Miracle-dz/UniFAR-FTUs huggingface dataset:
Specific and Charge Interactions Mediate Collagen Recognition by Oral Lactobacilli

The mechanisms by which oral lactobacilli, one of the three major genera of cariogenic bacteria, attach to tooth surfaces are unknown. We hypothesize that recognition of collagen, the major component of dentin, may be a mechanism which localizes these bacteria to exposed root surfaces as well as to carious lesions which have penetrated the dentin. We found that the majority of oral Lactobacillus spp. strains recognize and bind collagen type I. Binding of 125I-labeled collagen type I to two strains of L. casei rhamnosus has been characterized in some detail. These strains were previously characterized with respect to their attachment to dentin (Switalski and Butcher, 1994). The process of 125I-collagen binding was mediated via specific as well as charge interactions. The putative adhesin-mediated (specific) interaction involved a limited number of bacterial surface components (2 x 103/cell). Under conditions conducive for non-specific interactions (low ionic strength), the binding was higher by an order of magnitude. Collagen binding strains were found to adhere to collagen-coated surfaces, while strains unable to bind collagen adhered to a much lesser extent. Adherence of bacteria to collagen-coated surfaces could be competitively inhibited with collagen. These interactions may target collagen-binding strains of lactobacilli to dentin collagen in the oral cavity and thus play a role in the pathogenesis of root surface and/or coronal caries. Interference with this collagen-mediated attachment of lactobacilli may provide effective means of caries control, particularly in view of the fact that other oral acidogenic microbiota also interact with collagen.
Early-Stage Evolution of the Neo-Y Chromosome in Drosophila albomicans

Chia-Hao Cheng, Ching-Ho Chang, and Hwei-yu Chang (2011) Early-stage evolution of the neo-Y chromosome in Drosophila albomicans. Zoological Studies 50(3): 338-349. Numerous theories have specified that an originally autosomal neo-Y chromosome arm is expected to undergo degenerative evolution. Neosex chromosomes of Drosophila albomicans originated from 2 Robertsonian translocation events, one for X and the other for Y, between ancestral Drosophila sex chromosomes and a pair of autosomes homologous to the 3rd chromosomes of its sibling species D. nasuta. Since the neo-sex chromosome in D. albomicans is still evolutionarily young, we used genetic approaches to reveal changes in the entire neo-Y chromosome. Non-disjunction is an indicator used to investigate differences between homologous chromosomes. In this study, we first confirmed that no male recombination had occurred in hybrid males of these 2 sibling species. With the aid of molecular marker genotyping and direct karyotyping of aneuploid offspring produced through specially designed crosses and backcrosses of fertile hybrids, we found that the non-disjunction rate was significantly higher in hybrid males with the neo-Y chromosome than in hybrids without it. The high nondisjunction rate made it possible to generate 3,X,X/neo-Y F2 females and X,neo-Y/neo-Y F3 male offspring which can reveal recessive effects of the homozygous 3rd chromosome arm. Results of this aneuploid study revealed severe recessive inviability of the neo-Y chromosome. Our results further suggested that increased non-disjunction in hybrid males with the neo-Y chromosome is likely due to changes that occurred on the Y arm, whereas recessive deleterious alleles might be located on the 3rd arm of the neo-Y chromosome. Taken together, the elevated non-disjunction rate and severe recessive inviability revealed significant changes in the neo-Y chromosome at this early stage of chromosome evolution in D. albomicans. http://zoolstud.sinica. edu.tw/Journals/50.3/338.pdf
Expression of the gltP gene of Escherichia coli in a glutamate transport‐deficient mutant of Rhodobacter sphaeroides restores chemotaxis to glutamate

