Miracle-dz/UniFAR-FTUs huggingface dataset:
Faster solution to the maximum quartet consistency problem with constraint programming

Evolution is an important sub-area of study in biological science, whereby the evolutionary history, or phylogeny, would shed light on the genetic linkage and the functional correlation for the species under consideration. Many kinds of species data can be deployed for the task and many phylogeny reconstruction methods have been examined in the literature. A quartet approach is to build a local phylogeny for every 4 species, which is called a quartet for these 4 species, and then to assemble a phylogeny for the whole set of species satisfying the topological constraints imposed by these quartets built. In practice, those predicted quartets might not agree each other and the optimization problem, the well-known Maximum Quartet Consistency (MQC) problem, is to construct a phylogeny to satisfy a maximum number of the predicted quartets. An equivalent representation for the MQC problem through searching for a certain ultrametric matrix via Answer Set Programming has recently been proposed. This paper follows the approach and presents a number of optimization techniques to speed up the searching process. The experimental results on both the simulated and real datasets suggest that the new representation combined with Constraint Programming presents a unique perspective to the MQC problem.
Energy-Efficient Resource Allocation in NOMA Heterogeneous Networks

Non-orthogonal multiple access has attracted much recent attention due to its capability of improving the system spectral efficiency in wireless communications. Deploying NOMA in a heterogeneous network can satisfy users' explosive data traffic requirements, and NOMA will likely play an important role in the next generation mobile communication networks. However, NOMA brings new technical challenges on resource allocation due to the mutual cross-tier interference in heterogeneous networks. In this article, to study the trade-off between data rate performance and energy consumption in NOMA, we examine the problem of energy-efficient user scheduling and power optimization in NOMA heterogeneous networks. The energy-efficient user scheduling and power allocation schemes are introduced for the downlink NOMA heterogeneous network for perfect and imperfect CSI, respectively. Simulation results show that the resource allocation schemes can significantly increase the energy efficiency of NOMA heterogeneous networks for cases of both perfect CSI and imperfect CSI.
Klinefelter Syndrome—A Clinical Update

Context: Recently, new clinically important information regarding Klinefelter syndrome (KS) has been published. We review aspects of epidemiology, endocrinology, metabolism, body composition, and neuropsychology with reference to recent genetic discoveries. EvidenceAcquisition: PubMedwassearchedfor“Klinefelter,”“Klinefelter’s,”and“XXY”intitlesand abstracts.Relevantpaperswereobtainedandreviewed,aswellasotherarticlesselectedbytheauthors. EvidenceSynthesis: KSisthemostcommonsexchromosomedisorderinmales,affectingonein660 men. The genetic background is the extra X-chromosome, which may be inherited from either parent. Most genes from the extra X undergo inactivation, but some escape and serve as the putative genetic cause of the syndrome. KS is severely underdiagnosed or is diagnosed late in life, roughly 25% are diagnosed, and the mean age of diagnosis is in the mid-30s. KS is associated with an increased morbidity resulting in loss of approximately 2 yr in life span with an increased mortality from many different diseases. The key findings in KS are small testes, hypergonadotropic hypogonadism, and cognitive impairment. The hypogonadism may lead to changes in body composition and a risk of developing metabolic syndrome and type 2 diabetes. The cognitive impair-mentismainlyintheareaoflanguageprocessing.BoyswithKSareofteninneedofspeechtherapy, and many suffer from learning disability and may benefit from special education. Medical treatment is mainly testosterone replacement therapy to alleviate acute and long-term consequences of hypogonadism as well as treating or preventing the frequent comorbidity. Conclusions: More emphasis should be placed on increasing the rate of diagnosis and generating evidence for timing and dose of testosterone replacement. Treatment of KS should be a multidisciplinary task including pediatricians, speech therapists, general practitioners, psychologists, infertility specialists, urologists, and endocrinologists. ( J Clin Endocrinol Metab 98: 20–30, 2013)
Bordetella pertussis (Pertussis)

