Miracle-dz/UniFAR-FTUs huggingface dataset:
Letters to the Editor No " Bias " toward the Null Hypothesis in Most Conventional Multipoint Nonparametric Linkage Analyses Comparison of Linkage Statistics Analyses Using All 200 Families and Using Only the 147 Informative Families

To the Editor: We would like to comment on the Schork and Greenwood (2004) article dealing with the inherent “bias” toward the null hypothesis in the context of nonparametric linkage analysis. The authors point out that, in certain situations, a loss of evidence for linkage can result from the practice of assigning expected allele-sharing values to affected relative pairs that are uninformative for their identity-by-descent (IBD) status. They explained this by setting up a likelihood function and studying its properties by simulation, clearly illustrating the negative impact of using expected IBD values for uninformative pairs. However, we would like to point out that their likelihood does not reflect how the majority of nonparametric linkage analysis programs compute statistics in practice. Indeed, the “problem” has been known and well discussed for years. Some of the concerns we discuss here have also been raised by Cordell (2004). Schork and Greenwood (2004) set up the likelihood formulation as follows. Let ni be the number of sib pairs sharing i alleles IBD ( , 1, or 2). If all families had i p 0 unambiguous IBD sharing, then the LOD score evaluated at the sharing vector (p0, p1, p2) is calculated as
Thioredoxin-Interacting Protein Gene Expression via MondoA Is Rapidly and Transiently Suppressed during Inflammatory Responses

Whereas accumulating evidence indicates that a number of inflammatory genes are induced by activation of nuclear factor-κB and other transcription factors, less is known about genes that are suppressed by proinflammatory stimuli. Here we show that expression of thioredoxin-interacting protein (Txnip) is dramatically suppressed both in mRNA and protein levels upon stimulation with lipopolysaccharide in mouse and human macrophages. In addition to lipopolysaccharide, a Toll-like receptor 4 ligand, stimulation with other Toll-like receptor ligands such as CpG DNA also suppressed Txnip expression. Not only the Toll-like receptor ligands, but also other proinflammatory stimulators, such as interleukin-1β and tumor necrosis factor-α elicited the similar response in fibroblasts. Suppression of Txnip by lipopolysaccharide is accompanied by a decrease of the glucose sensing transcription factor MondoA in the nuclei and dissociation of the MondoA:Mlx complex that bound to the carbohydrate-response elements in the Txnip promoter in unstimulated cells. Lipopolysaccharide-mediated decrease of nuclear MondoA was inhibited in the presence of 2-deoxyglucose. Furthermore, blockage of glyceraldehyde-3-phosphate dehydrogenase by iodoacetate alleviated the suppression of Txnip mRNA by lipopolysaccharide, suggesting the involvement of glucose-metabolites in the regulation. Since Txnip is implicated in the regulation of glucose metabolism, this observation links between inflammatory responses and metabolic regulation.
Genome Sequence of Aedes aegypti, a Major Arbovirus Vector

We present a draft sequence of the genome of Aedes aegypti, the primary vector for yellow fever and dengue fever, which at ∼1376 million base pairs is about 5 times the size of the genome of the malaria vector Anopheles gambiae. Nearly 50% of the Ae. aegypti genome consists of transposable elements. These contribute to a factor of ∼4 to 6 increase in average gene length and in sizes of intergenic regions relative to An. gambiae and Drosophila melanogaster. Nonetheless, chromosomal synteny is generally maintained among all three insects, although conservation of orthologous gene order is higher (by a factor of ∼2) between the mosquito species than between either of them and the fruit fly. An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species.
Evolution of Sex-Dependent Gene Expression in Three Recently Diverged Species of Drosophila

