Miracle-dz/UniFAR-FTUs huggingface dataset:
Static type inference for parametric classes

Central features of object-oriented programming are method inheritance and data abstraction attained through hierarchical organization of classes. Recent studies show that method inheritance can be nicely supported by ML style type inference when extended to labeled records. This is based on the fact that a function that selects a field ƒ of a record can be given a polymorphic type that enables it to be applied to any record which contains a field ƒ. Several type systems also provide data abstraction through abstract type declarations. However, these two features have not yet been properly integrated in a statically checked polymorphic type system. This paper proposes a static type system that achieves this integration in an ML-like polymorphic language by adding a class construct that allows the programmer to build a hierarchy of classes connected by multiple inheritance declarations. Moreover, classes can be parameterized by types allowing “generic” definitions. The type correctness of class declarations is statically checked by the type system. The type system also infers a principal scheme for any type correct program containing methods and objects defined in classes.
Responses to Elevated c-di-GMP Levels in Mutualistic and Pathogenic Plant-Interacting Bacteria

Despite a recent burst of research, knowledge on c-di-GMP signaling pathways remains largely fragmentary and molecular mechanisms of regulation and even c-di-GMP targets are yet unknown for most bacteria. Besides genomics or bioinformatics, accompanying alternative approaches are necessary to reveal c-di-GMP regulation in bacteria with complex lifestyles. We have approached this study by artificially altering the c-di-GMP economy of diverse pathogenic and mutualistic plant-interacting bacteria and examining the effects on the interaction with their respective host plants. Phytopathogenic Pseudomonas and symbiotic Rhizobium strains with enhanced levels of intracellular c-di-GMP displayed common free-living responses: reduction of motility, increased production of extracellular polysaccharides and enhanced biofilm formation. Regarding the interaction with the host plants, P. savastanoi pv. savastanoi cells containing high c-di-GMP levels formed larger knots on olive plants which, however, displayed reduced necrosis. In contrast, development of disease symptoms in P. syringae-tomato or P. syringae-bean interactions did not seem significantly affected by high c-di-GMP. On the other hand, increasing c-di-GMP levels in symbiotic R. etli and R. leguminosarum strains favoured the early stages of the interaction since enhanced adhesion to plant roots, but decreased symbiotic efficiency as plant growth and nitrogen contents were reduced. Our results remark the importance of c-di-GMP economy for plant-interacting bacteria and show the usefulness of our approach to reveal particular stages during plant-bacteria associations which are sensitive to changes in c-di-GMP levels.
Dynamics of learning and recall at excitatory recurrent synapses and cholinergic modulation in rat hippocampal region CA3

Hippocampal region CA3 contains strong recurrent excitation mediated by synapses of the longitudinal association fibers. These recurrent excitatory connections may play a dominant role in determining the information processing characteristics of this region. However, they result in feedback dynamics that may cause both runaway excitatory activity and runaway synaptic modification. Previous models of recurrent excitation have prevented unbounded activity using biologically unrealistic techniques. Here, the activation of feedback inhibition is shown to prevent unbounded activity, allowing stable activity states during recall and learning. In the model, cholinergic suppression of synaptic transmission at excitatory feedback synapses is shown to determine the extent to which activity depends upon new features of the afferent input versus components of previously stored representations. Experimental work in brain slice preparations of region CA3 demonstrates the cholinergic suppression of synaptic transmission in stratum radiatum, which contains synapses of the longitudinal association fibers.
Research participation, protected time, and research output by family physicians in family medicine residencies.

