Miracle-dz/UniFAR-FTUs huggingface dataset:
Gut sterilization in experimental colitis leukocyte mediated colon injury, and effects on angiogenesis/lymphangiogenesis

Inappropriate responses to normal commensal bacteria trigger immune activation in both inflammatory bowel disease and experimental colitis. How gut flora contribute to the pathogenesis of inflammatory bowel disease is unclear, but may involve entrapment of leukocytes and remodeling of the vascular system. Here we evaluated how the progression and tissue remodeling in experimental colitis differ in a germ- free model of mouse colitis. Four treatment groups were used: control, antibiotic-treated (ABX), dextran sulfate colitis (DSS) and DSS pre- and co-treated with antibiotics (DSS + ABX). In days 0 - 3 of the study, germ-free mice received antibiotics (vancomycin, neomycin, and metronidazole). During the next 11 days, antibiotics were continued and DSS (3%) added to “colitis” groups. Disease activity, weight, stool form and blood were monitored daily. Mice were sacrificed and tissue samples harvested. Histopathological scores in controls (0.00) and in ABX (1.0+/–0.81) were significantly (p –0). Extents of injury, inflammation and crypt damage were all improved in DSS + ABX. The Disease Activity Index score (day 11) was significantly worse in the DSS group compared to the DSS + ABX group. Stool blood and form scores were also significantly improved among these groups. Importantly, myeloper- oxidase was significantly reduced in DSS + ABX, indicating that neutrophil infiltration was blocked. Colitis was associated with an increase in blood and lymphatic vessels; both of these events were also significantly reduced by gut sterilization. Our experiment shows that clinical and histopathological severity of colitis was significantly worse in the DSS colitis group compared to the DSS + ABX group, supporting the hypothesis that development of IBD is likely to be less severe with appropriate antibiotic treatment. In particular, gut sterilization effectively reduces leuko- cyte-dependent (PMN) injury to improve outcomes and may be an important target for therapy.
Real Options in Offshore Oil Field Development Projects

The average size of discovered petroleum reserves on the Norwegian continental shelf has declined steadily over the last years. As a consequence, the fields have become economically more marginal, and new and flexible development strategies are required. This paper describes a stochastic dynamic programming model for project evaluation under uncertainty, where emphasis is put on flexibility and its value. Both market risk and reservoir uncertainty are handled by the model, as well as different flexibility types. The complexity of the problem is a challenge and calls for simple descriptions of the main variables in order to obtain a manageable model size. Results from a case study reveal significant value of flexibility, and clearly illustrate the shortcoming of today’s common evaluation methods. Particularly capacity flexibility should not be neglected in future development projects where uncertainty surrounding the reservoir properties is substantial.
A Generic Model of Dyadic Social Relationships

We introduce a model of dyadic social interactions and establish its correspondence with relational models theory (RMT), a theory of human social relationships. RMT posits four elementary models of relationships governing human interactions, singly or in combination: Communal Sharing, Authority Ranking, Equality Matching, and Market Pricing. To these are added the limiting cases of asocial and null interactions, whereby people do not coordinate with reference to any shared principle. Our model is rooted in the observation that each individual in a dyadic interaction can do either the same thing as the other individual, a different thing or nothing at all. To represent these three possibilities, we consider two individuals that can each act in one out of three ways toward the other: perform a social action X or Y, or alternatively do nothing. We demonstrate that the relationships generated by this model aggregate into six exhaustive and disjoint categories. We propose that four of these categories match the four relational models, while the remaining two correspond to the asocial and null interactions defined in RMT. We generalize our results to the presence of N social actions. We infer that the four relational models form an exhaustive set of all possible dyadic relationships based on social coordination. Hence, we contribute to RMT by offering an answer to the question of why there could exist just four relational models. In addition, we discuss how to use our representation to analyze data sets of dyadic social interactions, and how social actions may be valued and matched by the agents.
B-type natriuretic peptide enhances vasculogenesis by promoting number and functional properties of early endothelial progenitor cells.