Sexual dimorphism in morphological, physiological, and behavioral traits is pervasive in animals, as is the observation of strong sexual dimorphism in genomewide patterns of gene expression in the few species where this has been studied. Studies of transcriptome divergence show that most interspecific transcriptional divergence is highly sex dependent, an observation consistent with the action of sex-dependent natural selection during species divergence. However, few transcriptome evolution studies have been conducted between recently diverged species (<1 MY). Here, we present analyses of sex-biased transcriptome divergence in sexually mature adults of three recently diverged species of Drosophila: Drosophila pseudoobscura, D. persimilis, and D. pseudoobscura bogotana. Data were collected using a custom designed Agilent oligonucleotide. Expression was detected in 12,507 genes. About 80% of the expressed genes show sex-biased expression in each species. Across species, 21% of the transcriptome shows switches between nonsex bias and sex bias, and just 0.9% of the transcriptome shows reversals of sex-biased expression. Over 80% of the expression divergence between species is due to changes in one sex only. About 15% of the expression divergence between species is due to changes in the same direction in both sexes and just 2% is due to changes in both sexes but in opposite directions. In agreement with previous studies, we observe a high level of sex-dependent transcriptome divergence and strong demasculinization of the two arms of the X chromosome in all species. However, in contrast to previous studies we find that male-biased genes do not have higher levels of expression divergence than non-sex-biased genes, and sex-biased genes show higher levels of expression divergence in the alternate sex, suggesting that sex-biased genes endure stronger selection when expressed in the alternate sex.
Modeling the mixtures of known noise and unknown unexpected noise for robust speech recognition

Real-world noise may be a mixture of known or trainable noise and unknown unexpected noise. This paper investigates the combination of the conventional noise-reduction techniques with the probabilistic union model to deal with this type of mixed noise for robust speech recognition. In particular, we have developed a multi-environment system to remove the known or trainable acoustic mismatch across different environments. The novelty of this system, in contrast to other multi-environment models, is that the acoustic model for each environment is built upon the probabilistic union model, so that this system is also capable of accommodating further unknown unexpected noise within a specific environment. We have tested the new system for connected digit recognition in different environments, each involving an environment-specific noise and some unknown untrained noise. The results indicate that the new system offers significantly improved performance for the environments involving unknown additional noise, in comparison to a baseline multi-environment system.
Persistent Epstein-Barr viral load in Epstein-Barr viral naïve pediatric heart transplant recipients: Risk of late-onset post-transplant lymphoproliferative disease

AIM To examine the risk of late-onset post-transplant lymphoproliferative disorder (PTLD) in the presence of persisting high Epstein-Barr virus (EBV) in EBV naïve pediatric heart transplant (HT) recipients. METHODS A retrospective review of the medical records of the 145 pediatric HT recipients who had serial EBV viral load monitoring at our center was performed. We defined EBV naive patients whose EBV serology either IgM or IgG in the blood were negative at the time of HT and excluded passive transmission from mother to child in subjects less than 6 mo of age. RESULTS PTLD was diagnosed in 8 out of 145 patients (5.5%); 6/91 (6.5%) in those who were EBV seropositive and 2/54 (3.7%) in the EBV naïve group at the time of HT (P = 0.71). We found 32/145 (22%) patients with persistently high EBV load during continuing follow-up; 20/91 (22%) in EBV seropositive group vs 12/54 (22%) in EBV naïve group (P = 0.97). There was no significant association between pre-HT serostatus and EBV load after transplant (P > 0.05). In the EBV seropositive group, PTLD was diagnosed in 15% (3/20) of patients with high EBV vs 4.2% (3/71) of patients with low or undetectable EBV load (P = 0.14) whereas in EBV naïve patients 8.3% (1/12) of those with high EBV load and 2.3% (1/42) with low or undetectable EBV load (P = 0.41). There was a highly significant association between occurrence of PTLD in those with high EBV load and duration of follow up (4.3 ± 3.9 years) after HT by Cochran-Armitage test for the entire cohort (P = 0.005). At least one episode of acute rejection occurred in 72% (23/32) of patients with high EBV vs 36% (41/113) patients with low or undetectable EBV after HT (P < 0.05). CONCLUSION There is an association between persistently high EBV load during post-HT follow up and the occurrence of late-onset PTLD in pediatric HT recipients irrespective of serostatus at the time of transplant. The occurrence of allograft rejection increased in patients with high EBV load presumably due to reduction in immunosuppression.
Rough Terrain Negotiable Mobile Platform with Passively Adaptive Double-Tracks and Its Application to Rescue Missions

