Miracle-dz/UniFAR-FTUs huggingface dataset:
Listeria monocytogenes Infection Overcomes the Requirement for CD40 Ligand in Exogenous Antigen Presentation to CD8+ T Cells1

In vivo priming of CD8+ T lymphocytes against exogenously processed model Ags requires CD4+ T cell help, specifically interactions between CD40 ligand (CD40L) expressed by activated CD4+ T cells and CD40, which is present on professional APC such as dendritic cells (DCs). To address this issue in the context of bacterial infection, we examined CD40L-CD40 interactions in CD8+ T cell priming against an exogenously processed, nonsecreted bacterial Ag. CD40L interactions were blocked by in vivo treatment with anti-CD40L mAb MR-1, which inhibited germinal center formation and CD8+ T cell cross-priming against an exogenous model Ag, OVA. In contrast, MR-1 treatment did not interfere with CD8+ T cell priming against a nonsecreted or secreted recombinant Ag expressed by Listeria monocytogenes. Memory and secondary responses of CD8+ T cells against nonsecreted and secreted bacterial Ags were also largely unimpaired by transient MR-1 treatment. When MR-1-treated mice were concurrently immunized with L. monocytogenes and OVA-loaded splenocytes, cross-priming of OVA-specific naive CD8+ T cells occurred. No significant decline in cross-priming against OVA was measured when either TNF or IFN-γ was neutralized in L. monocytogenes-infected animals, demonstrating that multiple signals exist to overcome CD40L blockade of CD8+ T cell cross-priming during bacterial infection. These data support a model in which DCs can be stimulated in vivo through signals other than CD40, becoming APC that can effectively stimulate CD8+ T cell responses against exogenous Ags during infection.
Natural History of Concussion in Sport

Background Evidence-based clinical data are required for safe return to play after concussion in sport. Purpose The objective of this study was to describe the natural history of concussion in sport and identify clinical features associated with more severe concussive injury, using return-to-sport decisions as a surrogate measure of injury severity. Study Design Cohort study (prognosis); Level of evidence, 3. Methods Male elite senior, elite junior, and community-based Australian Rules football players had preseason baseline cognitive testing (Digit Symbol Substitution Test, Trail-Making Test—Part B, and CogSport computerized test battery). Players were recruited into the study after a concussive injury sustained while playing football. Concussed players were tested serially until all clinical features of their injury had resolved. Results Of 1015 players, 88 concussions were observed in 78 players. Concussion-associated symptoms lasted an average of 48.6 hours (95% confidence interval, 39.5-57.7 hours) with delayed return to sport correlated with ≥4 symptoms, headache lasting ≥60 hours, or self-reported “fatigue/fogginess. ” Cognitive deficits using the Digit Symbol Substitution Test and Trail-Making Test—part B recovered concomitantly with symptoms, but computerized test results recovered 2 to 3 days later and remained impaired in 35% of concussed players after symptom resolution. Conclusion Delayed return to sport was associated with initially greater symptom load, prolonged headache, or subjective concentration deficits. Cognitive testing recovery varied, taking 2 to 3 days longer for computerized tests, suggesting greater sensitivity to impairment. Therefore, symptom assessment alone may be predictive of but may underestimate time to complete recovery, which may be better estimated with computerized cognitive testing.
Aliskiren, a Direct Renin Inhibitor, Improves Vascular Endothelial Function in Patients on Hemodialysis Independent of Antihypertensive Effect ∼ a Pilot Study∼