OBJECTIVE To test the hypothesis that B-type natriuretic peptide (BNP) acts as a potent vasculogenic agent by enhancing the number, proliferation, adhesion, and migration of endothelial progenitor cells (EPCs). BACKGROUND BNP is a neurohormonal peptide that predicts outcome and used for treatment in chronic heart failure patients. It has been shown to promote angiogenesis in experimental animals. EPCs have been demonstrated to contribute to postnatal angiogenesis and vasculogenesis. METHODS The number of EPC colony forming units (CFU) and levels of N-terminal ProBNP were assayed in patients with severe, yet controlled, New York Heart Association (NYHA) II-IV heart failure. The in vitro effects of BNP on early EPC-CFU numbers, proliferation, migration, adhesive, and vascular tube formation capacities were studied using human and murine systems. The effects of in vivo BNP administration on Sca-1/Flk-1 progenitors and on vasculogenesis in the hindlimb ischemia model were then assayed in wild-type mice. RESULTS A significant correlation was found between circulating N-terminal ProBNP levels and EPC-CFU numbers. We observed a dose-dependent effect of BNP on the numbers of CFU and proliferation capacity of human EPCs as well as on their adhesive, migratory, and tube formation properties, in vitro. Systemic BNP administration to mice led to a significant increase in bone marrow Sca-1/Flk-1 EPCs and improvement in blood flow and capillary density in the ischemic limbs of mice. CONCLUSIONS BNP promotes vessel growth by increasing the number of endothelial progenitors and enhancing their functional properties. These provasculogenic properties of BNP could account for some of its beneficial effects in chronic heart failure patients and may be harnessed for the purpose of improving collateral formation in ischemic subjects.
Fine Scale Spatiotemporal Clustering of Dengue Virus Transmission in Children and Aedes aegypti in Rural Thai Villages

Background Based on spatiotemporal clustering of human dengue virus (DENV) infections, transmission is thought to occur at fine spatiotemporal scales by horizontal transfer of virus between humans and mosquito vectors. To define the dimensions of local transmission and quantify the factors that support it, we examined relationships between infected humans and Aedes aegypti in Thai villages. Methodology/Principal Findings Geographic cluster investigations of 100-meter radius were conducted around DENV-positive and DENV-negative febrile “index” cases (positive and negative clusters, respectively) from a longitudinal cohort study in rural Thailand. Child contacts and Ae. aegypti from cluster houses were assessed for DENV infection. Spatiotemporal, demographic, and entomological parameters were evaluated. In positive clusters, the DENV infection rate among child contacts was 35.3% in index houses, 29.9% in houses within 20 meters, and decreased with distance from the index house to 6.2% in houses 80–100 meters away (p<0.001). Significantly more Ae. aegypti were DENV-infectious (i.e., DENV-positive in head/thorax) in positive clusters (23/1755; 1.3%) than negative clusters (1/1548; 0.1%). In positive clusters, 8.2% of mosquitoes were DENV-infectious in index houses, 4.2% in other houses with DENV-infected children, and 0.4% in houses without infected children (p<0.001). The DENV infection rate in contacts was 47.4% in houses with infectious mosquitoes, 28.7% in other houses in the same cluster, and 10.8% in positive clusters without infectious mosquitoes (p<0.001). Ae. aegypti pupae and adult females were more numerous only in houses containing infectious mosquitoes. Conclusions/Significance Human and mosquito infections are positively associated at the level of individual houses and neighboring residences. Certain houses with high transmission risk contribute disproportionately to DENV spread to neighboring houses. Small groups of houses with elevated transmission risk are consistent with over-dispersion of transmission (i.e., at a given point in time, people/mosquitoes from a small portion of houses are responsible for the majority of transmission).
Bayesian analysis of a matched case–control study with expert prior information on both the misclassification of exposure and the exposure–disease association

We propose a Bayesian adjustment for the misclassification of a binary exposure variable in a matched case–control study. The method admits a priori knowledge about both the misclassification parameters and the exposure–disease association. The standard Dirichlet prior distribution for a multinomial model is extended to allow separation of prior assertions about the exposure–disease association from assertions about other parameters. The method is applied to a study of occupational risk factors for new‐onset adult asthma. Copyright © 2009 John Wiley & Sons, Ltd.
X-Ray Fluorescence Molecular Imaging with Improved Sensitivity for Biomedical Applications

