Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Association Study Identifies HLA-DP as a Susceptibility Gene for Pediatric Asthma in Asian Populations

Asthma is a complex phenotype influenced by genetic and environmental factors. We conducted a genome-wide association study (GWAS) with 938 Japanese pediatric asthma patients and 2,376 controls. Single-nucleotide polymorphisms (SNPs) showing strong associations (P<1×10−8) in GWAS were further genotyped in an independent Japanese samples (818 cases and 1,032 controls) and in Korean samples (835 cases and 421 controls). SNP rs987870, located between HLA-DPA1 and HLA-DPB1, was consistently associated with pediatric asthma in 3 independent populations (P combined = 2.3×10−10, odds ratio [OR] = 1.40). HLA-DP allele analysis showed that DPA1*0201 and DPB1*0901, which were in strong linkage disequilibrium, were strongly associated with pediatric asthma (DPA1*0201: P = 5.5×10−10, OR = 1.52, and DPB1*0901: P = 2.0×10−7, OR = 1.49). Our findings show that genetic variants in the HLA-DP locus are associated with the risk of pediatric asthma in Asian populations.
Combining Catalyzed Reporter Deposition-Fluorescence In Situ Hybridization and Microautoradiography To Detect Substrate Utilization by Bacteria and Archaea in the Deep Ocean

ABSTRACT The recently developed CARD-FISH protocol was refined for the detection of marine Archaea by replacing the lysozyme permeabilization treatment with proteinase K. This modification resulted in about twofold-higher detection rates for Archaea in deep waters. Using this method in combination with microautoradiography, we found that Archaea are more abundant than Bacteria (42% versus 32% of 4′,6′-diamidino-2-phenylindole counts) in the deep waters of the North Atlantic and that a larger fraction of Archaea than of Bacteria takes up l-aspartic acid (19% versus 10%).
Temporal Autocorrelation in Univariate Linear Modeling of FMRI Data

In functional magnetic resonance imaging statistical analysis there are problems with accounting for temporal autocorrelations when assessing change within voxels. Techniques to date have utilized temporal filtering strategies to either shape these autocorrelations or remove them. Shaping, or "coloring," attempts to negate the effects of not accurately knowing the intrinsic autocorrelations by imposing known autocorrelation via temporal filtering. Removing the autocorrelation, or "prewhitening," gives the best linear unbiased estimator, assuming that the autocorrelation is accurately known. For single-event designs, the efficiency of the estimator is considerably higher for prewhitening compared with coloring. However, it has been suggested that sufficiently accurate estimates of the autocorrelation are currently not available to give prewhitening acceptable bias. To overcome this, we consider different ways to estimate the autocorrelation for use in prewhitening. After high-pass filtering is performed, a Tukey taper (set to smooth the spectral density more than would normally be used in spectral density estimation) performs best. Importantly, estimation is further improved by using nonlinear spatial filtering to smooth the estimated autocorrelation, but only within tissue type. Using this approach when prewhitening reduced bias to close to zero at probability levels as low as 1 x 10(-5).
Automated Post-Silicon Debugging of Design Bugs

As design size and complexity increase in the modern IC design, more design bugs escape the pre-silicon verification process and slip into the silicon. Efficient automation of postsilicon debugging procedures helps to reduce debugging time and to increase diagnosis accuracy. This paper presents an automated approach for post-silicon debugging of design bugs by integrating post-silicon trace analysis, model-based diagnosis, and diagnostic trace generation. The diagnosis accuracy increases by automated iteration of model-based diagnosis and diagnostic trace generation. Experimental results show the effectiveness of the approach in reducing the number of fault candidates without biasing the solution space.
Detecting Errors in English Article Usage with a Maximum Entropy Classifier Trained on a Large, Diverse Corpus

One of the most difficult challenges faced by non-native speakers of English is mastering the system of English articles. We trained a maximum entropy classifier to select among a/an, the, or zero article for noun phrases, based on a set of features extracted from the local context of each. When the classifier was trained on 6 million noun phrases, its performance was correct about 88% of the time. We also used the classifier to detect article errors in the TOEFL essays of native speakers of Chinese, Japanese, and Russian. Agreement with human annotators was about 88% (kappa = 0.36). Many of the disagreements were due to the classifier s lack of discourse information. Performance rose to 94% agreement (kappa = 0.47) when the system accepted noun phrases as correct in cases where its own confidence was low.
REGULATORY MECHANISMS OF CELLULAR RESPIRATION

