Miracle-dz/UniFAR-FTUs huggingface dataset:
Variability of the Influence of Physicochemical Factors Affecting Bacterial Adhesion to Polystyrene Substrata

The role of electrostatic and hydrophobic interactions and solid and liquid surface tensions in the adhesion of four bacterial species (Pseudomonas fluorescens, Enterobacter cloacae, Chromobacterium sp., and Flexibacter sp.) to hydrophobic polystyrene petri dishes and to more hydrophilic polystyrene tissue culture dishes was investigated. The effect of electrostatic interactions was investigated by determining the effects of different electrolyte solutions on attachment to and of different electrolyte and pH solutions on detachment from the polystyrene substrate. The significance of solid and liquid surface tensions and hydrophobic interactions was investigated by measuring the effects of different surfactants (including a concentration series of dimethyl sulfoxide) on adhesion and detachment. Adhesion varied with bacterial species, substratum, and electrolyte type and concentration, with no apparent correlation between adhesion and electrolyte valence or concentration. The influence of different pH and detergent solutions on bacterial detachment also varied with species, substratum, pH, and detergent type; however, the greatest degree of detachment of all strains from the surfaces was produced by detergent treatment. The results suggest that adhesion cannot be attributed to any one type of adhesive interaction. There was some evidence for both electrostatic and hydrophobic interactions, but neither interaction could wholly account for the data.
Development of representative magnetic resonance imaging-based atlases of the canine brain and evaluation of three methods for atlas-based segmentation.

OBJECTIVE To develop representative MRI atlases of the canine brain and to evaluate 3 methods of atlas-based segmentation (ABS). ANIMALS 62 dogs without clinical signs of epilepsy and without MRI evidence of structural brain disease. PROCEDURES The MRI scans from 44 dogs were used to develop 4 templates on the basis of brain shape (brachycephalic, mesaticephalic, dolichocephalic, and combined mesaticephalic and dolichocephalic). Atlas labels were generated by segmenting the brain, ventricular system, hippocampal formation, and caudate nuclei. The MRI scans from the remaining 18 dogs were used to evaluate 3 methods of ABS (manual brain extraction and application of a brain shape-specific template [A], automatic brain extraction and application of a brain shape-specific template [B], and manual brain extraction and application of a combined template [C]). The performance of each ABS method was compared by calculation of the Dice and Jaccard coefficients, with manual segmentation used as the gold standard. RESULTS Method A had the highest mean Jaccard coefficient and was the most accurate ABS method assessed. Measures of overlap for ABS methods that used manual brain extraction (A and C) ranged from 0.75 to 0.95 and compared favorably with repeated measures of overlap for manual extraction, which ranged from 0.88 to 0.97. CONCLUSIONS AND CLINICAL RELEVANCE Atlas-based segmentation was an accurate and repeatable method for segmentation of canine brain structures. It could be performed more rapidly than manual segmentation, which should allow the application of computer-assisted volumetry to large data sets and clinical cases and facilitate neuroimaging research and disease diagnosis.
Cardiac Vasoplegia Syndrome: Pathophysiology, Risk Factors and Treatment

Abstract:Vasoplegia syndrome is a well known complication after cardiac surgery and has a significant morbidity and mortality. It is characterized by profound vasodilation and loss of systemic vascular resistance leading to hypotension. The pathogenesis of vasoplegia involves the activation of contact, coagulation and complement systems and the activation of leukocytes, platelets and endothelial cells resulting in an imbalance in the regulation of the vascular tone leading to postcardiac surgery vasoplegia. Multiple risk factors have been identified that help predict vasoplegia. Treatment requires mainly vasopressors, but hypotension can be refractory to vasopressors. Some studies suggest that methylene blue can reverse refractory hypotension in these patients and may prevent the development of the syndrome, but more studies are needed with this drug. In this review, we will discuss the pathophysiology of the vasoplegia syndrome and associated risk factors for this complication and briefly outline current therapeutic strategies.
Local Bone Deformation at Two Predominant Sites for Stress Fractures of the Tibia: An In Vivo Study

