Miracle-dz/UniFAR-FTUs huggingface dataset:
Association between TLR2 and TLR4 Gene Polymorphisms and the Susceptibility to Inflammatory Bowel Disease: A Meta-Analysis

Background The associations between toll-like receptor 2 (TLR2) and toll-like receptor 4(TLR4) polymorphisms and inflammatory bowel disease (IBD) susceptibility remain controversial. A meta-analysis was performed to assess these associations. Methods A systematic search was performed to identify all relevant studies relating TLR2 and TLR4 polymorphisms and IBD susceptibility. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated. Subgroup analyses were performed by ethnicity and publication quality. Results Thirty-eight eligible studies, assessing 10970 cases and 7061 controls were included. No TLR2 Arg677Trp polymorphism was found. No significant association was observed between TLR2 Arg753Gln polymorphism and Crohn’s disease (CD) or ulcerative colitis (UC) in all genetic models. Interestingly, TLR4 Asp299Gly polymorphism was significantly associated with increased risk of CD and UC in all genetic models, except for the additive one in CD. In addition, a statistically significant association between TLR4 Asp299Gly polymorphism and IBD was observed among high quality studies evaluating Caucasians, but not Asians. Associations between TLR4 Thr399Ile polymorphisms and CD risk were found only in the allele and dominant models. The TLR4 Thr399Ile polymorphism was associated with UC risk in pooled results as well as subgroup analysis of high quality publications assessing Caucasians, in allele and dominant models. Conclusions The meta-analysis provides evidence that TLR2 Arg753Gln is not associated with CD and UC susceptibility in Asians; TLR4 Asp299Gly is associated with CD and UC susceptibility in Caucasians, but not Asians. TLR4 Thr399Ile may be associated with IBD susceptibility in Caucasians only. Additional well-powered studies of Asp299Gly and other TLR4 variants are warranted.
The Influence of Heel Height on Frontal Plane Ankle Biomechanics: Implications for Lateral Ankle Sprains

Background: Wearing high heel shoes is thought to increase an individual's likelihood of experiencing a lateral ankle sprain. The purpose of this study was to evaluate the influence of heel height on frontal plane kinematics, kinetics, and electromyographic (EMG) activity of the ankle joint during walking. Methods: Eighteen healthy women participated. Three-dimensional kinematics, ground reaction forces, and EMG signals of the tibialis anterior (TA) and peroneus longus (PL) were recorded as subjects ambulated in high (9.5 cm) and low (1.3 cm) heel shoes at a self-selected walking velocity. Peak ankle plantarflexion, peak ankle inversion angle, and the peak ankle inversion moment during the stance phase of gait were evaluated. The EMG variables of interest consisted of the normalized average signal amplitude of the TA and PL during the first 50% of the stance phase. Paired t-tests were used to assess differences between the two shoe conditions. Results: When compared to the low heel condition, wearing high heels resulted in significantly greater peak ankle plantarflexion and inversion angles (p < 0.001). In addition, the peak inversion moment and PL muscle activation was found to be significantly higher in the high heel condition (p < 0.001). No difference in TA muscle activity was found between shoe conditions (p = 0.30). Conclusion: The plantarflexed and inverted posture when wearing high heels may increase an individual's risk for experiencing a lateral ankle sprain. Clinical Relevance: Data obtained from this investigation highlights the need for increased awareness and proper education related to the wearing of high heel shoes.
Selective rather than inductive mechanisms favour specific replacement of Purkinje cells by embryonic cerebellar cells transplanted to the cerebellum of adult Purkinje cell degeneration (pcd) mutant mice