X-ray Fluorescence Molecular Imaging (XFMI) holds great promise as a low-cost molecular imaging modality for biomedical applications with high chemical sensitivity. However, for in vivo biomedical applications, a key technical bottleneck is the relatively low chemical sensitivity of XFMI, especially at a reasonably low radiation dose. In laboratory x-ray source based XFMI, one of the main factors that limits the chemical sensitivity of XFMI is the scattered x-rays. We will present our latest findings on improving the chemical sensitivity of XFMI using excitation beam spectrum optimization. XFMI imaging experiments on two mousesized phantoms were conducted at three different excitation beam spectra. Our results show that the minimum detectable concentration (MDC) of iodine can be readily increased by five times via excitation spectrum optimization. Findings from this investigation could find use for in vivo pre-clinical small-animal XFMI in the future. Keywords—Molecular imaging, X-ray fluorescence, chemical sensitivity, X-ray scattering.
Examining the Ability of Artificial Neural Networks Machine Learning Models to Accurately Predict Complications Following Posterior Lumbar Spine Fusion

Study Design. A cross-sectional database study. Objective. The aim of this study was to train and validate machine learning models to identify risk factors for complications following posterior lumbar spine fusion. Summary of Background Data. Machine learning models such as artificial neural networks (ANNs) are valuable tools for analyzing and interpreting large and complex datasets. ANNs have yet to be used for risk factor analysis in orthopedic surgery. Methods. The American College of Surgeons National Surgical Quality Improvement Program (ACS-NSQIP) database was queried for patients who underwent posterior lumbar spine fusion. This query returned 22,629 patients, 70% of whom were used to train our models, and 30% were used to evaluate the models. The predictive variables used included sex, age, ethnicity, diabetes, smoking, steroid use, coagulopathy, functional status, American Society for Anesthesiology (ASA) class ≥3, body mass index (BMI), pulmonary comorbidities, and cardiac comorbidities. The models were used to predict cardiac complications, wound complications, venous thromboembolism (VTE), and mortality. Using ASA class as a benchmark for prediction, area under receiver operating curves (AUC) was used to determine the accuracy of our machine learning models. Results. On the basis of AUC values, ANN and LR both outperformed ASA class for predicting all four types of complications. ANN was the most accurate for predicting cardiac complications, and LR was most accurate for predicting wound complications, VTE, and mortality, though ANN and LR had comparable AUC values for predicting all types of complications. ANN had greater sensitivity than LR for detecting wound complications and mortality. Conclusion. Machine learning in the form of logistic regression and ANNs were more accurate than benchmark ASA scores for identifying risk factors of developing complications following posterior lumbar spine fusion, suggesting they are potentially great tools for risk factor analysis in spine surgery. Level of Evidence: 3
Different postischemic protein expression of the GABA(A) receptor alpha2 subunit and the plasticity-associated protein MAP1B after treatment with BDNF versus G-CSF in the rat brain.

PURPOSE Recent data indicate that both brain-derived neurotrophic factor (BDNF) and granulocyte-colony stimulating factor (G-CSF) exert substantial neuroregenerative effects and improve functional outcome after ischemic stroke. In the present study, we checked for potential differences in the postischemic modulation of various excitatory and inhibitory neurotransmitter receptors as well as various marker molecules for structural plasticity by BDNF versus G-CSF. METHODS Adult male Wistar rats were subjected to photothrombotic ischemia and subsequently treated with NaCl, BDNF or G-CSF, respectively. After 6 weeks, postischemic protein expression of the NR1, GluR1 and alpha2 subunit of the NMDA, AMPA and GABA(A) receptor, respectively, was semiquantitatively determined ipsi- and contralateral to the ischemic lesion. Structural plasticity was further analyzed immunohistochemically using antibodies against MAP1B, MAP2 and synaptophysin. RESULTS Only BNDF caused a significantly reduced postischemic protein expression of the GABA(A) receptor alpha2 subunit and the NR1 subunit of the NMDA receptor in the hippocampus. Furthermore, BDNF compared to G-CSF increased MAP1B protein expression in the periischemic regenerative region. CONCLUSIONS Although both BDNF and G-CSF have been shown to improve postischemic functional outcome to a similar extent, exogenous administration results in different underlying structural reorganization processes suggesting specific modulations of plasticity-associated events by these trophic factors.
Intriguing Clues to a Scrapie-Mad Cow Link