Rhodobacter sphaeroides is chemotactic to glutamate and most other amino acids. In Escherichia coli, chemotaxis involves a membrane‐bound sensor that either binds the amino acid directly or interacts with the binding protein loaded with the amino acid. In R. sphaeroides, chemotaxis is thought to require both the uptake and the metabolism of the amino acid. Glutamate is accumulated by the cells via a binding protein‐dependent system. To determine the role of the binding protein and transport in glutamate taxis, mutants were created by Tn5 insertion mutagenesis and selected for growth in the presence of the toxic glutamine analogue γ‐glutamyl‐hydrazide. One of the mutants, R. sphaeroides MJ7, was defective in glutamate uptake but showed wild‐type levels of binding protein. The mutant showed no chemotactic response to glutamate. Both glutamate uptake and chemotaxis were recovered when the gltP gene, coding for the H+‐linked glutamate carrier of E. coli, was expressed in R. sphaeroides MJ7. It is concluded that the chemotactic response to glutamate strictly requires uptake of glutamate, supporting the view that intracellular metabolism is needed for chemotaxis in R. sphaeroides.
Regulation of Hypocretin (Orexin) Expression in Embryonic Zebrafish*

Hypocretins/orexins are neuropeptides involved in the regulation of sleep and energy balance in mammals. Conservation of gene sequence, hypothalamic localization of cell bodies, and projection patterns in adult zebrafish suggest that the architecture and function of the hypocretin system are conserved in fish. We report on the complete genomic structure of the zebrafish and Tetraodon hypocretin genes and the complete predicted hypocretin protein sequences from five teleosts. Using whole mount in situ hybridization, we have traced the development of hypocretin cells in zebrafish from onset of expression at 22 h post-fertilization through the first week of development. Promoter elements of similar size from zebrafish and Tetraodon were capable of driving efficient and specific expression of enhanced green fluorescent protein in developing zebrafish embryos, thus defining a minimal promoter region able to accurately mimic the native hypocretin pattern. This enhanced green fluorescent protein expression also revealed a complex pattern of projections within the hypothalamus, to the midbrain, and to the spinal cord. To further analyze the promoter, a series of deletion and substitution constructs were injected into embryos, and resulting promoter activity was monitored in the first week of development. A critical region of 250 base pairs was identified containing a core 13-base pair element essential for hypocretin expression.
Parenting Support and PTSD in Children of a War Zone

Background: The protective role of parenting factors on the mental well-being of children exposed to war trauma remains an under-researched area. Aim: To establish the relationship between perceived positive parenting support and post-traumatic stress disorder (PTSD) symptoms in children exposed to war trauma. Methods: A random sample of 412 children aged 12—16 years was selected from the Gaza Strip and was assessed using the Gaza Traumatic Events Checklist (GTEC), the SCID (DSM-IV) and the Perceived Parenting Support Scale (PPSS). Results: Palestinian children were exposed to different types of war-traumatic events. The number of exposed traumatic events was independently associated with the severity of post-traumatic symptoms scores or the diagnosis of PTSD, while perceived parenting support was found to act as a protective factor in this association. Conclusions: Interventions in war zones need to ensure the minimal possible disruption to communities and family units, and to involve parents in preventive or treatment programmes for children exposed to trauma.
The Usage Behavior and Intention Stability of Nurses: An Empirical Study of a Nursing Information System

Background: Many prior studies of technology adoption treat user intention as the single predictor of actual usage behavior. However, as many researchers of behavioral science have pointed out, multiple factors mediate the relationship between user intention and usage behavior. Purpose: The present article explores the factors that mediate the relationship between intention and actual behavior. We develop a conceptual framework that is based on the Technology Acceptance Model III and behavior theory to further elicit system usage behavior and to confirm “intention stability” and “past experience” as two significant mediating factors in this relationship. Methods: The target system was a nursing information system that had been recently adopted by a medical center in central Taiwan. Data were collected using a questionnaire survey conductedin two rounds. Two hundred forty-five valid questionnaires were returned (response rate: 49%). Mediated moderation was analyzed to explore the presence of mediators or moderators between intention and behavior. Results: The results support that intention stability is a mediated moderator and that prior experience is a moderator of the relationshipbetween intention and behavior. These two factors increased by over 13.6% the explanatory power of intention on actual behavior. Furthermore, this study expanded the scope of prior research by confirming intention stability as a moderating variable between intention and behavior. Finally, this study identified the moderating effect of past experience on the intention–behavior relationship, indicating that past experience enhances the predictive power of intention on behavior. Conclusions/Implications for Practice: The findings of this study may assist hospital managers to better understand the nursing information system usage behaviors of nursing staff and to develop ways to enhance the intention stability of these staff. Managers may improve the familiarity of nursing staff with the system by increasing their system-related practice time. More experience should enhance staff system skills and resolve problems such as the need for extra work hours or overtime because of initial system unfamiliarity. Improved work efficiency should then allow nurses to divert more time from administrative work to patient care and training. This positive circle of support is expected to increase the willingness of nurses to accept and take advantage of the system.
Chronic Obstructive Pulmonary Disease Patients Have Greater Systemic Responsiveness to Ex Vivo Stimulation with Swine Dust Extract and its Components Versus Healthy Volunteers