1. Heather L. Daniels, DO* 2. Camille Sabella, MD* 1. *Center for Pediatric Infectious Diseases, Cleveland Clinic Children’s, Cleveland, OH * Abbreviations: CDC: : Centers for Disease Control and Prevention DTaP: : diphtheria, tetanus, and acellular pertussis vaccine DTwP: : diphtheria, tetanus, and whole cell pertussis vaccine IHPS: : infantile hypertrophic pyloric stenosis PCR: : polymerase chain reaction Tdap: : tetanus toxoid, reduced diphtheria toxoid, and acellular pertussis vaccine Th: : T-helper After completing this article, readers should be able to: Bordetella pertussis is a fastidious gram-negative coccobacillus responsible for the respiratory infection commonly known as “whooping cough. ” The organism is spread by respiratory droplets and is highly contagious among close contacts. The typical incubation period is 7 to 10 days, but it may be as long as 21 days. Neither natural infection nor pertussis vaccination results in long-lasting immunity, contributing to endemic infection and 3- to 5-year cycles of pertussis epidemics. Several active components, which play a role in immunity and are responsible for the organism’s ability to cause disease, are produced by B pertussis . (1) Pertussis toxin, filamentous hemagglutinin, pertactin, and agglutinogen allow the organism to adhere to ciliated epithelium of the respiratory tract, where it exerts its effects. Pertussis toxin also induces cell cytoxicity, inhibits neutrophilic and monocytic responses, and delays induction of specific immune responses. Pertussis toxin is postulated to be responsible for the systemic manifestations of pertussis, …
Response: Commentary: Effects of dividing attention on memory for declarative and procedural aspects of tool use

Osiurak et al. (2016) presented a commentary on our previous research. However, we found that their commentary contained several inaccurate statements and misrepresented the purpose and implications of our work. Thus, we will begin by describing our research objectives and findings. We will then offer a critique of the position taken by Osiurak et al. regarding the processes of tool use. Finally, we will discuss how our research contributes to a better understanding of the processes involved in skilled tool use.
Real-time Coherent Video Style Transfer Final Report

Existing image style transfer models usually suffer from high temporal inconsistency when applied to videos. Some video style transfer models have been proposed to tackle this problem, yet they fail to guarantee high processing speed, desirable perceptual style quality and high temporal coherence at the same time. In this paper, we propose ReCoNet, a novel real-time video style transfer model, which can generate stylized videos in real-time speed with high temporal coherence while being able to reproduce rich artistic styles. In ReCoNet, a novel luminance warping constraint is added to the temporal loss at the output level to capture luminance changes between consecutive frames and increase stylization stability under illumination effects. We also purpose a new feature-maplevel temporal loss to further improve temporal consistency on the appearances of traceable objects. Experimental results demonstrate that our model can achieve outstanding performance both qualitatively and quantitatively.
Association Between Dementia Severity and Recommended Lifestyle Changes: A Retrospective Cohort Study

Objective: Early diagnosis of dementia leads to early treatment which is beneficial to patients and the community. We reviewed initial evaluations from the Spectrum Health Medical Group Neurocognitive Clinic (SHMGNC) to evaluate dementia stage at the time of diagnosis. Methods: We retrospectively reviewed 110 randomly chosen initial evaluations from September 2008 to December 2015 at the SHMGNC. Patients underwent a neurological examination, Montreal Cognitive Assessment, and a battery of neuropsychological testing. Results: Of all, 78.9% had moderate or severe dementia at diagnosis. The SHMGNC recommended lifestyle changes (medication assistance, financial assistance, driving restrictions, and institutional care) in 75.8% of patients with dementia. The severity of dementia was associated with the number of lifestyle changes recommended. Cohabitation with a caregiver did not lead to an early diagnosis of dementia. Conclusions: Patients are not undergoing evaluation at the onset of the dementia process. Diagnosis is delayed. Home-based, patient-centered care may improve early screening and detection of dementia.
Investigating live streaming data for student behaviour modelling