BACKGROUND AND OBJECTIVES The Future of Family Medicine project concluded that research must become a greater part of the culture of the specialty. We examined the participation of family physician residency faculty in research, their protected time, and their research output and how these varied by program type. METHODS This was a cross-sectional survey of all family medicine residency programs in the United States. The response rate was 66% (298/453). RESULTS The majority of programs reported at least one family physician who participates in research, though the medical school-based (MSB) programs reported a higher total number of faculty than the community-based, medical school affiliated (MSA) programs (9.53 versus 2.72) and percentage of faculty (56% versus 37%). Substantially more MSB programs reported that they had at least one family physician with significant protected time for research (48% versus 7% for > 25% protected time) or any protected time (69% for MSB versus 45% for MSA). MSB programs and MSA programs reported similar success at producing at least one poster or paper for national meetings within the last 3 years (63% versus 41%) but not for published papers (86% versus 43%). CONCLUSIONS We found that only about half of the family medicine residencies produced any nationally recognized research over a 3-year period and that this represents only a small improvement over the last 10 years. Our findings suggest that more support is needed if research is to become an integral part of the culture of family medicine.
Pharmacokinetics and pharmacodynamics of thiopentone

The induction doses of thiopentone in eight elderly male patients (60–80 years) were significantly lower (p < 0.01) than in eight young male patients (ranges 3.09–5.06 mg/kg body weight in the elderly and 4.88–8.11 mg/kg in the young). The sleep concentrations in venous as well as in arterial blood did not differ between the two groups. In the elderly the arterial concentrations were significantly higher than the venous (p < 0.05). A three compartment open model was used to describe the disappearance of the drug from the venous blood. Significant increases were found in V3(means 145.9 and 51.2 litres) and in T½β(means 781 and427 minutes) in the elderly. The redistribution rate constant, K1,2, was decreased in the elderly (p < 0.05).
Nucleotide Sequence Analysis of Hypervariable Junctions of Haemophilus influenzae Pilus Gene Clusters

ABSTRACT Haemophilus influenzae pili are surface structures that promote attachment to human epithelial cells. The five genes that encode pili, hifABCDE, are found inserted in genomes either between pmbA and hpt (hif-1) or between purE and pepN (hif-2). We determined the sequence between the ends of the pilus clusters and bordering genes in a number of H. influenzae strains. The junctions of the hif-1 cluster (limited to biogroup aegyptius isolates) are structurally simple. In contrast,hif-2 junctions are highly diverse, complex assemblies of conserved intergenic sequences (including genes hicA andhicB) with evidence of frequent recombination. Variation athif-2 junctions seems to be tied to multiple copies of a 23-bp Haemophilus intergenic dyad sequence. Thehif-1 cluster appears to have originated in biogroup aegyptius strains from invasion of the hpt-pmbA region by a DNA template containing the hif-2 genes with termini in the hairpin loop of flanking intergenic dyad sequences. The pilus gene clusters are an interesting model of a mobile “pathogenicity island” not associated with a phage, transposon, or insertion element.
Random Projection for High Dimensional Data Clustering: A Cluster Ensemble Approach

We investigate how random projection can best be used for clustering high dimensional data. Random projection has been shown to have promising theoretical properties. In practice, however, we find that it results in highly unstable clustering performance. Our solution is to use random projection in a cluster ensemble approach. Empirical results show that the proposed approach achieves better and more robust clustering performance compared to not only single runs of random projection/clustering but also clustering with PCA, a traditional data reduction method for high dimensional data. To gain insights into the performance improvement obtained by our ensemble method, we analyze and identify the influence of the quality and the diversity of the individual clustering solutions on the final ensemble performance.
Xenopus TACC1 is a microtubule plus‐end tracking protein that can regulate microtubule dynamics during embryonic development

Microtubule plus‐end dynamics are regulated by a family of proteins called plus‐end tracking proteins (+TIPs). We recently demonstrated that the transforming acidic coiled‐coil (TACC) domain family member, TACC3, can function as a +TIP to regulate microtubule dynamics in Xenopus laevis embryonic cells. Although it has been previously reported that TACC3 is the only TACC family member that exists in Xenopus, our examination of its genome determined that Xenopus, like all other vertebrates, contains three TACC family members. Here, we investigate the localization and function of Xenopus TACC1, the founding member of the TACC family. We demonstrate that it can act as a +TIP to regulate microtubule dynamics, and that the conserved C‐terminal TACC domain is required for its localization to plus‐ends. We also show that, in Xenopus embryonic mesenchymal cells, TACC1 and TACC3 are each required for maintaining normal microtubule growth speed but exhibit some functional redundancy in the regulation of microtubule growth lifetime. Given the conservation of TACC1 in Xenopus and other vertebrates, we propose that Xenopus laevis is a useful system to investigate unexplored cell biological functions of TACC1 and other TACC family members in the regulation of microtubule dynamics. © 2015 The Authors. Cytoskeleton, Published by Wiley Periodicals, Inc.
Using brain organoids to understand Zika virus-induced microcephaly

