Miracle-dz/UniFAR-FTUs huggingface dataset:
On a regulatory gene controlling the expression of the murine lambda1 light chain

We describe here two alleles, an allele of the lambda1 locus present in the SJL strain (rlambda1lo) and an allele of the lambda1 locus present in the BALB/c strain (rlambda1 +), of a regulatory gene locus which specifically influences the expression of the mouse lambda1 light chain structural gene. The rlambda1 regulatory gene is not linked to either the major histocompatibility complex or to the heavy-chain allogroup but appears to be linked to the lambda1 structural gene locus. In the homozygous state, the present of the rlambda1lo allele results in a 50- fold reduction in the number of lambda1 antigen-sensitive, bone-marrow derived lymphocytes (ASCs) compared to the presence of the rlambda1 + allele. However, those few lambda1ASCs present in rlambda1lo homozygotes can be induced normally to produce lambda1 light chains indistinguishable from those found in rlambda1 + homozygotes. The reduction in lambda1ASC's due to the rlambda1lo allele results both in a reduction in the amount of lambda1 Ig in the serum and also in a large variation in the magnitude of the lambda1 antibody response to alpha(1,3) dextran by individual animals. This variation permits the estimate that, on the average, 50 B cells of anti-alpha(1,3) specificity must be present per animal to permit a measurable response. Surprisingly, the expression of a gene locus regulating lambda1 light chain expression (rlambda1 locus) shows a clear gene dosage effect with rlambda1lo/rlambda1 + heterozygotes having 1/2 the number of lambda1ASCs and 1/2 the amount of serum lambda1 Ig as rlambda1 +/rlambda1 + homozygotes. This fact permits an analysis of the relationship between germ-line v-genes and their individual expression in serum Ig. The rlambda1 locus controls specifically a DNA-level event which occurs in stem cells as they become committed to lambda1 light chain expression. We postulate that the rlambda1 locus represents one of the DNA level recognition sites involved in the translocation event which places the vlambda1 and clambda1 structural genes in a transcriptional unit.
Application of Least-Squares Joint Imaging of Multiples and Primaries on Shallow Water-Bottom Data Sets

Data contaminated with strong shallow water-bottom multiples is rife with challenges. Application of Least-Squares Joint Imaging of Multiples and Primaries (LSJIMP) on such data sets yields mixed results. LSJIMP solves both the separation and integration simultaneously, as a global least-squares inverse problem. We point out some limitations of LSJIMP by testing it on synthetic data sets that emulate shallow water-bottom marine environments. Some slight modifications have been made, and we suggest some strategies that might make LSJIMP an effective algorithm. INTRODUCTION Multiples are often the most significant impediment to the successful construction and interpretation of an image of the primaries, especially in regions with anomalously strong reflectors (e.g., “hard” water bottom or salt bodies). But, since they penetrate deeply enough into the earth and illuminate different angular ranges and reflection points, a primary and its multiples are more than simply redundant. The problem of handling multiples becomes more challenging when we encounter shallow water-bottom with a large impedence contrast. In such cases a large amount of multiple energy is generated, most of which is surface related. Offshore Australia is a prime example of such a marine environment. An important class of multiple-suppression techniques create from the data a “model” of the multiples, which may then be adaptively subtracted from the data. Verschuur and Prein (1999) use Surface-Related Multiple Elimination (SRME) for multiplesuppression on an Australian data set infected with shallow water bottom multiples. The multiple-generating boundaries were more or less horizontal or gently dipping. Long et al. (2005) use SRME to revisit a poor-data-quality area in the northern Carnarvon Basin, offshore Western Australia, where both shortand long-period multiple energy prohibit imaging of the underlying geology. In some sense, shallow-water multiple suppression is easier. The multiples look a lot like primaries, so deconvolution with a gapped filter (gap size = waterbottom time) will solve the problem nicely. However, some of the more advanced multiple suppression methods, like high-resolution Radon and SRME, have a trouble with shallow water-bottom. The Radon transform relies on moveout differences between multiples and primaries, which are not present in shallow data, except near the surface, and SRME often requires many non-linear iterations in shallow-water environments. 1
Pareto-optimal phylogenetic tree reconciliation

