Miracle-dz/UniFAR-FTUs huggingface dataset:
A Microbial Relationship Between Irritable Bowel Syndrome and Depressive Symptoms

Irritable bowel syndrome (IBS) is associated with depressive symptoms, but this relationship is poorly understood. Emerging research suggests that gut microbes are associated with symptoms in persons with IBS. The purpose of this integrative review is to describe the state of the science of the microbial relationship between IBS and depressive symptoms. PubMed, CINAHL, PsychINFO, and Web of Science were searched using “irritable bowel syndrome,” “microbiome,” “depression,” and related terms. Included articles were published in peer reviewed journals in English from 2009 to 2018. Studies on inflammatory bowel conditions, extra-intestinal microbiomes, or animal models were excluded. Fourteen quantitative studies met inclusion criteria, were critically appraised, and were analyzed using the Whittemore and Knafl method. Analysis revealed a consistently lower microbial biodiversity and lower proportions of Bifidobacterium and Lactobacillus in persons with IBS and co-occurring depressive symptoms. Inclusion of participants with moderate or greater depressive symptoms scores distinguished the studies which reported microbe differences in depressive symptoms. The results of this integrative review underscore the need for studies with larger samples and inclusion of a larger range of depressive symptoms guided by an overarching conceptual framework, such as the biopsychosocial ecology framework. This effort needs to be combined with longitudinal designs in order to identify related microbial markers.
Evidence of stage progression in a novel, validated fluorescence-navigated and microsurgical-assisted secondary lymphedema rodent model

Secondary lymphedema (SL)is a frequent and devastating complication of modern oncological therapy and filarial infections. A lack of a reliable preclinical model to investigate the underlying mechanism of clinical stage progression has limited the development of new therapeutic strategies. Current first line treatment has shown to be merely symptomatic and relies on lifetime use of compression garments and decongestive physiotherapy. In this study, we present the development of a secondary lymphedema model in 35 rats using pre- and intraoperative fluorescence-guided mapping of the lymphatics and microsurgical induction. In contrast to the few models reported so far, we decided to avoid the use of radiation for lymphedema induction. It turned out, that the model is nearly free of complications and capable of generating a statistically significant limb volume increase by water displacement measurements, sustained for at least 48 days. A translational, accurate lymphatic dysfunction was visualized by a novel VIS-NIR X-ray ICG-Clearance-Capacity imaging technology. For the first-time SL stage progression was validated by characteristic histological alterations, such as subdermal mast cell infiltration, adipose tissue deposition, and fibrosis by increased skin collagen content. Immunofluorescence confocal microscopy analysis suggested that stage progression is related to the presence of a characteristic α SMA+/HSP-47+/vimentin+ fibroblast subpopulation phenotype. These findings demonstrate that the in-vivo model is a reliable and clinically relevant SL model for the development of further secondary lymphedema therapeutic strategies and the analysis of the veiled molecular mechanisms of lymphatic dysfunction.
Transport behavior of pressure-driven electrolyte solution through a surface-charged nanochannel

The transport behavior of a pressure-driven electrolyte solution through a surface-charged nanochannel is investigated using molecular dynamics (MD) simulations. Similar to pure water, the relationship between the applied pressure (P) and the average transport velocity ( vˉ) of the electrolyte solution is roughly linear, which matches with the theoretical solution very well. The friction coefficient λ is used to describe the transport behavior (a higher λ leads to a lower vˉ), which scales with the slope of the P- vˉ relationship and increases with the increases of both the charge density of the channel wall σ and the electrolyte concentration n. The physical mechanism is found as follows: the solid–liquid interaction energy between the channel wall and the liquid inside the channel decreases with both σ and n (being more negative), which makes it more difficult for the liquid boundary layer to slide against the channel wall, leading to a higher λ. In addition, the increase of σ also causes a significant decrease of the liquid–liquid interaction energy but the opposite effect is found with the increase of n. However, λ increases with the increase of both σ and n, suggesting that the relationship between λ and the liquid–liquid interaction energy is more complicated for an electrolyte solution, different from the corresponding result of pure water.
Epigenetic priming prior to pembrolizumab in mismatch repair-proficient advanced colorectal cancer.

