Miracle-dz/UniFAR-FTUs huggingface dataset:
Determination of enterotoxigenic gene profiles of Bacillus cereus strains isolated from dairy desserts by multiplex PCR.

The aim of this study was to investigate the presence of Bacillus cereus and to detect enterotoxigenic genes in dairy dessert samples utilising a multiplex PCR technique. A total of 100 samples, 25 keskul, 12 tavuk gogsu, 12 kazandibi, 30 supangle, 4 profiteroles and 17 sutlac were analysed. B. cereus contamination was found in 7 of 100 (7.0%) samples including 3 (25%) tavuk gogsu, 2 (6.6%) supangle, 1 (4%) keskul and 1 (5.8%) sutlac. The average number of B. cereus was between 2.0×101 5.0×102 cfu/g in these dairy dessert samples. A total of 20 isolates were collected from the 7 positive samples. The results indicated that 30% (6/20) of B. cereus isolates contain three enterotoxic HBL complex encoding genes hblA, hblC and hblD, whereas 70% (14/20) had no hbl genes. In addition, all three enterotoxic NHE complex encoding genes, nheA, nheB and nheC, were detected in 40% (8/20), two nhe genes (nheA and nheB) were found in 45% (9/20) and one nhe gene (two nheA and one nheB) was found in 15% (3/20) of the isolates. The ctyK1 gene was not detected in any sample. The presence of B. cereus and their enterotoxigenic genes in dairy desserts may be a potential risk for public health.
Selenium attenuates diclofenac‐induced testicular and epididymal toxicity in rats

The adverse effect of diclofenac administration on the male reproductive organ in both humans and rats has been reported. Selenium, a trace element vital in nutrition, plays a significant part in cellular redox homeostasis, including male reproduction. However, the impact of selenium on male reproductive toxicity associated with diclofenac administration is lacking in the literature. The current investigation assessed the modulatory effects of selenium on diclofenac‐mediated reproductive toxicity in rats. Rats were treated for fourteen consecutive days, either with diclofenac (10 mg/kg) or co‐treated with selenium (0.125 and 0.25 mg/kg) body weight. Sperm parameters, enzymes of testicular function, luteinizing, follicle‐stimulating hormone and testosterone were assessed in addition to oxidative stress indices and histopathological changes. Selenium significantly alleviated diclofenac‐induced decreases in sperm count and motility, testicular function enzymes and levels of luteinizing hormone and testosterone in serum. Moreover, selenium co‐administration at 0.125 and 0.25 mg/kg inhibited the diclofenac‐induced decrease of antioxidant enzyme activities and increased oxidative stress parameters—lipid peroxidation, reactive nitrogen and oxygen species—in epididymis and testes of rats. Selenium (0.25 mg/kg) alone ameliorated diclofenac‐mediated histological injuries in exposed rats. Collectively, selenium enhanced testicular and epididymal function in diclofenac‐treated rats by suppressing nitrosative and oxidative stress in rats.
Influence of pit-trap type on the interpretation of fauna diversity

We compare bias in the interpretation of sampled reptile and mammal assemblages caught using 20-L PVC buckets and PVC pipes (150 mm by 600 mm deep) when used as pit-traps. We report on 16 632 pipe- and 16 632 bucket-nights of pit-trap data collected over 11 survey periods spread over 2.5 years around Ora Banda in Western Australia. Buckets caught more reptiles and more of the common ‘small’ and ‘medium’-sized reptiles, whereas pipes caught more mammals and the larger of the small trappable mammals. The trappability of some families of reptiles and some mammal species differs between buckets and pipes. We conclude that different pit-trap types provide a bias in the interpretation of the sampled fauna assemblage. Differences in the interpretation of vertebrate faunal diversity were accentuated by low trapping effort but attenuated by high trapping effort. We recommend that both buckets and pipes be employed as pit-traps during fauna surveys (as well as alternatives such as funnel traps) to more fully document fauna assemblages being surveyed.
Fibroblast-specific Expression of a Kinase-deficient Type II Transforming Growth Factor β (TGFβ) Receptor Leads to Paradoxical Activation of TGFβ Signaling Pathways with Fibrosis in Transgenic Mice*

