Miracle-dz/UniFAR-FTUs huggingface dataset:
Letter to the Editor Partition-ligation–expectation-maximization Algorithm for Haplotype Inference with Single-nucleotide Polymorphisms

The mapping of SNPs in human genomes has generated a lot of interest from both the biomedical research community and industry. In conjunction with SNP mapping, researchers have shown that haplotypes possess considerably greater potential than the traditional single-SNP approach in disease-gene mapping and in our understanding of complex landscapes of linkage disequilib-rium (LD) (Goldstein 2001). In silico methods for hap-lotype reconstruction have attracted much attention because of their cost-effectiveness and accuracy (Tish-koff et al. 2000) and have played an important role in the definition of human haplotype block structure and in candidate-gene studies of complex traits (Tabor et al. 2002). In a recent publication, Niu et al. (2002) proposed a partition-ligation (PL) strategy and implemented it together with Gibbs sampling, to estimate haplotype phases for a large number of SNPs. Although the resulting program, HAPLOTYPER, has been in high demand from many research groups, a significant portion of researchers are also strongly interested in using an expectation-maximization (EM)–based algorithm. In the present letter, we describe how to combine the PL strategy with the EM algorithm and how to handle the local-mode problem. We also present a fast and robust method of computing the variance of the estimated haplotype frequencies. Some related issues concern the handling of missing data and the multiple imputations of haplotype phases. The EM algorithm is arguably the most popular statistical algorithm, because of its interpretability and stability. Compared to the Gibbs sampler, the EM approach is a deterministic procedure, requires less computing time, and is easier for convergence check. The output of the EM algorithm, if not trapped in a local mode, is the maximum-likelihood estimate (MLE), which possesses well-established statistical properties. However, the capability of most EM-based approaches is restricted to approximately one dozen loci, because of the memory constraint. A recently developed program, SNPHAP (see David Clayton's Web site [SNPHAP: A Program for Estimating Frequencies of Large Haplotypes of SNPs]), is an exception that, although different from the PL strategy , can handle many more linked loci by using a progressive extension technique. The essential steps of the PL strategy (Niu et al. 2002) are as follows: One first breaks down all of the marker loci into stretches of " atomistic " units and then uses either the EM algorithm or the Gibbs sampler to construct haplotypes for each unit and to rebuild the phase hierarchically, through a bottom-up approach. For example , …
Epigenetic Remodeling of Meiotic Crossover Frequency in Arabidopsis thaliana DNA Methyltransferase Mutants

Meiosis is a specialized eukaryotic cell division that generates haploid gametes required for sexual reproduction. During meiosis, homologous chromosomes pair and undergo reciprocal genetic exchange, termed crossover (CO). Meiotic CO frequency varies along the physical length of chromosomes and is determined by hierarchical mechanisms, including epigenetic organization, for example methylation of the DNA and histones. Here we investigate the role of DNA methylation in determining patterns of CO frequency along Arabidopsis thaliana chromosomes. In A. thaliana the pericentromeric regions are repetitive, densely DNA methylated, and suppressed for both RNA polymerase-II transcription and CO frequency. DNA hypomethylated methyltransferase1 (met1) mutants show transcriptional reactivation of repetitive sequences in the pericentromeres, which we demonstrate is coupled to extensive remodeling of CO frequency. We observe elevated centromere-proximal COs in met1, coincident with pericentromeric decreases and distal increases. Importantly, total numbers of CO events are similar between wild type and met1, suggesting a role for interference and homeostasis in CO remodeling. To understand recombination distributions at a finer scale we generated CO frequency maps close to the telomere of chromosome 3 in wild type and demonstrate an elevated recombination topology in met1. Using a pollen-typing strategy we have identified an intergenic nucleosome-free CO hotspot 3a, and we demonstrate that it undergoes increased recombination activity in met1. We hypothesize that modulation of 3a activity is caused by CO remodeling driven by elevated centromeric COs. These data demonstrate how regional epigenetic organization can pattern recombination frequency along eukaryotic chromosomes.
What are task-sets: a single, integrated representation or a collection of multiple control representations?