591 Background: Pembrolizumab results in compelling responses in MMR-deficient CRC. However, most advanced CRC patients have MMR proficient (MMR-p) tumors resistant to PD1 blockade. DNA methyltransferases (DNMT) and histone deacetylases (HDAC) result in silencing of tumor suppressor genes. Preclinical combined HDAC/DNMT inhibition induces susceptibility to immune checkpoints and inhibit tumor growth by re-expressing silenced tumor suppressors. Methods: Single institution, open-label, randomized pilot study (NCT02512172) enrolling patients with advanced MMR-p CRC who progressed on ≥ 1 line of chemotherapy. Patients were randomized to A: oral 5-azacitidine (5AZA, CC486), B: romidepsin or C: combined 5AZA and romidepsin. Patients had pre-treatment biopsy, 14 days of epigenetic therapy with repeat biopsy. All groups began pembrolizumab 200 mg combined with epigenetic therapy until disease progression. Toxicity was assessed using CTCAE v4.0. Results: From 2016 to 2018, 24 patients enrolled with median age of 60 (range 40-69) and median treatment cycles was 3 (range 1-16). There were 2 deaths on study (1 acute kidney injury/ sepsis, 1 cardiac arrest, both unrelated to study drugs). The most common treatment-related hematological AEs in all arms were anemia (63%), lymphopenia (50%) and thrombocytopenia (29%). Most common treatment-related non-hematological AEs in arm A (n = 7) were diarrhea (86%), nausea (86%), fatigue (71%) and anorexia (71%); Arm B (n = 8) were fatigue (63%), dysgeusia (63%), anorexia (63%) and vomiting (63%); and Arm C (n = 9) were nausea (100%), vomiting (100%), fatigue (78%) and anorexia (67%). Treatment-related non-laboratory AEs ≥ grade 3 occurred in 0 patients in Arm A, 3 patients (38%) in Arm B and 3 patients (33%) in Arm C. The most common laboratory AEs in all arms were raised alkaline phosphatase (38%), increased ALT (33%), hyperglycemia (29%), and hypophosphatemia (29%). Conclusions: In this study, the combination of epigenetic agents 5-azacitidine and romidepsin with pembrolizumab is considered safe and generally tolerable in patients with advanced p-MMR colorectal cancer. Further comparison of pre- and post-treatment biopsies is required to determine predictors of response. Clinical trial information: NCT02512172.
Evaluation of Efficacy and Safety of Intensive pulse Light (IPL) In Treatment of Hirsutism in Irsutism in Iraqi women with Some Epidemiological Data

Background: Hirsutism is the presence or an excess of terminal (thick and dark) hair growth in women, in a male - like pattern. Hirsutism affects about 5-10% of women during reproductive age. Many therapeutic measures are used in the treatment of hirsutism, which include, drugs therapy and cosmetic measures and this involved self-care methods and laser therapy, of which intensive pulse light is one of useful therapeutic method. Objective: To evaluate the efficacy and safety of intensive pulse light in the treatment of hirsutism with some epidemiological data in Iraqi women. Patients and Methods: A cohort study in which, one hundred and forty seven women with hirsutism of the face (moustache and chin) were seen and evaluated in a laser clinic of Baquba Teaching Hospital, during the period from January 2010 to June 2013, with a mean age of (29.76 ± 9) years . They were examined and evaluated for the grad of hirsutism, type of skin, menstrual cycle, marital status, childbearing, hormonal and steroid therapy and family history of hirsutism. The diagnosis of cause of hirsutism was made by clinical criteria and certain investigations according to the need. They were treated by intensive pulse light (IPL) and anti-hormonal drugs on need, according to the type of skin and severity of the hirsutism and followed up for six months after the end of therapy , the response was graded into four grades, excellent, good , moderate and poor Results : The study revealed that (42.85%) shows an excellent response, (42.17%) with good response, (14.28%) with moderate response and (7.48%) shows a poor response. Severe complications of therapy like blister and hyperpigmentation were rarely seen. The study shows that the idiopathic hirsutism was the common cause of hirsutism of the face (moustache and chin) in women (66.66%), then the polycystic ovary syndrome (24.49%) and hyperprolactenemia (8.85%). Conclusion : We concluded that intensive pulse light was an effective and safe method in treatment of hirsutism in women, whatever the cause and the idiopathic hirsutism was the common cause.
Perceived Usefulness, Ease of Use and Adequacy of Use of Mobile Technologies by Nigerian University Lecturers.

