Miracle-dz/UniFAR-FTUs huggingface dataset:
The use of discordant sibling pairs for finding genetic loci linked to obesity: practical considerations.

BACKGROUND Currently there is substantial interest in finding genetic loci linked to human obesity. However, the complexity of the genetic architecture for human body fatness and body weight make this a very challenging task. Recently, several authors have proposed the use of discordant sibling pairs to improve the power to detect linkage for obesity and other continuously distributed complex phenotypes. The use of discordant siblings pairs can markedly increase the power of statistical analyses to detect linkage. However, the use of discordant sibling pairs also presents several practical concerns. These include both the difficulty and cost of locating markedly discordant sibling pairs and the possibility that when such pairs are located, they may in fact be only half-siblings due to non-paternity. In this paper, I consider both of these issues. RESULTS Quantitative estimates of the probability of finding pairs of a given degree of discordance are presented based on the assumption of a normal distribution as well as on actual data. Quantitative estimates of the odds of selecting pairs that are actually half siblings as opposed to full siblings are also presented for different degrees of discordance. Finally, percentile scores for BMI are tabulated as these are necessary for researchers to implement certain sibling selection strategies.
Stimulated Platelets Release Factor(s) Affecting the In Vitro Response of Human Polymorphonuclear Cells

The metabolic and functional responses of human polymorphonuclear cells (PMNs) to thrombin‐activated platelet supernatants were studied. The incubation of PMNs with supernatants from stimulated platelets (SPS) caused a 50% decrease in both killing of Staphylococcus aureus and luminol‐enhanced chemiluminescence (CL) by PMNs stimulated by opsonized‐zymosan (OZ), Concanavalin A (Con A), or calcium ionophore A23187. The levels of PMN intracellular fluorescence measured by flow cytometry, using the fluorochrome dichlorofluorescin diacetate (DCF‐DA), were considerably less in the presence of SPS than in resting platelet supernatants (RPS). No influence of platelet supernatant on O2 consumption and O2 ‐ generation by OZ‐activated PMNs was observed. The incubation of PMNs with SPS caused a significant increase in the rate of chemotaxis and aggregation elicited by Con A, OZ, and phorbol myristate acetate (PMA). The supernatant from resting platelets did not show any of the above‐reported effects. Platelets previously degranulated by thrombin were unable to inhibit CL when activated with agonists. Studies on the differential release of the granules by platelets showed that the CL‐quenching activity paralleled the discharge of lysosomal content The release of myeloperoxidase (MPO) from PMNs elicited by OZ was reduced in the presence of SPS. The platelet supernatant did not affect the MPO activity if PMNs were lysed with Triton X‐100. The leakage of lactate dehydrogenase (LDH) from platelets was less than 3%, and no catalase or superoxide dismutase was released. This activity withstood lyophilization, but was destroyed by 10 min heating at 100°C or by treatment with proteolytic enzymes.
Automatic compositional verification of probabilistic safety properties for inter-organisational workflow processes

For many complex systems, it is important to verify formally their correctness; the aim is to guarantee the reliability and the correctness of such systems before their effective deployment. Several methods have been proposed to this effect using different formal tools such as Probabilistic Automata (PA). In this paper we focus on verification of service-based inter-organizational workflow (IOWF) processes which support collaboration and cooperation between WF processes attached to several partners, and specified using the business process execution language (BPEL4WS). Then, IOWF processes are translated to Probabilistic Automata (PA) models. More than verification support, PA provides a numerical evaluation of the IOWF process. We also propose the use of compositional verification to cope with the state space explosion problem. The IOWF behavior is checked against probabilistic safety properties. The verification and the analysis are performed in an automated way using the PRISM model checker and based on the assume-guarantee reasoning rule.
Contrasts in codon usage of latent versus productive genes of Epstein-Barr virus: data and hypotheses