ABSTRACT Technologies to differentiate human pluripotent stem cells into three-dimensional organized structures that resemble in vivo organs are pushing the frontiers of human disease modeling and drug development. In response to the global health emergency posed by the Zika virus (ZIKV) outbreak, brain organoids engineered to mimic the developing human fetal brain have been employed to model ZIKV-induced microcephaly. Here, we discuss the advantages of brain organoids over other model systems to study development and highlight recent advances in understanding ZIKV pathophysiology and its underlying pathogenesis mechanisms. We further discuss perspectives on overcoming limitations of current organoid systems for their future use in ZIKV research. Summary: This Spotlight article summarises the latest advances in using cerebral organoids to model Zika virus infection and the resulting pathology.
The relationship between ethical leadership and core job characteristics.

Summary In the current study, we draw on the original job characteristics model (JCM) and on an elaborated model of work design to examine relationships between ethical leadership, task significance, job autonomy, effort, and job performance. We suggest that leaders with strong ethical commitments who regularly demonstrate ethically normative behavior can have an impacton the JCM elementsof tasksignificance and autonomy, thereby affecting anemployee’s motivation (willingness to exert effort), which in turn will be evidenced by indications of enhanced task performance and organizational citizenship behavior. We conducted a field study by surveying pairs of co-workers in a diverse set of organizations. Results provide support for a fully mediated model whereby task significance and effort fully mediate relationships between ethical leadership and subordinates’ job performance. Implications for future research on job design are discussed. Copyright # 2010 John Wiley & Sons, Ltd. At the heart of the job characteristics model (JCM, Hackman & Oldham, 1976) is the premise that leaders canshape intrinsic motivation bytheway inwhich theystructuretheobjectivecharacteristics of the work itself. 1 The theoretical model of job design was rooted in an examination of the ‘‘basic conditions that promote high performance motivation and satisfaction at work,’’ in order ‘‘to determine how those conditions can be created’’ (Hackman & Oldham, 1976; p. 71). We argue that the conceptual and empirical developments of the JCM to date can be expanded to encompass a broader role for leaders. In particular, we suggest that leaders with strong ethical commitments who regularly demonstrate ethically normative behavior can have an impact on the JCM elements of task significance and autonomy, thereby affecting an employee’s motivation (willingness to exert effort), which in turn will be evidenced by indications of enhanced task performance and organizational citizenship behaviors.
PHASE FIELD MODELING OF SHEAR YIELDING AND CRAZING IN GLASSY POLYMER

Yunzhe Mao. M.S.M.E. , Purdue University, May 2014. Phase Field Modeling of Shear Yielding and Crazing in Glassy Polymer. Major Professor: Marisol Koslowski, School of Mechanical Engineering. Glassy polymers are very important in industrial and commercial components manufacturing. For instance, it is used to manufacture polymer-matrix composites, the type of composite used in the Dreamliner 787. But this kind of material is also limited by its tendency to fail in brittle manner. In this study, we use phase field model to characterize the yielding condition of glassy amorphous polymer under a wide range of loading conditions. The main failure mechanisms in amorphous glassy polymers, such as poly-methyl-methacrylate (PMMA), are crazing and shear yielding. Crazing is formed because of the nucleation of micro-voids in the location of stress concentrations and shear yielding plastic deformation in the form of shear band. A Phase field model based on Griffith’s theory is used to model the response of material under different loading condition ranging from pure deviatoric to isotropic volume expansion. The benefits of phase field modeling is that it can reduce the implementation complexity as it does not need to track the discontinuities in the displacement field. The model predictions for the macroscopic volumetric and deviatoric stress-strain response and phase field contour of PMMA are then compared with experimental data reported in ix the literature and atomistic simulation’s results whose yielding criterion is energy-based and does not make assumption on whether the deformation is dominated by deviatoric strain or volumetric strain but the rate of mechanical work per unit volume. Our results shows that phase field model can the response of crazing behavior accurately in three dimensions. The outcome indicate that a 27% reduction of phase field damage parameter will achieved before the crazing emerges and the material yielding for any loading condition.
Juvenile Male Rats Exposed to a Low-Dose Mixture of Twenty-Seven Environmental Chemicals Display Adverse Health Effects

