Miracle-dz/UniFAR-FTUs huggingface dataset:
Qualitative Semi‐Parametric Test for Genetic Associations in Case‐Control Designs Under Structured Populations

Recently, statistical methods have been proposed using genomic markers to control for population stratification in genetic association studies. However, these methods either have unacceptable low power when population stratification becomes strong or cannot control for population stratification well under admixture population models. In this paper, we propose a semiparametric association test to detect genetic association between a candidate marker and a qualitative trait of interest in case‐control designs. The performanceof the test is compared to other existing methods through simulations. The results show that our method gives correct type I error rate both under discrete population models and admixture population models, and our method is robust to the extent of the population stratification. In most of the cases we considered, our method has higher power and, in some cases, substantially higher power than that of existing methods.
Heat Shock Protein 72 (HSPA1B) Gene Polymorphism and Toll-Like Receptor (TLR) 4 Mutation Are Associated with Increased Risk of Urinary Tract Infection in Children

Innate immunity and urinary tract response play a central role in the development of urinary tract infection (UTI). Heat shock protein (HSP) 72 and Toll-like receptor (TLR) 4 are among the key elements of innate defence mechanisms. This study assesses the role of HSPA1B A(1267)G and TLR4 A(896)G polymorphisms using allele-specific polymerase chain reaction in 103 patients treated with recurrent UTI. Allelic prevalence was compared with reference values of 235 healthy controls. Clinical data were also statistically evaluated. TLR4 (896)AG genotype and TLR4 (896)G allele had also higher prevalence in UTI patients versus controls (p = 0.031 and 0.041, respectively). Our data indicates a relationship between the carrier status of HSPA1B (1267)G and TLR4 (896)G alleles and the development of recurrent UTI in childhood independently of other renal abnormalities, while raising further questions about the clinical and therapeutic relevance of these polymorphisms in everyday pediatric nephrology.
Vers un matériau virtuel pour les composites céramiques

A l'âge actuel des composites, les developpements industriels reposent en grande partie sur l'utilisation d'outils numeriques pour le dimensionnement et l'optimisation des structures et des materiaux. Face au challenge scientiﬁque que represente la construction de ces outils, on propose de rassembler les travaux menes par les communautes macro- et micro- mecanique. Pour cela, on considere des cadres de modelisation et de simulation suﬃsamment larges pour contenir l'ensemble des mecanismes, situes a diﬀerentes echelles et appartenant a diﬀerentes physiques, qui pilotent le comportement mecanique et la duree de vie des composites. Les modeles ainsi derives, appeles materiaux virtuels, sont i) utilisables tant en calcul de structure qu'en optimisation materiau, ii) extrapolants pour les chargements severes et les grandes durees de vie, iii) generiques pour des familles entieres de materiaux. La these presentee ici initie la construction d'un materiau virtuel pour les composites tisses a matrice ceramique auto-cicatrisante developpes par Snecma Propulsion Solide, et plusieurs briques ont ete etudiees. i) Au niveau macroscopique, le comportement mecanique est analyse au travers d'un modele ecrit dans le cadre de la theorie de l'endommagement anisotrope et unilateral. On discute d'abord du cadre meme de la theorie, diﬀerentes formulations et lois d'evolutions sont alors comparees. Puis on discute de l'implementation numerique des modeles proposes, et des exemples de calculs de structures industrielles sont presentes. ii) A l'echelle du tissu, pour traiter la ﬁssuration inter-ﬁl, une methode basee sur la mecanique de l'endommagement a taux limite en quasi-statique est analysee et illustree par des exemples de calculs a la propagation. iii) Toujours a cette echelle, la ﬁssuration intra-ﬁl transverse est introduite au travers d'un modele continu avec deformation inelastique, homogeneise a partir d'un modele discret avec frottements situe a l'echelle ﬁbre. Des exemples de calculs sur des tissus realistes sont presentes. iv) Pour ﬁnir, le point clef de la these : a l'echelle ﬁbre la duree de vie est analysee au travers d'une approche novatrice de la propagation sous-critique des defauts dans les ceramiques. Elle uniﬁe les propagations classique et sous-critique, ainsi que les propagations reaction- et diﬀusion-controlled, via un simple couplage entre la mecanique de la rupture et des problemes de diﬀusion/reaction. Elle est validee sur le cas des ﬁbres Hi-Nicalon.
NADC30-like Strain of Porcine Reproductive and Respiratory Syndrome Virus, China