This paper presents design and integration of the ROBHAZ-DT3, which is a newly developed mobile robot system with chained double-track mechanisms. A passive adaptation mechanism equipped between the front and rear body enables the ROBHAZ-DT3 to have good adaptability to uneven terrains including stairs. The passive adaptation mechanism reduces energy consumption when moving on uneven terrain as well as its simplicity in design and remote control, since no actuator is necessary for adaptation. Starting from this novel design, dynamic analysis and simulation were conducted to verify the mobility of the double-track mechanism and to obtain significant design parameters such as a suitable track size and an allowable attack angle. Based on this novel mobile platform, a rescue version of the ROBHAZ-DT3 with appropriate sensors and a semi-autonomous mapping and localization algorithm is developed to participate in the RoboCup2004 US-Open: Urban Search and Rescue Competition. From the various experiments in the realistic rescue arena, we can verify that the ROBHAZ-DT3 is reliable in travelling rugged terrain and the proposed mapping and localization algorithm are effective in the unstructured environment with uneven ground.
Loving one's job: Construct development and implications for individual well-being

We introduce the construct of loving one's job as an overlooked, but potentially informative, construct for organizational research. Following both empirical findings and theoretical developments in other domains we suggest that love of the job comprises a passion for the work itself, commitment to the employing organization, and high-quality intimate relationships with coworkers. We also suggest that love of the job is a taxonic rather than a dimensional construct – one either loves their job or does not. In addition, we propose that loving your job is on the whole beneficial to individual well-being. Within this broad context, however, we suggest that loving one's job may buffer the effect of some stressors while at the same time increase vulnerability to others. These suggestions provide some initial direction for research focused on the love of one's job.
DOES BILINGUALISM IMPROVE ACADEMIC PERFORMANCE? ESTIMATING THE RELATIONSHIP BETWEEN FOREIGN LANGUAGES SPOKEN AT HOME AND STUDENT TEST SCORES

During the 2013-14 school year, nearly 10 percent of students in U.S. public elementary and secondary schools are English-learners. Limitation in the scope of previous research prevents researchers from understanding whether a non-English language spoken at home has an effect on student test scores. Using the Early Childhood Longitudinal Study, Kindergarten 1998-99, this study examines the role of bilingualism – when a non-English language is spoken at home – plays in students’ academic performance and their developmental trajectories in early school years. Ordinary Least Square results show that despite starting with lower math and the reading scores in kindergarten, bilingual students fully close the math gap by 1 grade and reading gap by 5 grade. However, home and community factors, school factors, and student characteristics explain more of these differences than bilingualism.
Please Scroll down for Article Applied Economics Letters Betting on Weight Loss … and Losing: Personal Gambles as Commitment Mechanisms Betting on Weight Loss . . . and Losing: Personal Gambles as Commitment Mechanisms

This article may be used for research, teaching and private study purposes. Any substantial or systematic reproduction, redistribution , reselling , loan or sub-licensing, systematic supply or distribution in any form to anyone is expressly forbidden. The publisher does not give any warranty express or implied or make any representation that the contents will be complete or accurate or up to date. The accuracy of any instructions, formulae and drug doses should be independently verified with primary sources. The publisher shall not be liable for any loss, actions, claims, proceedings, demand or costs or damages whatsoever or howsoever caused arising directly or indirectly in connection with or arising out of the use of this material. Professional bookmakers rarely accept bets from individuals who directly control the outcome of the bet. We analyse a unique exception to this rule and a potential policy innovation in the battle against obesity: a weight loss betting market. If obese individuals have time-inconsistent preferences then commitment mechanisms, such as personal gambles, should help them restrain their short-term impulses and lose weight. Correspondence with the bettors confirms that this is their primary motivation. However, it appears that the bettors in our sample are not particularly skilled at choosing effective commitment mechanisms. Despite payoffs of as high as $7350, approximately 80% of people who spend money to bet on their own behaviour end up losing their bets. Empirical analysis of the betting market yields further insights. Males are treated very differently compared to females: being male is considered equivalent to having an extra 6 months to lose the same amount of weight. Movements in the market price also confirm the belief that rigidity is preferred to flexibility in setting successful weight loss targets.
Parent decision‐making around the genetic testing of children for germline TP53 mutations