Cell replacement after neuronal degeneration in the adult CNS depends on the availability of specific cues to direct specification, differentiation and integration of newly born neurons into mature circuits. Following recent reports indicating that neurogenic signals may be reactivated in the adult injured CNS, here we asked whether such signals are expressed in the cerebellum after Purkinje cell degeneration. Thus, we compared the fate of embryonic cerebellar cells transplanted to the cerebella of adult wild‐type and Purkinje cell degeneration (pcd) mutant mice. Donor cells were dissected from β‐actin‐enhanced green fluorescent protein (EGFP) transgenic mice and transplanted as a single cell suspension. In both hosts, grafted cells generated all major cerebellar phenotypes, with a precise localization in the recipient cortex or white matter. Nevertheless, the phenotypic distributions showed striking quantitative differences. Most notably, in the pcd cerebellum there was a higher amount of Purkinje cells, while other phenotypes were less frequent. Analysis of cell proliferation by 5‐bromo‐2′‐deoxyuridine (BrDU) incorporation revealed that in both hosts mitotic activity was strongly reduced shortly after transplantation, and virtually all donor Purkinje cells were actually generated before grafting. Together, these results indicate that some compensatory mechanisms operate in the pcd environment. However, the very low mitotic rate of transplanted cells suggests that the adult cerebellum, either wild‐type or mutant, does not provide instructive neurogenic cues to direct the specification of uncommitted progenitors. Rather, specific replacement in mutant hosts is achieved through selective mechanisms that favour the survival and integration of donor Purkinje cells at the expense of other phenotypes.
CLASS, SUBCLASS, AND ALLELIC EXCLUSION OF MEMBRANE-BOUND Ig OF HUMAN B LYMPHOCYTES

Membrane-bound immunoglobulins of peripheral blood B lymphocytes and of lymphocytes from an IgG chronic lymphocytic leukemia showed restriction to one immunoglobulin class, one IgG subclass, and one Gm allotype. Certain antigens in the C-terminal part of IgG Fc were not exposed on the cell surface.
Type II-Activated Murine Macrophages Produce IL-4

Background Type II activation of macrophages is known to support Th2 responses development; however, the role of Th2 cytokines (esp. IL-4) on type II activation is unknown. To assess whether the central Th2 cytokine IL-4 can alter type II activation of macrophages, we compared the ability of bone marrow-derived macrophages from wild type (WT) and IL-4Rα-deficient mice to be classically or type II-activated in vitro. Results We found that although both WT and IL-4Rα-deficient macrophages could be classically activated by LPS or type II activated by immune complexes plus LPS, IL-4Rα-deficient macrophages consistently produced much higher levels of IL-12p40 and IL-10 than WT macrophages. Additionally, we discovered that type II macrophages from both strains were capable of producing IL-4; however, this IL-4 was not responsible for the reduced IL-12p40 and IL-10 levels produced by WT mice. Instead, we found that derivation culture conditions (GM-CSF plus IL-3 versus M-CSF) could explain the different responses of BALB/c and IL-4Rα−/− macrophages, and these cytokines shaped the ensuing macrophage such that GM-CSF plus IL-3 promoted more IL-12 and IL-4 while M-CSF led to higher IL-10 production. Finally, we found that enhanced IL-4 production is characteristic of the type II activation state as other type II-activating products showed similar results. Conclusions Taken together, these results implicate type II activated macrophages as an important innate immune source of IL-4 that may play an important role in shaping adaptive immune responses.
Diffusion-based Regularisation Strategies for Variational Level Set Segmentation

Variational level set methods are formulated as energy minimisation problems, which are often solved by gradient-based optimisation methods, such as gradient descent. Unfortunately, the gradient obtained by applying the calculus of variations is not suitable, because it is only an element of the function space L 2 making it prone to lead into wrong local minima. Consequently, some regularisation strategy - be it the restriction to signed distance functions or the choice of smooth function spaces - is necessary. In this paper we propose diffusion-based regularisation strategies and compare them to the recently proposed ones of Charpiat et al. and Sundaramoorthi et al. From this comparison we derive two general regularisation paradigms at the level of update equations and show that the diffusion-based paradigm enjoys both theoretical and practical advantages, such as an improved convergence rate, while being of the same computational complexity as the other paradigm.
Bordetella bronchiseptica Pneumonia in an Extremely-Low-Birth-Weight Neonate