Epstein-Barr virus (EBV) has two different modes of existence: latent and productive. There are eight known genes expressed during latency (and hardly at all during the productive phase) and about 70 other ("productive") genes. It is shown that the EBV genes known to be expressed during latency display codon usage strikingly different from that of genes that are expressed during lytic growth. In particular, the percentage of S3 (G or C in codon site 3) is persistently lower (about 20%) in all latent genes than in nonlatent genes. Moreover, S3 is lower in each multicodon amino acid form. Also, the percentage of S in silent codon sites 1 of leucine and arginine is lower in latent than in nonlatent genes. The largest absolute differences in amino acid usage between latent and nonlatent genes emphasize codon types SSN and WWN (W means nucleotide A or T and N is any nucleotide). Two principal explanations to account for the EBV latent versus productive gene codon disparity are proposed. Latent genes have codon usage substantially different from that of host cell genes to minimize the deleterious consequences to the host of viral gene expression during latency. (Productive genes are not so constrained.) It is also proposed that the latency genes of EBV were acquired recently by the viral genome. Evidence and arguments for these proposals are presented.
Activities in dementia care: A comparative assessment of activity types

This exploratory study compares the impact of five activity types on the well-being of institutionalized people with dementia: the intergenerational art program Opening Minds through Art, art and music therapies, creative activities, non-creative activities, and no activities at all. We validated the Scripps Modified Greater Cincinnati Chapter Well-Being Observational Tool, and used that instrument to systematically observe N = 67 people with dementia as they participated in different activity types. People with dementia showed the highest well-being scores during Opening Minds through Art compared to all other activities. No significant well-being differences were found between creative activities led by licensed art/music therapist versus regular activity staff. Furthermore, no significant well-being differences were found between creative and non-creative activities that were both led by regular activity staff. Overall, people with dementia benefit from participating in activities, regardless of the type (creative or non-creative), or who conducts them (licensed therapists or activity staff). However, in order for people with dementia to reach significantly high levels of overall well-being, we recommend that activities are specifically designed for people with dementia and incorporate a 1:1 ratio between people with dementia and well-trained volunteers/staff members.
Effect of Two Recovery Methods on Repeated Closed-Handed and Open-Handed Weight-Assisted Pull-Ups

Abstract Bacon, NT, Wingo, JE, Richardson, MT, Ryan, GA, Pangallo, TC, and Bishop, PA. Effect of two recovery methods on repeated closed-handed and open-handed weight-assisted pull-ups J Strength Cond Res 26(5): 1348–1352, 2012—The purpose of this study was to examine 2 recovery modalities (with and without an ice bag treatment) on closed-handed and open-handed weight-assisted pull-ups in recreationally-trained rock climbers. Healthy and recreationally active volunteers (n = 9) completed 4 counterbalanced trials separated by 72 hours. Trials included 3 sets of closed-handed and open-handed weight-assisted pull-ups supported by 50% of body weight, until failure. Between each set, participants sat quietly in a chair and engaged in approximately 20 minutes of either passive or ice bag treatment. Ice bags were placed on the participants' arms and shoulders. Heart rate (HR), ratings of perceived exertion (RPE), session-RPE (S-RPE), and perceived recovery were also assessed. Hand-grip strength pretrial and posttrial was not different between ice bag conditions. Also, there were no differences between treatments for HR, RPE, perceived recovery, S-RPE, or comfort ratings. The overall number of open-handed pull-ups (mean ± SD = 19 ± 5) was lower than closed-handed pull-ups (34 ± 14; p < 0.001). Ice bag recovery attenuated the decrease in open-handed pull-up performance for sets 2 (22 ± 5; p = 0.004) and 3 (22 ± 5; p = 0.003) relative to set 3 using passive recovery only (i.e., no ice bag; 17 ± 6). There were no differences (p = 0.31) between treatments for closed-handed pull-ups. The findings support the recommendations to use ice bags for recovery between bouts of rock climbing that involve a predominantly open-handed grip to maintain performance.
Neoadjuvant chemotherapy in squamous cell carcinoma of the esophagus using low dose continuous infusion 5-fluorouracil and cisplatin: results of a prospective study.