This paper investigated the university lecturers’ perceived usefulness, ease of use and adequacy of use mobile technologies for research collaboration in South-west, Nigeria. Lecturers in the public universities in the South-west, Nigeria were purposively sampled. The study was descriptive type using survey method. 4 research questions were raised and answered. The research instrument was validated and reliability coefficient of 0.85, 0.92, 0.94 and 0.83 for perceived usefulness, ease of use, adequacy of use and frequency of use of mobile technologies for research collaboration was attained respectively using Cronbach Alpha. A total of 742 respondents were drawn from 13 federal and state universities in South-west, Nigeria. Data were collected using structured questionnaire. Mean and percentages were used to answer research questions 1-4. The findings revealed that university lecturers had positive perception toward the usefulness, ease of use and adequacy of use of mobile technologies. The study concluded that lecturers perceived mobile technologies to be essential and easy to use in facilitating research collaboration. It was recommended that the university lecturers should be encouraged to use mobile technologies effectively for research collaboration.
Distribution of lead in selected organs and tissues of albino rats exposed to acute lead toxicity

The study investigated the distribution of lead in the blood, liver, lung, kidney, heart and brain of albino rats, after oral administration of 1000, 1500 and 2000 ppm of lead solution for 7 consecutive days. The various organs were digested by standard procedures and lead concentrations in these organs were determined by Atomic absorption spectrophotometry. The results showed that although lead concentrations in the blood and other tissues of albino rats in the lead treated groups (Groups 2, 3 and 4) were significantly different from those of the control group (Group 1) p < 0.05, these difference were not proportional to the quantity of lead the animals were exposed to. It is therefore probable that factors other than quantity of exposure may be responsible for the distribution of lead in various organs of albino rats. Key words: Lead, blood, toxicity.
Cell type-specific novel long non-coding RNA and circular RNA in the BLUEPRINT hematopoietic transcriptomes atlas

Transcriptional profiling of hematopoietic cell subpopulations has helped to characterize the developmental stages of the hematopoietic system and the molecular bases of malignant and non-malignant blood diseases. Previously, only the genes targeted by expression microarrays could be profiled genome-wide. High-throughput RNA sequencing, however, encompasses a broader repertoire of RNA molecules, without restriction to previously annotated genes. We analyzed the BLUEPRINT consortium RNA-sequencing data for mature hematopoietic cell types. The data comprised 90 total RNA-sequencing samples, each composed of one of 27 cell types, and 32 small RNA-sequencing samples, each composed of one of 11 cell types. We estimated gene and isoform expression levels for each cell type using existing annotations from Ensembl. We then used guided transcriptome assembly to discover unannotated transcripts. We identified hundreds of novel non-coding RNA genes and showed that the majority have cell type-dependent expression. We also characterized the expression of circular RNA and found that these are also cell type-specific. These analyses refine the active transcriptional landscape of mature hematopoietic cells, highlight abundant genes and transcriptional isoforms for each blood cell type, and provide a valuable resource for researchers of hematologic development and diseases. Finally, we made the data accessible via a web-based interface: https://blueprint.haem. cam.ac. uk/bloodatlas/.
A computational framework for interpreting clusters through inductive learning: a case study

: In supervised learning the inductive algorithm seeks to develop a conceptual description, or prescriptive model, from examples or objects that have been pre-classiﬁed. On the other hand, in unsupervised learning, or clustering, the task of the algorithm is to group non-classiﬁed examples into clusters of examples, building a descriptive model. Central to all of the goals of clustering is the notion of similarity (or dissimilarity) between the individual objects being clustering. The key distinction between prediction and description is that prediction has as its objective a unique variable, known as the class attribute in supervised learning, while in descriptive problems no single variable is central to the problem. In this work we propose an approach, as well as a particular implementation of this approach, were a combination of traditional clustering and inductive learning are used to ﬁnd and interpret special patterns from a database in order to extract useful knowledge to represent real world domains. This approach helps the user to make explicit his/her prior knowledge relevant to the problem allowing to organize the set of objects in diﬀerent clusters into a set of classes considered to be semantically interpretable by the user.
Computational drug repurposing for the identification of SARS-CoV-2 main protease inhibitors