To the Editor: Porcine reproductive and respiratory syndrome (PRRS), which is characterized by reproductive failure in sows and respiratory disease in pigs of all ages, is a viral disease with serious economic consequences for the global pork industry (1). PRRS virus (PRRSV), the causative agent of this disease, was identified in Europe in 1991 and the United States in 1992 (2,3). PRRSV is an enveloped, positive-strand RNA virus of the family Arteriviridae. This virus is divided into European genotype 1 and North American genotype 2. Emerging novel PRRSV strains have caused many outbreaks of severe PRRS (4–7). We report emergence of a novel PRRSV (NADC30-like) in China that is genetically similar to the NADC30 strain isolated in the United States in 2008 (8).
Impacts of anthropogenic SOx, NOx and NH3 on acidification of coastal waters and shipping lanes

The acidification of the ocean by anthropogenic CO2 absorbed from the atmosphere is now well‐recognized and is considered to have lowered surface ocean pH by 0.1 since the mid‐18th century. Future acidification may lead to undersaturation of CaCO3 making growth of calcifying organisms difficult. However, other anthropogenic gases also have the potential to alter ocean pH and CO2 chemistry, specifically SOx and NOx and NH3. We demonstrate using a simple chemical model that in coastal water regions with high atmospheric inputs of these gases, their pH reduction is almost completely canceled out by buffering reactions involving seawater HCO3− and CO32− ions. However, a consequence of this buffering is a significant decrease in the uptake of anthropogenic CO2 by the atmosphere in these areas.
Benefits of and barriers to using patient-rated outcome measures in athletic training.

CONTEXT Patient-rated outcome measures (PROMs) are important for driving treatment decisions and determining treatment effectiveness. However, athletic trainers (ATs) rarely use them; understanding why may facilitate strategies for collection of these outcomes. OBJECTIVE To identify the benefits of and barriers to using PROMs in athletic training. DESIGN Cross-sectional study. SETTING Web-based survey. PATIENTS OR OTHER PARTICIPANTS A total of 1469 randomly sampled ATs (age = 36.8 ± 9.8 years; 48% female) working in the college/university, 2-year institution, secondary school, clinic, hospital, or industrial/occupational setting. INTERVENTION(S) An e-mail was sent to ATs inviting them to complete a survey regarding the use, benefits, and barriers of PROMs. Athletic trainers who indicated they used PROMs (AT-PRs) completed 65 questions about the benefits of and barriers to their use. Athletic trainers who indicated no use of PROMs (AT-NONs) completed 21 questions about barriers of use. MAIN OUTCOME MEASURE(S) Dependent variables were the endorsements for the benefits of and barriers to the use of PROMs. RESULTS A total of 458 ATs initiated the survey and 421 (AT-PR = 26%, AT-NON = 74%) completed it (response rate = 28.7%). The most frequently endorsed benefits by AT-PRs were enhancing communication with patients (90%) and other health care professionals (80%), directing patient care (87%), and increasing examination efficiency (80%). The most frequently endorsed barriers by AT-PRs were that PROMs are time consuming (44%), difficult (36%), and confusing (31%) for patients and time consuming for clinicians to score and interpret (29%). The most frequently endorsed problems by AT-NONs were that PROMs are time consuming for clinicians to score and interpret (31%), time consuming (46%) and irrelevant to patients (28%), and lacking a support structure for clinicians (29%). CONCLUSIONS These results suggest that, although benefits to using PROMs exist, there are also barriers. Barriers are similar for AT-PRs and AT-NONs. Strategies to decrease barriers and facilitate the use of PROMs warrant investigation.
Computational Identification and Characterization of Novel Genes from Legumes1[w]

