Miracle-dz/UniFAR-FTUs huggingface dataset:
A randomized placebo-controlled trial of Saccharomyces boulardii in combination with standard antibiotics for Clostridium difficile disease.

OBJECTIVE--To determine the safety and efficacy of a new combination treatment for patients with Clostridium difficile-associated disease (CDD). The treatment combines the yeast Saccharomyces boulardii with an antibiotic (vancomycin hydrochloride or metronidazole). DESIGN--A double-blind, randomized, placebo-controlled, parallel-group intervention study in patients with active CDD. Patients received standard antibiotics and S boulardii or placebo for 4 weeks, and were followed up for an additional 4 weeks after therapy. Effectiveness was determined by comparing the recurrence of CDD in the two groups using multivariate analysis to control for other risk factors for CDD. SETTING--National referral study of ambulatory or hospitalized patients from three main study coordinating centers. PATIENTS--A total of 124 eligible consenting adult patients, including 64 who were enrolled with an initial episode of CDD, and 60 who had a history of at least one prior CDD episode. Patients who were immunosuppressed due to acquired immunodeficiency syndrome or cancer chemotherapy within 3 months were not eligible. INTERVENTION--Treatment with oral S boulardii (1 g/d for 4 weeks) or placebo in combination with a standard antibiotic. MAIN OUTCOME MEASURE--Recurrence of active CDD. RESULTS--A history of CDD episodes dramatically increased the likelihood of further recurrences. Multivariate analysis revealed that patients treated with S boulardii and standard antibiotics had a significantly lower relative risk (RR) of CDD recurrence (RR, 0.43; 95% confidence interval, 0.20 to 0.97) compared with placebo and standard antibiotics. The efficacy of S boulardii was significant (recurrence rate 34.6%, compared with 64.7% on placebo; P = .04) in patients with recurrent CDD, but not in patients with initial CDD (recurrence rate 19.3% compared with 24.2% on placebo; P = .86). There were no serious adverse reactions associated with S boulardii. CONCLUSIONS--The combination of standard antibiotics and S boulardii was shown to be an effective and safe therapy for these patients with recurrent CDD; no benefit of S boulardii was demonstrated for those with an initial episode of CDD.
Improving Subgraph Recognition with Variational Graph Information Bottleneck

Subgraph recognition aims at discovering a compressed substructure of a graph that is most informative to the graph property. It can be formulated by optimizing Graph Information Bottleneck (GIB) with a mutual information estimator. However, GIB suffers from training instability and degenerated results due to its intrinsic optimization process. To tackle these issues, we reformulate the subgraph recognition problem into two steps: graph perturbation and subgraph selection, leading to a novel Variational Graph Information Bottleneck (VGIB) framework. VGIB first employs the noise injection to modulate the information flow from the input graph to the perturbed graph. Then, the perturbed graph is encouraged to be informative to the graph property. VGIB further obtains the desired subgraph by filtering out the noise in the perturbed graph. With the customized noise prior for each input, the VGIB objective is endowed with a tractable variational upper bound, leading to a superior empirical performance as well as theoretical properties. Extensive experiments on graph interpretation, explainability of Graph Neural Networks, and graph classification show that VGIB finds better subgraphs than existing methods11Code is avaliable on https://github.com/Samyu0304/VGIB.
Understanding the role of promoters in catalysis: operando XAFS/DRIFTS study of CeOx/Pt/Al2O3 during CO oxidation

Abstract A combined operando XAFS/DRIFTS study on CeOx/Pt/Al2O3 catalysts has been performed during CO oxidation and provides insights into the changes in nanoparticle structure and adsorbed species during the reaction profile. The onset of CO2 formation is shown to be concurrent with a rapid re-oxidation of the Pt nanoparticles, evidenced by XAFS spectroscopy, and the loss of bridge bonded CO adsorbed on Pt, as shown by simultaneous DRIFTS acquisition. The continued appearance of linear bound CO on the catalyst surface is shown to remain long after catalytic light off. The interaction of Pt and CeOx is evidenced by the improved performance towards CO oxidation, compared to the non-CeOx modified Pt/Al2O3, and changes in the CO adsorption properties on Pt previously linked to Pt-CeO2 interfaces.
Meta-analyses of effects of phytochemicals on digestibility and rumen fermentation characteristics associated with methanogenesis.