To better understand the role of disrupted transforming growth factor β (TGFβ) signaling in fibrosis, we have selectively expressed a kinase-deficient human type II TGFβ receptor (TβRIIΔk) in fibroblasts of transgenic mice, using a lineage-specific expression cassette subcloned from the pro-α2(I) collagen gene. Surprisingly, despite previous studies that characterized TβRIIΔk as a dominant negative inhibitor of TGFβ signaling, adult mice expressing this construct demonstrated TGFβ overactivity and developed dermal and pulmonary fibrosis. Compared with wild type cells, transgenic fibroblasts proliferated more rapidly, produced more extracellular matrix, and showed increased expression of key markers of TGFβ activation, including plasminogen activator inhibitor-1, connective tissue growth factor, Smad3, Smad4, and Smad7. Smad2/3 phosphorylation was increased in transgenic fibroblasts. Overall, the gene expression profile of explanted transgenic fibroblasts using cDNA microarrays was very similar to that of littermate wild type cells treated with recombinant TGFβ1. Despite basal up-regulation of TGFβ signaling pathways, transgenic fibroblasts were relatively refractory to further stimulation with TGFβ1. Thus, responsiveness of endogenous genes to TGFβ was reduced, and TGFβ-regulated promoter-reporter constructs transiently transfected into transgenic fibroblasts showed little activation by recombinant TGFβ1. Responsiveness was partially restored by overexpression of wild type type II TGFβ receptors. Activation of MAPK pathways by recombinant TGFβ1 appeared to be less perturbed than Smad-dependent signaling. Our results show that expression of TβRIIΔk selectively in fibroblasts leads to paradoxical ligand-dependent activation of downstream signaling pathways and causes skin and lung fibrosis. As well as confirming the potential for nonsignaling receptors to regulate TGFβ activity, these findings support a direct role for perturbed TGFβ signaling in fibrosis and provide a novel genetically determined animal model of fibrotic disease.
Increasing collaborative research output between early-career health researchers in Africa: lessons from the CARTA fellowship program

ABSTRACT In 2008 nine African Universities and four African research institutions, in partnership with non-African institutions started the Consortium for Advanced Research Training in Africa (CARTA) to strengthen doctoral training and research capacity on health in Africa. This study describes particular aspects of the CARTA program that promotes collaboration between the PhD fellows in the program, and determines the patterns of collaborative publications that resulted from the intervention. We reviewed program monitoring and evaluation documents and conducted a bibliometric analysis of 806 peer-reviewed publications by CARTA fellows published between 2011 and 2018. Results indicate that recruiting multidisciplinary fellows from various institutions, encouraging registration of doctoral-level fellows outside home institutions, and organizing joint research seminars stimulated collaborative research on health-related topics. Fellows collaborated among themselves and with non-CARTA researchers. Fellows co-authored 75 papers (10%) between themselves, of which 53 (71%) and 42 (56%) included fellows of different cohorts and different disciplines respectively, and 19 (25%) involved fellows of different institutions. CARTA graduates continued to publish with each other after graduating – 11% of the collaborative publications occurred post-graduation – indicating that the collaborative approach was maintained after exiting from the program. However, not all fellows contributed to publishing collaborative papers. The study recommends concerted effort towards enhancing collaborative publications among the CARTA fellows, both doctoral and post-doctoral, which can include holding research exchange forums and collaborative grant-writing workshops.
Incidence and distribution of Apple chlorotic leaf spot virus in the main fruit growing areas of Iran

A survey for the presence of Apple chlorotic leaf spot virus (ACLSV) in apple (Malus pumila), pear (Pyrus communis) and quince (Cydonia oblonga) was conducted in the provinces of Tehran, Isfahan, Khorasan, East and West Azerbaijan, the main pome fruit growing areas in Iran. Samples were taken from 1078 apple, 92 pear and 23 quince trees and tested by double antibody sandwich-ELISA for the presence of ACLSV using commercial kits (Bioreba, Switzerland). ACLSV was detected in 200 apple samples (18.55%) but in none of the other samples. Some of the positive samples came from trees bearing small and malformed leaves with necrotic lesions, whereas others were from symptomless plants. The highest incidence of ACLSV was in the province of Isfahan (30.9%), followed by West Azerbaijan (17.78%), Tehran (14.1%) and East Azerbaijan (11.68%). To confirm virus identification, total RNA was extracted from leaf samples and subjected to reverse transcription polymerase chain reaction using primers specific for a region of the ACLSV genome that encodes part of the coat protein (CP). A 358 bp DNA fragment corresponding to a fragment of the ACLSV CP gene was amplified from extracts of infected trees but not from those of healthy trees.
Production and Fate of Bacteria in the Oceans