Motivation: Phylogenetic tree reconciliation is a widely used method for reconstructing the evolutionary histories of gene families and species, hosts and parasites and other dependent pairs of entities. Reconciliation is typically performed using maximum parsimony, in which each evolutionary event type is assigned a cost and the objective is to find a reconciliation of minimum total cost. It is generally understood that reconciliations are sensitive to event costs, but little is understood about the relationship between event costs and solutions. Moreover, choosing appropriate event costs is a notoriously difficult problem. Results: We address this problem by giving an efficient algorithm for computing Pareto-optimal sets of reconciliations, thus providing the first systematic method for understanding the relationship between event costs and reconciliations. This, in turn, results in new techniques for computing event support values and, for cophylogenetic analyses, performing robust statistical tests. We provide new software tools and demonstrate their use on a number of datasets from evolutionary genomic and cophylogenetic studies. Availability and implementation: Our Python tools are freely available at www.cs. hmc.edu/∼hadas/xscape. Contact: mukul@engr.uconn. edu Supplementary information: Supplementary data are available at Bioinformatics online.
Depositional processes of impactites from the YAX‐1 drill core in the Chicxulub impact structure inferred from vertical profiles of PDF orientations and grain size distributions of shocked quartz

Core samples from the Chicxulub impact structure provide insights into the formation processes of a shallow‐marine‐target, complex crater. Although previous studies investigated the impactites (generally suevitic and polymict breccias) of the Yaxcopoil‐1 (YAX‐1) drill core in the Chicxulub impact structure, the interpretation of its deposition remains controversial. Here, we analyze planar deformation features (PDFs), grain size, and abundance of shocked quartz throughout the YAX‐1 impactite sequence (794–895 m in depth). PDF orientations of most quartz grains in YAX‐1 impactites show a distribution of both low angles ({10 1¯ 4}, {10 1¯ 3}, {10 1¯ 2}) and high angles (orientations higher than 55° to c‐axis), while the lower part of the impactite sequence contains quartz showing only PDF orientations of low angles. High‐abundance, coarse‐grained shocked quartz is found from the lower to middle parts of the impactites, whereas it abruptly changes to low‐abundance, fine‐grained shocked quartz within the upper part. In the uppermost part of the impactites, repeated oscillations in contents of these two components are observed. PDF orientation pattern suggests most of the shocked quartz grains experienced a range of shock pressure, except two samples in the lower part of impactites, which experienced only a high level of shock. We suggest that the base and lower part of the impactite sequence were formed by ejecta curtain and melt surge deposits, respectively. Our results are also consistent with the interpretation that the middle part of the impactite sequence is fallback ejecta from the impact plume. Additionally, we support the contention that massive seawater resurges into the crater occurred during the deposition of the upper and uppermost part of the impactites.
Effects of plyometric training on maximal-intensity exercise and endurance in male and female soccer players

Abstract In a randomised controlled trial design, effects of 6 weeks of plyometric training on maximal-intensity exercise and endurance performance were compared in male and female soccer players. Young (age 21.1 ± 2.7 years) players with similar training load and competitive background were assigned to training (women, n = 19; men, n = 21) and control (women, n = 19; men, n = 21) groups. Players were evaluated for lower- and upper-body maximal-intensity exercise, 30 m sprint, change of direction speed and endurance performance before and after 6 weeks of training. After intervention, the control groups did not change, whereas both training groups improved jumps (effect size (ES) = 0.35–1.76), throwing (ES = 0.62–0.78), sprint (ES = 0.86–1.44), change of direction speed (ES = 0.46–0.85) and endurance performance (ES = 0.42–0.62). There were no differences in performance improvements between the plyometric training groups. Both plyometric groups improved more in all performance tests than the controls. The results suggest that adaptations to plyometric training do not differ between men and women.
European Conference on Information Systems ( ECIS ) 5-15-2012 CONSUMERS ' PERCEPTIONS OF A VIRTUAL HEALTH CHECK : AN EMPIRICAL INVESTIGATION