Humans are exposed to a large number of environmental chemicals in their daily life, many of which are readily detectable in blood or urine. It remains uncertain if these chemicals can cause adverse health effects when present together at low doses. In this study we have tested whether a mixture of 27 chemicals administered orally to juvenile male rats for three months could leave a pathophysiological footprint. The mixture contained metals, perfluorinated compounds, PCB, dioxins, pesticides, heterocyclic amines, phthalate, PAHs and others, with a combined dose of 0.16 (Low dose), 0.47 (Mid dose) or 1.6 (High dose) mg/kg bw/day. The lowest dose was designed with the aim of obtaining plasma or urine concentrations in rats at levels approaching those observed in humans. Some single congeners were administered at doses representative of combined doses for chemical groups. With this baseline, we found effects on weight, histology and gene expression in the liver, as well as changes to the blood plasma metabolome in all exposure groups, including low-dose. Additional adverse effects were observed in the higher dosed groups, including enlarged kidneys and alterations to the metabolome. No significant effects on reproductive parameters were observed.
Mitotic Recombination: Why? When? How? Where?

DNA damage repair, loss of heterozygosity, and chromosome rearrangement are important aspects of genome stability, and all are tied to mitotic recombination. Despite the importance of mitotic recombination, the most basic questions about this process remain poorly understood. This is in part because mitotic recombination, in contrast to meiotic recombination, is rare on a per cell division basis [1]. A number of systems have been devised to detect or select for mitotic recombination. In this issue of PLoS Genetics, Lee et al. [2] describe a novel system that represents a major step forward in the study of spontaneous mitotic recombination events. Their studies have given us new insights into the why, when, how, and where of mitotic recombination. Mitotic recombination was first described by Stern in his classic Drosophila experiments [3]. For Stern, “recombination” referred only to reciprocal crossovers (RCOs) (Figure 1A). A severe limitation of most RCO assays is that only one of the two reciprocal products can be recovered. Barbera and Petes [4] devised a clever method to recover both products of RCOs in Saccharomyces cerevisiae. They used this method to measure rates of spontaneous and induced mitotic recombination. Lee et al. have brought increased power to this assay by performing it in diploids with ∼0.5% heterology between the sequences of homologous chromosomes. This design allowed mapping of RCOs at high resolution, and also allowed study of another aspect of recombination—gene conversion (Figure 1C and 1D). Their analysis led to several key findings that provide unique and sometimes surprising insights into questions about mitotic recombination. Figure 1 Reciprocal crossovers and gene conversion.
Assistive technologies at home for people with a memory disorder

The aim of this study was to assess in practice whether assistive technologies support and facilitate the work of a family caregiver or care staff, and whether these technologies support the independence of a person with a memory disorder. A comprehensive set of supportive devices and alarm systems were experimentally tested in the care of five test subjects in an assisted living facility by eight nurses, and in the care of four test subjects in a home environment by three family caregivers and one care team. Questionnaires, diaries and logged data were used to evaluate the benefits of the devices. Simple aids and alarm systems that did not need much adjusting were considered most useful by caregivers and nurses, though multiple false alarms occurred during the test period. Technical connection problems, complex user interface, and inadequate sound quality were the primary factors reducing the utility of the tested devices. Further experimental research is needed to evaluate the utility of assistive technologies in different stages of a memory disorder.
Vision in a Phase 3 Trial of Natalizumab for Multiple Sclerosis: Relation to Disability and Quality of Life