Modelling technology integration in the teaching and learning environment is a complex, uncertain and dynamic practice. A large amount of student behaviour data has been gathered literately for different processing purposes. Yet, considerable questions are still remaining due to the huge data volume, diversification and uncertainty. In this work, we implement a big-data analytical framework for online behaviour modelling, particularly taking streaming data of students' online activity from their laptop usage as an illustrative example. The proposed framework covers details from accessing streaming records to storing heterogeneous data. Furthermore, the work also demonstrates the use of a TF-IDF based feature generation and fuzzy representation strategy to discover critical patterns via this behaviour data. The accuracy of the modelling work is evaluated using students' score on a national-wide test. Experimental results show that the employed TF-IDF feature is much stabler than other traditional features, thereby achieving a better modelling performance. In summary, the simulation result demonstrates the flexibility and applicability of the proposed framework for processing complex behaviour data, and revealing important patterns for decision making.
The Mediating Effects of Self-handicapping on Eating Disorder Symptomatology

With the high prevalence of eating disorders (ED) and the functional impairment that they cause, there is a pressing need to more fully identify their risk factors and mechanisms. While perfectionism and negative affect are known risk factors for ED, the mechanisms by which they develop are not well understood. The present study examined the roles of self-handicapping, thought suppression, and maladaptive emotion regulation strategies, as potential mechanisms through which perfectionism and negative affect confer risk for ED. A sample of 161 female undergraduates completed measures of perfectionism, negative affect, thought suppression, self-handicapping, eating disorder tendencies, and an Implicit Association Test that measured negative attitudes towards high calorie foods. Results showed that self-handicapping, but not thought suppression, mediated the effects of perfectionism and negative affect on self-reported ED tendencies. Contrary to expectation, perfectionism predicted lower levels of self-handicapping. Overall, the results suggest that self-handicapping may be an important link in the pathway through which ED develop.
Examining the Role of Health Literacy in Optimizing the Care of Pregnant Women with Diabetes

Abstract Diabetes during pregnancy is a substantial and growing public health problem disproportionately affecting women in racial/ethnic minority communities. Health literacy and numeracy are skills needed to function in the health care environment. By definition, health literacy is the degree to which individuals have the capacity to obtain, process, and understand basic health information and services needed to make appropriate health decisions. Health literacy is increasingly recognized as an important mediator of health disparities in the United States, yet it has been rarely studied during pregnancy. Thus, this article aims to describe the problem of inadequate health literacy, outline the relationships between inadequate health literacy and poor health outcomes, and discuss diabetes-specific associations with health literacy. Although literacy has been insufficiently studied during pregnancy, a limited body of work suggests inadequate health literacy may be associated with lesser knowledge and self-care behaviors among pregnant women with diabetes. Health literacy-focused clinical “pearls” for the care of pregnant women with diabetes include: to use multiple educational modalities, to employ teach-back methods, to validate understanding, to provide specific and concrete counseling, and to offer focused, limited messaging. Lastly, future research directions regarding diabetes, health literacy, and pregnancy are addressed.
GABAergic Gene Expression in Postmortem Hippocampus from Alcoholics and Cocaine Addicts; Corresponding Findings in Alcohol-Naïve P and NP Rats