Abstract Bordetella bronchiseptica, a gram-negative coccobacillus, is a common veterinary pathogen. In both domestic and wild animals, this bacterium causes respiratory infections including infectious tracheobronchitis in dogs and atrophic rhinitis in swine. Human infections are rare and have been documented in immunocompromised hosts. Here, we describe an extremely-low-birth-weight infant with B. bronchiseptica pneumonia. This is the first report that describes the microorganism's responsibility in causing nosocomial infection in a preterm neonate. He recovered uneventfully after a course of meropenem. It is possible that the bacteria colonize the respiratory tracts of our health care workers or parents who may have had contact with pets and then transmitted the bacterium to our patient. Follow-up until 21 months of age showed normal growth and development. He did not suffer from any significant residual respiratory disease.
Saturated R134a flow boiling inside a 4.3 mm inner diameter microfin tube

The refrigerant charge minimization in refrigerating and air-conditioning systems represents a challenging issue due to the new environmental national and international regulations. The use of smaller smooth tubes, such as with the outer diameter around 5 mm, is becoming more and more common in many applications. More recently, the microfin tubes have also started to be reduced in size to cope with the continuously increasing demand of new, efficient, and compact heat exchangers for air-conditioning and refrigeration equipment. This work investigates the performance of R134a during saturated flow boiling inside a microfin tube with internal diameter at the fin tip of 4.3 mm. Boiling heat transfer coefficients, frictional pressure drops, and critical vapor qualities were measured at 30°C of saturation temperature, by varying the refrigerant mass velocity between 100 and 800 kg m−2 s−1 and the vapor quality from 0.1 to 0.95 at four different heat fluxes: 15, 30, 60, and 90 kW m−2. Moreover, the reliability of several models for flow boiling heat transfer and pressure drop estimations was assessed by comparing the experimental results with the calculations.
Musicians are more consistent: Gestural cross-modal mappings of pitch, loudness and tempo in real-time

Cross-modal mappings of auditory stimuli reveal valuable insights into how humans make sense of sound and music. Whereas researchers have investigated cross-modal mappings of sound features varied in isolation within paradigms such as speeded classification and forced-choice matching tasks, investigations of representations of concurrently varied sound features (e.g., pitch, loudness and tempo) with overt gestures—accounting for the intrinsic link between movement and sound—are scant. To explore the role of bodily gestures in cross-modal mappings of auditory stimuli we asked 64 musically trained and untrained participants to represent pure tones—continually sounding and concurrently varied in pitch, loudness and tempo—with gestures while the sound stimuli were played. We hypothesized musical training to lead to more consistent mappings between pitch and height, loudness and distance/height, and tempo and speed of hand movement and muscular energy. Our results corroborate previously reported pitch vs. height (higher pitch leading to higher elevation in space) and tempo vs. speed (increasing tempo leading to increasing speed of hand movement) associations, but also reveal novel findings pertaining to musical training which influenced consistency of pitch mappings, annulling a commonly observed bias for convex (i.e., rising–falling) pitch contours. Moreover, we reveal effects of interactions between musical parameters on cross-modal mappings (e.g., pitch and loudness on speed of hand movement), highlighting the importance of studying auditory stimuli concurrently varied in different musical parameters. Results are discussed in light of cross-modal cognition, with particular emphasis on studies within (embodied) music cognition. Implications for theoretical refinements and potential clinical applications are provided.
Breeding for Enhanced Zinc and Iron Concentration in CIMMYT Spring Wheat Germplasm

Micronutrient malnutrition, resulting from dietary deficiency of important minerals such as zinc (Zn) and iron (Fe), is a widespread food-related health problem. Genetic enhancement of crops with elevated levels of these micronutrients is one of the most cost effective ways of solving global micronutrient malnutrition problem. Develop - ment and dissemination of high Zn and Fe containing high-yielding, disease-resistant wheat varieties by International Maize and Wheat Improvement Center (CIMMYT) is initially targeted for the Indo-Gangetic plains of South Asia, a region with high population density and high micronutrient malnutrition. The most promising sources for grain Zn and Fe concentrations are wild relatives, primitive wheats and landraces. Synthetic hexaploids were developed at CIMMYT by crossing Aegilops taushii and high Zn and Fe containing accessions of T. dicoccon. Current breeding
Long-term Survival Outcomes of Laparoscopic Versus Open Gastrectomy for Gastric Cancer: A Systematic Review and Meta-analysis

