Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary History of GS3, a Gene Conferring Grain Length in Rice

Unlike maize and wheat, where artificial selection is associated with an almost uniform increase in seed or grain size, domesticated rice exhibits dramatic phenotypic diversity for grain size and shape. Here we clone and characterize GS3, an evolutionarily important gene controlling grain size in rice. We show that GS3 is highly expressed in young panicles in both short- and long-grained varieties but is not expressed in leaves or panicles after flowering, and we use genetic transformation to demonstrate that the dominant allele for short grain complements the long-grain phenotype. An association study revealed that a C to A mutation in the second exon of GS3 (A allele) was associated with enhanced grain length in Oryza sativa but was absent from other Oryza species. Linkage disequilibrium (LD) was elevated and there was a 95.7% reduction in nucleotide diversity (θπ) across the gene in accessions carrying the A allele, suggesting positive selection for long grain. Haplotype analysis traced the origin of the long-grain allele to a Japonica-like ancestor and demonstrated introgression into the Indica gene pool. This study indicates a critical role for GS3 in defining the seed morphologies of modern subpopulations of O. sativa and enhances the potential for genetic manipulation of grain size in rice.
Interaction with a Therapy Dog Enhances the Effects of Social Story Method in Autistic Children

AbstractThis study explored the effects of a combination between two methods that have proved to enhance the social abilities of autistic children—Social Story and Animal Assisted Therapy. The main hypothesis of this investigation was that a naturally enriched social environment (i.e., the presence of a therapy dog) improves the effectiveness of Social Story method. Two social skills were targeted: (1) the ability to greet a social partner and (2) the ability to introduce oneself to a social partner, by using a standard single-subject research design. Three preschool autistic children were included in the study. The dependent variables were the frequency of the appropriate social interactions relevant to the target social skill, the level of prompt needed to provide the expected social response, and the frequency of social initiations. The presence of the therapy dog while reading the social story increased the frequency of social initiations and decreased the level of social prompt needed to elicit social responses from children with autism.
Pathogen trafficking pathways and host phosphoinositide metabolism

Phosphoinositide (PI) glycerolipids are key regulators of eukaryotic signal transduction, cytoskeleton architecture and membrane dynamics. The host cell PI metabolism is targeted by intracellular bacterial pathogens, which evolved intricate strategies to modulate uptake processes and vesicle trafficking pathways. Upon entering eukaryotic host cells, pathogenic bacteria replicate in distinct vacuoles or in the host cytoplasm. Vacuolar pathogens manipulate PI levels to mimic or modify membranes of subcellular compartments and thereby establish their replicative niche. Legionella pneumophila, Brucella abortus, Mycobacterium tuberculosis and Salmonella enterica translocate effector proteins into the host cell, some of which anchor to the vacuolar membrane via PIs or enzymatically turnover PIs. Cytoplasmic pathogens target PI metabolism at the plasma membrane, thus modulating their uptake and antiapoptotic signalling pathways. Employing this strategy, Shigella flexneri directly injects a PI‐modifying effector protein, while Listeria monocytogenes exploits PI metabolism indirectly by binding to transmembrane receptors. Thus, regardless of the intracellular lifestyle of the pathogen, PI metabolism is critically involved in the interactions with host cells.
A Markov Decision Process Analysis of the Cold Start Problem in Bayesian Information Filtering

We consider the information filtering problem, in which we face a stream of items, and must decide which ones to forward to a user to maximize the number of relevant items shown, minus a penalty for each irrelevant item shown. Forwarding decisions are made separately in a personalized way for each user. We focus on the cold-start setting for this problem, in which we have limited historical data on the user's preferences, and must rely on feedback from forwarded articles to learn which the fraction of items relevant to the user in each of several item categories. Performing well in this setting requires trading exploration vs. exploitation, forwarding items that are likely to be irrelevant, to allow learning that will improve later performance. In a Bayesian setting, and using Markov decision processes, we show how the Bayes-optimal forwarding algorithm can be computed efficiently when the user will examine each forwarded article, and how an upper bound on the Bayes-optimal procedure and a heuristic index policy can be obtained for the setting when the user will examine only a limited number of forwarded items. We present results from simulation experiments using parameters estimated using historical data from arXiv.org.
Does regulatory enforcement work? A panel analysis of OSHA enforcement

