Miracle-dz/UniFAR-FTUs huggingface dataset:
Calretinin immunohistochemistry in Hirschsprung's disease: An adjunct to formalin-based diagnosis.

AIM This study was designed to assess the utility of calretinin immunohistochemistry in the diagnosis of Hirschsprung's disease. MATERIAL AND METHODS Eleven definitive resection materials from 10 Hirschsprung's disease patients and 3 initial full-thickness rectal biopsies of these patients were retrieved from the pathology archives. Additionally, 15 distal colon and 13 proximal colon full-thickness samples from 23 non-Hirschsprung's disease patients were also evaluated as the control group. All material was reevaluated by light microscopy for the presence or absence of ganglion cells and immunostained with calretinin, including proximal surgical margins and aganglionic zone samples from each resection material. RESULTS Immunohistochemistry for calretinin provided highly compatible results with hematoxylin-eosin findings in Hirschsprung's disease and non-Hirschsprung's disease patients, except in one Hirschsprung's disease patient with very rare nerve stainings at the distal surgical margin. CONCLUSIONS Calretinin immunohistochemistry was found to be highly sensitive and specific in detecting aganglionic segments. New research should be conducted in order to clarify calretinin staining patterns of the transitional zone, rare Hirschsprung's disease types, pure hypoganglionosis patients, and the anorectal junction, and for the mapping of fetal and neonatal colonic specimens. The technique seemed very effective for lowering the need for excessive sectioning and practical regarding the erratic nature of the acetylcholinesterase staining.
The Extent of Farm Drainage in the United States

Introduction Modern production agriculture in much of the central and eastern United States would not be possible without the extensive drainage network that has been built up starting ~1870. While an unqualified success for increasing agricultural production, research over the past quarter century has illustrated the important role drainage plays in determining the quality of surface water. Much of the nitrate that enters the Mississippi river and contributes to hypoxia in the northern Gulf of Mexico comes from tile drainage of agricultural fields in the Midwest. Because of its distributed nature, extended installation history, incomplete maps of subsurface drains, and the lack of a systematic survey in recent years, the current extent of drained cropland in the US is poorly known. In this study, we investigate using the information contained in the NRCS STATSGO soils database in conjunction with the 1992 National Land Cover Dataset (NLCD) compiled by the USGS to estimate the distribution and extent of agricultural drainage across the U.S.
Prevalence of eating disorders and psychiatric comorbidity in a clinical sample of type 2 diabetes mellitus patients.

BACKGROUND A few studies have shown high rates of eating disorders and psychiatric morbidity in patients with type 2 diabetes mellitus. OBJECTIVE Disturbed eating behavior and psychiatric comorbidity in a sample of T2DM patients. METHODS Seventy type 2 diabetes mellitus patients between 40 and 65 years of age (mean, 52.9 +/- 6.8) from a diabetes outpatient clinic were sequentially evaluated. The Structured Clinical Interview for DSM-IV, Binge Eating Scale and Beck Depression Inventory were used to assess eating disorders and other psychiatric comorbidity. In addition to the descriptive analysis of the data, we compared groups divided based on the presence of obesity (evaluated by the body mass index) or an eating disorder. RESULTS Twenty percent of the sample displayed an eating disorder. Binge eating disorder was the predominant eating disorder diagnosis (10%). Overall, the group of obese patients with type 2 diabetes mellitus presented rates of psychiatric comorbidity comparable to those seen in their nonobese counterparts. However, the presence of an eating disorder was associated with a significant increase in the frequency of anxiety disorders (57.1% x 28.6%; p = 0.044). CONCLUSIONS In our study sample, the occurrence of eating disorders was increased compared to rates observed in the general population, with the predominance of binge eating disorder. The presence of an eating disorder in type 2 diabetes mellitus patients was associated with higher rates of anxiety disorders.
Effects of proton pump inhibitors and histamine-2 receptor antagonists on response to fidaxomicin or vancomycin in patients with Clostridium difficile-associated diarrhoea