Performing two randomly alternating tasks typically results in higher reaction times (RTs) following a task switch, relative to a task repetition. These task switch costs (TSC) reflect processes of switching between control settings for different tasks. The present study investigated whether task sets operate as a single, integrated representation or as an agglomeration of relatively independent components. In a cued task switch paradigm, target detection (present/absent) and discrimination (blue/green/right-/left-tilted) tasks alternated randomly across trials. The target was either a color or an orientation singleton among homogeneous distractors. Across two trials, the task and target-defining dimension repeated or changed randomly. For task switch trials, agglomerated task sets predict a difference between dimension changes and repetitions: joint task and dimension switches require full task set reconfiguration, while dimension repetitions permit re-using some control settings from the previous trial. By contrast, integrated task sets always require full switches, predicting dimension repetition effects (DREs) to be absent across task switches. RT analyses showed significant DREs across task switches as well as repetitions supporting the notion of agglomerated task sets. Additionally, two event-related potentials (ERP) were analyzed: the Posterior-Contralateral-Negativity (PCN) indexing spatial selection dynamics, and the Sustained-Posterior-Contralateral-Negativity (SPCN) indexing post-selective perceptual/semantic analysis. Significant DREs across task switches were observed for both the PCN and SPCN components. Together, DREs across task switches for RTs and two functionally distinct ERP components suggest that re-using control settings across different tasks is possible. The results thus support the “agglomerated-task-set” hypothesis, and are inconsistent with “integrated task sets. ”
Does impaired primacy recall equal impaired long‐term storage?: Serial position effects in Huntington's disease and Alzheimer's disease

Immediate recall, delayed recall, and delayed recognition of items from the primacy (beginning) and recency (terminal) regions of a word list were examined in Huntington's disease (HD) patients, Alzheimer's disease (AD) patients, and age‐matched normal controls. The HD patients, relative to middle‐aged controls, exhibited poor immediate recall of primacy words, but intact retention over time of the words they had recalled initially, and intact recognition of all primacy words. These results suggest that poor primacy recall may not always signify impairment in long‐term storage (LTS), as is often presumed. Relative to elderly controls, AD patients also showed severely impaired immediate recall of primacy words but, unlike HD patients, exhibited markedly deficient retention and recognition of these words. Thus, in AD patients, it is likely that impaired LTS is a major factor contributing to poor primacy recall. Diverging patterns of results were also found for HD and AD patients' recency item recall and rec.
Stage-specific transcriptome of the malaria parasite in the red blood cell cycle

The World Health Organization has estimated that in 2015 there were 214 million cases of malaria that led to approximately 438,000 deaths. The development of novel therapeutics largely relies on a better understanding of parasite biology and pathogenesis. Our analyses on time-series RNA-Seq data identified stage-specific genes expressed across the blood-stage in the malaria parasite, Plasmodium falciparum: in the ring and the early trophozoite stage, genes associated with hemoglobin degradation and transcription were highly expressed; in the trophozoite and early schizont stage, genes involved in glycolysis, the TCA cycle, mitochondrion organization, deoxyribonucleotide metabolic processes as well as DNA replication were upregulated; in the schizont stage, genes associated with merozoite invasion and actin filament organization were over-expressed. Our results revealed an orchestrated transcriptional machinery and a “just-in-time” mechanism for transcriptional regulation in the blood stage of the
Head-to-Head Comparison of Transcranial Random Noise Stimulation, Transcranial AC Stimulation, and Transcranial DC Stimulation for Tinnitus