Recent research suggests that aerobic, heterotrophic bacteria in the marine euphotic zone are not merely decomposers of detritus. The bacterial biomass in the coastal and open oceans is large and productive, suggesting that bacteria are important as producers of organic matter. It appears likely that the bacterial production is removed quantitatively by small predators. (Accepted for publication 16 March 1983)
Measuring management practices in primary health care facilities – development and validation of management practices scorecard in Nigeria

ABSTRACT Background In low- and middle-income countries, there is scarcity of validated and reliable measurement tools for health facility management, and many interventions to improve primary health care (PHC) facilities are designed without adequate evidence base on what management practices are critical. Objective This article developed and validated a scorecard to measure management practices at primary health care facilities under the performance-based financing (PBF) scheme in Nigeria. Methods Relevant management practice domains and indicators for PHC facilities were determined based on literature review and a prior qualitative study conducted in Nigeria. The domains and indicators were tested for face validity via experts review and organized into an interviewer-administered scorecard. A stratified random sampling of PHC facilities in three States in Nigeria was conducted to assess the reliability and construct validity of the scorecard. Inter-rater reliability using inter-class correlation (ICC) (1, k) was assessed with one-way ANOVA. Exploratory factor analysis (EFA) was conducted to assess the construct validity, and an updated factor structure were developed. Results 32 indicators and 6 management practice domains were initially described. Ordinal responses were derived for each indicator. Data on the scorecard were obtained from 111 PHC facilities. The ICC of mean ratings for each team of judges was 0.94. The EFA identified 6 domains (Stakeholder engagement and communication; Community-level activities; Update of plan and target; Performance management; Staff attention to planning, target, and performance; and Drugs and financial management) and reduced the number of indicators to 17. The average communality of selected items was 0.45, and item per factor ratio was 17:6. Conclusions Despite a few areas for further refinement, this paper presents a reliable and valid scorecard for measuring management practices in PHC facilities. The scorecard can be applied for routine supervisory visits to PHC facilities, and can help accumulate knowledge on facility management, how it affects performance, and how it may be strengthened.
Efecto del ácido salicílico y la nutrición mineral sobre la calidad de plántulas de chile habanero

Effect of the salicylic acid and nutrition on quality of habanero pepper seedlings. The objective of this study was to evaluate the effect of salicylic acid and N P K fertilization on the growth and mineral status of habanero pepper seedlings (Capsicum chinense Jacq.). The study was developed in Yucatan, Mexico in November 2008 and December 2009. Seedlings were exposed to four treatments: T1) without salicylic acid and fertilization; T2) application of 10 -8 M salicylic acid; T3) application of 190 mg/l de NPK and T4) application of 10 -8 M of salicylic acid + 190 mg/l of NPK. The quality of seedlings was evaluated by measuring growth characteristic of shoot and root. The content of N, P, K, Ca, Mg, Cu, Fe, Zn and Mn was analyzed in whole seedlings. The slenderness and the index of quality of Dickson were also considered. The results showed significant differences (P≤0.05) on shoot growth. Applications of fertilizer caused increase on shoot dry weight. Plant height, number of leaves, stem diameter, and foliar area were not significantly different between T3 and T4. Significant differences were observed on root dry weight, specific root length, root weight density and root length density. All variables except specific root length were significantly higher with the fertilizer treatment. The latest had the highest value in the treatment T4. Significant differences (P≤0.05) were observed in tissue mineral content. Seedlings treated with T3 showed the highest content of N, P, Ca, Mg and Mn. The content of K, Zn and Fe was not significantly different between T3 and T4. In conclusion, the application of salicylic acid favored seedling growth but it did not improve significantly the quality of habanero pepper seedlings.
Neuroendocrine subtypes of small cell lung cancer differ in terms of immune microenvironment and checkpoint molecule distribution