Objective It has been established that use of proton pump inhibitors (PPIs) is associated with an increased risk of acquiring Clostridium difficile-associated diarrhoea (CDAD). However, it is not known whether the use of PPIs or histamine-2 receptor antagonists (H2RAs) concurrently with CDAD-targeted antibiotic treatment affects clinical response or recurrence rates. Design In two phase 3 trials, patients with toxin-positive CDAD were randomised to receive fidaxomicin 200 mg twice daily or vancomycin 125 mg four times daily for 10 days. Only inpatients with CDAD (due to complete medication record availability) were included in this post hoc analysis: 701 patients, of whom 446 (64%) used PPIs or H2RAs during study drug treatment or follow-up. Baseline factors that were statistically significant in univariate analyses were analysed in multivariate analyses of effects on clinical response and recurrence. Results Multivariate analysis showed that leukocytosis, elevated creatinine and hypoalbuminemia, but not PPI or H2RA use, were significant factors associated with poor clinical responses. Treatment group was the single significant predictor of recurrence; the probability of recurrence after fidaxomicin therapy was half that following vancomycin therapy. Conclusions Acid-suppressing drugs, used by nearly two-thirds of inpatients with CDAD, did not worsen clinical response or recurrence when used concurrently with fidaxomicin or vancomycin. Therefore, development of CDAD does not require discontinuation of anti-acid treatment in patients who have an indication for continuing PPI or H2RA therapy, such as gastro-oesophageal reflux disease and risk of gastrointestinal bleed.
Possible Association between SORL1 and Alzheimer Disease?

Shibata et al. [1] reported that the variants in neuronal sortilin-related receptor (SORL1) were not associated with Alzheimer disease (AD) in a Japanese cohort comprising 180 cases and 130 age-matched controls. The authors performed a genotypic association analysis using 7 single nucleotide polymorphisms (SNPs) that were previously reported to be statistically significant by Rogaeva et al. [2] and subsequently by others [3,4,5]. The authors reported no association with AD. However, they did observe a weak association (p = 0.05) for SNP 8 (rs668387) when restricted to APOE ∊4 noncarriers. We conducted an allelic association analysis of the same data, which shows that 2 SNPs (8 and 24) were significantly associated with AD with p values less than 0.05. Specifically, when all subjects were examined, SNP 24 (rs2282649) and SNP 8 (rs668387) were significant (p < 0.05). However, using a model restricted to elderly APOE ∊4 noncarriers, the association became somewhat stronger (SNP 8, p = 0.0163; SNP 24, p = 0.0375). More importantly, the associated variants in the study by Shibata et al. [1] were identical to those in the study by Rogaeva et al. [2]. For SNP 24, the T allele was associated with AD in Caucasians as well as in Japanese people. For SNP 8, the C allele was associated with AD in Caribbean Hispanics, Caucasians, Israeli Arabs, and Japanese people. In contrast to the original conclusions, this study does support the association between variants in SORL1 and AD in a Japanese population. Although the findings are only marginally significant given the small sample size, this study continues to support the association in both the 3′ and 5′ regions of SORL1.
The Weakest Failure Detectors to Solve Quittable Consensus and Nonblocking Atomic Commit

We define quittable consensus, a natural variation of the consensus problem, where processes have the option to agree on “quit” if failures occur, and we relate this problem to the well-known problem of nonblocking atomic commit. We then determine the weakest failure detectors for these two problems in all environments, regardless of the number of faulty processes.
Towards realistic performance evaluation of Mobile Ad Hoc Network

Mobile Ad-Hoc Network (MANET) is a self-configuring network of mobile nodes connected by wireless links to form an arbitrary topology without the use of existing infrastructure. In order to facilitate communication between a pair of nodes, routing protocols are used. The performance of routing protocols is evaluated using simulation tools such as QUALNET, NS-2 and MATLAB etc. Simulation tool provides researchers with a number of significant benefits, including repeatable scenarios, isolation of parameters, and exploration of a variety of metrics. We wish to make these simulations more realistic for ad hoc network. To do the same different shapes such as square, elliptical, circular and rectangular of the simulation region were taken. In addition to different shapes, we used the concept of obstacle. These obstacles restrict node movement as well as obstruct the communication path between nodes. Simulation results show that for same number of nodes deployed having equal areas and with different shapes the throughput will have inverse relationship with perimeter. The result can be very useful while designing a routing protocol.
Three New Escherichia coli Phages from the Human Gut Show Promising Potential for Phage Therapy

