Miracle-dz/UniFAR-FTUs huggingface dataset:
Short communication: Diversity of staphylococci isolated from sheep mastitis in northern Algeria.

Mastitis in ruminants is an important disease with major effects on both the economy and animal welfare. It is caused by major pathogens such as Staphylococcus aureus and minor pathogens such as coagulase-negative staphylococci. The objective of this study was to identify and characterize staphylococci as a cause of sheep mastitis in Algeria. In this study, 123 milk samples were collected directly from the udder of sheep suffering from clinical mastitis in 2 provinces in Algeria. Recovered isolates were identified using MALDI-TOF mass spectrometry. Virulence-associated and antimicrobial resistance genes as well as clonal complexes (CC) of S. aureus were determined using microarray-based analysis. A total of 45 staphylococci isolates were cultivated from sheep milk samples, and 28 S. aureus were identified as methicillin susceptible (62.2%). Seventeen other Staphylococcus isolates of different species were identified using MALDI-TOF mass spectrometry. Subsequent microarray analysis typed the methicillin-susceptible S. aureus to 6 CC: CC8-MSSA, CC97-MSSA, CC130/521-MSSA, CC479-MSSA, CC522-MSSA, and CC705-MSSA. The accessory gene regulator agrIII and the ruminant leukocidin genes lukF-P83 and lukM were found in all isolates of CC130/521, CC479, CC522, and CC705. The toxic shock syndrome toxin gene tst1 was detected exclusively in CC130/521. Additionally, virulence-associated genes (sea, sed, sak, hld, hlgA, edinB, and others) were detected. The presence of antibiotic resistance genes [blaZ, erm(B), and tet(K)] was detected in small numbers of staphylococci. Staphylococci possessing these genes are considered potential hazards for farm animals, farmers, and consumers. Data concerning the prevalence and diversity of staphylococci causing mastitis in sheep from Algeria are lacking. Presented results on different aspects about staphylococci in Algerian sheep populations should at least partially close that gap. However, further extensive studies covering more geographical regions are needed to assess the epidemiological risk.
Indirect, but not direct, down-regulation of visual long-term memory encoding through strategic biasing of attentional allocation.

Visual long-term memory allows us to store a virtually infinite amount of visual information (Brady, Konkle, Alvarez, & Oliva, 2008; Standing, 1973). Despite its massive storage capacity, our ability to encode visual long-term memory fluctuates from moment-to-moment, and for that reason, not every piece of visual information that we wish to encode gets stored into our visual long-term memory. At the same time, we occasionally encounter visual information that we do not wish to remember. To what extent can we control our memory encoding ability at will? Here, we showed that although there are multiple mechanisms to directly up-regulate memory encoding, it is more difficult, if not impossible, to down-regulate memory encoding directly. However, we are capable of down-regulating memory encoding indirectly by biasing attentional allocation away from the encoding of an unwanted stimulus and toward the encoding of a simultaneously encoded item. However, this strategy is effective only if it is exerted prior to perceptual encoding of the unwanted stimulus. Thus, our findings not only support the existence of the biased competition mechanism of voluntary control of memory encoding but also reveals its critical period in indirectly down-regulating memory encoding of unwanted information. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
Contribution of the colicin receptor CirA to biofilm formation, antibotic resistance, and pathogenicity of Salmonella Enteritidis

Salmonella Enteritidis is an important foodborne pathogen that can infect a wide range of animal species including human beings, resulting in great losses to commercial husbandry and human health. CirA is an outer membrane receptor involved in iron uptake and colicin1A/B‐mediated competitive killing. Although iron uptake is crucial to bacterial virulence, limited literature is available about the role of CirA in infection. In the present work, we aimed to evaluate the role of CirA during S. Enteritidis infection. For this purpose, we generated a CirA‐deficient mutant of the S. Enteritidis strain C50336 and examined its biological characteristics. The results showed that cirA gene inactivation caused sharply decreased biofilm formation and apparently impaired antibiotic resistance. Furthermore, the cirA gene deletion mutant showed markedly reduced adhesion and invasion to human epithelial cell line Caco‐2 cells and decreased proliferation in mouse macrophage cell line RAW264.7 cells. Moreover, attenuated virulence was determined by a mouse model, with an LD50 increase of approximately 1,000‐fold. These data indicated that CirA plays critical roles in the S. Enteritidis infection process.
Patient, Caregiver, and Clinician Perceptions of Ventricular Assist Device Self-care Education Inform the Development of a Simulation-based Mastery Learning Curriculum.