Aims: Aliskiren inhibits the first step in the renin-angiotensin system (RAS) and recently has been shown to modulate vascular diseases via RAS-dependent and independent pathways. This study aimed to determine the effect of aliskiren-associated direct renin inhibition on endothelial function in patients on hemodialysis via flow-mediated dilatation (FMD) and platelet-derived microparticles (PDMP), as biomarkers of atherosclerosis. Methods: A 12-week prospective study was performed with 24 patients on hemodialysis who were administered 150 mg orally aliskiren once daily for 12 weeks. Results: No significant difference were observed between pre-dialysis, home, and weekly averaged blood pressure at baseline and at 12 weeks (151.5 ± 8.5/80.9 ± 12.9 mmHg vs 150.3 ± 15.3/78.9 ± 21.2 mmHg, 151.4 ± 9.7/82.3 ± 14.7 mmHg vs 151.2 ± 17.7/81.4 ± 10.6 mmHg, and 156.0 ± 18.3/81.9 ± 9.4 mmHg vs 152.5 ± 18.9/81.7 ± 12.3 mmHg, respectively). FMD significantly increased from 2.54% ± 1.45% at baseline to 3.11% ± 1.37% at 12 weeks (P = 0.0267), and PDMP significantly decreased from 13.9 ± 5.8 U/mL at baseline to 10.9 ± 4.5 U/mL at 12 weeks (P = 0.0002). Conclusion: Aliskiren improved vascular endothelial function and platelet-endothelium activation in patients on hemodialysis independent of antihypertensive effect.
Evaluative Conditioning: Arti-fact or -fiction?—A Reply to Baeyens, De Houwer, Vansteenwegen, and Eelen (1998)

Baeyens et al.(1998) claim that Field and Davey's (1997) controversial study of conceptual conditioning offers little threat to current conceptions of evaluative conditioning. This article addresses some of the questions posed by Baeyenset al.First, some criticisms of the conceptual conditioning study appear to be based on a misunderstanding of the procedure. Second, we address the issues surrounding the so-called Type-X procedure. Specifically, we begin by reviewing the status of studies that have used a procedure different from the Type-X procedure. It is then argued that, although the Type-X procedure has been used in only a portion of EC research, it has been used primarily in those studies whose outcome has been used to argue that evaluative conditioning (EC) is functionally distinct from autonomic conditioning. We then review the evidence from non-Type-X procedures that EC is a distinct form of learning. Finally, an attempt is made to explain why between-subject controls should be used as a matter of course in this field of research.
Does Hepatitis C Virus Infection Increase Risk for Stroke? A Population-Based Cohort Study

Background The relationship between hepatitis C virus infection and risk of stroke remains inconsistent. This study evaluates the risk of stroke in association with chronic hepatitis C infection in a longitudinal population-based cohort. Methods We identified 4,094 adults newly diagnosed with hepatitis C infection in 2002–2004 from the Taiwan National Health Insurance Research Database. Comparison group consisted of 16,376 adults without hepatitis C infection randomly selected from the same dataset, frequency matched by age and sex. Events of stroke from 2002–2008 were ascertained from medical claims (International Classification of Diseases, Ninth Revision, Clinical Modification, ICD-9-CM, codes 430–438). Multivariate adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated for potential associated factors including HCV infection, age, sex, low-income status, urbanization, cessation of cigarette smoking, alcohol-related illness, obesity, history of chronic diseases and medication use. Findings During 96,752 person-years of follow-up, there were 1981 newly diagnosed stroke cases. The HRs of stroke associated with medical conditions such as hypertension, diabetes and heart disease were 1.48 (95% CI 1.33 to 1.65), 1.23 (95% CI 1.11 to 1.36) and 1.17 (95% CI 1.06 to 1.30), respectively, after adjustment for covariates. The cumulative risk of stroke for people with hepatitis C and without hepatitis C infections was 2.5% and 1.9%, respectively (p<0.0001). Compared with people without hepatitis C infection, the adjusted HR of stroke was 1.27 (95% CI 1.14 to 1.41) for people with hepatitis C infection. Conclusion Chronic hepatitis C infection increases stroke risk and should be considered an important and independent risk factor.
Total Intermittent Pringle Maneuver during Liver Resection Can Induce Intestinal Epithelial Cell Damage and Endotoxemia