Local bone deformation was registered at two predominant injury sites for tibial stress fractures in a healthy female volunteer. Two instrumented strain gauge staples were inserted under local anesthesia to the anterior middiaphysis (AM) and to the posteromedial part of the distal tibia (PD). Calibration and reliability of the instrumented staple system have previously been demonstrated in vitro. Concomitant ground reaction forces were registered with a Kistler force plate. Studying peak values, it was shown that during a voluntary 30-cm forward jump, PD deformation was greater during forefoot landing (2700–4200 microstrain) than during a heel strike landing (1200–1900 microstrain) and also compared with the concomitant AM deformation under both above testing conditions (1300–1900 microstrain). The stance phase during walking resulted in PD deformation of 950 microstrain, whereas the concomitant AM deformation was 334 microstrain. The greatest AM deformation (mean, 2128 microstrain) was registered during ground contact after a voluntary vertical drop from a height of 45 cm, concomitant with a PD deformation of 436 microstrain. These data are the first to show different local deformations at various sites of the tibia in vivo. The PD deformation was larger than previously noted from other parts of the tibia, whereas the middiaphysis data are consistent with other reports. The results may support the clinical assumption of different etiologies for stress fractures at these predominant sites.
The Demand for a Sound Baseline in GPU Memory Architecture Research

Modern GPUs adopt massive multithreading and multi-level cache hierarchies to hide long operation latencies, especially off-chip memory access latencies. However, poor cache indexing and cache line allocation policy as well as a small number of miss-status handling registers (MSHRs) can exacerbate the problem of cache thrashing and cache-missrelated resource congestion. Besides, modulo address mapping among memory partitions may cause severe partition camping, resulting in underutilization of DRAM bandwidth and capacity of banked L2 cache. Furthermore, prior GPU cache bypassing studies unrealistically assume there is no limit on the number of in-flight bypassed requests, which may lead to pathological experimental results in simulation. In this work, we investigate the performance impact of the aforementioned factors and demonstrate the necessity for a sound baseline in GPU memory architecture research. Our results show that advanced cache indexing functions can greatly reduce conflict misses and improve cache efficiency; the allocation-on-fill policy brings a better performance than allocation-on-miss. Besides, the performance does not consistently improve with more MSHRs. Instead, there can be performance degradation in certain scenarios. In addition, Xor mapping can greatly mitigate the problem of memory partition camping. Furthermore, the fact that a limited number of inflight bypassed requests can be supported should be taken into account in GPU cache bypassing studies, for more reliable results and conclusions.
Major Urinary Protein Complex of Normal Mice: Origin

Mouse serum contains protein having the same charge density and molecular size as the major urinary protein complex of mice. Mouse liver (but not eight other tissues examined) incorporated amino acids labeled with carbon-14 into the complex in vitro. The degree of incorporation was greater in livers from males than from females, and was internmediate in livers from females treated with testosterone.
Correlation and Path Coefficient Analyses in Sugarcane Genotypes of Ethiopia

To study the relations of certain morphological and sugar quality characters with sugarcane yield, an experiment was conducted at Wonji and Metehara Sugar Estates, Ethiopia between March 2012 and October 2013. The experiment, comprising of 400 sugarcane genotypes of which 174 were local that were collected from different regional states of Ethiopia and 226 introduced, was laid out in partial balanced lattice design with two replications. Data was collected on cane yield and its components, sugar yield and sugar quality traits. ANOVA, correlation and path coefficient analysis were done. Analysis of variance revealed significant differences (P < 0.01) for all the characters studied. Cane yield showed strong positive and highly significant (P < 0.01) correlation with millable cane number (r = 0.832), single cane weight (r = 0.528), stalk height (r = 0.517) and sugar yield (r = 0.987). There was also positive significant (P = 0.05) correlation of tiller count and cane diameter with cane yield. Path analysis revealed the highest positive direct effect of millable cane number (0.812) on cane yield followed by single cane weight (0.682) and pol percent (0.550). However, stalk diameter and brix percent had considerable negative direct effects and indirect positive effects through single cane weight on cane yield. Therefore, in view of their significant positive association with cane yield, indirect effects of stalk diameter and brix percent via single cane weight should be considered during selection. Genotypes should be selected on the basis of millable cane number, single cane weight and pol percent for getting higher cane and sugar yield.
Age-Related Nuclear Translocation of P2X6 Subunit Modifies Splicing Activity Interacting with Splicing Factor 3A1