BACKGROUND Patients who undergo ventricular assist device (VAD) implantation and their caregivers must rapidly learn a significant amount of self-care skills and knowledge. OBJECTIVE The aim of this study was to explore patient, caregiver, VAD coordinator, and physician perspectives and perceptions of existing VAD self-care training to inform development of a simulation-based mastery learning (SBML) curriculum to teach patients and caregivers VAD self-care skills and knowledge. METHODS We conducted semistructured, in-person interviews with patients with a VAD, their caregivers, VAD coordinators, and physicians (cardiac surgeons, an infectious disease physician, and advanced heart failure cardiologists). We used a 2-cycle team-based iterative inductive approach to coding and analysis. RESULTS We interviewed 16 patients, 12 caregivers, 7 VAD coordinators, and 11 physicians. Seven major themes were derived from the interviews including (1) identification of critical curricular content, (2) need for standardization and assessment, (3) training modalities, (4) benefits of repetition, (5) piercing it all together, (6) need for refresher training, and (7) provision of training before implant. CONCLUSIONS Findings from this study suggest that SBML is a natural fit for the high-risk tasks needed to save VAD self-care. The 7 unique training-related themes derived from the qualitative data informed the design and development of a VAD SBML self-care curriculum.
Direct visualization of native CRISPR target search in live bacteria reveals Cascade DNA surveillance mechanism

CRISPR-Cas systems encode RNA-guided surveillance complexes to find and cleave invading DNA elements. While it is thought that invaders are neutralized minutes after cell entry, the mechanism and kinetics of target search and its impact on CRISPR protection levels have remained unknown. Here we visualized individual Cascade complexes in a native type I CRISPR-Cas system. We uncovered an exponential relationship between Cascade copy number and CRISPR interference levels, pointing to a time-driven arms race between invader replication and target search, in which 20 Cascade complexes provide 50% protection. Driven by PAM-interacting subunit Cas8e, Cascade spends half its search time rapidly probing DNA (∼30 ms) in the nucleoid. We further demonstrate that target DNA transcription and CRISPR arrays affect the integrity of Cascade and impact CRISPR interference. Our work establishes the mechanism of cellular DNA surveillance by Cascade that allows the timely detection of invading DNA in a crowded, DNA-packed environment. One sentence summary The results from in vivo tracking of single CRISPR RNA-surveillance complexes in the native host cell explain their ability to rapidly recognize invader sequences.
Tubos de látex: esterilidade pós-reprocessamento em vapor saturado sob pressão

Among the dentistry and medical articles the tubular dispositive requires special attention to the reprocessing due to lumen cleaning difficulty, and also organic material retention allowing biofilm establishment. The aim of this study was to evaluate the sterility of 30 latex pipes submitted to the sterilization process by vapor in autoclave" in a hospital of Goiania-GO. The latex pipe was cut transversely in 2 pieces of 1cm, one at the extreme(E) and middle (M). They were inoculated in BHI (Brain Heart Infusion) and incubated at 37oC for 20 days. The samples with positive growth were seeded on sheep blood agar for microbial isolation. The colonies were characterized by morphology and biochemical tests. Microorganisms were detected in 5 latex pipes samples (16.7%), from these, 3 samples (10%) obtained from middle pieces, and 2 from extreme pieces (6.7%). The contaminants were identified as Gram-positive bacilli (BGP), coagulase negative staphylococcus (ECN), and coagulase positive staphylococcus (ECP). Multiple reprocessed of these articles are distinguished what facilitates to consuming, collapse, drying, formation of cracks, and microorganisms retention. According to our results, the latex pipes reprocess using vapor in autoclave might be a risk to the users.
Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery

Abstract While abnormalities related to carbohydrates (glycans) are frequent for patients with rare and undiagnosed diseases as well as in many common diseases, these glycan-related phenotypes (glycophenotypes) are not well represented in knowledge bases (KBs). If glycan-related diseases were more robustly represented and curated with glycophenotypes, these could be used for molecular phenotyping to help to realize the goals of precision medicine. Diagnosis of rare diseases by computational cross-species comparison of genotype–phenotype data has been facilitated by leveraging ontological representations of clinical phenotypes, using Human Phenotype Ontology (HPO), and model organism ontologies such as Mammalian Phenotype Ontology (MP) in the context of the Monarch Initiative. In this article, we discuss the importance and complexity of glycobiology and review the structure of glycan-related content from existing KBs and biological ontologies. We show how semantically structuring knowledge about the annotation of glycophenotypes could enhance disease diagnosis, and propose a solution to integrate glycophenotypes and related diseases into the Unified Phenotype Ontology (uPheno), HPO, Monarch and other KBs. We encourage the community to practice good identifier hygiene for glycans in support of semantic analysis, and clinicians to add glycomics to their diagnostic analyses of rare diseases.
Systemic Inflammation and Nutritional Status in Patients on Palliative Cancer Care: A Systematic Review of Observational Studies

Objective: This systematic literature review explores the results of studies that have analyzed the association between inflammation and nutritional status in patients with cancer in palliative care. Methods: The bibliographic research was performed in May 2019, according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Group guidelines. The inclusion criteria were papers that (1) had an online abstract available, (2) were original, (3) used a cohort or cross-sectional design, (4) involved patients with advanced cancer in palliative care, and (5) assessed the association between inflammation and nutritional status. The quality assessment was performed using the Newcastle-Ottawa Scale. Results: Nine studies were selected. Weight loss (WL; n = 7) was the most common nutritional marker employed and C-reactive protein (CRP; n = 6) was the most common inflammatory marker. There was considerable variability (39.0%-92.2%) in the proportion of patients who had WL in a 6-month period, while CRP >5 mg/dL was common in 45.3% to 73.9% of patients. Systemic inflammation was related to nutritional status, highlighting the relationship between CRP and WL and lean mass (LM). Patients with CRP >10 mg/L have been found to have a lower LM (P < .001) and a faster rate of loss of LM at a faster rate during the disease trajectory (P = .030). Conclusion: Nutritional status is associated with systemic inflammatory response. Inflammatory markers should be considered an additional parameter for the nutritional diagnosis of patients with cancer in palliative care.
Critical Review: Do children with bilateral cochlear implants have better sound localization abilities than those children implanted unilaterally?

The aim of this critical review was to examine the literature regarding the effects of bilateral versus unilateral cochlear implantation on sound localization abilities in children aged 2 to 16 years. Overall, the findings suggest that bilateral cochlear implants offer some benefits for sound localization that are not achievable with unilateral implantations. Further research, using well-designed studies with a sufficient sample size is still needed to further quantify the benefits of bilateral cochlear implants for sound localization in this population.
Morphological and Molecular Characterization of Larval and Adult Stages of Eustrongylides excisus (Nematoda: Dioctophymatoidea) with Histopathological Observations.

The genus Eustrongylides includes nematodes known as the etiological agent of the "big red worm disease. " The aim of this work was to identify Eustrongylides spp. larvae from fish and adults from great cormorant (Phalacrocorax carbo) sampled at Lake Trasimeno, Italy, by morphological and molecular analysis. Histopathological description of the lesions in birds was also provided. We described adults of Eustrongylides excisus for the first time in Italy, and we also linked larval stages 3 and 4 to adults. The use of molecular tools combined with the traditional taxonomy will help the identification of the species, including species inquirendae. Moreover, molecular analysis can also help to investigate the role of intermediate and paratenic hosts, to deepen the knowledge about geographical distribution of the different Eustrongylides spp. and to define the zoonotic potential of E. excisus, which has not yet been identified as causal agent of human cases.
Long noncoding RNA XIST participates hypoxia-induced angiogenesis in human brain microvascular endothelial cells through regulating miR-485/SOX7 axis.