Small cell lung cancer (SCLC) has recently been subcategorized into neuroendocrine (NE)‐high and NE‐low subtypes showing ‘immune desert’ and ‘immune oasis’ phenotypes, respectively. Here, we aimed to characterize the tumor microenvironment according to immune checkpoints and NE subtypes in human SCLC tissue samples at the protein level. In this cross‐sectional study, we included 32 primary tumors and matched lymph node (LN) metastases of resected early‐stage, histologically confirmed SCLC patients, which were previously clustered into NE subtypes using NE‐associated key RNA genes. Immunohistochemistry (IHC) was performed on formalin‐fixed paraffin‐embedded TMAs with antibodies against CD45, CD3, CD8, MHCII, TIM3, immune checkpoint poliovirus receptor (PVR), and indoleamine 2,3‐dioxygenase (IDO). The stroma was significantly more infiltrated by immune cells both in primary tumors and in LN metastases compared to tumor nests. Immune cell (CD45+ cell) density was significantly higher in tumor nests (P = 0.019), with increased CD8+ effector T‐cell infiltration (P = 0.003) in NE‐low vs NE‐high tumors. The expression of IDO was confirmed on stromal and endothelial cells and was positively correlated with higher immune cell density both in primary tumors and in LN metastases, regardless of the NE pattern. Expression of IDO and PVR in tumor nests was significantly higher in NE‐low primary tumors (vs NE‐high, P < 0.05). We also found significantly higher MHC II expression by malignant cells in NE‐low (vs NE‐high, P = 0.004) tumors. TIM3 expression was significantly increased in NE‐low (vs NE‐high, P < 0.05) tumors and in LN metastases (vs primary tumors, P < 0.05). To our knowledge, this is the first human study that demonstrates in situ that NE‐low SCLCs are associated with increased immune cell infiltration compared to NE‐high tumors. PVR, IDO, MHCII, and TIM3 are emerging checkpoints in SCLC, with increased expression in the NE‐low subtype, providing key insight for further prospective studies on potential biomarkers and targets for SCLC immunotherapies.
Crude enzymes supplementation in fibrous diet improves performance of commercial broilers

A total of 280, 1-day-old mixed sex broiler chicks were randomly allotted to seven dietary treatment groups. Basal diet was formulated with high fibrous contents (6.72%). Increasing levels of cell-free fermentation broth containing cellulases were mixed in basal diet of groups B, C, D and E (equivalent to 1.2×104 IU, 2.4×104 IU, 3.6×104 IU and 4.8×104 IU cellulases/kg, respectively). Where as in diet of group F, fermentation broth containing 3×104 IU protease and 1.2×104 IU cellulases were added per kilogram. In diet of group G fermentation broth containing 3×104 IU protease and 2.4×104 IU cellulases were added per kilogram. Significant improvement (P<0.05) in weight gain and feed conversion ratio (FCR) was observed in all treatment groups. Combination of protease and cellulases in diet was proved better in first 4 weeks. However, effects of cellulases were equally good (but at higher dose) in last 2 weeks compared to the groups supplemented with mixture of cellulases and protease. Increasing doses of enzymes reduced the viscosity of ingesta and also in vitro-simulated digested feed. Vent pasting seen at its maximum in control group was also reduced to zero with decreasing severity under the effect of increasing enzyme levels. Combined use of indigenously produced cellulases and protease was successful to tackle problems of high fibrous broiler diet.
An investigation of the ecology of the map turtle, Graptemys geographica (Le Sueur), in the northern part of its range

Data obtained during the course of a 3-year study on a population of map turtles, Graptemys geographica, in Lac des Deux Montagnes, Quebec, Canada, suggest that the population size is approximately 351 turtles, that the sex composition is biased in favour of males, and that juveniles compose at least 8% of the total population. Map turtles emerge soon after ice breakup. During the prenesting period, males exhibit less movement over shorter distances than do females. In mid-May, female turtles start to move into the two bays used for nesting. The nesting season is about 2 weeks in duration, commencing in mid-June. The mean size of three clutches was 12. After nesting there appears to be a marked dispersal of both male and female turtles, with females moving more frequently and greater distances than males. By September the turtles have returned to the bays in the study area and remain until freeze-up. Bay utilization by the turtles is discussed in terms of food resources and human recreational use.
Effect of Stocked Fish on Rice Leaffolder Cnaphalocrocis medinalis and Rice Caseworm Nymphula depunctalis Populations in Intensive Rice Culture