This study tests the impact of OSHA enforcement on workplace injuries. Using data on injuries and OSHA inspections for a panel of 6,842 large manufacturing plants between 1979 and 1985, we find significant specific deterrence effects. Inspections imposing penalties induce a 22% decline in injuries in the inspected plant during the following few years. We suggest that narrow deterrence perspectives have led to unduly pessimistic assumptions about enforcement effectiveness and that a managerial attention model is more consistent with our findings. In a technical appendix we describe the Chamberlain technique, a powerful analytic approach for panel data that provides tests and corrections for potential biases endemic in enforcement studies, including unmeasured heterogeneity among units, serially correlated dependent variables, and endogeneity of inspections. We argue that more empirical studies of enforcement impacts are necessary to provide an appropriate perspective for descriptive and analytic studies appraising regulatory behavior.
Expression of Mesenchyme-Specific Gene HMGA2 in Squamous Cell Carcinomas of the Oral Cavity

Carcinoma cells of epithelial origin are predisposed to acquire a fibroblastic feature during progression of neoplasm referred to as the epithelial-mesenchymal transition. HMGA2 is an architectural transcriptional factor that is expressed in the undifferentiated mesenchyme and initiates mesenchymal tumor formation. However, the biological consequence of the expression in the pathology of epithelial-type carcinomas is controversial. The present study was conducted to dissect the expression pattern in oral squamous cell carcinomas. HMGA2 was detected exclusively in carcinoma cell lines and tissues, but not in normal keratinocytes and gingival, by conventional reverse transcription-PCR. Quantitative real-time reverse transcription-PCR demonstrated 160-fold more HMGA2 expression in carcinoma tissues than in normal gingiva and 11-fold more HMGA2 expression in carcinoma cell lines than in normal keratinocytes. HMGA2 expression was observed by immunohistochemistry in 73.8% of 42 carcinomas and localized to the invasive front, where the cells exhibit the epithelial-mesenchymal transition. Fourteen patients who had been classified into a group without lymph node metastasis were positive for HMGA2 staining, and the disease recurred. Furthermore, carcinomas from all 23 patients who died of tumor recurrence stained for HMGA2, and HMGA2 staining was correlated to long-term survival of patients (P < 0.01). Multivariate risk factor analysis demonstrated that HMGA2 expression was an independent prognostic value for disease-specific overall survival (P < 0.01). These results suggest that HMGA2 contributes to the aggressiveness of carcinoma and that detection of HMGA2 expression is a useful predictive and prognostic tool in clinical management of oral carcinomas.
A Reinforcement learning-based cognitive MAC protocol

A Multi-Channel Cognitive MAC Protocol for adhoc cognitive networks that uses a distributed learning reinforcement scheme is proposed in this paper. The proposed protocol learns the Primary User (PU) traffic characteristics and then selects the best channel to transmit. The scheme, which addresses overlay cognitive networks,avoids collision with the PU nodes and manages to exceed the performance of the less adaptive statistical channel selection schemes in normal and especially bursty traffic environments. The simulation analysis results have shown that the performance of our proposed scheme outperforms that of the CREAM-MAC scheme.
Competing with Humans at Fantasy Football: Team Formation in Large Partially-Observable Domains

We present the first real-world benchmark for sequentially-optimal team formation, working within the framework of a class of online football prediction games known as Fantasy Football. We model the problem as a Bayesian reinforcement learning one, where the action space is exponential in the number of players and where the decision maker's beliefs are over multiple characteristics of each footballer. We then exploit domain knowledge to construct computationally tractable solution techniques in order to build a competitive automated Fantasy Football manager. Thus, we are able to establish the baseline performance in this domain, even without complete information on footballers' performances (accessible to human managers), showing that our agent is able to rank at around the top percentile when pitched against 2.5M human players.
Misexpression of FATTY ACID ELONGATION1 in the Arabidopsis Epidermis Induces Cell Death and Suggests a Critical Role for Phospholipase A2 in This Process[W]