BACKGROUND Long non-coding RNAs (lncRNAs) X-inactive specific transcript (XIST) has identified to involve into the tumor cell angiogenesis. However, whether XIST contributes to Human Brain Microvascular Endothelial Cells (HBMEC) angiogenesis as well as potential mechanisms are largely unclear. METHODS The expression of XIST, miR-485-3p and SRY-box 7 (SOX7) in HBMEC were altered by transfection. The cell viability, cell migration and tube formation of HBMEC were measured, respectively. The cross-regulations between XIST, miR-485-3p, SOX7, and vascular endothelial growth factor (VEGF) signaling pathway were investigated by RT-qPCR and Western blot assay. RESULTS In this study, we characterized the upregulation of XIST in HBMEC under hypoxia condition. Meanwhile, XIST silencing impaired hypoxia-induced cell proliferation, migration and tube formation. Besides, our integrated experiments identified that XIST may competitively bind with miR-485-3p and then modulate the derepression of downstream target SRY-box 7 (SOX7). Mechanically, knockdown of XIST impaired hypoxia-induced angiogenesis via miR-485-3p/SOX7 axis and subsequent suppression of VEGF signaling pathway. CONCLUSION Altogether, the present study suggested that XIST is required to maintain VEGF signaling expression in HBMEC under hypoxia condition and plays a vital role in hypoxia-induced angiogenesis via miR-485-3p/SOX7 axis.
A Simple Method for Measuring Adenosine Triphosphate in Acute Cholangitis Patients to Determine the Need for Emergency Biliary Drainage

Objective Acute cholangitis is occasionally life-threatening and requires immediate treatment. For the management of acute cases, globally accepted diagnostic criteria and the use of severity grading, as defined in the Tokyo Guidelines 2018 (TG18), are recommended. This study was performed to explore the association between acute cholangitis and the level of adenosine 5'-triphosphate (ATP) in blood as determined with a simple measurement method. Methods Twenty-three consecutive patients admitted for acute cholangitis and 14 healthy individuals were enrolled. Based on the TG18, the patients were categorized according to the degree of severity as Grade I, II, or III. We measured the amount of ATP in blood samples using a bioluminescence meter and evaluated the correlation with the degree of severity. Results The ATP/total hemoglobin (tHgb) level showed a significant decline in association with an increase in severity, as that in the healthy controls was 236.60 ± 8.10 and in the Grade I, II, and III groups was 238.56 ± 6.98, 186.88 ± 7.62, and 154.60 ± 11.01, respectively (p<0.01). While no significant difference was observed between the healthy controls and Grade I patients (p=0.649), there was a statistically significant difference between Grade I and Grade II (p<0.01) in the ATP/tHgb level. According to a receiver operating characteristic analysis, the area under the curve for ATP/tHgb, used as an index for predicting the need for emergency biliary drainage (Grade II, III cases), was the highest among various examined factors. Conclusion The present novel measurement method was found to be simple to perform and useful for detecting acute cholangitis patients with a low ATP level who may require emergency biliary drainage.
Growth performance, carcass traits and digestive function of broiler chickens fed diets with graded levels of corn resistant starch

ABSTRACT 1. This study was conducted to assess the effects of graded levels of dietary corn resistant starch (RS) on growth performance, carcass traits, nutrient retention, digestive organ index, intestinal morphology, digestive enzyme activities, and mRNA expression of certain nutrient transporters in broiler chickens. 2. A total of 320, 1-d-old Arbor Acres broiler chickens were randomly assigned to five dietary treatments, with eight replicates of eight birds in each. These treatments included one corn-soybean control diet, a corn-soybean based diet containing 20% corn starch, and three diets supplemented with 4%, 8% and 12% RS by replacing corn starch with 6.67%, 13.33% and 20% of Hi-Maize 260® (identified as control, RS1, RS2, RS3 and RS4, respectively). The feeding period lasted 42 days. 3. Performance parameters including feed consumption, feed conversion, body weight gain and percentage of abdominal fat at d 42 of age, nutrient retention (including dry matter, fat, total starch and nitrogen free extract), and apparent metabolisable energy was measured from d 18 to 20 and d 39 to 41 and showed negative linear responses to increasing dietary RS level (P < 0.05). Birds fed the RS3 and RS4 diets showed higher relative weight of duodenum, jejunum and ileum, as well as lower villus height and villus height/crypt depth compared to the control (P < 0.05). The activity of pancreatic trypsin of birds at d 21 and 42 of age decreased linearly in response to the increase of dietary RS level (P < 0.01). There were linear changes in up-regulated mRNA expression of SGLT-1 and down-regulated mRNA expression of GLUT-2 with increasing proportion of RS at d 21 and 42 of age (P < 0.05), respectively. 4. It was concluded that feeding broilers with diets containing higher concentrations of RS impaired the development of small intestine, which resulted in lower apparent total tract retention of nutrients and poorer body weight gain, feed efficiency and carcass traits of broiler chickens.
Tissue-dependent DNA methylation of carp uncoupling protein 1 promoter.