After years of the development of information systems (IS) designed primarily for healthcare managers and professionals, there is an increasing interest in reaching consumers and patients directly through consumer health information technology (IT). Consumer-centric health information systems enable individuals to manage their health better and maintain a healthier lifestyle. However, the foremost challenge in developing systems for health behavior change is that there is modest knowledge of how individuals interact with these systems and how they process and act on information. In addition, technologies cannot have the capacity to help facilitate self-monitoring and self-management or improve consumers' health outcomes if the consumers do not adopt them. The objective of this study is to investigate consumers’ perceptions of a virtual health check. Specifically, we propose and test factors affecting perceived persuasiveness of the system and whether perceived persuasiveness predicts intention to adopt virtual health coaching. A theoretically driven research model is constructed, and a structural equation modeling (SEM) approach, namely partial least squares (PLS), is used to test the model against the data gathered from 130 subjects. The results of the study lend support to the proposed model. Studying the adoption, use, and impact of innovative consumer health IT is worthwhile, as it will guide future implementations.
VKORC1 and VKORC1L1: Why do Vertebrates Have Two Vitamin K 2,3-Epoxide Reductases?

Among all cellular life on earth, with the exception of yeasts, fungi, and some prokaryotes, VKOR family homologs are ubiquitously encoded in nuclear genomes, suggesting ancient and important biological roles for these enzymes. Despite single gene and whole genome duplications on the largest evolutionary timescales, and the fact that most gene duplications eventually result in loss of one copy, it is surprising that all jawed vertebrates (gnathostomes) have retained two paralogous VKOR genes. Both VKOR paralogs function as entry points for nutritionally acquired and recycled K vitamers in the vitamin K cycle. Here we present phylogenetic evidence that the human paralogs likely arose earlier than gnathostomes, possibly in the ancestor of crown chordates. We ask why gnathostomes have maintained these paralogs throughout evolution and present a current summary of what we know. In particular, we look to published studies about tissue- and developmental stage-specific expression, enzymatic function, phylogeny, biological roles and associated pathways that together suggest subfunctionalization as a major influence in evolutionary fixation of both paralogs. Additionally, we investigate on what evolutionary timescale the paralogs arose and under what circumstances in order to gain insight into the biological raison d’être for both VKOR paralogs in gnathostomes.
A Clinical Nomogram Predicting Pathologic Lymph Node Involvement in Esophageal Cancer Patients

Background:Esophageal cancer patients with pathologic lymph-node involvement (pN1) generally have a poor prognosis with surgery alone. We, therefore, constructed a nomogram to predict the risk of pN1 prior to surgical resection and externally validated the clinical utility of the model. Methods:A total of 273 esophageal adenocarcinoma patients treated with surgery alone were reviewed from 2 different institutions (University of Texas M. D. Anderson Cancer Center = 164, training set; University of Rochester School of Medicine and Dentistry = 109, validation set). Pretreatment clinical parameters were used to construct a nomogram for predicting the risk of pN1. Internal and external validation of the nomogram was performed to assess clinical utility. Results:Of the 164 patients in the training set, 56 patients (34%) had lymph-node involvement (pN1). Significant factors associated with pN1 on univariable logistic regression analysis (using a P < 0.05) included endoscopically determined clinical tumor depth (cT), clinical nodal (cN) status, and clinical tumor length (cL). Multivariable analysis suggested the significant independent factors were cT (odds ratio, 5.6; 95% confidence interval, 1.7–18.6; P < 0.01) and cL >2 cm (odds ratio, 7.0; 95% confidence interval, 2.7–18.1; P < 0.001). Regression tree analysis was used to determine the best cutoff for cL. A nomogram was created for pN1 using these clinical parameters and was internally validated by bootstrapping with a predicted accuracy of 85.1%. External validation performed on the validation set demonstrated an original C-index of 0.777 suggesting good clinical utility. Conclusions:Our analyses demonstrate that the risk of pathologic nodal involvement in esophageal adenocarcinoma patients can be estimated by this clinical nomogram, which will allow the identification of patients at high-risk of harboring positive lymph-nodes, who may be candidates for en bloc resection and/or neoadjuvant treatment.
Locomotor activity following lateral frontal lesions in rhesus monkeys.

