show that the aggregation of prolamin–GFP fusion proteins does not depend on the tissues, suggesting that the prolamin–GFP fusion proteins accumulate in the ER by forming into aggregates. The findings bear out the importance of the assembly of prolamin molecules and the interaction of prolamin with BiP in the formation of ER-derived PBs.
Fibroblast growth factor‐19: Development, analytical characterization and clinical evaluation of a new ELISA test

Objective. Since fibroblast growth factor 19 (FGF‐19) is a potent metabolic regulator that influences glucose and lipid homeostasis, our aim was to develop an ELISA assay for measuring FGF‐19 in human serum and to investigate its concentrations in healthy volunteers and patients suffering from metabolic syndrome. Material and methods. A sandwich ELISA method was developed for quantitative determination of human FGF‐19 in serum samples. Blood pressure, waist circumference, FGF‐21 serum levels, serum cholesterol, triacylglycerols, HDL‐cholesterol, LDL‐cholesterol, insulin, glucose, adiponectin, uric acid, creatinine, hs‐CRP and calculated BMI and Quicki insulin sensitivity index were measured in 153 healthy volunteers and 66 persons with metabolic syndrome. Results. Neither sex nor age influenced FGF‐19 serum concentration in the healthy volunteers. Probands with metabolic syndrome had 65 % lower FGF‐19 serum values than the healthy ones (medians 158.6 versus 242.4 ng/L; p<0.01). FGF‐19 correlated with glucose (r = −0.35, p<0.01), HDL (r = 0.24, p = 0.045), triacylglycerols (r = −0.19, p = 0.05) and with a number of other risk facors for metabolic syndrome (r = −0.28, p = 0.01). When adjusted to the concentrations of triacylglycerols, BMI and glucose, and finally to all data pertinent to FGF‐19 (according to correlation analysis), our data indicate that FGF‐19 is an independent marker of metabolic syndrome. Conclusions. The present study demonstrates the analytical properties of the ELISA FGF‐19 assay and its usefulness when studying the metabolic syndrome. Serum concentrations of FGF‐19 could be new key predictors of metabolic syndrome and thereby even a new negative risk factor of atherosclerosis.