Oxidizing agents of sulfhydryl groups such as iodosobenzoate, alkylating agents such as iodoacetamide, and mercaptide-forming agents such as cadmium chloride, mercuric chloride, p-chloromercuribenzoate, sodium arsenite, and p-carboxyphenylarsine oxide, added in small concentrations to a suspension of sea urchin sperm produced an increase in respiration. When the concentration was increased there was an inhibition. These effects are explained by postulating the presence in the cells of two kinds of sulfhydryl groups: soluble sulfhydryl groups, which regulate cellular respiration, and fixed sulfhydryl groups, present in the protein moiety of enzymes. Small concentrations of sulfhydryl reagents combine only with the first, thus producing an increase in respiration; when the concentration is increased, the fixed sulfhydryl groups are also attacked and inhibition of respiration is the consequence. Other inhibitors of cell respiration, such as cyanide and urethanes, which do not combine with —SH groups, did not stimulate respiration in small concentration.
Exploring Social and Emotional Aspects of Giftedness in Children.

Parents of gifted children have few guidelines about how to deal with issues resulting from their children's giftedness. Not only intellectual, but also, social and emotional issues provide challenges for parents. Five social/emotional traits of giftedness (divergent thinking ability, excitability, sensitivity, perceptiveness and entelechy) are described, and the specific issues that parents must face to enable their children to reach their full potential are explored.
Word Sense Disambiguation Using Aggregated Similarity Based on WordNet Graph Representation

The term of word sense disambiguation, WSD, is introduced in the context of text document processing. A knowledge based approach is conducted using WordNet lexical ontology, describing its structure and components used for the process of identification of context related senses of each polysemy words. The principal distance measures using the graph associated to WordNet are presented, analyzing their advantages and disadvantages. A general model for aggregation of distances and probabilities is proposed and implemented in an application in order to detect the context senses of each word. For the non-existing words from WordNet, a similarity measure is used based on probabilities of co-occurrences. The module of WSD is proposed for integration in the step of processing documents such as supervised and unsupervised classification in order to maximize the correctness of the classification. Future work is related to the implementation of different domain oriented ontologies.
Enveloping pedagogies: the codification of instructional technologies

Abstract A multitude of new technologies and curricula are being introduced in schools as the panacea for equalizing student differences and facilitating student success. However, we can find a pattern in how teachers have historically employed instructional innovations in the spaces of their classrooms. This article examines the manner in which two White elementary teachers codify instructional technologies with institutional systems of knowledge. Drawing on poststructuralist theories of discourse and practice, the author analyses the speech acts and pedagogical practices of these teachers to identify the process and knowledge in which they codify instructional resources with a psychological/individual discourse in order to give them meaning. The article illuminates how the social practice of codifying curriculum materials, computer technology and texts within this system of reasoning bounds how instructional resources can be used, and by whom. Furthermore, the analysis builds upon other empirical work to describe the entwinement of the codes that envelop instructional technologies and those that inscribe subjectivities upon students.
Achieving Optimal Accuracy in Frameless Functional Neurosurgical Procedures

mention of these figures in the present study, making it difficult to compare this common source of error between studies. With proper registration, the 1-mm error sphere should completely encompass the head ( fig. 1 ), and registration errors should be less than 0.5 mm, with an ideal error being approximately 0.2–0.3 mm. We reject registration errors above 0.8 mm, which imply that there has either been some dislodgement of the fiducials due to loosening or improper placement, or there has been some error in localizing the identical point in image space and surgical space. Choosing the center of the fiducials in image space is not intuitive ( fig. 2 ) and requires practice and experience, with expert assistance recommended during the learning phase. The tool used for alignment of the NeXframe platform in this study (‘Guide Frame DT’) is difficult to align properly within the registration divot on the reference frame, which can lead to angular errors of several degrees. Over the past 3 years, this instrument has been abandoned in favor of the alignment tool packaged with the NeXframe, which does not suffer from these limitations. This important point is not discussed as a source of possible error. It would be informative to know if the Stealth navigational platform used in this study was properly calibrated. Instrument We read with interest the recent paper by Bjartmarz and Rehncrona, ‘Comparison of accuracy and precision between frame-based and frameless stereotactic navigation for deep brain stimulation electrode implantation’ [1] . We applaud the authors for endeavoring to provide a direct comparison of the two techniques; however, their methodology is missing certain details which we have found helpful in achieving optimal accuracy during frameless DBS placement. We believe it is vitally important to take careful note of registration accuracy and predicted volume of 1 mm error. There is no Received: August 27, 2007 Accepted: July 1, 2008 Published online: October 8, 2008
Manifold Regularization

In this lecture we introduce a class of learning algorithms, collectively called manifold regularization algorithms, suited for predicting/classifying data embedded in high-dimensional spaces. We introduce manifold regularization in the framework of semi-supervised learning, a generalization of the supervised learning setting in which our training set may consist of unlabeled as well as labeled examples.
Exploring the Essence of Spirituality: A Phenomenological Study of Eight Students with Eight Different Worldviews