Objectives The intermittent Pringle maneuver (IPM) is frequently applied to minimize blood loss during liver transection. Clamping the hepatoduodenal ligament blocks the hepatic inflow, which leads to a non circulating (hepato)splanchnic outflow. Also, IPM blocks the mesenteric venous drainage (as well as the splenic drainage) with raising pressure in the microvascular network of the intestinal structures. It is unknown whether the IPM is harmful to the gut. The aim was to investigate intestinal epithelial cell damage reflected by circulating intestinal fatty acid binding protein levels (I-FABP) in patients undergoing liver resection with IPM. Methods Patients who underwent liver surgery received total IPM (total-IPM) or selective IPM (sel-IPM). A selective IPM was performed by selectively clamping the right portal pedicle. Patients without IPM served as controls (no-IPM). Arterial blood samples were taken immediately after incision, ischemia and reperfusion of the liver, transection, 8 hours after start of surgery and on the first post-operative day. Results 24 patients (13 males) were included. 7 patients received cycles of 15 minutes and 5 patients received cycles of 30 minutes of hepatic inflow occlusion. 6 patients received cycles of 15 minutes selective hepatic occlusion and 6 patients underwent surgery without inflow occlusion. Application of total-IPM resulted in a significant increase in I-FABP 8 hours after start of surgery compared to baseline (p<0.005). In the no-IPM group and sel-IPM group no significant increase in I-FABP at any time point compared to baseline was observed. Conclusion Total-IPM in patients undergoing liver resection is associated with a substantial increase in arterial I-FABP, pointing to intestinal epithelial injury during liver surgery. Trial Registration ClinicalTrials.gov NCT01099475
Identification and Discrimination of Burkholderia pseudomallei, B. mallei, and B. thailandensis by Real-Time PCR Targeting Type III Secretion System Genes

ABSTRACT Burkholderia pseudomallei and B. mallei are two highly pathogenic bacteria, responsible for melioidosis and glanders, respectively. The two are closely related and can also be mistaken for B. thailandensis, a nonpathogenic species. To improve their differential identification, we describe a hydrolysis probe-based real-time PCR method using the uneven distribution of type III secretion system genes among these three species.
Research on fault tolerance for the static segment of FlexRay protocol

FlexRay is the next generation communication protocol in automotive network. But the development was hindered because most of the researches ignored transient fault in message transmission. In this work, a complete framework is presented to increases the reliability by retransmitting messages in the static segment. It includes system model, mathematical abstraction and a heuristic algorithm. Given a specification of the system model, our work will not only get the system satisfy the reliability goal but also optimize the bandwidth utilization rate. Simulation results show that our approach performs better than the existing algorithm in bandwidth utilization rate (-19.1%), reliability (+0.07%) and running time (-37.2%). In our opinion, this algorithm is so generic that it can be widely used in other time-triggered and reliability critical applications.
The storage vs repair bandwidth trade-off for multiple failures in clustered storage networks

We study the trade-off between storage overhead and inter-cluster repair bandwidth in clustered storage systems, while recovering from multiple node failures within a cluster. A cluster is a collection of m nodes, and there are n clusters. For data collection, we download the entire content from any k clusters. For repair of t ≥ 2 nodes within a cluster, we take help from ℓ local nodes, as well as d helper clusters. We characterize the optimal trade-off under functional repair, and also under exact repair for the minimum storage and minimum inter-cluster bandwidth (MBR) operating points. Our bounds show the following interesting facts: 1) When t|(m − ℓ) the tradeoff is the same as that under t = 1, and thus there is no advantage in jointly repairing multiple nodes, 2) When t |(m − ℓ), the optimal file-size at the MBR point under exact repair can be strictly less than that under functional repair. 3) Unlike the case of t = 1, increasing the number of local helper nodes does not necessarily increase the system capacity under functional repair.
Exclusive Contracts and Protection of Investments

We consider the effect of a renegotiable exclusive contract restricting a buyer to purchase from only one seller on the levels of noncontractible investments undertaken in their relationship. Contrary to some informal claims in the literature, we find that in this setting exclusivity has no direct effect on "internal" investments, i.e. those that are specific to the relationship. The direct effect of exclusivity is instead to increase the "external" investments of the seller (those which enhance the value of the buyer's trade with other sellers) and to reduce those of the buyer. Exclusivity may have an indirect effect on internal investments; the direction of this effect depends on the nature of any complementarities or substitutabilities between external and internal trades and investments. We relate these findings to existing informal discussions of the role of exclusivity in protecting investments. We also examine the effects of exclusivity on aggregate welfare, the private incentives of the buyer-seller coalition to use it, and the resulting externality on other potential suppliers.
Incidence of chronic obstructive pulmonary disease in a cohort of young adults according to the presence of chronic cough and phlegm.