Very-long-chain fatty acids (VLCFAs) are important functional components of various lipid classes, including cuticular lipids in the higher plant epidermis and lipid-derived second messengers. Here, we report the characterization of transgenic Arabidopsis thaliana plants that epidermally express FATTY ACID ELONGATION1 (FAE1), the seed-specific β-ketoacyl-CoA synthase (KCS) catalyzing the first rate-limiting step in VLCFA biosynthesis. Misexpression of FAE1 changes the VLCFAs in different classes of lipids but surprisingly does not complement the KCS fiddlehead mutant. FAE1 misexpression plants are similar to the wild type but display an essentially glabrous phenotype, owing to the selective death of trichome cells. This cell death is accompanied by membrane damage, generation of reactive oxygen species, and callose deposition. We found that nuclei of arrested trichome cells in FAE1 misexpression plants cell-autonomously accumulate high levels of DNA damage, including double-strand breaks characteristic of lipoapoptosis. A chemical genetic screen revealed that inhibitors of KCS and phospholipase A2 (PLA2), but not inhibitors of de novo ceramide biosynthesis, rescue trichome cells from death. These results support the functional role of acyl chain length of fatty acids and PLA2 as determinants for programmed cell death, likely involving the exchange of VLCFAs between phospholipids and the acyl-CoA pool.
Systemic sclerosis prevalence and comorbidities in the US, 2001-2002.

OBJECTIVE Large, population-based assessments of systemic sclerosis (SSc) prevalence and comorbidity in the United States (US) are rare. We explored autoimmune disease and other comorbidity patterns among SSc patients in the US from 2001 to 2002 and compared these with controls. RESEARCH DESIGN AND METHODS Two US datasets with patient-level medical and drug claims were used to assess SSc prevalence and comorbidity: IMS Health Integrated Administrative Claims Database (IMS Health) and the MarketScan Commercial Claims and Encounters Database (MarketScan). SSc patients and comorbidities were identified by International Classification of Diseases (ICD), 9th revision diagnostic codes appearing on medical claims. Patients without SSc diagnostic codes (controls) were selected and matched 4:1 to SSc patients based on sex, age, Census Bureau region, and previous insurance coverage. The prevalence relative risk (RR) statistic compared comorbidity occurrence between SSc patients and controls, with 95% confidence intervals estimated using the Mantel-Haenszel method. Several sensitivity analyses tested methods used for identifying SSc cases and the prevalence of comorbidities. RESULTS In both databases, SSc prevalence was 0.05% using the standard population model, 0.03% under sensitivity analysis. Among SSc patients the risks for inflammatory bowel disease (IBD) and multiple sclerosis (MS) were notably higher across datasets than for those without SSc: RR 3.2-6.6 for MS, RR 2.1-2.2 for IBD, in MarketScan and IMS Health, respectively (p < 0.05 for all). The chronic disease burden of SSc patients was much higher than that of controls, as confirmed by two chronicity measures (Chronic Disease Score, Elixhauser Comorbidity Index). The risks for cardiovascular, renal, liver and several neuropsychiatric diseases were higher for SSc patients across both datasets. Sensitivity analyses supported these findings. CONCLUSIONS These data provide a population-based estimate of US prevalence of SSc and document the higher risk for certain other autoimmune diseases among SSc patients when compared to controls. Patients with SSc also had a higher chronic disease burden than those without SSc. These findings are limited by the unknown validity of ICD-9 codes for SSc case identification, unbalanced regional representation, and a likely 'healthy worker' effect in these databases.
A Common Reference Framework for Analyzing/Comparing Proteins and Ligands. Fingerprints for Ligands And Proteins (FLAP): Theory and Application