Tinnitus is the perception of a sound in the absence of an external sound stimulus. This phantom sound has been related to plastic changes and hyperactivity in the auditory cortex. Different neuromodulation techniques such as transcranial magnetic stimulation and transcranial direct current stimulation (tDCS) have been used in an attempt to modify local and distant neuroplasticity as to reduce tinnitus symptoms. Recently, two techniques of pulsed electrical stimulation using weak electrical currents – transcranial alternating current stimulation (tACS) and transcranial random noise stimulation (tRNS) – have also shown significant neuromodulatory effects. In the present study we conducted the first head-to-head comparison of three different transcranial electrical stimulation (tES) techniques, namely tDCS, tACS, and tRNS in 111 tinnitus patients by placing the electrodes overlying the auditory cortex bilaterally. The results demonstrated that tRNS induced the larger transient suppressive effect on the tinnitus loudness and the tinnitus related distress as compared to tDCS and tACS. Both tDCS and tACS induced small and non-significant effects on tinnitus symptoms, supporting the superior effects of tRNS as a method for tinnitus suppression.
Reflections on Personal Responsibility: Sorority Members At Risk for Interpersonal Violence

This study explores the phenomenon of interpersonal violence associated with alcohol abuse and sorority membership at a midsized state university in the West. Using Millennial theory as the conceptual framework, 180 reflection papers from women in two sororities were analyzed using qualitative content analysis to determine how they applied harm reduction education and participated in social activities when consuming alcohol. The results indicate little harm reduction application among the cohort, reproduced bystander behavior norms, how organizational challenges contribute to injury, and alcohol consumption promoted heavily as a benefit of membership. The study suggests implications for further research and practice.
Empowering caregivers: Impact analysis of FamilyLink Education Programme (FLEP) in Hong Kong, Taipei and Bangkok

Background: Education and support for caregivers is lacking in Asia and the peer-led FamilyLink Education Programme (FLEP) is one of the few provisions to address this service gap. This study aims to evaluate quantitatively its efficacy in reducing subjective burdens and empowering the participants. Method: One hundred and nine caregiver participants in three Asian cities were successfully surveyed at pre-intervention, post-intervention and six-month intervals with a number of standard inventories. Mixed analysis of variance (ANOVA) procedures showed significant programme impact over time intervals for all sites, and subsequently an empowerment measurement model was tested. Results: FLEP was found effective in reducing worry and displeasure, significantly improving intra-psychic strain, depression and all empowerment measures. The measurement model had an acceptable good fit. Baseline difference showed no interference with the programme efficacy. Conclusions: Apart from the initial support for FLEP, the current study also provides some hindsight on the empowerment practice in mental health for Asia, whose sociocultural political contexts are vastly different from that of the developed countries. It remains to be seen whether qualitative data or more stringent research design will yield consistent results and whether FLEP can also work in rural areas.
Anxiogenic action of caffeine: an experimental study in rats

The anxiogenic action of caffeine (10, 25 and 50 mg/kg, i.p.) was investigated in rats and compared with that of yohimbine (2 mg/kg, i.p.). The experimental methods used were the open-field, elevated plus-maze, social interaction and novelty-suppressed feeding latency tests. Caffeine produced a dose-related profile of behavioural changes, which were qualitatively similar to those induced by yohimbine and which indicate an anxiogenic activity in rodents. Thus, both the drugs reduced ambulation and rears, and increased immobility and defaecation in the open-field test. They decreased the number of entries and time spent on the open arms of the elevated-plus maze, reduced social interaction in paired rats and increased the feeding latency in an unfamiliar environment in 48-h food-deprived rats. Lorazepam, a well known benzodiazepine anxiolytic agent, attenuated the anxiogenic effects of caffeine and yohimbine. Subchronic administration of caffeine (50 mg/kg, i.p.) for 21 days, in different groups of animals, induced a significant degree of tolerance in the elevated plus-maze test, which was statistically significant after 14 and 21 days' treatment. Yohimbine, however, did not induce similar tolerance. When caffeine (50 mg/kg, i.p.) was withdrawn after 21 days' administration, to a separate group of rats, significant withdrawal anxiety was observed 48 h later as noted in the elevated plus-maze test. The investigations support clinical evidence of caffeine-induced anxiety, tolerance to anxiety on continued use, and withdrawal anxiety in chronic caffeine-containing beverage users.
A survey of fishes associated with Hawaiian deep-water Halimeda kanaloana (Bryopsidales: Halimedaceae) and Avrainvillea sp. (Bryopsidales: Udoteaceae) meadows