AbstractMany meta-analyses have confirmed the technical feasibility and favorable short-term surgical outcomes of laparoscopic gastrectomy (LG) for gastric cancer patients, but the long-term survival outcome of LG remains controversial compared with open gastrectomy (OG). This study aimed to compare the 5-year overall survival (OS), recurrence, and gastric cancer–related death of LG with OG among gastric cancer patients.PubMed was searched to February 2014.The resectable gastric cancer patients who underwent curative LG or OG were eligible. The studies that compared 5-year OS, recurrence, or gastric cancer–related death in the LG and OG groups were included.A meta-analysis, meta-regression, sensitivity analysis, subgroup analysis, and stage-specific analysis were performed to estimate the survival outcome between the two groups and identify the potential confounders. Quality assessment was based on a tailored comparability scoring system.Twenty-three studies with 7336 patients were included. The score of comparability between two groups and the extent of lymphadenectomy were two independent confounders. Based on the well-balanced studies, the 5-year OS (OR = 1.07, 95% CI 0.90–1.28, P = 0.45), recurrence (OR = 0.83, 95% CI 0.68–1.02, P = 0.08), and gastric cancer–related death (OR = 0.86, 95% CI 0.65–1.13, P = 0.28) rates were comparable in LG and OG. Several subsets such as the publication year, study region, sample size, gastrectomy pattern, extent of lymphadenectomy, number of nodes harvested, and proportion of T1–2 or N0–1 did not influence the estimates, if they were well balanced. Particularly, the stage-specific estimates obtained comparable results between the two groups.Randomized controlled trials comparing LG with OG remain sparse to assess their long-term survival outcomes.The major contributions of this systematic review compared with other meta-analyses are a comprehensive collection of available long-term survival outcomes within a much larger number of observations and a more precise consideration of confounders. Current knowledge indicates that the long-term survival outcome of laparoscopic gastric cancer surgery is comparable to that of open surgery among early or advanced stage gastric cancer patients, and LG is acceptable with regard to oncologic safety.
Childhood Cancer in Developing Countries

The problem of childhood cancer cannot be evaluated separately from developmental levels and states of health of the countries. Rapid increase in population, poverty, poor hygiene, lack of education, and multitude health problems impede the development of pediatric oncology and success of the management of childhood cancer in developing countries. More than 85% pediatric cancer cases occur in developing countries that use less than 5% of world resources. The rate will exceed 90% in the next two decades, due to the increase of youth population in favor of developing countries. Incidence rates, pathology, and clinical characteristics of various cancers seem different in developing and developed countries. Different environments, life styles, dietary habits, and hygienic conditions are the main reasons for those differences. Unprecedented changes in diagnostic techniques, treatment methods and supportive care have occurred during the last decades. Consequently, management has improved and the mortality rates have decreased. Most of the children with cancer living in developing countries could not profit from those advances in pediatric oncology because of the cost.
The sphingosine 1‐phosphate receptor S1P4 regulates cell shape and motility via coupling to Gi and G12/13

Sphingosine 1‐phosphate (S1P) receptors represent a novel subfamily of G‐protein‐coupled receptors binding S1P specifically and with high affinity. Although their in vivo functions remain largely unknown, in vitro extracellular application of S1P induces distinct S1P receptor‐dependent cellular responses including proliferation, differentiation, and migration. We have analyzed signaling pathways engaged by S1P4, which is highly expressed in the lymphoid system. Here we show that S1P4 couples directly to Gαi and even more effectively to Gα12/13‐subunits of trimeric G‐proteins, but not to Gαq unlike other S1P receptors. Consequently, CHO‐K1 cells ectopically expressing S1P4 potently activate the small GTPase Rho and undergo cytoskeletal rearrangements, inducing peripheral stress fiber formation and cell rounding, upon S1P stimulation. Overexpression of S1P4 in Jurkat T cells induces pertussis toxin‐sensitive cell motility even in the absence of exogenously added S1P. In addition, S1P4 is internalized upon binding of S1P. The capacity of S1P4 to mediate cellular responses, such as motility and shape change through Gαi‐ and Gα12/13‐coupled signaling pathways may be important for its in vivo function which is currently under investigation. © 2003 Wiley‐Liss, Inc.
[Prevalence of pathologic gastroesophageal reflux in regurgitant infants].