A fast new algorithm (Fingerprints for Ligands And Proteins or FLAP) able to describe small molecules and protein structures using a common reference framework of four-point pharmacophore fingerprints and a molecular-cavity shape is described in detail. The procedure starts by using the GRID force field to calculate molecular interaction fields, which are then used to identify particular target locations where an energetic interaction with small molecular features would be very favorable. The target points thus calculated are then used by FLAP to build all possible four-point pharmacophores present in the given target site. A related approach can be applied to small molecules, using directly the GRID atom types to identify pharmacophoric features, and this complementary description of the target and ligand then leads to several novel applications. FLAP can be used for selectivity studies or similarity analyses in order to compare macromolecules without superposing them. Protein families can be compared and clustered into target classes, without bias from previous knowledge and without requiring protein superposition, alignment, or knowledge-based comparison. FLAP can be used effectively for ligand-based virtual screening and structure-based virtual screening, with the pharmacophore molecular recognition. Finally, the new method can calculate descriptors for chemometric analysis and can initiate a docking procedure. This paper presents the background to the new procedure and includes case studies illustrating several relevant applications of the new approach.
Continuity of care and colorectal cancer screening by Vietnamese American patients.

BACKGROUND Colorectal cancer (CRC) screening rates among Asian Americans are 30-50% lower than among Whites. Using practice management and electronic medical records data from a community health center, we examined the association of CRC screening with continuity of care and comorbidity. These variables have not previously been studied in Asian American and limited-English proficient populations. METHODS After obtaining IRB approval, we extracted data in 2009 on age-eligible Vietnamese patients who had one or more clinic visits in the prior 24 months. Our analysis examined associations between CRC screening (per current US Preventive Services Task Force guidelines) and clinic site, demographics, insurance status, continuity of care, comorbidities, and provider characteristics. RESULTS We identified a total of 1,016 eligible patients (604 at Clinic 1 and 412 at Clinic 2). Adherence to CRC screening was lower for patients who were male; lacked insurance; had only one medical visit in the past 12 months; and had no assigned primary care provider. Our multivariable models showed higher screening rates among patients who were female; had public health insurance; and had more than one medical visit in the past 12 months, regardless of high or low continuity of care. CONCLUSIONS We found no association between higher continuity of care and CRC screening. Additional primary care systems research is needed to guide cancer screening interventions for limited-English proficient patients.
Limits on perceptual abstraction in reading: Asymmetric transfer between surface forms differing in typicality.

In 2 experiments and a rating study we examined asymmetric transfer of repetition benefit between two easily readable surface forms. Typed second occurrences showed benefit that was similar for words and pseudowords and did not depend on the surface form of the first occurrence. Handwritten second occurrences showed benefit only for words, and benefit was larger when first occurrences were handwritten than when typed. This pattern, which was unrelated to explicit memory, characterized both naming and lexical decision, and benefit transferred between tasks. These results tax current episodic accounts of repetition benefit that are based on retrieving perceptual records or conceptual interpretations, and they tax strongly abstractionist accounts that are based on extremely general visual analysis
CRITICAL EXAMINATION OF CANDIDATES' DIVERSITY COMPETENCE: RIGOROUS AND SYSTEMATIC ASSESSMENT OF CANDIDATES' EFFICACY TO TEACH DIVERSE STUDENT POPULATIONS

The National Center for Educational Statistics (NCES, 2010) continues to report substantial underachievement of diverse student populations in the nation's schools. After decades of focus on diversity and multicultural education, with integrating field and clinical practice, candidates continue to graduate without adequate knowledge, skills and dispositions to teach diverse students. The National Council of Accreditation of Teacher Education (NCATE) requires teacher education programs to engage in assessment practices that examine candidates' competence to teach diverse students and to inform the unit. In this article the authors discuss the need to triangulate the results of performance-based assessment and to systematically examine the growth of candidates' competence to teach every student. They propose a rigorous and systematic unit (i.e., teacher education program unit) assessment practice, using reliable and valid instruments to measure candidates' efficacy to teach diverse students, which will provide effective data for teacher education programs to become proactive to improve programs.
KIF5C S176 Phosphorylation Regulates Microtubule Binding and Transport Efficiency in Mammalian Neurons