It is often claimed that fish stocked in rice fields have a significant impact on the rice pest population. However, there is little experimental evidence for this. We used the data of six experiments to find out whether a polyculture of silver barb Barbodes gonionotus (Bleeker), common carp Cyprinus carpio (L.) and Nile tilapia Oreochromis niloticus (L.) has any effect on the population of rice leaffolders Cnaphalocrocis medinalis (Guenée) and rice caseworms Nymphula depunctalis (Guenée), two common pests in intensively cultured rice fields. Fish had no effect on the rice leaffolder population, but significantly lowered the number of rice caseworm adults and larvae. We concluded that fish have some effect on the arthropod pest population in rice fields, although, most probably, only on sluggish pests living in the water or on the water surface.
Eutrophication as a driver of microbial community structure in lake sediments.

Lake sediments are globally important carbon sinks. Although the fate of organic carbon (OC) in lake sediments depends significantly on microorganisms, only few studies have investigated controls on lake sedimentary microbial communities. Here we investigate the impact of anthropogenic eutrophication, which affects redox chemistry and organic matter (OM) sources in sediments, on microbial communities across five lakes in central Switzerland. Lipid biomarkers and distributions of microbial respiration reactions indicate strong increases in aquatic OM contributions and microbial activity with increasing trophic state. Across all lakes, 16S rRNA genes analyses indicate similar depth-dependent zonations at the phylum- and class-level that follow vertical distributions of OM sources and respiration reactions. Yet, there are notable differences, such as higher abundances of nitrifying Bacteria and Archaea in oligotrophic lake. Furthermore, analyses at order-level and below suggest changes in OM sources due to eutrophication cause permanent changes in bacterial community structure. By contrast, archaeal communities are differentiated according to trophic state in recently deposited layers, but converge in older sediments deposited under different trophic regimes. Our study indicates an important role for trophic state in driving lacustrine sediment microbial communities and reveals fundamental differences in the temporal responses of sediment Bacteria and Archaea to eutrophication. This article is protected by copyright. All rights reserved.
Experimental metatranscriptomics reveals the costs and benefits of dissolved organic matter photo-alteration for freshwater microbes.

Microbes and sunlight convert terrigenous dissolved organic matter (DOM) in surface waters to greenhouse gases. Prior studies show contrasting results about how biological and photochemical processes interact to contribute to the degradation of DOM. In this study, DOM leached from the organic layer of tundra soil was exposed to natural sunlight or kept in the dark, incubated in the dark with the natural microbial community, and analyzed for gene expression and DOM chemical composition. Microbial gene expression (metatranscriptomics) in light and dark treatments diverged substantially after 4 h. Gene expression suggested that sunlight exposure of DOM initially stimulated microbial growth by (a) replacing the function of enzymes that degrade higher molecular weight DOM such as enzymes for aromatic carbon degradation, oxygenation, and decarboxylation, and (b) releasing low molecular weight compounds and inorganic nutrients from DOM. However, growth stimulation following sunlight exposure of DOM came at a cost. Sunlight depleted the pool of aromatic compounds that supported microbial growth in the dark treatment, ultimately causing slower growth in the light treatment over 5 days. These first measurements of microbial metatranscriptomic responses to photo-alteration of DOM provide a mechanistic explanation for how sunlight exposure of terrigenous DOM alters microbial processing and respiration of DOM. This article is protected by copyright. All rights reserved.
Evolution and Migraine

Evolution and migraine are discussed in the outstanding article “Did Going North Give Us Migraine”. The accompanying editorial, “Toward a Philosophy of Migraine” is remarkably thought provoking. Analyzing evolutionary processes with regards to disease is more than an academic exercise. Taking evolution into account is vital for a complete understanding of the disease. Interpreting the evolutionary underpinnings of an illness may help us in developing safe and effective treatments.