OBJECTIVE To determine the prevalence of pathologic gastroesophageal reflux in a group of regurgitant infants attended at Helena Moura Hospital, Recife, State of Pernambuco, Brazil. The clinical criteria employed were based on Rome II criteria. METHOD The study design was transversal. The patients were all children of less than 1 year of age with a history of episodes of regurgitation for at least 3 weeks. The study group was comprised of 798 children who attended the program between January and August of 2002. The diagnostic criteria were based on Rome II criteria. RESULTS The prevalence of pathologic gastroesophageal reflux was 11.15% (89/798) (95% CI 9.10-13.48). It was higher during the first two trimesters of life, 14.62% (31/212) (95% CI 10.33-19.86) in the first trimester, and 13.76% (38/276) (95% CI 10.07-18.21) in the second trimester. CONCLUSION The prevalence of pathologic gastroesophageal reflux within the group of children examined concurred with previously published studies, with predominance, therefore, of regurgitant infants.
OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software

Orthology, refining the concept of homology, is the cornerstone of evolutionary comparative studies. With the ever-increasing availability of genomic data, inference of orthology has become instrumental for generating hypotheses about gene functions crucial to many studies. This update of the OrthoDB hierarchical catalog of orthologs (http://www.orthodb.org) covers 3027 complete genomes, including the most comprehensive set of 87 arthropods, 61 vertebrates, 227 fungi and 2627 bacteria (sampling the most complete and representative genomes from over 11,000 available). In addition to the most extensive integration of functional annotations from UniProt, InterPro, GO, OMIM, model organism phenotypes and COG functional categories, OrthoDB uniquely provides evolutionary annotations including rates of ortholog sequence divergence, copy-number profiles, sibling groups and gene architectures. We re-designed the entirety of the OrthoDB website from the underlying technology to the user interface, enabling the user to specify species of interest and to select the relevant orthology level by the NCBI taxonomy. The text searches allow use of complex logic with various identifiers of genes, proteins, domains, ontologies or annotation keywords and phrases. Gene copy-number profiles can also be queried. This release comes with the freely available underlying ortholog clustering pipeline (http://www.orthodb.org/software).
Overexpression of bone morphogenetic protein-6 (BMP-6) in the epidermis of transgenic mice: inhibition or stimulation of proliferation depending on the pattern of transgene expression and formation of psoriatic lesions

Bone morphogenetic protein-6 (BMP-6) belongs to the family of TGF-beta- related growth factors. In the developing epidermis, expression of BMP- 6 coincides with the onset of stratification. Expression persists perinatally but declines after day 6 postpartum, although it can still be detected in adult skin by reverse transcriptase-polymerase chain reaction (RT-PCR) analysis. We constitutively overexpressed BMP-6 in suprabasal layers of interfollicular epidermis in transgenic mice using a keratin 10 promoter. All mice expressing the transgene developed abnormalities in the skin, indicating an active transgene-derived factor. Depending on the pattern of transgene expression, the effects on proliferation and differentiation were completely opposite. Strong and uniform expression of the BMP-6 transgene resulted in severe repression of cell proliferation in embryonic and perinatal epidermis but had marginal effects on differentiation. Weaker and patchy expression of the transgene evoked strong hyperproliferation and parakeratosis in adult epidermis and severe perturbations of the usual pattern of differentiation. These perturbations included changes in the expression of keratins and integrins. Together with an inflammatory infiltrate both in the dermis and in the epidermis, these aspects present all typical histological and biochemical hallmarks of a human skin disease: psoriasis.
Semi-Supervised Clustering via Matrix Factorization

The recent years have witnessed a surge of interests of semi-supervised clustering methods, which aim to cluster the data set under the guidance of some supervisory information. Usually those supervisory information takes the form of pairwise constraints that indicate the similarity/dissimilarity between the two points. In this paper, we propose a novel matrix factorization based approach for semi-supervised clustering. In addition, we extend our algorithm to co-cluster the data sets of different types with constraints. Finally the experiments on UCI data sets and real world Bulletin Board Systems (BBS) data sets show the superiority of our proposed method.