BACKGROUND Surgery is the treatment of choice for localized esophageal squamous cell carcinoma (ESCC). Despite curative surgical resection, the majority of patients develop local and systemic recurrence with poor 5-year survival. AIMS To study the role of low dose continuous infusion (CI) 5-fluorouracil (5-FU) and cisplatin as neoadjuvant chemotherapy in ESCC. SETTINGS AND DESIGN A non-randomized prospective study conducted over a period of two years (1996-1998) in the Department of Surgery, All India Institute of Medical Sciences, India. MATERIAL AND METHODS Twenty-two patients with ESCC were included in the study. Chemotherapy consisted of a continuous 30-day infusion of 5-FU (350 mg/m2/day) and cisplatin (7.5 mg/m2/day), 5 days/week for 4 weeks. All patients had surgery following chemotherapy. RESULTS A full course of chemotherapy was completed in 18 patients (82%). Chemotherapy was not completed due to non-compliance (n=2), thrombophlebitis (n=1), and vomiting (n=1). Grade-1 haematological and hepato-toxicity was observed in four patients. Thirteen patients developed thrombophlebitis. After chemotherapy, improvement in dysphagia was observed in 13 of 22 (59%) patients. Radiological partial response was observed in 8 patients (36.4%). 19 patients underwent surgical resection (86.4%) with zero mortality. Post-operative morbidity was observed in six patients (27%). Complete and partial pathological response was observed in two (11%) and one patient (5.5%) respectively. The overall median survival was 18 months and 4-year survival was 42%. CONCLUSIONS Low dose CI 5-FU and cisplatin is well tolerated with minimal toxicity. Histopathological response rates and survival figures are comparable with the more toxic neoadjuvant chemotherapeutic regimens.
A new microsporidian parasite, Potaspora morhaphis n. gen., n. sp. (Microsporidia) infecting the Teleostean fish, Potamorhaphis guianensis from the River Amazon. Morphological, ultrastructural and molecular characterization

SUMMARY A fish-infecting Microsporidia Potaspora morhaphis n. gen., n. sp. found adherent to the wall of the coelomic cavity of the freshwater fish, Potamorhaphis guianensis, from lower Amazon River is described, based on light microscope and ultrastructural characteristics. This microsporidian forms whitish xenomas distinguished by the numerous filiform and anastomosed microvilli. The xenoma was completely filled by several developmental stages. In all of these stages, the nuclei are monokaryotic and develop in direct contact with host cell cytoplasm. The merogonial plasmodium divides by binary fission and the disporoblastic pyriform spores of sporont origin measure 2·8±0·3×1·5±0·2 μm. In mature spores the polar filament was arranged into 9–10 coils in 2 layers. The polaroplast had 2 distinct regions around the manubrium and an electron-dense globule was observed. The small subunit, intergenic space and partial large subunit rRNA gene were sequenced and maximum parsimony analysis placed the microsporidian described here in the clade that includes the genera Kabatana, Microgemma, Spraguea and Tetramicra. The ultrastructural morphology of the xenoma, and the developmental stages including the spores of this microsporidian parasite, as well as the phylogenetic analysis, suggest the erection of a new genus and species.
Mitigating NLD for Wireless Networks: Effect of Nonlinear Power Amplifiers on Future Wireless Communication Networks

Efficient utilization of limited bandwidth with high-data-rate transmission while serving a large number of users is a prime requirement for present and future wireless communication systems. To meet this rising demand, orthogonal frequency-division multiplexing (OFDM) and cooperative communication have emerged as promising solutions due to their robustness in severely degraded channel conditions, link reliability, and spectral efficiency. Both OFDM and cooperative systems have challenged RF front-end specifications such as bandwidth and power-efficiency requirements for end users as well as for the base station due to the high peak-to-average power ratio (PAPR). In present and future communication systems, the power amplifier (PA) is a key component at the transmitter. To obtain maximum power efficiency, the PA is operated near its saturation point, which leads to nonlinear distortion (NLD), which is further exaggerated due to the high PAPR of the input signal. This NLD is expected to increase in future fifth-generation (5G) communication networks, due to the use of large bandwidth at millimeter-wave (mmW) frequencies.
Identification of modulators of autophagic flux in an image-based high content siRNA screen