Effects of bilateral frontal lesions on locomotor activity were studied under various stimulus conditions. 8 monkeys were tested after, and 13 monkeys before and after, partial ablation of lateral frontal granular cortex or as unoperated controls. Ss with lesions that included sulcus principals were hyperreactive to light. Their locomotor activity in light as well as darkness was more enhanced by relatively familiar auditory stimuli, and more depressed by relatively novel stimuli than that of unoperated Ss, or of Ss with lateral frontal lesions which spared sulcus principalis.
Ambivalent effect of member portraits in virtual groups

Knowledge exchange with shared databases can be seen as a public-goods dilemma. People are reluctant to contribute information because they save time, effort and perhaps social power if they withhold their knowledge and socially loaf. But if all people choose this individually efficient strategy, then no information exchange can take place, and the group is less effective than it would have been if all members contributed. Thus, in the knowledge-exchange situation, group norms and individual norms oppose each other. In order to strengthen people's orientation towards the group, virtual collaborative tools sometimes provide member portraits. But based on the Social Identity Model of Deindividuation Effect (SIDE)-Model, ambivalent effects of these member portraits are expected according to people's social categorization: when people identify more strongly with the group, such portraits enhance participation, whereas when people have a stronger individual identity, they undermine participation. This study links the concepts of social value orientation to identity salience. The assumption is that in the information-exchange dilemma, the social value orientation of a group member will determine whether group identity or individual identity becomes salient for that group member. We then extend the SIDE-model to the domain of social loafing and expect that portraits of the group members will have different effects for people with individual orientation and for people with prosocial orientation. An experiment confirmed this expectation and revealed a significant interaction between social value orientation and portraits. Especially striking is the result that for prosocials the provision of member portraits leads to an increase in social loafing. This is analogous to the predictions of the SIDE-model.
Immunomodulation Induced by Stem Cell Mobilization and Harvesting in Healthy Donors: Increased Systemic Osteopontin Levels after Treatment with Granulocyte Colony-Stimulating Factor

Peripheral blood stem cells from healthy donors mobilized by granulocyte colony-stimulating factor (G-CSF) and harvested by leukapheresis are commonly used for allogeneic stem cell transplantation. The frequency of severe graft versus host disease is similar for patients receiving peripheral blood and bone marrow allografts, even though the blood grafts contain more T cells, indicating mobilization-related immunoregulatory effects. The regulatory phosphoprotein osteopontin was quantified in plasma samples from healthy donors before G-CSF treatment, after four days of treatment immediately before and after leukapheresis, and 18–24 h after apheresis. Myeloma patients received chemotherapy, combined with G-CSF, for stem cell mobilization and plasma samples were prepared immediately before, immediately after, and 18–24 h after leukapheresis. G-CSF treatment of healthy stem cell donors increased plasma osteopontin levels, and a further increase was seen immediately after leukapheresis. The pre-apheresis levels were also increased in myeloma patients compared to healthy individuals. Finally, in vivo G-CSF exposure did not alter T cell expression of osteopontin ligand CD44, and in vitro osteopontin exposure induced only small increases in anti-CD3- and anti-CD28-stimulated T cell proliferation. G-CSF treatment, followed by leukapheresis, can increase systemic osteopontin levels, and this effect may contribute to the immunomodulatory effects of G-CSF treatment.
AMPA/Kainate Receptor-Mediated Downregulation of GABAergic Synaptic Transmission by Calcineurin after Seizures in the Developing Rat Brain