Throughout most facets of American life, there has been a renewed interest in and expression of spirituality. Religiosity and spirituality have been at the center of recent international events (e.g., September 11th) and political discussions (e.g., continuing debates about school prayer and the role of religion in the political process). As a consequence, campus communities are striving to make sense of spirituality and religious tolerance as well as their roles in helping American students understand themselves as part of a diverse democracy. This phenomenological study addresses these issues by asking eight students representing eight different worldviews (i.e., Agnosticism, Atheism, Buddhism, Hinduism, Judaism, Muslim, Protestantism, and Roman Catholicism) about what spirituality means to them. Photo elicitation and semistructured interviewing are used as the primary means for collecting data. Results show that common to all eight perspectives is the idea that spirituality is the human attempt to make meaning of the self in connection to and with the external world. Implications for student development practice and future research are discussed.
Out of DSM: Depathologizing Homosexuality

In 1973, the American Psychiatric Association (APA) removed the diagnosis of “homosexuality” from the second edition of its Diagnostic and Statistical Manual (DSM). This resulted after comparing competing theories, those that pathologized homosexuality and those that viewed it as normal. In an effort to explain how that decision came about, this paper reviews some historical scientific theories and arguments that first led to the placement of homosexuality in DSM-I and DSM-II as well as alternative theories that eventually led to its removal from DSM III and subsequent editions of the manual. The paper concludes with a discussion of the sociocultural aftermath of that 1973 decision.
Drug Treatment, Health, and Social Service Utilization by Substance Abusing Women From a Community-Based Sample

Background:Substance abuse is an escalating problem among poor urban Latina women; little is known about their access to drug treatment and to needed social and health services. Objective:Our objectives were to (1) examine the need and use of substance abuse treatment, health services, government entitlement programs, and social service programs among cocaine and heroin using Puerto Rican women and (2) identify whether service use predicts their prospective entry into drug treatment. Research Design:This was a 3-wave longitudinal study of community substance abusing women evaluated on substance abuse and dependence using diagnostic measures, and hair and urine toxicological screens. Information was collected on self-reported need and receipt of substance abuse treatment, social services, general health services, and government entitlement programs. Subjects:A community sample of cocaine-, crack-, and/or heroin-using women from copping areas in low-income urban centers of Puerto Rico were interviewed in 1997–1998 with 2 follow-up periods. Results:Drug treatment, health, and social service utilization were low relative to need for services throughout all data waves. Social service utilization predicted prospective entry into drug treatment but not contacts with general health services or government entitlement programs. Conclusion:Drug-abusing women in low-income urban areas in Puerto Rico have substantial unmet substance abuse treatment, health, and social service needs. Mandated treatment by social service agencies may explain their clients’ higher likelihood of entering drug treatment. Building linkages between service sectors to augment entry into drug treatment is essential for meeting the complex needs of this underserved population.
Multiple sclerosis and viruses

Discussing the problem of multiple sclerosis and viruses should not be limited to reviewing the epidemiological evidence in favor, or against, a particular candidate, such as Epstein‐Barr virus or human herpes virus 6. In this text, I discuss the difficulty of going from association to causation in human epidemiology; the fact that viruses can trigger or prevent autoimmunity; the problem of our very limited knowledge of the viruses that we harbor as part of our metagenome; and the role of such viral flora in multifactorial diseases and also, possibly, in health. ANN NEUROL 2010;68:6–8
Experimentally Induced Security Influences Responses to Psychological Pain

We tested the hypothesis that experimentally induced security changes people's response to psychological pain (operationalized in terms of hurt feelings) in ways that depend on their attachment style. Seventy undergraduates were randomly assigned to receive (a) security-enhancing subliminal primes (the words love, secure, affection) or (b) neutral subliminal primes (lamp, staple, building). As expected, interactions emerged between priming condition and attachment style. In the neutral priming condition, avoidant attachment was associated with a tendency to dismiss hurtful events, inhibit expressions of distress, and react hostilely; as expected, security priming caused avoidance to be associated with greater openness to the pain of a hurtful experience. A significant interaction also emerged between attachment anxiety and security priming. In the neutral priming condition, attachment anxiety was associated with less constructive reactions and more intense feelings of rejection, more crying, and more nega.
Conduction disturbances and increased atrial vulnerability in Connexin40-deficient mice analyzed by transesophageal stimulation.