Li‐Fraumeni syndrome is a rare genetic cancer predisposition syndrome caused by germline TP53 mutations. Up to 20% of mutation carriers develop cancer during childhood. The benefits of TP53 mutation testing of children are a matter of debate and knowledge of parent decision‐making around such testing is limited. The current study examined how parents make decisions regarding TP53 testing for their children.
Rituximab-associated hepatitis B virus (HBV) reactivation in lymphoproliferative diseases: meta-analysis and examination of FDA safety reports.

BACKGROUND Rituximab has been associated with hepatitis B virus reactivation (HBV-R). However, the characteristics and scope of this association remain largely undefined. METHODS We completed a comprehensive literature search of all published rituximab-associated HBV-R cases and from the Food and Drug Administration (FDA) Adverse Event Reporting System (AERS) MedWatch database. Literature and FDA cases were compared for completeness, and a meta-analysis was completed. RESULTS One hundred and eighty-three unique cases of rituximab-associated HBV-R were identified from the literature (n = 27 case reports, n = 156 case series). The time from last rituximab to reactivation was 3 months (range 0-12), although 29% occurred >6 months after last rituximab. Within FDA data (n = 118 cases), there was a strong signal for rituximab-associated HBV-R [proportional reporting ratio = 28.5, 95% confidence interval (CI) 23.9-34.1; Empiric Bayes Geometric Mean = 26.4, 95% CI 21.4-31.1]. However, the completeness of data in FDA reports was significantly inferior compared with literature cases (P < 0.0001). Among HBV core antibody (HBcAb(+)) series, the pooled effect of rituximab-based therapy showed a significantly increased risk of HBV-R compared with nonrituximab-treated patients (odds ratio 5.73, 95% CI 2.01-16.33; Z = 3.33, P = 0.0009) without heterogeneity (χ(2) = 2.12, P = 0.5473). CONCLUSIONS The FDA AERS provided strong HBV-R safety signals; however, literature-based cases provided a significantly more complete description. Furthermore, meta-analysis of HBcAb(+) series identified a more than fivefold increased rate of rituximab-associated HBV-R.
Maternal association and influence of DHFR 19 bp deletion variant predisposes foetus to anencephaly susceptibility: a family-based triad study

Abstract Objective: Previous studies have not used family-based methods to evaluate maternal-paternal genetic effects of the folate metabolizing enzyme, dihydro folate reductase (DHFR) essential during embryogenesis. Present study focuses on evaluating the association and influence of parental genetic effects of DHFR 19 bp deletion in the development of foetal neural tube defects (NTDs) using family-based triad approach. Materials and methods: The study population (n = 924) including 124 NTD case-parent trios (n = 124 × 3 = 372) and 184 healthy control-parent trios (n = 184 × 3 = 552) from Telangana, India, was genotyped for DHFR 19 bp deletion. Statistical analysis was used by SPSS and parent-of-origin effects (POE). Results: Foetuses with deletion genotype (DD) were at risk of developing anencephaly (OR = 3.26, p = 0.020). Among parents, increased maternal risk of having an anencephaly foetus (OR = 2.66, p = 0.028) was observed in mothers with DD genotype. In addition, POE analysis also demonstrated higher risk of maternal transmission of the deletion allele to anencephaly foetus compared with paternal transmission (OR = 6.00, p = 0.016). Interestingly, maternal-paternal-offspring genotype incompatibility revealed maternal deletion genotype (DD) in association with paternal heterozygous deletion genotype (WD) significantly increased risk for NTDs (OR = 5.29, p = 0.013). Conclusions: This study, using family-based case-parent and control-parent triad approach, is the first to report influence of maternal transmission of DHFR 19 bp deletion in the development of anencephaly in the foetus.
Text Classification from Positive and Unlabeled Documents Based on GA