PARIS-- In the 27 April issue of The Independent newspaper, a headline suggested that the mystery of the origins of bovine spongiform encephalopathy (BSE), or "mad cow disease," was solved, proclaiming that "Tests Show BSE Caused by Infected Sheep. " The truth is far more complex, say scientists, who nonetheless laud the unpublished research described in the article as a possible step toward understanding how the puzzling disease got started.
CATARACT SURGERY

Objectives: This study is conducted to determine the prevalence of hepatitis Band hepatitis C virus infection in patients presenting for cataract surgery and to see the pattern ofliver function tests in hepatitis positive and negative patients. Design: Descriptive study, Settingand Period: The study was conducted from September 2015 to February 2016 at Al-Shifa eyehospital, Rawalpindi, Pakistan. Methods: All the patients presenting for cataract surgery wereincluded in the study. Liver function tests were performed using automatic chemistry analyzerwhile hepatitis B surface antigen and antibodies to hepatitis C virus were checked using thirdgeneration ELISA. Results: A total of 315 patients were included in the study. Male to femaleratio was 1.18:1. Out of these 315 cases, there were 45 (14.29%) patients who tested positivefor hepatitis and all of these 45 cases were positive for anti-HCV antibodies with 18 (40%) malesand 27 (60%) females, showing high predilection for female gender. Majority of patients, about171 (54.29%), were in the age range of 21-40 years, followed by 57 (18.10%) patients in theage group of 40-50 years. The mean age of hepatitis positive patients was 33.33±13.37 years.Regarding liver function tests, the alanine transaminase levels (ALT) were 77.9 and 132 U/L inhepatitis negative and hepatitis positive patients respectively. Enzyme levels were 1.65 timeshigher in hepatitis positive patients than in hepatitis negative patients. Rest of the parameterswas within normal limits. Conclusion: Hepatitis B and C virus infections are common cause ofliver dysfunction in our country. Hepatitis C virus infection is more prevalent than Hepatitis Bvirus infection. Hepatitis infection can lead to raised ALT levels even when other parameters ofliver function tests are within normal limits. Therefore, all patients who have raised ALT levelsmust undergo hepatitis screening.
NLRPs, microbiota, and gut homeostasis: unravelling the connection

Within the NOD‐like receptor (NLR) family, there are several NLRP (NLR family, pyrin domain‐containing) proteins that are involved in the formation of inflammasomes. These multi‐protein complexes are a key part of the network of cellular events required for secretion of the pro‐inflammatory cytokines IL‐1β and IL‐18. The NLRP3 inflammasome is the best‐characterized member of the family and has recently been implicated in gut homeostasis and determining the severity of inflammation in inflammatory bowel disease (IBD) and inflammation‐associated colorectal cancer. This led to the discovery that NLRP6 and NLRP12 also contribute to the maintenance of intestinal homeostasis and modulation of the gut microbiota, which in turn influences the intestine and distant organs. In this review, we bring together the latest data on the potential roles of NLRP family members in gut health and disease and identify the most pressing questions that remain to be answered to further our understanding of human diseases including IBD, inflammation‐associated cancers, and metabolic syndromes linked with obesity. Copyright © 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Evolutionary Testing Using an Extended Chaining Approach