Chronic obstructive pulmonary disease (COPD) is characterized by an airway and systemic inflammatory response. Bioaerosols/organic dusts are important agricultural pollutants that may lead to COPD. These environments are complex, containing a rich source of various microbial components. The objective of this study was to determine whether individuals with COPD have enhanced systemic responsiveness to settled swine facility organic dust extract (ODE) or its main pathogenic components (peptidoglycan [PGN], lipopolysaccharide [LPS]) versus healthy volunteers. A modified whole blood assay (WBA) that included occupational levels of ODE and concentrations of LPS and PGN found in ODE was used to determine systemic responsiveness (mediator release), and sputum inflammatory markers were measured to explore for systemic and airway associations. Sputum samples were evaluated for cell counts, and tumor necrosis factor (TNF)-α, interleukin (IL)-8/CXCL8, IL-6, and IL-10. Ex vivo whole blood stimulation with ODE, LPS, and PGN each resulted in significant mediator release in all subjects, with the highest occurring with ODE; PGN resulted in significantly enhanced TNF-α and IL-8 as compared to LPS. COPD subjects demonstrated greater systemic responsiveness using the modified WBA versus healthy controls. Within COPD subjects, blood baseline TNF-α, IL-8, and IL-10 and ODE-, PGN-, and LPS-stimulated IL-8 levels significantly correlated with lung function. In conclusion, dust-induced mediator release was robust, and PGN, in part, resembled dust-induced mediator release. Subjects with COPD demonstrated increased mediator release following ex vivo whole blood stimulation with bioaerosol components, suggesting that circulating blood cells in COPD subjects may be primed to respond greater to microbial/inflammatory insult.
A novel circularly polarized microstrip antenna with a circular slot

A novel circularly polarized microstrip slot antenna is designed in this paper. The circularly polarized radiation is generated by the use of annular grooved tandem coupling on the ground plane. The feeder network consists of a microstrip line and a cross-shaped patche. According to the simulation results of HFSS software, the relative bandwidth reaches 4.8%. The proposed antenna has the characteristics of simple structure, miniaturization and excellent performance.
[13C]glucose breath testing provides a noninvasive measure of insulin resistance: calibration analyses against clamp studies.

BACKGROUND Exhaled (13)CO2 following ingestion of [(13)C]glucose with a standard oral glucose tolerance load correlates with blood glucose values but is determined by tissue glucose uptake. Therefore exhaled (13)CO2 may also be a surrogate measure of the whole-body glucose disposal rate (GDR) measured by the gold standard hyperinsulinemic euglycemic clamp. SUBJECTS AND METHODS Subjects from across the glycemia range were studied on 2 consecutive days under fasting conditions. On Day 1, a 75-g oral glucose load spiked with [(13)C]glucose was administered. On Day 2, a hyperinsulinemic euglycemic clamp was performed. Correlations between breath parameters and clamp-derived GDR were evaluated, and calibration analyses were performed to evaluate the precision of breath parameter predictions of clamp measures. RESULTS Correlations of breath parameters with GDR and GDR per kilogram of fat-free mass (GDRffm) ranged from 0.54 to 0.61 and 0.54 to 0.66, respectively (all P<0.001). In calibration analyses the root mean square error for breath parameters predicting GDR and GDRffm ranged from 2.32 to 2.46 and from 3.23 to 3.51, respectively. Cross-validation prediction error (CVPE) estimates were 2.35-2.51 (GDR) and 3.29-3.57 (GDRffm). Prediction precision of breath enrichment at 180 min predicting GDR (CVPE=2.35) was superior to that for inverse insulin (2.68) and the Matsuda Index (2.51) but inferior to that for the log of homeostasis model assessment (2.21) and Quantitative Insulin Sensitivity Check Index (2.29) (all P<10(-5)). Similar patterns were seen for predictions of GDRffm. CONCLUSIONS (13)CO2 appearance in exhaled breath following a standard oral glucose load with added [(13)C]glucose provides a valid surrogate index of clamp-derived measures of whole-body insulin resistance, with good accuracy and precision. This noninvasive breath test-based approach can provide a useful measure of whole-body insulin resistance in physiologic and epidemiologic studies.
Sarcopenia in patients undergoing maintenance hemodialysis: incidence rate, risk factors and its effect on survival risk