With the emergence of multi-drug resistant bacteria the use of bacteriophages (phages) is gaining renewed interest as promising anti-microbial agents. The aim of this study was to isolate and characterize phages from human fecal samples. Three new coliphages, ɸAPCEc01, ɸAPCEc02 and ɸAPCEc03, were isolated. Their phenotypic and genomic characteristics, and lytic activity against biofilm, and in combination with ciprofloxacin, were investigated. All three phages reduced the growth of E. coli strain DPC6051 at multiplicity of infection (MOI) between 10−3 and 105. A cocktail of all three phages completely inhibited the growth of E. coli. The phage cocktail also reduced biofilm formation and prevented the emergence of phage-resistant mutants which occurred with single phage. When combined with ciprofloxacin, phage alone or in cocktail inhibited the growth of E. coli and prevented the emergence of resistant mutants. These three new phages are promising biocontrol agents for E. coli infections.
Annotating Genes of Known and Unknown Function by Large-Scale Coexpression Analysis1[W][OA]

About 40% of the proteins encoded in eukaryotic genomes are proteins of unknown function (PUFs). Their functional characterization remains one of the main challenges in modern biology. In this study we identified the PUF encoding genes from Arabidopsis (Arabidopsis thaliana) using a combination of sequence similarity, domain-based, and empirical approaches. Large-scale gene expression analyses of 1,310 publicly available Affymetrix chips were performed to associate the identified PUF genes with regulatory networks and biological processes of known function. To generate quality results, the study was restricted to expression sets with replicated samples. First, genome-wide clustering and gene function enrichment analysis of clusters allowed us to associate 1,541 PUF genes with tightly coexpressed genes for proteins of known function (PKFs). Over 70% of them could be assigned to more specific biological process annotations than the ones available in the current Gene Ontology release. The most highly overrepresented functional categories in the obtained clusters were ribosome assembly, photosynthesis, and cell wall pathways. Interestingly, the majority of the PUF genes appeared to be controlled by the same regulatory networks as most PKF genes, because clusters enriched in PUF genes were extremely rare. Second, large-scale analysis of differentially expressed genes was applied to identify a comprehensive set of abiotic stress-response genes. This analysis resulted in the identification of 269 PKF and 104 PUF genes that responded to a wide variety of abiotic stresses, whereas 608 PKF and 206 PUF genes responded predominantly to specific stress treatments. The provided coexpression and differentially expressed gene data represent an important resource for guiding future functional characterization experiments of PUF and PKF genes. Finally, the public Plant Gene Expression Database (http://bioweb.ucr.edu/PED) was developed as part of this project to provide efficient access and mining tools for the vast gene expression data of this study.
Recognition Strategies of Group 3 Innate Lymphoid Cells

During the early phase of an inflammatory response, innate cells can use different strategies to sense environmental danger. These include the direct interaction of specific activating receptors with pathogen-encoded/danger molecules or the engagement of cytokine receptors by pro-inflammatory mediators produced by antigen presenting cells in the course of the infection. These general recognition strategies, which have been extensively described for innate myeloid cells, are shared by innate lymphoid cells (ILC), such as Natural Killer (NK) cells. The family of ILC has recently expanded with the discovery of group 2 (ILC2) and group 3 ILC (ILC3), which play an important role in the defense against extracellular pathogens. Although ILC3 and NK cells share some phenotypic characteristics, the recognition strategies employed by the various ILC3 subsets have been only partially characterized. In this review, we will describe and comparatively discuss how ILC3 sense environmental cues and how the triggering of different receptors may regulate their functional behavior during an immune response.
Time-Delay Identification in a Chaotic Semiconductor Laser With Optical Feedback: A Dynamical Point of View