P2X receptors are ligand-gated ion channels sensitive to extracellular nucleotides formed by the assembling of three equal or different P2X subunits. In this work we report, for the first time, the accumulation of the P2X6 subunit inside the nucleus of hippocampal neurons in an age-dependent way. This location is favored by its anchorage to endoplasmic reticulum through its N-terminal domain. The extracellular domain of P2X6 subunit is the key to reach the nucleus, where it presents a speckled distribution pattern and is retained by interaction with the nuclear envelope protein spectrin α2. The in vivo results showed that, once inside the nucleus, P2X6 subunit interacts with the splicing factor 3A1, which ultimately results in a reduction of the mRNA splicing activity. Our data provide new insights into post-transcriptional regulation of mRNA splicing, describing a novel mechanism that could explain why this process is sensitive to changes that occur with age.
Lactation, seasonality, and mother's postpartum weight change in Bangladesh: An analysis of maternal depletion

Longitudinally collected data from rural Bangladesh was used to investigate the effects of lactation, reproductive patterns, and seasonality on maternal weight and postpartum weight change. Results of multivariate analyses demonstrate that weight change exhibits a strong seasonal pattern, with losses in winter (December through March) and the rainy season (July through November) and gains in other months. The rate of weight loss peaks between 5 and 9 months postpartum, declines to near zero by 16 months postpartum, and becomes positive thereafter. However, season and duration interact, so that women who reach the stage of most intensive nutritional demand at a time of low food supply relative to energy output lose considerably more weight than women who reach that stage when food supplies are more adequate. Currently lactating women lose weight more rapidly than nonlactating women. Weight loss is slower among women with low initial weight. Prior reproductive patterns are associated with both weight at the time of conception and weight gain during pregnancy, which together determine weight at the beginning of the lactation interval. Each additional birth is associated with a decrease of 280 g in weight at conception, whereas interpregnancy intervals of < 18 months are associated with an 800‐g deficit at the time of that conception compared to longer intervals. Weight gain during pregnancy is greater among women with high parity, short interpregnancy intervals, and lower weight at conception, but not enough to compensate for the prepregnancy deficit. © 1994 Wiley‐Liss, Inc.
Rumen Cellulosomics: Divergent Fiber-Degrading Strategies Revealed by Comparative Genome-Wide Analysis of Six Ruminococcal Strains

Background A complex community of microorganisms is responsible for efficient plant cell wall digestion by many herbivores, notably the ruminants. Understanding the different fibrolytic mechanisms utilized by these bacteria has been of great interest in agricultural and technological fields, reinforced more recently by current efforts to convert cellulosic biomass to biofuels. Methodology/Principal Findings Here, we have used a bioinformatics-based approach to explore the cellulosome-related components of six genomes from two of the primary fiber-degrading bacteria in the rumen: Ruminococcus flavefaciens (strains FD-1, 007c and 17) and Ruminococcus albus (strains 7, 8 and SY3). The genomes of two of these strains are reported for the first time herein. The data reveal that the three R. flavefaciens strains encode for an elaborate reservoir of cohesin- and dockerin-containing proteins, whereas the three R. albus strains are cohesin-deficient and encode mainly dockerins and a unique family of cell-anchoring carbohydrate-binding modules (family 37). Conclusions/Significance Our comparative genome-wide analysis pinpoints rare and novel strain-specific protein architectures and provides an exhaustive profile of their numerous lignocellulose-degrading enzymes. This work provides blueprints of the divergent cellulolytic systems in these two prominent fibrolytic rumen bacterial species, each of which reflects a distinct mechanistic model for efficient degradation of cellulosic biomass.
Antiangiogenic kringles derived from human plasminogen and apolipoprotein(a) inhibit fibrinolysis through a mechanism that requires a functional lysine-binding site