Abstract Background Sarcopenia is a degenerative syndrome mainly characterized by the atrophy of skeletal muscle, along with the decrease of muscle strength and function. However, there are currently few studies concerning sarcopenia in patients undergoing maintenance hemodialysis dialysis (MHD). This study was aimed to investigate the incidence of sarcopenia in MHD patients and its influencing factors, as well as its impact on survival risk. Method All 131 MHD patients enrolled in our study were tested with bioelectrical impedance analysis (BIA) and grip strength. Demographic data was collected and anthropometric measurement and laboratory examination were conducted. Results The total incidence of sarcopenia within the 131 MHD patients was 13.7% and the incidence of sarcopenia in patients over 60 years was 33.3%. The dialysis duration, with or without diabetes, serum phosphorus and pre-albumin levels of sarcopenic patients were significantly different from those of non-sarcopenicones; the modified quantitative subjective global assessment (MQSGA) scores of sarcopenic patients were higher than those without sarcopenia. Multivariate analysis showed that dialysis duration, diabetes and serum phosphorus level were independent risk factors for sarcopenia in MHD patients. Kaplan–Meier survival analysis showed a one-year survival of 88.9% in sarcopenic patients, which was significantly lower than non-sarcopenic patients. Conclusion The incidence of sarcopenia in MHD patients was high and increased gradually with age. Dialysis duration, diabetes, serum phosphorus level and malnutrition predisposed the patients to sarcopenia. One-year follow-up found that the mortality risk of sarcopenic patients was higher than that of non-sarcopenic patients.
Personal Identification by Pedestrians Behavior

The recent progress of motion sensor system enables to the personal identification from the human behavior observed from the sensor. Kinect is a motion sensing input device developed by Microsoft for Xbox 360 and Xbox One. The personal identification using the Microsoft Kinect sensor, shortly Kinect, is presented in this study. The use of the Kinect estimates the pedestrian's body size and walk behavior. The human body sizes such as height, width and so on and the walking behavior such as joint angle, stride length and so on are taken as the explanatory variables. The models which identifies pedestrians from the explanatory variables are defined by the traditional neural network (NN) and Support Vector Machine (SVM). In the numerical experiments, the pedestrian's body sizes and walking behavior pictures are taken from fifteen examinees. The pedestrian's walking direction is specified as 0°, 90°, 180° and 225° and then, the accuracy was compared. The results show that the identification accuracy is the best in case of 180°-walking direction and that the accuracy of the support vector machine is better than that of the neural network.
Code Complexity versus Performance for GPU-accelerated Scientific Applications