Increased phosphorylation of the KIF5 anterograde motor is associated with impaired axonal transport and neurodegeneration, but paradoxically also with normal transport, though the details are not fully defined. JNK phosphorylates KIF5C on S176 in the motor domain; a site that we show is phosphorylated in brain. Microtubule pelleting assays demonstrate that phosphomimetic KIF5C(1-560)S176D associates weakly with microtubules compared to KIF5C(1-560)WT. Consistent with this, 50% of KIF5C(1-560)S176D shows diffuse movement in neurons. However, the remaining 50% remains microtubule bound and displays decreased pausing and increased bidirectional movement. The same directionality switching is observed with KIF5C(1-560)WT in the presence of an active JNK chimera, MKK7-JNK. Yet, in cargo trafficking assays where peroxisome cargo is bound, KIF5C(1-560)S176D-GFP-FRB transports normally to microtubule plus ends. We also find that JNK increases the ATP hydrolysis of KIF5C in vitro. These data suggest that phosphorylation of KIF5C-S176 primes the motor to either disengage entirely from microtubule tracks as previously observed in response to stress, or to display improved efficiency. The final outcome may depend on cargo load and motor ensembles.
On the Robustness of the Modality ­Effect: Attempting to Replicate a Basic Finding

Abstract.Two experiments were conducted to replicate the modality effect and to test two opposing theoretical explanations: From the visuo-spatial load hypothesis (as implied by the Cognitive Theory of Multimedia Learning), we derived the prediction that the modality effect depends on the need to simultaneously store and process text and pictorial information in the same working memory subsystem, which implies that the modality effect is not influenced by text length. However, based on the concurrent auditory recency hypothesis, we expected the modality effect to occur with very short texts only, irrespective of whether a picture is present. Adopting a German translation of the learning materials used by Moreno and Mayer (1999), we failed to detect a modality effect for sequential text-picture-presentation in Experiment 1. In Experiment 2, a modality effect was expected for simultaneous presentation of the same texts and pictures, yet again remained absent. We conclude with the suggestion that the apparen.
High impact of mobile units for mass HIV testing in Africa.

Despite the usefulness of voluntary counselling and testing centres implemented in Africa their limited capacity does not allow for vast testing of the general population. Therefore in order to increase the number of individuals tested for HIV with the aim of enhancing the scaling up we developed a strategy based on bringing the healthcare package much closer to the people by using mobile HIV testing units. We herein report the Cameroon experience of mobile HIV testing unit strategy demonstrating its effectiveness in reaching a great number of individuals including those without usual access to HIV testing facilities. (excerpt)
Fine Structure of the Human Translocation Protein 1 (HTP1/TLOC1) Gene

We characterized the genomic region corresponding to the human translocation protein 1 (HTP1/TLOC1) cDNA previously reported. An experiment using rapid amplification of cDNA ends revealed that the transcription initiation site was at 12 bp upstream from the translation initiation codon ATG. Using direct‐sequencing PCR, we determined precise intron/exon boundaries and intron‐exon composition of the gene. The gene region spanned 28 kb and was composed of eight exons and seven introns. The lengths of exons and introns range from 48 to > 1707 bp and from 0.25 to 8.2 kb, respectively. The translation initiation codon and the termination codon were located in exons 1 and 8, respectively. The nucleotide sequences of the introns were also determined in the region around the intron/exon boundaries for 63 to 442 bp. All of the sequences around the intron/exon boundaries were consistent with the 5′ and 3′ consensus sequences for splice junctions of transcribed genes. Putative lariat sequences were identified between 28 and 64 nucleotides from the 3′ splice junction for all seven introns. DNA walking experiments revealed a promoter region of 600 bp. The promoter region did not contain an apparent TATA box or a CAT box but did contain Evi‐1, GATA, v‐Myb, MZF1, and AP‐1 binding sites‐factors known as regulatory factors on expression of the gene in blood cells. Therefore, this gene may be one such gene.