The invasive macroalgal species Avrainvillea sp. and native species Halimeda kanaloana form expansive meadows that extend to depths of 80 m or more in the waters off of O‘ahu and Maui, respectively. Despite their wide depth distribution, comparatively little is known about the biota associated with these macroalgal species. Our primary goals were to provide baseline information on the fish fauna associated with these deep-water macroalgal meadows and to compare the abundance and diversity of fishes between the meadow interior and sandy perimeters. Because both species form structurally complex three-dimensional canopies, we hypothesized that they would support a greater abundance and diversity of fishes when compared to surrounding sandy areas. We surveyed the fish fauna associated with these meadows using visual surveys and collections made with clove-oil anesthetic. Using these techniques, we recorded a total of 49 species from 25 families for H. kanaloana meadows and surrounding sandy areas, and 28 species from 19 families for Avrainvillea sp. habitats. Percent endemism was 28.6% and 10.7%, respectively. Wrasses (Family Labridae) were the most speciose taxon in both habitats (11 and six species, respectively), followed by gobies for H. kanaloana (six species). The wrasse Oxycheilinus bimaculatus and cardinalfish Apogonichthys perdix were the most frequently-occurring species within the H. kanaloana and Avrainvillea canopies, respectively. Obligate herbivores and food-fish species were rare in both habitats. Surprisingly, the density and abundance of small epibenthic fishes were greater in open sand than in the meadow canopy. In addition, species richness was also higher in open sand for Avrainvillea sp. We hypothesize that the dense holdfasts and rhizoids present within the meadow canopy may impede benthic-dwelling or bioturbator species, which accounted for 86% and 57% of individuals collected in sand adjacent to H. kanaloana and Avrainvillea sp. habitats, respectively. Of the 65 unique species recorded in this study, 16 (25%) were detected in clove oil stations alone, illustrating the utility of clove-oil anesthetic in assessing the diversity and abundance of small-bodied epibenthic fishes.
Social stakes of urban renewal: recent French housing policy

The social implications of urban restructuring, especially the spatial approach of urban renewal, are important indicators for the building stock, as this impacts on demolition and reconstruction. The social stakes of urban renewal reside in both its political intent and its social effects. Ongoing socio-economic difficulties have led to a shift in French public policy on disadvantaged neighbourhoods, moving from the promotion of local social and economic development to an increasing fear of concentrating local communities or ‘ghettos’. Social mix has become a policy objective for these neighbourhoods, and urban renewal as the means to achieve it. Although the effects of this policy are currently hard to assess, three social stakes can nonetheless be identified, partly based on the results of ongoing research at Les Minguettes, a suburb of Lyon, France. First, contemporary urban renewal tends to erode the stock of affordable housing, without bringing noticeable improvements in housing conditions. Second, this policy weakens the inhabitants' social capital, a resource strongly locally anchored in working-class milieus. Finally, social mix tends to transform local forms of coexistence in unpredictable ways, with no guarantee of the anticipated positive cooperation between locals and newcomers. L'approche spatiale de la rénovation urbaine, une politique de gestion du parc bâti consistant principalement à démolir et reconstruire des logements, a des implications sociales importantes. Les enjeux sociaux de la rénovation urbaine résident à la fois dans ses intentions politiques et dans ses conséquences sociales. Les difficultés socioéconomiques actuelles ont conduit à un changement de la politique publique française à l'égard des quartiers défavorisés, qui est passée de la promotion du développement social et économique local à une crainte croissante des regroupements communautaires ou de la formation de «ghettos». La mixité sociale est devenue un objectif des politiques visant ces quartiers et la rénovation urbaine le moyen d'y parvenir. Bien que les effets de cette politique soient actuellement difficiles à évaluer, trois enjeux sociaux peuvent néanmoins être identifiés, en se basant pour partie sur les résultats de recherches en cours aux Minguettes, en banlieue de Lyon, en France. Tout d'abord, la rénovation urbaine d'aujourd'hui a tendance à grignoter le parc des logements abordables, sans que cela se traduise par des améliorations sensibles des conditions de logement. En second lieu, cette politique affaiblit le capital social des habitants, une ressource fortement ancrée localement dans les milieux populaires. Enfin, la mixité sociale a tendance à transformer les formes locales de coexistence de manière imprévisible, sans garantie de la coopération positive escomptée entre les anciens et les nouveux habitants. Mots clés: parc bâti, démolition, politique du logement, quartier, capital social, mixité sociale, rénovation urbaine, France
Cross-cultural practice