BACKGROUND Recently, it has been reported that connexin40 (Cx40) deficiency in targeted mouse mutants is associated with a prolongation of P-wave and QRS complex duration on surface electrograms. The specific effects of Cx40 deficiency on sinus node function, sinoatrial, and atrioventricular conduction properties as well as on atrial vulnerability have not yet been investigated systematically by electrophysiological analysis. METHODS AND RESULTS Fifty-two mice (18 Cx40(+/+), 15 Cx40(+/-), and 19 Cx40(-/-) mice) were subjected to rapid atrial transesophageal stimulation after anesthesia with avertin. A significant prolongation of sinus node recovery time was noticed in Cx40(-/-) mice compared with Cx40(+/-) and Cx40(+/+) mice (287.8+/-109.0 vs 211.1+/-61.8 vs 204.4+/-60.9 ms; P<0.05). In addition, Wenckebach periodicity occurred at significantly longer atrial pacing cycle lengths in Cx40(-/-) mice than in Cx40(+/-) or Cx40(+/+) mice (93. 3+/-11.8 vs 83.9+/-9.7 vs 82.8+/-8.0 ms, P<0.05). Analysis of 27 Cx40(-/-) mice showed a significant increase in intra-atrial conduction time and atrioventricular conduction time compared with 52 Cx40(+/-) and 31 wild-type (Cx40(+/+)) mice. Furthermore, in Cx40(-/-) mice, atrial tachyarrhythmias could be induced frequently by atrial burst pacing, whereas no atrial arrhythmias were inducible in heterozygous or wild-type mice. CONCLUSIONS This study demonstrates that Cx40 deficiency is associated with sinoatrial, intra-atrial, and atrioventricular conduction disturbances. In atrial myocardium of the mouse, Cx40 deficiency results in increased atrial vulnerability and might contribute to arrhythmogenesis.
Online and Batch Learning of Generalized Cosine Similarities

In this paper, we define an online algorithm to learn the generalized cosine similarity measures for kNN classification and hence a similarity matrix A corresponding to a bilinear form. In contrary to the standard cosine measure, the normalization is itself dependent on the similarity matrix which makes it impossible to use directly the algorithms developed for learning Mahanalobis distances, based on positive, semi-definite (PSD) matrices. We follow the approach where we first find an appropriate matrix and then project it onto the cone of PSD matrices, which we have adapted to the particular form of generalized cosine similarities, and more particularly to the fact that such measures are normalized. The resulting online algorithm as well as its batch version is fast and has got better accuracy as compared with state-of-the-art methods on standard data sets.
Social-Aware Energy-Efficient Data Dissemination with D2D Communications

With the high penetration rate of smart mobile devices, it is appealing to exploit device-to-device (D2D) communications for data dissemination, e.g., in disaster alerts and event notifications. The popularity of social networks also offers good opportunities to improve the efficiency of data dissemination. Though there have been some existing works on data dissemination with D2D and mobile social networks, many focus on mitigating the D2D co-channel interference to achieve high resource utilization. As mobile devices are power-limited, it is important to consider the energy efficiency and finishing time in data dissemination. In this paper, we aim at developing an effective solution for D2D data dissemination to balance between total energy consumption and transmission completion time. In particular, we propose novel algorithms for seed selection and transmission scheduling with a single seed or multiple seeds. Simulation results demonstrate that our solution outperforms two reference schemes in total energy consumption while achieving a good balance for transmission completion time.
Specifications for a Social and Technical Environment for Improving Design Process Communication

The architecture, engineering, and construction (AEC) industry can generate tremendous value by improving design processes. Observed case studies and design literature suggest that processes can improve through collaboration, sharing and understanding (defined here as Design Process Communication). Industry has not widely adopted process communication techniques, though other research fields provide points of departure for promoting better communication. Organization Science studies how institutions exchange information and knowledge. Human Computer Interaction, informed by Cognitive Science, explains how computers can aid and supplement human’s ability to find and manage information. Process Modeling research shows how to best represent design processes. The paper links this research to develop a specification for a social and technological environment - a Design Process Communication Methodology. The environment is computable, distributed, embedded, modular, personalized, scalable, shared, social, transparent, and usable. The Methodology lays the foundation for improving building design process efficiency and effectiveness from concept to construction documentation.
Detecting and indexing moving objects for behavior analysis by video and audio interpretation. (La détection et l'indexation des objets en mouvement pour l'analyse du comportement par vidéo et audio interprétation)

In this thesis a system for analyzing moving objects behavior for surveillance applications is proposed: videos are processed in order to extract and analyze moving objects trajectories for identifying abnormal trajectories, associated to abnormal behaviors. Whereas the information extracted from the videos are not sufficient or not sufficiently reliable, the proposed system is enriched by a module in charge of recognizing audio events of interest such as shoots, screams or broken glasses. Finally, all the extracted information are suitably stored in order to allow an efficient retrieval from the human operator. Five different standard datasets have been used for testing the different modules proposed in this thesis; the obtained results, both in terms of accuracy and computational efficiency, confirm the effectiveness and the real applicability of the proposed approach.