Abstract Many proteins in the fibrinolysis pathway contain antiangiogenic kringle domains. Owing to the high degree of homology between kringle domains, there has been a safety concern that antiangiogenic kringles could interact with common kringle proteins during fibrinolysis leading to adverse effects in vivo. To address this issue, we investigated the effects of several antiangiogenic kringle proteins including angiostatin, apolipoprotein(a) kringles IV9-IV10-V (LK68), apolipoprotein(a) kringle V (rhLK8) and a derivative of rhLK8 mutated to produce a functional lysine-binding site (Lys-rhLK8) on the entire fibrinolytic process in vitro and analyzed the role of lysine binding. Angiostatin, LK68 and Lys-rhLK8 increased clot lysis time in a dose-dependent manner, inhibited tissue-type plasminogen activator-mediated plasminogen activation on a thrombin-modified fibrinogen (TMF) surface, showed binding to TMF and significantly decreased the amount of plasminogen bound to TMF. The inhibition of fibrinolysis by these proteins appears to be dependent on their functional lysine-binding sites. However, rhLK8 had no effect on these processes owing to an inability to bind lysine. Collectively, these results indicate that antiangiogenic kringles without lysine binding sites might be safer with respect to physiological fibrinolysis than lysine-binding antiangiogenic kringles. However, the clinical signi-ficance of these findings will require further validation in vivo.
A comparison of three vasopressors for tight control of maternal blood pressure during cesarean section under spinal anesthesia: Effect on maternal and fetal outcome

Purpose: Maintaining systolic blood pressure (SBP) at 100% of baseline is best for fetal and maternal outcome. We hypothesized that irrespective of the vasopressor used, maintaining SBP at 100% of baseline with phenylephrine (P), metaraminol (M), or ephedrine (E) will produce the best fetal pH after cesarean section (LSCS) under subarachnoid block (SAB). Materials and Methods: Ninety ASA 1 women scheduled for elective LSCS were randomly allocated to receive P, M, or E. SAB was established with patient in left lateral position using 2.5 cc of 0.5% hyperbaric bupivacaine. Immediately following SAB, patients received a bolus of the study drug (E = 5 mg, M = 0.5 mg, P = 30 mcg) followed by infusion (E = 2.5 mg/min, M = 0.25 mg/min, P = 15 mcg/min) to maintain SBP at 100% baseline. Umbilical blood gases, maternal hemodynamic parameters, and complications were recorded. Results: The umbilical pH was comparable in all the three groups (P > 0.05). The mean SBP from spinal block until delivery was similar over time for all the three groups. The incidence of reactive hypertension was more in group M (P < 0.05) than in group E and group P. Total drug consumption to meet target blood pressure till delivery was 39.3 ± 14.6 mg in group E, 1.7 ± 0.9 mg in group M, and 283.6 ± 99.8 mcg in group P. The incidence of nausea and vomiting was comparable in the three groups. Conclusion: All the three vasopressors were equally effective in maintaining maternal blood pressure as well as umbilical pH during spinal anesthesia for cesarean section without any detrimental effects on fetal and maternal outcome.
Genetic trends and breed overlap derived from multiple-breed genetic evaluations of beef cattle for growth traits.

Genetic evaluations for a multiple-breed population of beef cattle were used to estimate genetic trends for five breeds, and genetic differences and overlap among 14 breeds. Genetic evaluations studied were for direct contributions to birth weight, gain from birth to 200 and 365 d, and maternal contribution to gain from birth to 200 d. Almost all genetic trends were positive, but the magnitude of the trends varied among breeds. Trends were nonlinear between 1985 and 1995 for most breed and trait combinations. The rates of increase in genetic trends were generally higher for the lighter weight breeds, and lighter weight breeds had faster growth rate genetic trends at 1995 than the heavier breeds. Genetic trend estimates for yearling gain at 1995 were 2.46, 2.23, 1.73, 1.70, and 1.46 kg/yr for Angus, Hereford, Limousin, Charolais, and Simmental, respectively. Corresponding birth weight genetic trends were . 130, . 226, . 049, . 130, and . 048 kg/yr. Mean genetic differences between breeds have been decreasing in magnitude due to these differences in genetic trends between heavier and lighter breeds. Genetic variation for the traits studied seemed to be greater within than between breeds for calves born and cows calving between 1993 and 1995. Genetic trends at 1995 suggest that ratios of within:between breed variation will increase and that across-breed genetic improvement initiatives for growth traits will become more important in the future.
Regulatory Roles of IL-2 and IL-4 in H4/Inducible Costimulator Expression on Activated CD4+ T Cells During Th Cell Development1