Social work practitioners in developing countries have difficulty in comprehending Western knowledge in day-to-day practice. This study examined by interpretive methods how Indian social workers in an alcohol treatment center, which was patterned after an American treatment model, deal with technology transfer. Dharma, karma and making pragmatic judgements as to “what works” were found to be the predominant influences in the social worker’s utilization of knowledge and everyday practice.
Eecient Probabilistically Checkable Proofs and Applications to Approximation

We construct multi-prover proof systems for NP which use only a constant number of provers to simultaneously achieve low error, low randomness and low answer size. As a consequence, we obtain asymptotic improvements to approximation hardness results for a wide range of optimization problems including minimum set cover, dominating set, maximum clique, chromatic number, and quartic programming; and constant factor improvements on the hardness results for MAXSNP problems. In particular, we show that approximating minimum set cover within any constant is NP-complete; approximating minimum set cover within (logn) implies NP DTIME(n ); approximating the maximum of a quartic program within any constant is NP-hard; approximating maximum clique within n implies NP BPP; approximating chromatic number within n implies NP BPP; and approximating MAX3SAT within 113=112 is NP-complete. Department of Computer Science & Engineering, Mail Code 0114, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093. E-mail: mihir@cs.ucsd. edu. y MIT Laboratory for Computer Science, 545 Technology Square, Cambridge, MA 02139, USA. e-mail: shafi@theory. lcs.mit.edu. Partially supported by NSF FAW grant No. 9023312-CCR, DARPA grant No. N00014-92-J-1799, and grant No. 89-00312 from the United States Israel Binational Science Foundation (BSF), Jerusalem, Israel. z AT&T Bell Laboratories, Room 2C324, 600 Mountain Avenue, P. O. Box 636, Murray Hill, NJ 07974-0636, USA. email: lund@research.att. com. x MIT Laboratory for Computer Science, 545 Technology Square, Cambridge, MA 02139, USA. e-mail: acr@theory.lcs. mit.edu. Supported by a NSF Graduate Fellowship and by NSF grant 92-12184, AFOSR 89-0271, and DARPA N00014-92-J-1799.
A comparison of urinary neutrophil gelatinase-associated lipocalin in patients undergoing on- versus off-pump coronary artery bypass graft surgery.

OBJECTIVE The purpose of this study was to compare urinary neutrophil gelatinase-associated lipocalin (NGAL) levels in off-pump and on-pump coronary artery bypass graft (CABG) surgery. DESIGN A matched cohort study. SETTING A tertiary university hospital. PARTICIPANTS Thirty adult patients undergoing CABG surgery without cardiopulmonary bypass (off-pump) matched to 30 patients with on-pump CABG surgery by age, preoperative serum creatinine, Parsonnet score, ejection fraction, body mass index, and number of coronary artery grafts. INTERVENTIONS None, observational. MEASUREMENTS AND MAIN RESULTS Urinary NGAL, a novel, highly sensitive biomarker for renal injury, was measured before and immediately after surgery and then 3, 18, and 24 hours later. There were no differences in urinary NGAL at any time point between patients subjected to off-pump or on-pump CABG surgery; the peak urinary NGAL in patients who underwent off-pump CABG surgery was 94.7 +/- 30.9 ng/mL compared with 122.7 +/- 57.0 ng/mL in patients with on-pump CABG surgery (p = 0.6). Peak serum creatinine and the incidence of acute kidney injury also were not different between the groups. CONCLUSIONS Urinary NGAL was not different in patients undergoing off-pump and on-pump CABG surgery despite a very good match between the groups with respect to pre- and intraoperative risk factors.