Accepted 7 July 2020ABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus responsible for the known COVID-19 disease. Since currently no definitive therapies or vaccines for the SARS-CoV-2 virus are available, there is an urgent need to identify effective drugs against SARS-CoV-2 infection. One of the best-known targets available is the main protease of this virus, crucial for the processing of polyproteins codified by viral RNA. In this work, we used a computational virtual screening procedure for the repurposing of commercial drugs available in the DrugBank database as inhibitors of the SARS-CoV-2 main protease. Molecular docking calculations and molecular dynamics (MD) simulations have been applied. The computational model was validated through a self-docking procedure. The screening procedure highlighted five interesting drugs that showed a comparable or higher docking score compared to the crystallographic compound and maintained the protein binding during the MD runs. Amongst these drugs, Ritonavir has been used in clinical trials with patients affected by COVID-19 and Nelfinavir showed anti-SARS-CoV-2 activity. The five identified drugs could be evaluated experimentally as inhibitors of the SARS-CoV-2 main protease in view of a possible COVID-19 treatment. Communicated by Ramaswamy H. Sarma
Secondary Palate Development in the Dog (Canis lupus familiaris)

Objective: To investigate the gestational timing of morphologic events in normal canine secondary palate development as a baseline for studies in dog models of isolated cleft palate (CP). Methods: Beagle and beagle/cocker spaniel-hybrid fetal dogs were obtained by cesarean-section on various days of gestation, timed from the initial rise of serum progesterone concentration. Morphology of fetal heads was determined by examining serial coronal sections. Results: On gestational day 35 (d35), the palatal shelves pointed ventrally alongside the tongue. On d36, palatal shelves were elongated and elevated to a horizontal position above the tongue but were not touching. On d37, palatine shelves and vomer were touching, but the medial epithelial seam (MES) between the apposed shelves remained. Immunostaining with epithelial protein markers showed that the MES gradually dissolved and was replaced by mesenchyme during d37-d44, and palate fusion was complete by d44. Examination of remnant MES suggested that fusion of palatal shelves began in mid-palate and moved rostrally and caudally. Conclusion: Palate development occurs in dogs in the steps described in humans and mice, but palate closure occurs at an intermediate time in gestation. These normative data will form the basis of future studies to determine pathophysiologic mechanisms in dog models of CP. Added clinical significance is the enhancement of dogs as a large animal model to test new approaches for palate repair, with the obvious advantage of achieving full maturity within 2 years rather than 2 decades.
Role of ROCK/NF-κB/AQP8 signaling in ethanol-induced intestinal epithelial barrier dysfunction

The present study aimed to investigate the signaling pathways and the underlying molecular mechanisms involved in ethanol-induced intestinal epithelial barrier (IEB) dysfunction. Therefore, an in vitro experimental model of IEB was established using an ethanol-treated Caco-2 intestinal epithelial cell monolayer. The results confirmed that Rho-associated kinases (ROCKs), namely ROCK1 and ROCK2, were involved in the underlying pathway of ethanol-induced IEB dysfunction. Ethanol exposure significantly increased the expression of both ROCK isoforms and the activity of nuclear factor κB (NF-κB). Furthermore, ROCK1- and ROCK2-specific small interfering RNAs (siRNAs), and the NF-κB inhibitor ammonium pyrrolidine dithiocarbamate partially inhibited transepithelial electrical resistance in Caco-2 cells in an in vitro IEB model. In addition, ROCK1- and ROCK2-specific siRNAs inhibited the activity of NF-κB, thereby downregulating the expression of aquaporin 8 (AQP8). Taken together, the results of the present study suggested that ROCK1/ROCK2-mediated activation of NF-κB and upregulation of AQP8 expression levels may represent a novel mechanism of ethanol-induced impairment of IEB function.
Chromosome number variation in the polyploid Cerastium alpinum-C. arcticum complex (Caryophyllaceae)