Hypoxia is the most common cause of perinatal seizures and can be refractory to conventional anticonvulsant drugs, suggesting an age-specific form of epileptogenesis. A model of hypoxia-induced seizures in immature rats reveals that seizures result in immediate activation of the phosphatase calcineurin (CaN) in area CA1 of hippocampus. After seizures, CA1 pyramidal neurons exhibit a downregulation of GABAA receptor (GABAAR)-mediated inhibition that was reversed by CaN inhibitors. CaN activation appears to be dependent on seizure-induced activation of Ca2+-permeable AMPA receptors (AMPARs), because the upregulation of CaN activation and GABAAR inhibition were attenuated by GYKI 52466 [1-(4-aminophenyl)-4-methyl-7,8-methylenedioxy-5H-2,3-benzodiazepine hydrochloride] or Joro spider toxin. GABAAR β2/3 subunit protein was dephosphorylated at 1 h after seizures, suggesting this subunit as a possible substrate of CaN in this model. Finally, in vivo administration of the CaN inhibitor FK-506 significantly suppressed hypoxic seizures, and posttreatment with NBQX (2,3-dihydroxy-6-nitro-7-sulfonyl-benzo[f]quinoxaline) or FK-506 blocked the hypoxic seizure-induced increase in CaN expression. These data suggest that Ca2+-permeable AMPARs and CaN regulate inhibitory synaptic transmission in a novel plasticity pathway that may play a role in epileptogenesis in the immature brain.
Results of Monocular Surgery Under Peribulbar Anesthesia for Large-Angle Horizontal Strabismus

OBJECTIVE: To evaluate the results of monocular surgery under peribulbar anesthesia for large-angle horizontal strabismus. INTRODUCTION: Monocular surgery may preserve some muscles if a repeat operation is required, may help to avoid the exposure of the dominant eye to the inherent risks of a surgical procedure and may reduce surgical time. METHODS: We evaluated ninety-two consecutive patients who underwent monocular surgery under peribulbar anesthesia for large-angle horizontal strabismus (angle of 40 prism diopters or greater). Patients were divided into group 1- esotropia and group 2 –exotropia. The postoperative follow-up was at 6 months, when the residual deviation was evaluated. In cases of residual deviations of over 15 PD (prism diopter), a second procedure was indicated. RESULTS: In all patients with preoperative deviations up to 60 PD, residual deviations were under 15 PD. Some patients with preoperative deviations of 65 PD (two in group 1 and four in group 2) and all patients with deviations over 65 PD had residual deviations over 15 PD. The 13 patients who underwent a second procedure experienced successful outcomes. Our ROC curve analysis showed that the cutoff point for obtaining a successful surgical result was 62.5 PD. No patient presented with a major limitation in respect of ocular movement. CONCLUSIONS: Monocular surgery under peribulbar anesthesia can be an alternative for horizontal large-angle strabismus given deviations of up to 60 PD. Monocular surgery did not result in successful outcomes for deviations of over 65 PD.
NICHE CONSTRUCTION THROUGH GERMINATION CUEING: LIFE‐HISTORY RESPONSES TO TIMING OF GERMINATION IN ARABIDOPSIS THALIANA

Abstract Germination responses to seasonal conditions determine the environment experienced by postgermination life stages, and this ability has potential consequences for the evolution of plant life histories. Using recombinant inbred lines of Arabidopsis thaliana, we tested whether life‐history characters exhibited plasticity to germination timing, whether germination timing influenced the strength and mode of natural selection on life‐history traits, and whether germination timing influenced the expression of genetic variation for life‐history traits. Adult life‐history traits exhibited strong plasticity to season of germination, and season of germination significantly altered the strength, mode, and even direction of selection on life‐history traits under some conditions. None of the average plastic responses to season of germination or season of dispersal were adaptive, although some genotypes within our sample did exhibit adaptive responses. Thus, recombination between inbred lineages created some novel adaptive genotypes with improved responses to the seasonal timing of germination under some, but not all, conditions. Genetically based variation in germination time tended to augment genetic variances of adult life‐history traits, but it did not increase the heritabilities because it also increased environmentally induced variance. Under some conditions, plasticity of life‐history traits in response to genetically variable germination timing actually obscured genetic variation for those traits. Therefore, the evolution of germination responses can influence the evolution of life histories in a general manner by altering natural selection on life‐history traits and the genetic variation of these traits.