The Fabaceae, the third largest family of plants and the source of many crops, has been the target of many genomic studies. Currently, only the grasses surpass the legumes for the number of publicly available expressed sequence tags (ESTs). The quantity of sequences from diverse plants enables the use of computational approaches to identify novel genes in specific taxa. We used BLAST algorithms to compare unigene sets from Medicago truncatula, Lotus japonicus, and soybean (Glycine max and Glycine soja) to nonlegume unigene sets, to GenBank's nonredundant and EST databases, and to the genomic sequences of rice (Oryza sativa) and Arabidopsis. As a working definition, putatively legume-specific genes had no sequence homology, below a specified threshold, to publicly available sequences of nonlegumes. Using this approach, 2,525 legume-specific EST contigs were identified, of which less than three percent had clear homology to previously characterized legume genes. As a first step toward predicting function, related sequences were clustered to build motifs that could be searched against protein databases. Three families of interest were more deeply characterized: F-box related proteins, Pro-rich proteins, and Cys cluster proteins (CCPs). Of particular interest were the >300 CCPs, primarily from nodules or seeds, with predicted similarity to defensins. Motif searching also identified several previously unknown CCP-like open reading frames in Arabidopsis. Evolutionary analyses of the genomic sequences of several CCPs in M. truncatula suggest that this family has evolved by local duplications and divergent selection.
Simulating the 128‐ka Antarctic Climate Response to Northern Hemisphere Ice Sheet Melting Using the Isotope‐Enabled HadCM3

Warmer than present Antarctic and Southern Ocean temperatures during the last interglacial, approximately 128,000 years ago, have been attributed to changes in north‐south ocean heat transport, causing opposing hemispheric temperature anomalies. We investigate the magnitude of Antarctic warming and Antarctic ice core isotopic enrichment in response to Northern Hemisphere meltwater input during the early last interglacial. A 1,600‐year HadCM3 simulation driven by 0.25 Sv of meltwater input reproduces 50–60% of the peak Southern Ocean summer sea surface temperature anomaly, sea ice retreat, and ice core isotope enrichment. We also find a robust increase in the proportion of cold season precipitation during the last interglacial, leading to lower isotopic values at the Antarctic ice core sites. These results suggest that a HadCM3 simulation including 0.25 Sv for 3,000–4,000 years would reconcile the last interglacial observations, providing a potential solution for the last interglacial missing heat problem.
Feeding Modalities and the Onset of the Neonatal Abstinence Syndrome

Breast milk has been reported to ameliorate the severity and outcome of neonatal abstinence syndrome (NAS). The mechanism of this beneficial effect of breast milk on NAS remains unclear, as the negligible amount of methadone transmitted via breast milk is unlikely to have an impact on NAS. The aim of this study was to compare the impact of different feeding modalities on the onset of NAS. A retrospective medical record review was conducted on 194 methadone-maintained mother/infant dyads. Infants were categorized on the first 2 days of life as predominantly breastfed, fed expressed human breast milk (EBM), or formula fed. The feeding categories were then analyzed using the onset of NAS as the outcome measure. After adjusting for confounders, there was no significant effect of the modality of feeding on the rates of NAS requiring treatment (p = 0.11). Breastfeeding significantly delayed the onset of NAS (p = 0.04). The act of breastfeeding in the first 2 days of life had no effect on whether an infant required treatment for NAS when compared to those fed EBM or formula. This only suggests that the advantages of breastfeeding on NAS cannot be substantiated in a small cohort and should not discourage breastfeeding.
Identification of Listeria monocytogenes Genes Expressed in Response to Growth at Low Temperature