Automatic text classification is one of the most important tools in Information Retrieval. As the traditional methods for text classification cannot find the best feature set, the GA is applied to the feature selection because it can get the global optimal solution. This paper presents a novel text classifier from positive and unlabeled documents based on GA. Firstly, we identify reliable negative documents by improved 1-DNF algorithm. Secondly, we build a set of classifiers by iteratively applying SVM algorithm on training example sets. Thirdly, we discuss an approach to evaluate the weighted vote of all classifiers generated in the iteration steps to construct the final classifier based on GA instead of choosing one of the classifiers as the final classifier. GA evolving process can discover the best combination of the weights. The experimental result on the Reuter data set shows that the performance is exciting.
Opening of Mitochondrial KATP Channels Attenuates the Ouabain-Induced Calcium Overload in Mitochondria

We tested whether opening of mitochondrial ATP-sensitive K+ (mitoKATP) channels depolarizes mitochondrial membrane potential (&Dgr;&PSgr;m) and thereby prevents the mitochondrial Ca2+ overload. With the use of a Nipkow disk confocal system, the mitochondrial Ca2+ concentration ([Ca2+]m) and &Dgr;&PSgr;m in rat ventricular myocytes were measured by loading cells with Rhod-2 and JC-1, respectively. Exposure to ouabain (1 mmol/L) for 30 minutes produced mitochondrial Ca2+ overload, and the intensity of Rhod-2 fluorescence significantly increased to 173±16% of baseline (P <0.001). Treatment of myocytes with the mitoKATP channel opener diazoxide (100 &mgr;mol/L) blunted the ouabain-induced mitochondrial Ca2+ overload (131±10% of baseline;P <0.001 versus ouabain). Moreover, diazoxide significantly depolarized the &Dgr;&PSgr;m and reduced the intensity of JC-1 fluorescence during application of ouabain to 89±2% of baseline (P <0.05). These effects of diazoxide were blocked by the mitoKATP channel blocker 5-hydroxydecanoate (500 &mgr;mol/L). These results indicate that opening of mitoKATP channels prevents a mitochondrial Ca2+ overload in association with &Dgr;&PSgr;m depolarization and thereby protects myocardium against ischemic damage.
Web Facts and Fantasy

There is a great deal of research about improving Web server performance and building better, faster servers, but little research in characterizing servers and the load imposed upon them. While some tremendously popular and busy sites, such as netscape.com, playboy.com, and altavista.com, receive several million hits per day, most servers are never subjected to loads of this magnitude. This paper presents the analysis of internet Web server logs for a variety of different types of sites. We present a taxonomy of the different types of Web sites and characterize their access patterns and, more importantly, their growth. We then use our server logs to address some common perceptions about the Web. We show that, on a variety of sites, contrary to popular belief, the use of CGI does not appear to be increasing and that long latencies are not necessarily due to server loading. We then show that, as expected, persistent connections are generally useful, but that dynamic time-out intervals may be unnecessarily complex and that allowing multiple persistent connections per client may actually hinder resource utilization compared to allowing only a single persistent connection.
A complexity theory approach to evolvable production systems

Evolvable Production Systems differ from Reconfigurable and Holonic Manufacturing Systems by implying ontology-based process-specific modularity at fine granularity with local intelligence and a distributed control solution based on the Multi-Agent paradigm. Understanding the dynamics of such complex production systems is not feasible with traditional engineering. For creating the manufacturing systems of the future, engineers need to dare a leap in their ways of thinking. Complexity Theory and Artificial Intelligence can be a valuable source of inspiration for manufacturing engineers. This article illustrates how ideas from these scientific areas fit the problems and open questions of manufacturing. Some concepts, as Self-Organization and Emergence, need adaptation to be applicable in production systems; others simply require the right perspective. Finally, a vision of future EPS is outlined.