BACKGROUND A meta-analysis study was conducted to investigate the changes in rumen fermentation characteristics when methane inhibition by phytochemicals is employed. The whole database containing 185 treatment means from 36 published studies was divided into four subsets according to the major phytochemicals used in the studies, i.e. saponins, tannins, essential oils (EO) and organosulfur compounds (OS). RESULTS Changes in protozoal numbers showed linear relationships with changes in methane production by saponins (R(2) = 0.48), tannins (R(2) = 0.30) and EO (R(2) = 0.20) but not OS. Concentrations of total volatile fatty acids (VFA) and acetate did not show any relationship (P > 0.1) with changes in methane due to saponins. However, propionate production increased linearly with increasing inhibition of methane (R(2) = 0.31), which resulted in a linear (R(2) = 0.26) decrease in acetate/propionate ratio (A/P) with decreasing methane production. Concentrations of total VFA, acetate and propionate did not change with changes in methane production by tannins. However, A/P showed a significant linear relationship (R(2) = 0.27) with decreasing methane formation. Concentrations of total VFA (R(2) = 0.44) and propionate (R(2) = 0.15) changed linearly and positively with changes in methane production by EO. However, acetate production (R(2) = 0.22) and A/P (R(2) = 0.17) increased linearly with increasing inhibition of methane by EO. Changes in concentrations of total VFA (R(2) = 0.60) and acetate (R(2) = 0.35) decreased linearly while those of propionate increased linearly (R(2) = 0.23) with increasing inhibition of methane by OS. Consequently, A/P decreased linearly (R(2) = 0.30) with decreasing methane production by OS. Digestibilities of organic matter (OM) and neutral detergent fibre were not affected by inhibition of methane production by saponins, EO and OS, but digestibility of OM decreased with decreasing methane production by tannins. CONCLUSION The inhibition of methane production by phytochemicals results in changes in rumen fermentation that differ depending on the types of phytochemicals.
The Relative Trustworthiness of Inferential Tests of the Indirect Effect in Statistical Mediation Analysis

A content analysis of 2 years of Psychological Science articles reveals inconsistencies in how researchers make inferences about indirect effects when conducting a statistical mediation analysis. In this study, we examined the frequency with which popularly used tests disagree, whether the method an investigator uses makes a difference in the conclusion he or she will reach, and whether there is a most trustworthy test that can be recommended to balance practical and performance considerations. We found that tests agree much more frequently than they disagree, but disagreements are more common when an indirect effect exists than when it does not. We recommend the bias-corrected bootstrap confidence interval as the most trustworthy test if power is of utmost concern, although it can be slightly liberal in some circumstances. Investigators concerned about Type I errors should choose the Monte Carlo confidence interval or the distribution-of-the-product approach, which rarely disagree. The percentile bootstrap confidence interval is a good compromise test.
Clinical trials and drug promotion: Selective reporting of study 329

Selective reporting is prevalent in the medical literature, particularly in industry-sponsored research. In this paper, we expose selective reporting that is not evident without access to internal company documents. The published report of study 329 of paroxetine in adolescents sponsored by GlaxoSmithKline claims that "paroxetine is generally well tolerated and effective for major depression in adolescents". By contrast, documents obtained during litigation reveal that study 329 was negative for efficacy on all 8 protocol specified outcomes and positive for harm.
Clinicopathological Features of Patients with Concomitant Intraductal Papillary Mucinous Neoplasm of the Pancreas and Pancreatic Endocrine Neoplasm

Background/Aims: The occurrence of concomitant pancreatic endocrine neoplasm (PEN) and intraductal papillary neoplasm (IPMN) of the pancreas has rarely been reported. We describe our experience with 3 patients with this association and review the existing literature. Methods: From 1990 to 2005, 65 patients who underwent surgery for a PEN or IPMN were retrospectively reviewed. Forty-three patients had a PEN, 19 had an IPMN and 3 had both an IPMN and PEN. The 3 patients with concomitant IPMN and PEN are the focus of the current study and their clinicopathological features are reported together with 7 patients previously reported in the literature. Results: There were 10 patients with a median age of 62 years (range 40–73). The male:female ratio was equal. Seven of 10 patients were symptomatic and the most common symptoms were abdominal pain (n = 5), jaundice (n = 2) and loss of weight (n = 2). The median size of the endocrine neoplasms was 14 mm (range 2–30) and they occurred in the head (n = 3), body (n = 2) and tail (n = 5). Seven of the PENs were classified as benign, 2 were potentially malignant, and 1 was frankly malignant with lymph node involvement. None of the endocrine neoplasms were functioning. The IPMNs were found in the tail (n = 4), head (n = 3), head and body (n = 1), body (n = 1) and the entire pancreas (n = 1). Five of these neoplasms were benign, 2 were borderline and 3 were malignant (1 carcinoma in situ). Conclusion: The occurrence of concomitant IPMN and PEN is more frequent than would be expected. However, it is difficult in the present analysis to determine if this association is more than just fortuitous.
[Relation of IL-17 polymorphisms and serum levels in patients with chronic HCV infection].