We found a tight correlation among the levels of H4/inducible costimulator (ICOS) expression, IL-4 production, and GATA-3 induction, using activated CD4+ T cells obtained from six different murine strains. BALB/c-activated CD4+ T cells expressed ∼10-fold more H4/ICOS on their surfaces and produced ∼10-fold more IL-4 upon restimulation than C57BL/6-activated CD4+ T cells. BALB/c naive CD4+ T cells were shown to produce much higher amounts of IL-2 and IL-4 upon primary stimulation than C57BL/6 naive CD4+ T cells. Neutralization of IL-4 with mAbs in culture of BALB/c naive CD4+ T cells strongly down-regulated both H4/ICOS expression on activated CD4+ T cells and IL-4 production upon subsequent restimulation. Conversely, exogenous IL-4 added to the culture of BALB/c or C57BL/6 naive CD4+ T cells up-regulated H4/ICOS expression and IL-4 production upon restimulation. In addition, retroviral expression of GATA-3 during the stimulation of naive CD4+ T cells from C57BL/6 or IL-4−/− mice increased H4/ICOS expression on activated CD4+ T cells. A similar effect of IL-2 in the primary culture of BALB/c naive CD4+ T cells appeared to be mediated by IL-4, the production of which was regulated by IL-2. These data suggest that IL-4 induced by IL-2 is critical to the maintenance of high H4/ICOS expression on BALB/c-activated CD4+ T cells.
Measuring Birding Specialization: A Confirmatory Factor Analysis

This purpose of this paper was to test a three-dimensional model of recreational specialization developed by Scott and Shafer (2001a). The model suggests recreational specialization could be conceptualized in terms of three distinct dimensions: behavior, skill and knowledge, and commitment. The model was tested using data from avid American birdwatchers (members of the American Birding Association). Results revealed behavior, skill and knowledge, and commitment were moderately related but did not always covary. In addition, the three-dimensional model was a better fit to the data than a traditional single additive model. These results supported previous arguments suggesting researchers need to explore the distinct impact of each dimension of specialization, rather than using additive indices, on various dependent variables. Future researchers may explore whether or not the model can be generalized to other populations of birders (e.g., less skilled birdwatchers) and other groups of recreationists (e.g., anglers, hunters, mountain climbers).
Gastric epithelial cell proliferation and cagA status in Helicobacter pylori gastritis at different gastric sites

Objective. Helicobacter pylori infection causes hyperproliferation which is believed to predispose to the development of gastric carcinoma. The aim of this study was to analyze epithelial cell proliferation topographically in H. pylori gastritis in relationship to cagA status. Material and methods. The proliferative index (PI: Ki-67-labeled nuclei/total number of foveolar nuclei) was determined in gastric mucosa biopsies taken at the antrum (lesser and greater curvatures), incisura, and corpus (greater curvature) from 78 patients with H. pylori gastritis and 20 H. pylori-negative patients. H. pylori and cagA status were determined by polymerase chain reaction (PCR) and serology. Results. PIs were significantly higher in H. pylori- and cagA-positive patients, in comparison with H. pylori- and cagA-negative patients, at all sites (p≤0.002 and p≤0.009) and in the antrum in comparison to the corpus, in both H. pylori-negative (p=0.04) and positive patients (p<10−3). At the antral lesser curvature, PIs were higher than in all the other sites, both in H. pylori- (p≤0.002) and cagA-positive groups (p≤0.02). The PI correlated directly and significantly with inflammation in infected patients (r=0.45, p<10−3) and in cagA-positive patients (r=0.41, p=0.005). The PI was significantly higher in the antrum of infected patients with atrophy (p=0.03) and intestinal metaplasia (p=0.05) than in those without atrophy and intestinal metaplasia, respectively. Conclusions. We demonstrated that H. pylori infection and cagA-positive strains promote epithelial proliferation that was correlated with host inflammatory reaction and mostly at the antral lesser curvature, which is recognized as the area where most carcinomas arise.