Chromosome numbers of Cerastium alpinum, C. arcticum, and C. nigrescens were studied from the main part of their distribution area. No chromosome number variation was found within C. alpinum, which seems to be octoploid throughout its range. Dodecaploid chromosome numbers (2n = 108) were found in both C. arcticum and C. nigrescens. A higher, possibly aneuploid, chromosome number was reported for plants from Southwest Greenland, and the intermediate chromosome number of 2n = 90 was found in potential hybrids between C. alpinum and C. nigrescens. Despite sporadic reports of deviating chromosome numbers, the chromosome number variation within the C. alpinum-C. arcticum complex seems to be restricted mainly to the octo- and dodecaploid levels.
The interaction between circular RNA hsa_circ_0000285 and miR-599 in thyroid cancer.

Since this article has been suspected of research misconduct and the corresponding authors did not respond to our request to prove originality of data and figures, "The interaction between circular RNA hsa_circ_0000285 and miR-599 in thyroid cancer, by D. Yang, Y. Jin, S. Cheng, Y. Yang, published in Eur Rev Med Pharmacol Sci 2020; 24 (9): 4882-4889-DOI: 10.26355/eurrev_202005_21177-PMID: 32432751" has been withdrawn. The Publisher apologizes for any inconvenience this may cause. https://www.europeanreview. org/article/21177.
Comparison of Effectiveness and Safety of Antiarrhythmic Drugs Class IC and III in Patients After Electrical Cardioversion

Abstract Patients with atrial fibrillation are faced with an increased risk of thromboembolic events, myocardial infarction, chronic heart failure and death. For some patients with atrial fibrillation, direct current cardioversion (DCCV) is a strategy that can be used to reacquire sinus rhythm. Our aim was to analyse the most commonly used medications after an electrical cardioversion, the reasons for not using them, the effects of pharmacotherapy on recurrence rates, and compare results with data from studies in 2014. The prospective study includes patients with electrocardiographically confirmed atrial fibrillation who underwent direct current cardioversion, hospitalised at Pauls Stradiņš Clinical University Hospital (Rīga, Latvia). The average age was 64.6 years. 50% of the patients were female. During the six-month study period, 14.3% patients were using amiodarone, 8.3% patients were on etacizine, 7.1% received propafenone, and 57.1% used beta blockers in monotherapy or in combination. Warfarin was used in 28.0% patients, direct oral anticoagulants (DOAC’s) in 29.9%, 21,4% of patients received aspirin and 16.7% did not use any antithrombotic therapy. Comparing the recurrence rate in patients using different antiarrhythmic drugs, amiodarone showed a statistically significant superiority compared to etacizine and propafenone (p = 0.02). The obtained data showed that over four years, the use of anticoagulants increased by 11.6%.
Monosomic Analysis of Synthesized Hexaploid Wheats

Polyploidy is a common phenomenon in higher plants. For a study of its evolutionary significance, a comparative gene analysis of amphidiploids and their ancestral species constitutes an effective method. Furthermore, this type of work will yield information on the origin of genes now present in the amphidiploids. The comparative gene analysis of common wheat (genome formula : AABBDD) and their ancestors, Emmer wheat (AABB) and Aegilops squarrosa (DD), is now possible for two reasons. First, a number of hexaploid wheats have been artificially synthesized from various species of Emmer wheats and various varieties of Ae. squarrosa (McFadden & Sears 1945, 1947; Kihara et al. 1950; Tanaka 1961) and, secondly, the monosomic series of a common wheat established by Sears (1954) has made gene analysis of hexaploid wheats very easy. In common wheats a large amount of information has already been accumulated on chromosomal location of genes (cf. summary by Morris 1960, 1961). In order to obtain comparable information on the location of genes in Emmer wheat and Ae. squarrosa, the author carried out a monosomic analysis of four strains of synthesized hexaploid wheats. Results of the analysis are presented and discussed in comparison with those obtained in common wheat.