OBJECTIVE To investigate the association of single nucleotide polymorphisms (SNPs) in the interleukin 17 (IL-17) gene and serum protein levels in patients with chronic hepatitis C virus (HCV) infection. METHODS A total of 228 patients with chronic HCV infection and 81 healthy controls were enrolled in the study. The frequencies of IL-17 rs8193036 and rs2275913 polymorphisms were detected by the TaqMan SNP genotyping assay. Serum levels of IL-17 protein were detected by ELISA. Pairwise comparisons were made by the Chi-square test, and the significance of between-group differences was assessed by the Student's t-test with P less than 0.05. RESULTS The patients with chronic HCV infection and the healthy controls showed similar frequencies of the rs8193036 C/T allele (x2 = 1.428, P = 0.232) and the rs2275913 A/G allele (x2 = 0.106, P = 0.744). In addition, the two groups showed similar distribution of the rs8193036 CC (chronic HCV infection: 46.49% vs. healthy controls: 41.98%), CT (45.61% vs. 44.44%) and TT (7.89% vs. 13.58%) genotypes (x2 = 2.346, P = 0.309), and of the rs2275913 AA (16.23% vs. 13.58%), AG (48.25% vs. 50.62%) and GG (35.53% vs. 35.80%) genotypes (x2 = 0.340, P = 0.844). Subgroup analysis of chronic HCV infection patients stratified according to HCV genotypes 1 and 2 showed no differences in the distribution of rs8193036 and rs2275913 alleles (x2 = 1.127, P = 0.288; x2 = 1.088, P = 0.297) and genotypes (x2 = 2.825, P = 0.246; x2 = 0.970, P = 0.616). However, the chronic HCV infection group did show significantly higher levels of serum IL-17 than the controls (97.67+/-39.68 vs. 71.60+/-19.78 pg/ml, t = 2.414, P = 0.033). CONCLUSION Chronic HCV infection is associated with increased serum IL-17; however, the IL-17 polymorphisms rs8193036 and rs2275913 were not associated with chronic HCV infection susceptibility in this study's Chinese cohort.
Asynchronous Distributed Algorithms for Solving Linear Algebraic Equations

Two asynchronous distributed algorithms are presented for solving a linear equation of the form <inline-formula> <tex-math notation="LaTeX">$Ax=b$</tex-math></inline-formula> with at least one solution. The equation is simultaneously and asynchronously solved by <inline-formula><tex-math notation="LaTeX">$m$</tex-math></inline-formula> agents assuming that each agent knows only a subset of the rows of the partitioned matrix <inline-formula> <tex-math notation="LaTeX">$[A\ \ b]$</tex-math></inline-formula>, the estimates of the equation's solution generated by its neighbors, and nothing more. Neighbor relationships are characterized by a time-dependent directed graph whose vertices correspond to agents and whose arcs depict neighbor relationships. Each agent recursively updates its estimate of a solution at its own event times by utilizing estimates generated by its neighbors which are transmitted with delays. The event time sequences of different agents are not assumed to be synchronized. It is shown that for any matrix-vector pair <inline-formula><tex-math notation="LaTeX">$(A, b)$</tex-math></inline-formula> for which the equation has a solution and any repeatedly jointly strongly connected sequence of neighbor graphs defined on the merged sequence of all agents’ event times, the algorithms cause all agents’ estimates to converge exponentially fast to the same solution to <inline-formula><tex-math notation="LaTeX">$Ax=b$</tex-math> </inline-formula>. The first algorithm requires a specific initialization step at each agent, and the second algorithm works for arbitrary initializations. Explicit expressions for convergence rates are provided, and a relation between local initializations and limiting consensus solutions is established, which is used to solve the least 2-norm solution.
OF THE EXPERIMENTAL ANALYSIS OF BEHAVIOR STIMULUS CONTROL IN FIXED RATIO MA TCHING-TO-SAMPLE 1