ABSTRACT Listeria monocytogenes is a food-borne bacterial pathogen that is able to grow at refrigeration temperatures. To investigate microbial gene expression associated with cold acclimation, we used a differential cDNA cloning procedure known as selective capture of transcribed sequences (SCOTS) to identify bacterial RNAs that were expressed at elevated levels in bacteria grown at 10°C compared to those grown at 37°C. A total of 24 different cDNA clones corresponding to open reading frames in the L. monocytogenes strain EGD-e genome were obtained by SCOTS. These included cDNAs for L. monocytogenes genes involved in previously described cold-adaptive responses (flaA and flp), regulatory adaptive responses (rpoN, lhkA, yycJ, bglG, adaB, and psr), general microbial stress responses (groEL, clpP, clpB, flp, and trxB), amino acid metabolism (hisJ, trpG, cysS, and aroA), cell surface alterations (fbp, psr, and flaA), and degradative metabolism (eutB, celD, and mleA). Four additional cDNAs were obtained corresponding to genes potentially unique to L. monocytogenes and showing no significant similarity to any other previously described genes. Northern blot analyses confirmed increased steady-state levels of RNA for all members of a subset of genes examined during growth at a low temperature. These results indicated that L. monocytogenes acclimation to growth at 10°C likely involves amino acid starvation, oxidative stress, aberrant protein synthesis, cell surface remodeling, alterations in degradative metabolism, and induction of global regulatory responses.
Plane-sweep algorithms for the K group nearest-neighbor query

One of the most representative and studied queries in Spatial Databases is the (K) Nearest-Neighbor (NNQ), that discovers the (K) nearest neighbor(s) to a query point. An extension that is important for practical ap­plications is the (K) Group Nearest Neighbor Query (GNNQ), that discovers the (K) nearest neighbor(s) to a group of query points (considering the sum of distances to all the members of the query group). This query has been studied during the recent years, considering data sets indexed by efficient spatial data structures. We study (K) GNNQs, considering non-indexed data sets, since this case is frequent in practical applications. And we present two (RAM-based) Plane-Sweep algorithms, that apply optimizations emerging from the geometric properties of the problem. By extensive experimentation, using real and synthetic data sets, we highlight the most efficient algorithm.
Optimizing memory accesses for spatial computation

We present the internal representation and optimizations used by the CASH compiler for improving the memory parallelism of pointer-based programs. CASH uses an SSA-based representation for memory, which compactly summarizes both control-flow- and dependence information. In CASH, memory optimization is a four-step process: (1) first an initial, relatively coarse representation of memory dependences is built; (2) next, unnecessary memory dependences are removed using dependence tests; (3) third, redundant memory operations are removed (4) finally, parallelism is increased by pipelining memory accesses in loops. While the first three steps above are very general, the loop pipelining transformations are particularly applicable for spatial computation, which is the primary target of CASH. The redundant memory removal optimizations presented are: load/store hoisting (subsuming partial redundancy elimination and common-subexpression elimination), load-after-store removal, store-before-store removal (dead store removal) and loop-invariant load motion. One of our loop pipelining transformations is a new form of loop parallelization, called loop decoupling. This transformation separates independent memory accesses within a loop body into several independent loops, which are allowed dynamically to slip with respect to each other A new computational primitive, a token generator is used to dynamically control the amount of slip, allowing maximum freedom, while guaranteeing that no memory dependences are violated.
Efficacy of tranexamic acid on blood loss during bimaxilary osteotomy: A randomized double blind clinical trial

Background: Tranexamic acid has been used to reduce bleeding and the subsequent need for blood transfusion in many surgeries. Because orthognathic surgery can be associated with significant bleeding, this study evaluated the efficacy of prophylactic intravenous (IV) tranexamic acid on blood loss during bimaxillary osteotomy. Methods: Thirty-two consecutive patients, scheduled for elective bimaxillary osteotomy, were included in the study and 16 were randomly assigned to each group. They received tranexamic acid (20 mg/kg) or equal volume of placebo (normal saline) intravenously just before induction of anesthesia. Intraoperative blood loss, pre and post operative hemoglobin (Hb) and hematocrit (Hct) concentration, duration of surgery, hospital stay time, and rate of blood transfusion were recorded for each patient. Results: Intraoperative blood loss in the tranexamic group and control group were 585.9 and 790 mL respectively (P=0.008). Postoperative Hb concentration at the 6th hour was greater in the tranexamic group (P=0.008). There was no significant difference in the Hct concentration between the study groups. There was no significant difference in blood transfusion rate, hospital stay time and duration of surgery between the study groups. Conclusion: Preoperative IV administration of tranexamic acid reduces the amount of blood loss during bimaxillary osteotomy.
Case study: feasibility of multisystemic therapy as a treatment for urban adolescents with poorly controlled type 1 diabetes.