DNA methylation of enhancers and promoters generally inhibits gene transcription. DNA methylation occurs predominantly at the dinucleotide CpG, a methyl group that is covalently bonded to cytosine. We have previously demonstrated tissue-restricted expression of the uncoupling protein 1 (Ucp1) in common carp. Here, we characterized the methylation status of the upstream region of the transcriptional initiation site of the carp Ucp1 gene in the liver, brain, kidney, skeletal muscle, and scale. In addition, we explored the direct role of methylation on Ucp1 transcription. Ucp1 expression was higher in the liver than that in other tissues including the kidney, skeletal muscle, and scale. The extent of methylation at nt -2178 and nt -2103 was lower in the liver and kidney than that in the brain, skeletal muscle, and scale. In addition, methylation at the upstream proximal-region of the Ucp1 gene was generally less frequent in the liver compared to that in the other organs. The transcriptional activation assay using the CpG-free luciferase-based reporter suggested that the methylation of the distal and proximal regions of the carp Ucp1 gene did not affect Ucp1 transcription. Unexpectedly, mutation of cytidylic acid to guanylic acid at nt -108 decreased Ucp1 promoter activity. The present results reveal that the status of DNA methylation of the upstream region of the carp Ucp1 gene is different among different tissues, but suggest that the DNA methylation do not directly repress the transcription of Ucp1.
Tsukamurella asaccharolytica sp. nov., Tsukamurella conjunctivitidis sp. nov. and Tsukamurella sputi sp. nov., isolated from patients with bacteraemia, conjunctivitis and respiratory infection in Hong Kong.

Three bacterial strains, HKU70T, HKU71T and HKU72T, were isolated from the conjunctival swab, blood and sputum samples of three patients with conjunctivitis, bacteraemia and respiratory infection, respectively, in Hong Kong. The three strains were aerobic, Gram-stain positive, catalase-positive, non-sporulating and non-motile bacilli and exhibited unique biochemical profiles distinguishable from currently recognized Tsukamurella species. 16S rRNA, secA, rpoB and groEL gene sequence analyses revealed that the three strains shared 99.6-99.9, 94.5-96.8, 95.7-97.8 and 97.7-98.9 % nucleotide identities with their corresponding closest Tsukamurella species respectively. DNA-DNA hybridization confirmed that they were distinct from other known species of the genus Tsukamurella (26.2±2.4 to 36.8±1.2 % DNA-DNA relatedness), in line with results of in silico genome-to-genome comparison (32.2-40.9 % Genome-to-Genome Distance Calculator and 86.3-88.9 % average nucleotide identity values]. Fatty acids, mycolic acids, cell-wall sugars and peptidoglycan analyses showed that they were typical of members of Tsukamurella. The G+C content determined based on the genome sequence of strains HKU70T, HKU71T and HKU72T were 69.9, 70.2 and 70.5 mol%, respectively. Taken together, our results supported the proposition and description of three new species, i.e. Tsukamurella sputi HKU70T (=JCM 33387T=DSM 109106T) sp. nov., Tsukamurella asaccharolytica HKU71T (=JCM 33388T=DSM 109107T) sp. nov. and Tsukamurella conjunctivitidis HKU72T (=JCM 33389T=DSM 109108T) sp. nov.