Background: Low-contrast visual acuity (LCVA), a sensitive measure of visual function in multiple sclerosis (MS), demonstrated treatment effects as a secondary outcome measure in the Phase 3 trial of natalizumab, AFFIRM. In these posttrial analyses, we studied the relation of visual function to quality of life (QOL), magnetic resonance imaging (MRI) measures, and Expanded Disability Status Scale (EDSS) scores. Methods: At baseline and at 52 and 104 weeks in AFFIRM, patients underwent binocular testing of LCVA (1.25% and 2.5% contrast) and high-contrast visual acuity (HCVA). Vision-specific QOL was assessed by the Impact of Visual Impairment Scale (IVIS), whereas the SF-36 Health Survey and Visual Analog Scale were administered as generic QOL measures and the EDSS as a measure of neurologic impairment. Results: Among QOL measures, IVIS scores showed the most significant correlations with visual dysfunction at all time points in the trial (r= −0.25 to −0.45, P < 0.0001 for LCVA and HCVA). Higher MRI T1- and T2-lesion volumes were also associated with worse vision scores at all time points (P < 0.0001). Clinically meaningful worsening (progression) of LCVA was noted in substantial proportions of patients in AFFIRM and was prevalent even among those without EDSS progression over 2 years (21.9% with LCVA progression at 2.5% contrast; 26.2% at 1.25% contrast). HCVA worsened in only 3.7% of patients without EDSS progression. Conclusions: Loss of visual function, particularly as measured by LCVA, was common in AFFIRM, occurring in >20% of patients. Both LCVA and HCVA scores reflect vision-specific aspects of QOL, but LCVA provides information about disability progression not entirely captured by the EDSS. Vision represents a key dimension of outcome assessment for MS and adds valuable information on disability and QOL that can be useful to clinicians.
Human Visceral Leishmaniasis in Kermanshah Province, Western Iran, During 2011-2012

Background Visceral leishmaniasis (VL) or kala-azar is a parasitic disease caused by the species of Leishmania donovani complex. It is endemic in some parts of provinces of Iran. According to the reported cases of VL in Kermanshah Province in recent years, this study was conducted to determine the seroprevalence of VL in high risk villages of the province. Methods Totally, 1622 serum samples obtained from children under 15 years old and 178 from adults in 22 villages of studied areas. Serum samples were examined by direct agglutination test (DAT) for the detection of anti-Leishmania antibodies. Data were analyzed using SPSS software ver.11. 5. Results Only 6 serum samples (0.33%) showed anti-Leishmania antibodies against L.infantum at titers ≥ 1/3200. Four of the seropositive cases had a history of kala-azar and Leishman bodies were seen in their bone marrows. The highest (0.5%) and lowest (0.29%) seroprevalence was seen in the age groups of 5-9 and 10-14 years old, respectively. None of the adults were seropositive. There were not any significant differences between the rate of seropositivity in males (0.36%) and females (0.31%). 66.7% of seropositive individuals showed clinical manifestations. The most important symptoms in Kala-azar patients were fever, hepato-spleenomegally and anemia. Conclusion Kala-azar is occurred sporadically in Kermanshah Province. But presence of significant number of positive sera confirms the necessity for attention of people and clinicians to kala-azar.
Generalized Spatial Pulse Position Modulation for Optical Wireless Communications

In this paper, we investigate the performance of a spatial modulation scheme that combines the energy efficiency of pulse position modulation (PPM) with the spectral efficiency of generalized space shift keying (GSSK) for optical wireless communication system. The combined scheme is called generalized spatial pulse position modulation (GSPPM). We present the error performance analysis and validate the results through simulation. Error performance results show that the upper bound derived in the theoretical analysis is tight for all cases when the symbol error rate is below 0.1. The influence of parameters such as channel path gain and number of PPM slots on GSPPM's performance is illustrated. GSPPM is compared with some of the existing spatial modulation techniques, and results show that GSPPM provides an attractive trade-off between energy and spectral efficiency.