Pigeons were maintained on a fixed ratio (FR 9) schedule of reinforcement for correct matchingto-sample responses. Included in the test situation was a vertical array of lights, illuminated in relation to the successive steps of the fixed ratio. All five subjects showed regular decrements in matching errors across the sequence of unreinforced responses within the ratio cycle. In the form of a randomly introduced probe, the stimulus situation (array of lights) appropriate to having seven of the FR 9 steps already completed was occasionally introduced at the beginning of an FR cycle. Reinforcement followed the illumination of the two remaining lights by two correct matches. The number of errors in this probe condition was sharply lower than the errors characteristic of the first two steps of the basic FR 9.
Modelling the role of task in the control of gaze

Gaze changes and the resultant fixations that orchestrate the sequential acquisition of information from the visual environment are the central feature of primate vision. How are we to understand their function? For the most part, theories of fixation targets have been image based: The hypothesis being that the eye is drawn to places in the scene that contain discontinuities in image features such as motion, colour, and texture. But are these features the cause of the fixations, or merely the result of fixations that have been planned to serve some visual function? This paper examines the issue and reviews evidence from various image-based and task-based sources. Our conclusion is that the evidence is overwhelmingly in favour of fixation control being essentially task based.
Pobreza y Desastres Naturales en Colombia, 1970-2011: Una Aproximación desde los Municipios y los Hogares

Este documento, analiza el impacto de los desastres sobre las dimensiones del Indice de Pobreza Multidimensional (IPM) a nivel municipal y del hogar en Colombia, con el objetivo de determinar la correlacion y la posible relacion causal entre estas variables. Tomando datos municipales de corte transversal del IPM, sus 15 variables de privacion para el 2005, y un agregado de desastres ocurridos por municipio desde 1976 hasta 2005, se encuentran que los desastres naturales tienen un impacto significativo sobre la pobreza en Colombia. Adicionalmente, usando datos de las encuestas de calidad de vida (ECV) realizadas para los anos 1997, 2003, 2008 y 2010 se replica el ejercicio utilizando los hogares como unidad de analisis. Particularmente el estudio da luces sobre la necesidad de tomar acciones especificas para minimizar el numero de muertes, reducir la vulnerabilidad en sectores de educacion y sobre la ninez y la juventud y atender de manera expedita los efectos negativos sobre las condiciones de los hogares mas afectados por estos eventos.
Biohydrogenation of dietary n-3 PUFA and stability of ingested vitamin E in the rumen, and their effects on microbial activity in sheep

The present study investigated the susceptibility of dietary n-3 PUFA to ruminal biohydrogenation, the stability of ingested vitamin E in the rumen and the subsequent uptake of PUFA and vitamin E into plasma. Six cannulated sheep were assigned to six diets over five 33d periods, in an incomplete 6×5 Latin square. The diets, based on dried grass, were formulated to supply 50g fatty acids/kg DM using three lipid sources: Megalac® (calcium soap of palm fatty acid distillate; Volac Ltd, Royston, Herts., UK), linseed (formaldehyde-treated; Trouw Nutrition, Northwich, Ches., UK) and linseed–fish oil (formaldehyde-treated linseed+fish oil). The diets were supplemented with 100 or 500mg α-tocopheryl acetate/kg DM. Fat source or level of vitamin E in the diet did not alter microbial activity in the rumen. Biohydrogenation of linoleic acid (18:3n-6; 85–90%), linolenic acid (18:3n-3; 88–93%), docosahexaenoic acid (22:6n-3; 91%) and EPA (20:5n-3; 92%) was extensive. Feeding formaldehyde-treated linseed elevated concentrations of 18:3n-3 in plasma, whilst 22:6n-3 and 20:5n-3 were only increased by feeding the linseed–fish oil blend. Duodenal recovery of ingested vitamin E was high (range 0·79–0·92mg/mg fed). High dietary vitamin E was associated with increased plasma α-tocopherol (2·57 v. 1·46μg/ml for 500 and 100mg α-tocopheryl acetate/kg DM respectively), although all concentrations were low. Plasma vitamin E levels, however, tended to decrease as the type and quantity of PUFA in the diet increased. The present study illustrates that nutritionally beneficial PUFA in both fish and linseed oils are highly susceptible to biohydrogenation in the rumen. Although α-tocopheryl acetate resisted degradation in the rumen, plasma vitamin E status remained deficient to borderline, suggesting either that uptake may have been impaired or metabolism post-absorption increased.
Characterization of c‐Kit and nestin expression during islet cell development in the prenatal and postnatal rat pancreas