ABSTRACT Autophagy is the primary process for recycling cellular constituents through lysosomal degradation. In addition to nonselective autophagic engulfment of cytoplasm, autophagosomes can recognize specific cargo by interacting with ubiquitin-binding autophagy receptors such as SQSTM1/p62 (sequestosome 1). This selective form of autophagy is important for degrading aggregation-prone proteins prominent in many neurodegenerative diseases. We carried out a high content image-based siRNA screen (4 to 8 siRNA per gene) for modulators of autophagic flux by monitoring fluorescence of GFP-SQSTM1 as well as colocalization of GFP-SQSTM1 with LAMP2 (lysosomal-associated membrane protein 2)-positive lysosomal vesicles. GFP-SQSTM1 and LAMP2 phenotypes of primary screen hits were confirmed in 2 cell types and profiled with image-based viability and MTOR signaling assays. Common seed analysis guided siRNA selection for these assays to reduce bias toward off-target effects. Confirmed hits were further validated in a live-cell assay to monitor fusion of autophagosomes with lysosomes. Knockdown of 10 targets resulted in phenotypic profiles across multiple assays that were consistent with upregulation of autophagic flux. These hits include modulators of transcription, lysine acetylation, and ubiquitination. Two targets, KAT8 (K[lysine] acetyltransferase 8) and CSNK1A1 (casein kinase 1, α 1), have been implicated in autophagic regulatory feedback loops. We confirmed that CSNK1A1 knockout (KO) cell lines have accelerated turnover of long-lived proteins labeled with 14C-leucine in a pulse-chase assay as additional validation of our screening assays. Data from this comprehensive autophagy screen point toward novel regulatory pathways that might yield new therapeutic targets for neurodegeneration.
Developing efficient parsers in Prolog: the CLF manual (v1.0)

This document describes a couple of tools that help to quickly design and develop computer (formalized) languages. The first one use Flex to perform lexical analysis and the second is an extention of Prolog DCGs to perfom syntactical analysis. Initially designed as a new component for the Centaur system, these tools are now available independently and can be used to construct efficient Prolog parsers that can be integrated in Prolog or heterogeneous systems. This is the initial version of the CLF documentation. Updated version will be available online when necessary.
The Long-Term Impact of the Earned Income Tax Credit on Children's Education and Employment Outcomes

Using 4 decades of variation in the federal and state Earned Income Tax Credit (EITC), we estimate the impact of exposure to EITC expansions in childhood on education and employment outcomes in adulthood. Reduced-form results suggest that an additional $1,000 in EITC exposure when a child is 13–18 years old increases the likelihood of completing high school (1.3%), completing college (4.2%), and being employed as a young adult (1.0%) and earnings by 2.2%. Our analysis reveals that the primary channel through which the EITC improves these outcomes is increases in pretax family earnings.
Reducing substance use improves adolescents' school attendance.

AIMS Substance use initiation and frequency are associated with reduced educational attainments among adolescents. We examined if decreases in substance use substantially improve youths' school attendance. DESIGN A total of 1084 US adolescents followed quarterly for 1 year after entering substance abuse treatment. METHODS Random and fixed effects regression models were used to differentiate the lagged effects of drug use from other time-varying and time-invariant covariates. Self-reports of alcohol, marijuana, stimulants, sedatives, hallucinogens and other drug use were used to predict subsequent school attendance, after controlling for demographic and drug use history characteristics, problem indices and other covariates. FINDINGS Reductions in the frequency of alcohol, stimulants and other drug use and the elimination of marijuana use were each associated independently with increased likelihoods of school attendance. CONCLUSIONS Because years of completed schooling is highly correlated with long-term social and economic outcomes, the possibility that reductions in substance use may improve school attendance has significant implications for the cost-effectiveness of substance abuse treatment and other interventions designed to reduce adolescents' substance use.
The Integrated Land Price Forecast and Influential Factors Analysis in Xinjiang Based on the Gray System Theory