Background By performing identical studies in humans and rats, we attempted to distinguish vulnerability factors for addiction from neurobiological effects of chronic drug exposure. We focused on the GABAergic system within the hippocampus, a brain region that is a constituent of the memory/conditioning neuronal circuitry of addiction that is considered to be important in drug reinforcement behaviors in animals and craving and relapse in humans. Methodology Using RNA-Seq we quantified mRNA transcripts in postmortem total hippocampus from alcoholics, cocaine addicts and controls and also from alcohol-naïve, alcohol preferring (P) and non-preferring (NP) rats selectively bred for extremes of alcohol-seeking behavior that also show a general addictive tendency. A pathway-targeted analysis of 25 GABAergic genes encoding proteins implicated in GABA synthesis, metabolism, synaptic transmission and re-uptake was undertaken. Principal Findings Directionally consistent and biologically plausible overlapping and specific changes were detected: 14/25 of the human genes and 12/25 of the rat genes showed nominally significant differences in gene expression (global p values: 9×10−14, 7×10−11 respectively). Principal FDR-corrected findings were that GABBR1 was down-regulated in alcoholics, cocaine addicts and P rats with congruent findings in NSF, implicated in GABAB signaling efficacy, potentially resulting in increased synaptic GABA. GABRG2, encoding the gamma2 subunit required for postsynaptic clustering of GABAA receptors together with GPHN, encoding the associated scaffolding protein gephryin, were both down-regulated in alcoholics and cocaine addicts but were both up-regulated in P rats. There were also expression changes specific to cocaine addicts (GAD1, GAD2), alcoholics (GABRA2) and P rats (ABAT, GABRG3). Conclusions/Significance Our study confirms the involvement of the GABAergic system in alcoholism but also reveals a hippocampal GABA input in cocaine addiction. Congruent findings in human addicts and P rats provide clues to predisposing factors for alcohol and drug addiction. Finally, the results of this study have therapeutic implications.
Attention bias modification treatment for pediatric anxiety disorders: a randomized controlled trial.

OBJECTIVE While attention bias modification (ABM) is a promising novel treatment for anxiety disorders, clinical trial data remain restricted to adults. The authors examined whether ABM induces greater reductions in pediatric anxiety symptoms and symptom severity than multiple control training interventions. METHOD From a target sample of 186 treatment-seeking children at a hospital-based child anxiety clinic, 40 patients with an ongoing anxiety disorder who met all inclusion criteria were enrolled in the study. Children were randomly assigned to one of three conditions: ABM designed to shift attention away from threat; placebo attention training using stimuli identical to those in the ABM condition; and placebo attention training using only neutral stimuli. All participants completed four weekly 480-trial sessions (1,920 total trials). Before and after the attention training sessions, children's clinical status was determined via semistructured interviews and questionnaires. Reduction in the number of anxiety symptoms and their severity was compared across the three groups. RESULTS Change in the number of anxiety symptoms and their severity differed across the three conditions. This reflected significant reductions in the number of anxiety symptoms and symptom severity in the ABM condition but not in the placebo attention training or placebo-neutral condition. CONCLUSIONS ABM, compared with two control conditions, reduces pediatric anxiety symptoms and severity. Further study of efficacy and underlying mechanisms is warranted.
Strigolactones: mediators of osmotic stress responses with a potential for agrochemical manipulation of crop resilience

After quickly touching upon general aspects of strigolactone biology and functions, including structure, synthesis, and perception, this review focuses on the role and regulation of the strigolactone pathway during osmotic stress, in light of the most recent research developments. We discuss available data on organ-specific dynamics of strigolactone synthesis and interaction with abscisic acid in the acclimatization response, with emphasis on the ecophysiological implications of the effects on the stomatal closure process. We highlight the importance of considering roots and shoots separately as well as combined versus individual stress treatments; and of performing reciprocal grafting experiments to work out organ contributions and long-distance signalling events and components under more realistic conditions. Finally, we elaborate on the question of if and how synthetic or natural strigolactones, alone or in combination with crop management strategies such as grafting, hold potential to maximize crop resilience to abiotic stresses.
Characterizing HIV Medication Adherence for Virologic Success Among Individuals Living With HIV/AIDS: Experience With the CNS HIV Antiretroviral Therapy Effects Research (CHARTER) Cohort