It has been well documented that there are abundant endocrine progenitor cells in the neonatal pancreas. However, little is known of their relative proportions or even their phenotypes. The aim of this study was to examine the normal distribution and characteristics of putative endocrine precursor cells, identified by c‐Kit or nestin expression, within the prenatal and postnatal rat pancreas during islet cell development. Here, we provide evidence of the existence of a subset of ductal, islet, and acinar cells with an immature morphology and high proliferative capacity that expressed c‐Kit or nestin. The proportion of islet cells expressing c‐Kit or nestin was highest at embryonic day 18 (25 ± 4% and 28 ± 6%) and decreased significantly by postnatal day 28 (P < 0.01), 1.3 ± 0.2% and 5.7 ± 1%, respectively. The expression of nestin mRNA decreased throughout development, while c‐Kit mRNA expression was found to slightly increase in the developing pancreas. Coexpression patterns indicated that c‐Kit and nestin form two distinct cell populations in the postnatal pancreas, and infrequently coexpress with other pancreatic cell‐specific markers. Furthermore, decreased c‐Kit and nestin expression in the islets in postnatal life correlated with an increase in cells immunopositive for Pdx‐1 compared with birth (36 ± 5% vs. 60 ± 3%, P < 0.01), which accompanied a doubling in the proportion of Glut‐2–positive cells (39.4 ± 4% vs. 68.8 ± 3%, P < 0.01), both of which are mature β‐cell markers. Taken together, these findings suggest that c‐Kit‐ and nestin‐expressing cells represent endocrine precursor cells that undergo marked changes in population dynamics during the transition from prenatal to postnatal pancreatic development in the rat. Characterization of the phenotype, relative abundance and location of these cells within the developing pancreas is an important step toward creating a strategy for isolating stem cell populations and modeling islet cell differentiation in vitro. Developmental Dynamics 229:813–825, 2004. © 2004 Wiley‐Liss, Inc.
Hibernating Mammals Pass the Acid Test: Multiple Independent Evolutions of Enhanced Proton Block of Sodium Channels in Acid-Sensing Pain Receptors

ate and protons (H + ). Naked mole rats have evolved excellent pH regulation to counter this problem [Park, pers. commun. ], but exposure to such high levels of carbonic acid on the moist skin, untouched by internal buffering, would potentially burn the eyes and respiratory membranes of animals by activating the free nerve endings of small-diameter trigeminal nerve fibers (this is why carbonated soda pop stings the eyes and tickles the throat). Acid activates a variety of channels (ASIC, TRPV) [Holzer, 2011] that depolarize the trigeminal terminals. Depolarization of the terminals then recruits two voltage-gated sodium channels (Na v 1.7 and Na v 1.8) to trigger action potentials sending a message of ‘pain’ to the CNS. However, as an adaptation to this high CO 2 environment, naked mole rats show no behavioral avoidance of or nociceptor activation by acid [Park et al., 2008; LaVinka and Park, 2012]. Smith et al. [2011] elegantly elucidated a molecular mechanism for this protection. Surprisingly, the acid-sensing channels, the most obvious location for adaptive molecular change, did not differ between naked mole rats and mice. However, the sodium channel Na v 1.7 showed an enhanced Stephen Jay Gould famously described a Gedankenexperiment of rewinding and replaying the ‘tape of life’ to see whether life would inexorably evolve as we know it, or whether chance, instead, would result in a drastically different world. And as biologists have pointed out, examining instances of independent (parallel or convergent) trait evolution is as close as it gets to attaining this goal. We can point to a plethora of traits that have evolved independently: wings, a hydrodynamic body shape in rapid swimmers, spines and wax in desert plants, thumbs in pandas and primates, etc. But in the molecular age, we must push one layer deeper: do identical or similar changes at the molecular level underlie independently derived similarities at the organismal level [Zakon, 2002]? A recent paper on evolutionary change in voltage-gated sodium channels in pain receptors gives a resounding ‘Yes! ’ Naked mole rats (Heterocephalus glaber) live jam-packed in large subterranean colonies. One consequence of this is that they breathe stale air high in CO 2 ; this potentially results in acidosis in body tissues as the CO 2 mixes with water, forming carbonic acid, which dissociates into carbonPublished online: June 18, 2014