RATIONALE The few prospective studies aimed at assessing the incidence of chronic obstructive pulmonary disease (COPD) in relation to the presence of chronic cough/phlegm have produced contrasting results. OBJECTIVES To assess the incidence of COPD in a cohort of young adults and to test whether chronic cough/phlegm and dyspnea are independent predictors of COPD. METHODS An international cohort of 5,002 subjects without asthma (ages 20-44 yr) with normal lung function (FEV(1)/FVC ratio >/= 70%) from 12 countries was followed from 1991-2002 in the frame of the European Community Respiratory Health Survey II. Incident cases of COPD were those who had an FEV(1)/FVC ratio less than 70% at the end of the follow-up, but did not report having had a doctor diagnose asthma during the follow-up. MAIN RESULTS The incidence rate of COPD was 2.8 cases/1,000/yr (95% confidence interval [CI], 2.3-3.3). Chronic cough/phlegm was an independent and statistically significant predictor of COPD (incidence rate ratio [IRR], 1.85; 95% CI, 1.17-2.93) after adjusting for smoking habits and other potential confounders, whereas dyspnea was not associated with the disease (IRR = 0.98; 95% CI, 0.64-1.50). Subjects who reported chronic cough/phlegm both at baseline and at the follow-up had a nearly threefold-increased risk of developing COPD with respect to asymptomatic subjects (IRR = 2.88; 95% CI, 1.44-5.79). CONCLUSIONS The incidence of COPD is substantial even in young adults. The presence of chronic cough/phlegm identifies a subgroup of subjects with a high risk of developing COPD, independently of smoking habits.
Universal schema for entity type prediction

Categorizing entities by their types is useful in many applications, including knowledge base construction, relation extraction and query intent prediction. Fine-grained entity type ontologies are especially valuable, but typically difficult to design because of unavoidable quandaries about level of detail and boundary cases. Automatically classifying entities by type is challenging as well, usually involving hand-labeling data and training a supervised predictor. This paper presents a universal schema approach to fine-grained entity type prediction. The set of types is taken as the union of textual surface patterns (e.g. appositives) and pre-defined types from available databases (e.g. Freebase)---yielding not tens or hundreds of types, but more than ten thousands of entity types, such as financier, criminologist, and musical trio. We robustly learn mutual implication among this large union by learning latent vector embeddings from probabilistic matrix factorization, thus avoiding the need for hand-labeled data. Experimental results demonstrate more than 30% reduction in error versus a traditional classification approach on predicting fine-grained entities types.
A Systematic Review Characterizing On-Farm Sources of Campylobacter spp. for Broiler Chickens

Campylobacter and antimicrobial-resistant Campylobacter are frequently isolated from broiler chickens worldwide. In Canada, campylobacteriosis is the third leading cause of enteric disease and the regional emergence of ciprofloxacin-resistant Campylobacter in broiler chickens has raised a public health concern. This study aimed to identify, critically appraise, and synthesize literature on sources of Campylobacter in broilers at the farm level using systematic review methodology. Literature searches were conducted in January 2012 and included electronic searches in four bibliographic databases. Relevant studies in French or English (n = 95) conducted worldwide in any year and all study designs were included. Risk of Bias and GRADE criteria endorsed by the Cochrane collaboration was used to assess the internal validity of the study and overall confidence in the meta-analysis. The categories for on-farm sources were: broiler breeders/vertical transfer (number of studies = 32), animals (n = 57), humans (n = 26), environment (n = 54), and water (n = 63). Only three studies examined the antimicrobial resistance profiles of Campylobacter from these on-farm sources. Subgroups of data by source and outcome were analyzed using random effect meta-analysis. The highest risk for contaminating a new flock appears to be a contaminated barn environment due to insufficient cleaning and disinfection, insufficient downtime, and the presence of an adjacent broiler flock. Effective biosecurity enhancements from physical barriers to restricting human movement on the farm are recommended for consideration to enhance local on-farm food safety programs. Improved sampling procedures and standardized laboratory testing are needed for comparability across studies. Knowledge gaps that should be addressed include farm-level drug use and antimicrobial resistance information, further evaluation of the potential for vertical transfer, and improved genotyping methods to strengthen our understanding of Campylobacter epidemiology in broilers at the farm-level. This systematic review emphasizes the importance of improved industry-level and on-farm risk management strategies to reduce pre-harvest Campylobacter in broilers.
Epidemiology and Successful Control of a Large Outbreak Due to Klebsiella pneumoniae Producing ExtendedSpectrum β-Lactamases