Fitness functions derived from certain types of white-box test goals can be inadequate for evolutionary software test data generation (Evolutionary Testing), due to a lack of search guidance to the required test data. Often this is because the fitness function does not take into account data dependencies within the program under test, and the fact that certain program statements may need to have been executed prior to the target structure in order for it to be feasible. This paper proposes a solution to this problem by hybridizing Evolutionary Testing with an extended Chaining Approach. The Chaining Approach is a method which identifies statements on which the target structure is data dependent, and incrementally develops chains of dependencies in an event sequence. By incorporating this facility into Evolutionary Testing, and by performing a test data search for each generated event sequence, the search can be directed into potentially promising, unexplored areas of the test object's input domain. Results presented in the paper show that test data can be found for a number of test goals with this hybrid approach that could not be found by using the original Evolutionary Testing approach alone. One such test goal is drawn from code found in the publicly available libpng library.
A biphasic change in ribosomal conformation during transneuronal degeneration is altered by inhibition of mitochondrial, but not cytoplasmic protein synthesis

Following loss of eighth nerve input, 20–40% of neurons in the neonatal chick cochlear nucleus, nucleus magnocellularis (NM), undergo cell death. Intracellular changes that precede the death of NM neurons include increased oxidative metabolism and mitochondrial volume, decreased cytoplasmic protein synthesis, and destruction of ribosomes. Six hours following afferent deprivation, dying NM neurons demonstrate complete loss of ribosomes and cessation of protein synthesis, suggesting that the rapid destruction of ribosomes leads to neuronal death. Increased NM neuron death occurs when mitochondrial upregulation is prevented by chloramphenicol, a mitochondrial protein synthesis inhibitor. This finding suggests that increased oxidative capacity is required for neuronal survival following loss of afferent input. To study changes in the ribosomes of afferent-deprived NM neurons, we obtained a monoclonal antibody to ribosomal RNA. This monoclonal antibody, Y10B, labels ribosomes of all NM neurons receiving normal synaptic activity. Following removal of afferent input, NM neurons demonstrate a biphasic change in their pattern of Y10B label. During the initial phase, there is a uniform decrease in the density of Y10B label. In the second phase, some NM neurons recover the capacity to bind the Y10B antibody while others remain unlabeled. During this second phase, NM neurons putatively destined to die, based on their failure to synthesize protein, are unlabeled by the Y10B antibody. New gene expression is not necessary to initiate the change in ribosomal immunoreactivity that leads deafferented NM neurons toward cell death. Blocking cytoplasmic protein synthesis with cycloheximide had no effect on the biphasic change in Y10B labeling of afferent-deprived NM neurons. Treating chicks with chloramphenicol, however, prevented the recovery of Y10B immunoreactivity in NM neurons during the second phase of the response to afferent deprivation.
Continuous-Flow Synthesis of Deuterium-Labeled Antidiabetic Chalcones: Studies towards the Selective Deuteration of the Alkynone Core

Flow chemistry-based syntheses of deuterium-labeled analogs of important antidiabetic chalcones were achieved via highly controlled partial C≡C bond deuteration of the corresponding 1,3-diphenylalkynones. The benefits of a scalable continuous process in combination with on-demand electrolytic D2 gas generation were exploited to suppress undesired over-reactions and to maximize reaction rates simultaneously. The novel deuterium-containing chalcone derivatives may have interesting biological effects and improved metabolic properties as compared with the parent compounds.
ISO 9001 diffusion analysis according to activity sectors

Purpose – The purpose of this paper is to analyse the evolution of the world‐wide diffusion, according to industrial sectors of activity, of the ISO 9000 family of quality standards.Design/methodology/approach – Using data provided by the ISO itself, the evolution of the world‐wide diffusion of the ISO 9000 family of standards from 1998 to 2008 is studied. Using two indices of instability, these data are then analysed in terms of individual industrial sectors to assess the heterogeneity of diffusion across different sectors of activity.Findings – The results show that the diffusion of ISO 9001 follows a logistic curve in all sectors, although the current stage of diffusion (in terms of initial stage, expansion stage, and saturation stage) differs between different sectors of activity. The sectors have been classified into three groups according to their possible future evolution.Research limitations/implications – Because the analysis of prediction is based on mathematical models, the validity of the data.