A critical issue in optical chaos-based communications is the possibility to identify the parameters of the chaotic emitter and, hence, to break the security. In this paper, we study theoretically the identification of a chaotic emitter that consists of a semiconductor laser with an optical feedback. The identification of a critical security parameter, the external-cavity round-trip time (the time delay in the laser dynamics), is performed using both the auto-correlation function and delayed mutual information methods applied to the chaotic time-series. The influence on the time-delay identification of the experimentally tunable parameters, i.e., the feedback rate, the pumping current, and the time-delay value, is carefully studied. We show that difficult time-delay-identification scenarios strongly depend on the time-scales of the system dynamics as it undergoes a route to chaos, in particular on how close the relaxation oscillation period is from the external-cavity round-trip time.
SPECIFIC IMMUNE RESPONSE GENES OF THE GUINEA PIG

The immunogenicity of three random copolymers of amino acids with L-glutamic acid and L-alanine (GA), L-glutamic acid and L-tyrosine (GT), or L-glutamic acid, L-alanine, and L-tyrosine (GAT), administered in complete Freund's adjuvant, was studied in several inbred and random-bred guinea pig strains. The animals were tested for delayed sensitivity and their sera were assayed for the presence of antibody directed against the immunizing polymer. All of the guinea pigs developing delayed hypersensitivity also had significant antibody levels in their sera. Inbred strain 2 guinea pigs responded to immunization with GA, but failed to form detectable responses to GT. Inbred strain 13 animals, on the other hand, responded to GT, but not to GA. The (2 x 13)F1 hybrids responded to both GA and GT with both delayed hypersensitivity and circulating antibody. Thus, the ability of these inbred guinea pigs to respond immunologically to GA or GT is controlled by distinct autosomal dominant genes. A variable percentage of random-bred guinea pigs, depending on their source as well as their strain, responded to immunization with GA and with GT. All guinea pigs, both inbred and random bred, responded to immunization with GAT. The ability to respond immunologically to GAT, therefore, does not seem to be under simple genetic control. However, the levels of anti-GAT antibody found in the sera of animals lacking the ability to respond to GA were much lower than those detected in GA responder animals.
PMCA2 via PSD-95 Controls Calcium Signaling by α7-Containing Nicotinic Acetylcholine Receptors on Aspiny Interneurons

Local control of calcium concentration within neurons is critical for signaling and regulation of synaptic communication in neural circuits. How local control can be achieved in the absence of physical compartmentalization is poorly understood. Challenging examples are provided by nicotinic acetylcholine receptors that contain α7 nicotinic receptor subunits (α7-nAChRs). These receptors are highly permeable to calcium and are concentrated on aspiny dendrites of interneurons, which lack obvious physical compartments for constraining calcium diffusion. Using functional proteomics on rat brain, we show that α7-nAChRs are associated with plasma membrane calcium-ATPase pump isoform 2 (PMCA2). Analysis of α7-nAChR function in hippocampal interneurons in culture shows that PMCA2 activity limits the duration of calcium elevations produced by the receptors. Unexpectedly, PMCA2 inhibition triggers rapid calcium-dependent loss of α7-nAChR clusters. This extreme regulatory response is mediated by CaMKII, involves proteasome activity, depends on the second intracellular loop of α7-nAChR subunits, and is specific in that it does not alter two other classes of calcium-permeable ionotropic receptors on the same neurons. A critical link is provided by the scaffold protein PSD-95 (postsynaptic density-95), which is associated with α7-nAChRs and constrains their mobility as revealed by single-particle tracking on neurons. The PSD-95 link is required for PMCA2-mediated removal of α7-nAChR clusters. This three-component combination of PMCA2, PSD-95, and α7-nAChR offers a novel mechanism for tight control of calcium dynamics in neurons.
Elevated O3 and TYLCV Infection Reduce the Suitability of Tomato as a Host for the Whitefly Bemisia tabaci