ABSTRACT An outbreak due to extended-spectrum β-lactamase-producingKlebsiella pneumoniae (ESBL-KP) was detected from May 1993 to June 1995. A total of 145 patients, particularly patients in intensive care units (ICUs) (107 patients [72%]), were colonized or infected. Infection developed in 92 (63%) patients, and primary bacteremia caused by ESBL-KP was the most frequent infection (40 of 92 patients [43%]). A single clone of ESBL-KP was identified by pulsed-field gel electrophoresis analysis throughout the whole period, and no molecular epidemiological relationship could be found between the epidemic strain and non-ESBL-KP isolates. To determine risk factors for ESBL-KP infection weekly rectal swabs were obtained in three serial incidence surveys (470 patients); the probabilities of carriage of ESBL-KP in the digestive tract were 33% (October and November 1993), 40% (May and June 1994), and 0% (October and November 1995) at 10 days of ICU admission. A logistic regression model identified prior carriage of ESBL-KP in the digestive tract (odds ratio, 3.4; 95% confidence interval 1.1 to 10.4) as an independent variable associated with ESBL-KP infection. A statistically significant correlation was observed between the restricted use of oxyimino-β-lactams (189 defined daily doses [DDD]/1,000 patient-days to 24 DDD/1,000 patient-days) and the trends of ESBL-KP infection (r = 0.7; P = 0.03).
Contributions of imprecision in PET‐MRI rigid registration to imprecision in amyloid PET SUVR measurements

Quantitative measurement of β‐amyloid from amyloid PET scans typically relies on localizing target and reference regions by image registration to MRI. In this work, we present a series of simulations where 50 small random perturbations of starting location and orientation were applied to each subject's PET scan, and rigid registration using spm_coreg was performed between each perturbed PET scan and its corresponding MRI. We then measured variation in the output PET‐MRI registrations and how this variation affected the resulting SUVR measurements. We performed these experiments using scans of 1196 participants, half using 18F florbetapir and half using 11C PiB. From these experiments, we measured the magnitude of the imprecision in the rigid registration steps used to localize measurement regions, and how this contributes to the overall imprecision in SUVR measurements. Unexpectedly, we found for both tracers that the imprecision in these measurements depends on the degree of amyloid tracer uptake, and thus also indirectly on Alzheimer's disease clinical status. We then examined common choices of reference regions, and we show that SUVR measurements using supratentorial white matter references are relatively resistant to this source of error. We also show that the use of partial volume correction further magnifies the effects of registration imprecision on SUVR measurements. Together, these results suggest that this rigid registration step is an attractive target for future work in improving measurement techniques. Hum Brain Mapp 38:3323–3336, 2017. © 2017 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.
Distinct ferroelectric smectic liquid crystals consisting of banana shaped achiral molecules

The synthesis of a banana-shaped molecule is reported and it is found that the smectic phase which it forms is biaxial with the molecules packed in the best direction into a layer. Because of this characteristic packing, spontaneous polarization appears parallel to the layer and switches on reversal of an applied electric field. This is the first obvious example of ferroelectricity in an achiral smectic phase and is ascribed to the C2v symmetry of the molecular packing.