OBJECTIVE To determine the feasibility of using multisystemic therapy (MST), an intensive, home-based psychotherapy, to improve poor metabolic control among four adolescents with type 1 diabetes. METHOD A multiple baseline, repeated measures design was used. Blood glucose readings were obtained every 2 weeks during a baseline period, a 7-month intervention, and a month-long postintervention period. Glycosylated hemoglobin (GHb) was measured at baseline and follow-up and was contrasted between two participants who received MST and two participants who did not receive the intervention. RESULTS Intervention participants showed improvements in health status, as well as fewer hospitalizations and emergency room visits. CONCLUSIONS Findings from this case study suggest that MST has the potential to improve treatment adherence and metabolic control among teens with poorly controlled type 1 diabetes.
Bandit structured prediction for learning from partial feedback in statistical machine translation

We present an approach to structured prediction from bandit feedback, called Bandit Structured Prediction, where only the value of a task loss function at a single predicted point, instead of a correct structure, is observed in learning. We present an application to discriminative reranking in Statistical Machine Translation (SMT) where the learning algorithm only has access to a 1-BLEU loss evaluation of a predicted translation instead of obtaining a gold standard reference translation. In our experiment bandit feedback is obtained by evaluating BLEU on reference translations without revealing them to the algorithm. This can be thought of as a simulation of interactive machine translation where an SMT system is personalized by a user who provides single point feedback to predicted translations. Our experiments show that our approach improves translation quality and is comparable to approaches that employ more informative feedback in learning.
Parametric Learning of Texture Filters by Stacked Fisher Autoencoders

Deep learning has recently contributed significantly to large-scale recognition of several modalities like image, video and speech. Stacked autoencoders are a family of powerful convolutional neural nets to build scalable generative models for automatic feature learning. In this paper, we propose a network of novel overcomplete autoencoders called Fisher autoencoders. In contrast to convolutional autoencoders which learn some latent representations, we train a set of projections for the model variables using banks of filters. The Fisher autoencoders are independently computed in stacks of variable depth based on the complexity of patterns under study and the ability of each individual filter to extract deep features. We select texture understanding as one of the most difficult tasks in pattern recognition and conduct our experiments in a standard platform to assure fair comparisons with other methods. Our results show considerable improvements over the most recent benchmarks on several texture datasets for our Fisher autoencoders evaluated against improved Fisher vectors on Dense SIFT (DSIFT) and DeCAF-VGG deep local descriptors.
Secondary closure of an extraction socket using the double-membrane guided bone regeneration technique with immediate implant placement

Purpose Immediate implantation presents challenges regarding site healing, osseointegration, and obtaining complete soft-tissue coverage of the extraction socket, especially in the posterior area. This last issue is addressed herein using the double-membrane (collagen membrane+high-density polytetrafluoroethylene [dPTFE] membrane) technique in two clinical cases of posterior immediate implant placement. Methods An implant was placed immediately after atraumatically extracting the maxillary posterior tooth. The gap between the coronal portion of the fixture and the adjacent bony walls was filled with allograft material. In addition, a collagen membrane (lower) and dPTFE membrane (upper) were placed in a layer-by-layer manner to enable the closure of the extraction socket without a primary flap closure, thus facilitating the preservation of keratinized mucosa. The upper dPTFE membrane was left exposed for 4 weeks, after which the membrane was gently removed using forceps without flap elevation. Results There was considerable plaque deposition on the outer surface of the dPTFE membrane but not on the inner surface. Moreover, scanning electron microscopy of the removed membrane revealed only a small amount of bacteria on the inner surface of the membrane. The peri-implant tissue was favorable both clinically and radiographically after a conventional dental-implant healing period. Conclusions Secondary closure of the extraction socket and immediate guided bone regeneration using the double-membrane technique may produce a good clinical outcome after immediate placement of a dental implant in the posterior area.