According to the Integrated land price 2006-2010 in Xinjiang,In order to provide a scientific basis for the control of the integrated land price,we explore to establish a forecast GM(1,1) model of integrated land price in Xinjiang and analysis its Influential factors based on grey prediction theory and grey association analysis theory.By the model results,we can get that the Real Estate Price Indices and the urbanization rate are the two main factors prompt Xinjiang integrated land price rise.The forecast results also show that,although the government applied pressure,integrated land price in Xinjiang will not crash in short-term but rise steadily.
Autoregulation of the Plasmid Addiction Operon of Bacteriophage P1*

The P1 plasmid addiction operon increases the apparent stability of a plasmid that carries it by killing plasmid-free (cured) segregants. The operon consists of a gene encoding an endotoxin responsible for eath n uring (doc), preceded by a gene encoding a relatively unstable antidote that can revent ost eath (phd). When the copy number of the operon was increased, expression of a lacZ reporter fused to the promoter of the operon decreased, indicating that expression of the operon was stabilized by an autoregulatory circuit. Transcription of the lacZ reporter was repressed about 10-fold when phd, without doc, was expressed from an exogenous promoter. DNase I footprinting showed that Phd binds a perfect 10-base pair palindromic DNA sequence and, at higher concentrations, an adjacent, imperfect palindrome. The palindromic sites are located between the −10 region of the putative promoter and the start codon of phd. Electrophoretic mobility of DNA containing the promoter region was retarded in the presence of Phd and further retarded in the presence of Phd and Doc. When doc was co-expressed with phd, repression of the lacZ fusion was enhanced more than 100-fold. Thus, both products of the addiction operon participate in its autoregulation.
Transactional programming in a multi-core environment

With single thread performance starting to plateau, HW architects have turned to chip level multiprocessing (CMP) to increase processing power. All major microprocessor companies are aggressively shipping multi-core products in the mainstream computing market. Moore's law will largely be used to increase HW thread-level parallelism through higher core counts in a CMP environment. CMPs bring new challenges into the design of the software system stack. In this tutorial, we talk about the shift to multi-core processors and the programming implications. In particular, we focus on transactional programming. Transactions have emerged as a promising alternative to lock-based synchronization that eliminates many of the problems associated with lock-based synchronization. We discuss the design of both hardware and software transactional memory and quantify the tradeoffs between the different design points. We show how to extend the Java and C languages with transactional constructs, and how to integrate transactions with compiler optimizations and the language runtime (e.g., memory manager and garbage collection).
Cell wall proteomics of the green alga Haematococcus pluvialis (Chlorophyceae)

The green microalga Haematococcus pluvialis can synthesize and accumulate large amounts of the ketocarotenoid astaxanthin, and undergo profound changes in cell wall composition and architecture during the cell cycle and in response to environmental stresses. In this study, cell wall proteins (CWPs) of H. pluvialis were systematically analyzed by sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE) coupled with peptide mass fingerprinting (PMF) and sequence‐database analysis. In total, 163 protein bands were analyzed, which resulted in positive identification of 81 protein orthologues. The highly complex and dynamic composition of CWPs is manifested by the fact that the majority of identified CWPs are differentially expressed at specific stages of the cell cycle along with a number of common wall‐associated ‘housekeeping’ proteins. The detection of cellulose synthase orthologue in the vegetative cells suggested that the biosynthesis of cellulose occurred during primary wall formation, in contrast to earlier observations that cellulose was exclusively present in the secondary wall of the organism. A transient accumulation of a putative cytokinin oxidase at the early stage of encystment pointed to a possible role in cytokinin degradation while facilitating secondary wall formation and/or assisting in cell expansion. This work represents the first attempt to use a proteomic approach to investigate CWPs of microalgae. The reference protein map constructed and the specific protein markers obtained from this study provide a framework for future characterization of the expression and physiological functions of the proteins involved in the biogenesis and modifications in the cell wall of Haematococcus and related organisms.