Antiretroviral therapy (ART) has changed HIV-related illness from terminal to chronic by suppressing viral load which results in immunologic and clinical improvement. Success with ART is dependent on optimal adherence, commonly categorized as > 95%. As medication type, class and frequency of use continue to evolve, we assessed adherence levels related to viral suppression. Using a cross-sectional analysis with secondary data (n = 381) from an ongoing multi-site study on impact of ART on the Central Nervous System (CNS), we compared self-reported adherence rates with biological outcomes of HIV-RNA copies/ml, and CD4 cell/mm3. Adherence to ART measures included taking all prescribed medication as directed on schedule and following dietary restrictions. While depression was a barrier to adherence, undetectable viral suppression was achieved at pill adherence percentages lower than 95%. Practice, research and policy implications are discussed in the context of patient-, provider-, and system-level factors influencing adherence to ART.
Conformational differences in protein disulfide linkages between normal hair and hair from subjects with trichothiodystrophy: A quantitative analysis by Raman microspectroscopy

Raman spectra of normal hair shafts and hair shafts from patients exhibiting trichothiodystrophy (TTD) were obtained using line focus laser illumination. Because hair from TTD patients has a significant decrease in the content of the sulfur‐containing amino acids in comparison to normal hair, the 550–500 cm−1 disulfide stretching mode region of the Raman spectrum was examined in detail. A quantitative spectral analysis demonstrates significant increases in the two energetically less favored gauche–gauche–trans (g‐g‐t) and trans–gauche–trans (t‐g‐t) forms. These observations suggest that the increased amounts of these less stable disulfide conformers are contributing factors to or associated with the hair brittleness observed for this congenital disorder. Structure–spectra correlations for the three dominant disulfide conformers are confirmed by quantum chemical calculations using modern density functional theory (DFT). © 2006 Wiley Periodicals, Inc. Biopolymers 82: 615–622, 2006
A comparison study of multivariate fixed models and Gene Association with Multiple Traits (GAMuT) for next‐generation sequencing

In this paper, extensive simulations are performed to compare two statistical methods to analyze multiple correlated quantitative phenotypes: (1) approximate F‐distributed tests of multivariate functional linear models (MFLM) and additive models of multivariate analysis of variance (MANOVA), and (2) Gene Association with Multiple Traits (GAMuT) for association testing of high‐dimensional genotype data. It is shown that approximate F‐distributed tests of MFLM and MANOVA have higher power and are more appropriate for major gene association analysis (i.e., scenarios in which some genetic variants have relatively large effects on the phenotypes); GAMuT has higher power and is more appropriate for analyzing polygenic effects (i.e., effects from a large number of genetic variants each of which contributes a small amount to the phenotypes). MFLM and MANOVA are very flexible and can be used to perform association analysis for (i) rare variants, (ii) common variants, and (iii) a combination of rare and common variants. Although GAMuT was designed to analyze rare variants, it can be applied to analyze a combination of rare and common variants and it performs well when (1) the number of genetic variants is large and (2) each variant contributes a small amount to the phenotypes (i.e., polygenes). MFLM and MANOVA are fixed effect models that perform well for major gene association analysis. GAMuT can be viewed as an extension of sequence kernel association tests (SKAT). Both GAMuT and SKAT are more appropriate for analyzing polygenic effects and they perform well not only in the rare variant case, but also in the case of a combination of rare and common variants. Data analyses of European cohorts and the Trinity Students Study are presented to compare the performance of the two methods.
Construction and Use of Glycan Microarrays

Glycosylation is an important post‐translational modification that influences many biological processes critical for development, normal physiologic function, and diseases. Unfortunately, progress toward understanding the roles of glycans in biology has been slow due to the challenges of studying glycans and the proteins that interact with them. Glycan microarrays provide a high‐throughput approach for the rapid analysis of carbohydrate‐macromolecule interactions. Protocols detailed here are intended to help laboratories with basic familiarity of DNA or protein microarrays to begin printing and performing assays using glycan microarrays. Basic and advanced data processing are also detailed, along with strategies for improving reproducibility of data collected with glycan arrays. Curr. Protoc. Chem Biol. 2:37‐53. © 2010 by John Wiley & Sons, Inc.