Summary form only given. Graphics Processing Units (GPUs) are becoming widely used as parallel accelerators in high-performance computing. GPU programming until recently, has been done by using low-level programming models such as CUDA and OpenCL. The directive-based OpenACC programming model has been growing in popularity due to its higher level of abstraction. This technique, which uses “directive” or “pragma” statements to annotate source code written in traditional high-level languages such as Fortran, C, and C++, is intended to allow a single code base to work across multiple computational platforms. We attempt to compare code complexity and performance of CUDA, OpenCL, and OpenACC implementations for three benchmark codes – the Game of Life (GOL) example code, the LULESH hydrodynamics proxy application, and the CloverLeaf mini-app from the Mantevo suite For the GOL C, CUDA C, and OpenCL codes and the LULESH C++, CUDA, and OpenCL codes, we measured source lines of code (SLOC) and cyclomatic complexity using the Oxbow toolkit static analysis tools. We ran the commercial McCabe IQ tool on the CloverLeaf Fortran90, Fortran90 + OpenACC, and Fortran portion of CloverLeaf_CUDA to measure cyclomatic complexity, design complexity, and essential complexity. We found that the CUDA and OpenCL implementations have significantly more lines of code than the corresponding OpenACC implementations but that the measured cyclomatic complexity is not always higher. The CUDA and OpenCL implementations generally have better performance, but there is not a drastic difference if the OpenACC code is optimized. We conclude that the available metrics and tools for measuring complexity of GPU programs are inadequate, since they do not quantify the portability and maintainability of the codes, and that specialization and extensions are needed.
Pelvic girdle and fin of Tiktaalik roseae

Significance The earliest tetrapods have robust limbs, particularly hind limbs that are enlarged and supported by a number of modifications to the pelvic girdle. In contrast, the closest relatives of tetrapods maintain small and weakly ossified pelvic appendages as compared with the pectorals. This observation has led to the “front wheel drive” hypothesis that held that the closest relatives of tetrapods emphasized pectoral support and locomotion whereas significant pelvic support and locomotion was a tetrapod innovation. The discovery of pelvic girdle and fin material of the tetrapodomorph Tiktaalik roseae reveals a transitional stage in the origin of the pelvic girdle and appendage: although retaining primitive skeletal architecture, these elements are enhanced in size and robusticity much like tetrapods. A major challenge in understanding the origin of terrestrial vertebrates has been knowledge of the pelvis and hind appendage of their closest fish relatives. The pelvic girdle and appendage of tetrapods is dramatically larger and more robust than that of fish and contains a number of structures that provide greater musculoskeletal support for posture and locomotion. The discovery of pelvic material of the finned elpistostegalian, Tiktaalik roseae, bridges some of these differences. Multiple isolated pelves have been recovered, each of which has been prepared in three dimensions. Likewise, a complete pelvis and partial pelvic fin have been recovered in association with the type specimen. The pelves of Tiktaalik are paired and have broad iliac processes, flat and elongate pubes, and acetabulae that form a deep socket rimmed by a robust lip of bone. The pelvis is greatly enlarged relative to other finned tetrapodomorphs. Despite the enlargement and robusticity of the pelvis of Tiktaalik, it retains primitive features such as the lack of both an attachment for the sacral rib and an ischium. The pelvic fin of Tiktaalik (NUFV 108) is represented by fin rays and three endochondral elements: other elements are not preserved. The mosaic of primitive and derived features in Tiktaalik reveals that the enhancement of the pelvic appendage of tetrapods and, indeed, a trend toward hind limb-based propulsion have antecedents in the fins of their closest relatives.
Phylogeography and mitochondrial DNA (mtDNA) diversity in North American collared lemmings (Dicrostonyx groenlandicus)

Variation in the nucleotide sequence of the mitochondrial control region (250 bp) and the cytochrome b region (870 bp) was examined in collared lemmings (Dicrostonyx groenlandicus) from 19 localities in northern Alaska and the Canadian Arctic. The division of D. groenlandicus in two phylogeographical groups with limited divergence across the Mackenzie River is consistent with the separation of this species in more than one refugial area located to the northwest of the Laurentide ice sheet during the last glaciation. Populations of D.groenlandicus from formerly glaciated areas are no less variable than those in nonglaciated areas. Instead, the low intrapopulation and intraregional diversity estimates in D. groenlandicus are probably a result of regional bottleneck events due to range contractions during Holocene warming events. These results are consistent with findings previously reported on collared lemmings (D. torquatus) from the Eurasian Arctic.