The effects of elevated atmospheric ozone (O3) levels on herbivorous insects have been well studied, but little is known about the combined effects of elevated O3 and virus infection on herbivorous insect performance. Using open-top chambers in the field, we determined the effects of elevated O3 and Tomato yellow leaf curl virus (TYLCV) infection on wild-type (Wt) tomato and 35S tomato (jasmonic acid (JA) defense-enhanced genotype) in association with whitefly, Bemisia tabaci Gennadius biotype B. Elevated O3 and TYLCV infection, alone and in combination, significantly reduced the contents of soluble sugars and free amino acids, increased the contents of total phenolics and condensed tannins, and increased salicylic acid (SA) content and the expression of SA-related genes in leaves. The JA signaling pathway was upregulated by elevated O3, but downregulated by TYLCV infection and O3 + TYLCV infection. Regardless of plant genotype, elevated O3, TYLCV infection, or O3 + TYLCV infection significantly decreased B. tabaci fecundity and abundance. These results suggest that elevated O3 and TYLCV infection, alone and in combination, reduce the nutrients available for B. tabaci, increase SA content and SA-related gene expression, and increase secondary metabolites, resulting in decreases in fecundity and abundance of B. tabaci in both tomato genotypes.
Follistatin‐like 1 promotes cardiac fibroblast activation and protects the heart from rupture

Follistatin‐like 1 (Fstl1) is a secreted protein that is acutely induced in heart following myocardial infarction (MI). In this study, we investigated cell type‐specific regulation of Fstl1 and its function in a murine model of MI. Fstl1 was robustly expressed in fibroblasts and myofibroblasts in the infarcted area compared to cardiac myocytes. The conditional ablation of Fstl1 in S100a4‐expressing fibroblast lineage cells (Fstl1‐cfKO mice) led to a reduction in injury‐induced Fstl1 expression and increased mortality due to cardiac rupture during the acute phase. Cardiac rupture was associated with a diminished number of myofibroblasts and decreased expression of extracellular matrix proteins. The infarcts of Fstl1‐cfKO mice displayed weaker birefringence, indicative of thin and loosely packed collagen. Mechanistically, the migratory and proliferative capabilities of cardiac fibroblasts were attenuated by endogenous Fstl1 ablation. The activation of cardiac fibroblasts by Fstl1 was mediated by ERK1/2 but not Smad2/3 signaling. This study reveals that Fstl1 is essential for the acute repair of the infarcted myocardium and that stimulation of early fibroblast activation is a novel function of Fstl1.
Assessing soil quality issues for crop production function based on farmers’ perception: An experience from Itapaji Watershed in Southwestern Nigeria

To successfully manage soil quality for sustainable crop production, there is need to identify issues affecting it. These are problems facing the capacity of soil to perform its functions and thus reducing its productivity. In addition, the similarities and differences between farmers’ perception of soil quality issues and that of soil scientist are very pertinent. This study, which was carried out at Itapaji watershed in Ikole local government area of Ekiti state, aims at identifying soil quality issues using participatory approach and conventional method. Diagnostic survey was carried out using participatory approach involving farmers’ judgement using questionaires. The resultswere analysed to identify the soil quality issues from farmers’ perspectives. For conventional method, major soil types were identified and soil quality issues were identified using soil management assessment framework. The relationship between the soil issues from farmers’ interview and soil analysis were established by correlation analysis at α0. 05. Soil quality issues identified by farmers are soil compaction, low soil fertility, termite infestation, crop wilt, hardpan formation, erosion, poor drainage and land use intensification. Low soil fertility is the most prominent with about 36.2 % impact on crop production in the watershed. Conventionally from soil analysis, CEC and organic matter are low which indicate low soil fertility; there is high acidity, shallow soil depth with presence of plinthite and hard pan. The farmers’ perception of soil quality and that of soil scientists correlate well (r = 0.70). There is therefore need for promotion of farmers’ participation by providing a forum for articulation of their opinions in mitigating low soil quality.