Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamics of the human gut phageome during the antibiotics therapy

Antibiotics are widely used in all sorts of the medical procedures. Without them, modern medical practice is not possible. As much as they are inevitable, they have severe adverse effects in promoting the antibiotic resistance. Each antibiotic therapy has a profound impact on the human gut. Firstly antibiotics select resistant bacteria what results in rapid changes of the taxonomical composition of the human gut. Secondly, the antibiotic pressure prompts the horizontal gene transfer including transduction that is intermediated by the phages, what advances spread of the resistance. Although the taxonomical composition restores after a month from the therapy, the bacteria get enriched with the genes conferring resistance to antibiotics. We have analyzed changes in the microbiome and phageome of the two people throughout the antibiotic therapy and subsequent recovery time. Analysis of the phage genomes is bioinformatically tricky as phages have complex genomic structures and there are no reliable reference databases. Therefore, we developed a novel comprehensive pipeline for the time-series analysis of the metagenomic datasets focusing on the function and changes in the phage sequences. We observed the phages respond to the antibiotic therapy, and are enriched with antibiotic-resistant genes.
An Unusual Localization of Lunate in a Transcaphoid Volar Lunate Dislocation: Current Concepts

Perilunate dislocation and fracture dislocations are rare injuries corresponding to 10% of all carpal injuries. They usually come with high-energy trauma, with associated injuries representing 61%. Volar lunate dislocation or fracture-dislocation accounts for 3% of perilunate injuries. We present a case of a 42-year-old polytrauma male, transmitted to our department 48 hours after a car accident with a trans-scaphoid volar lunate dislocation. During operation, the lunate was displaced volarly to the ulnar side of the wrist, forward to the styloid process of the distal ulna, while the scaphoid fracture appeared at the waist with comminution, and the proximal pole of the scaphoid protruded under the dorsal capsule. Carpal injuries are often missed out in polytrauma patients, and these injuries are underestimated because of the severity of the other visceral or extremity lesions. Untreated or improperly treated, those injuries lead to serious morbidity and loss of function. Therefore, good functional prognosis with decreased percentage of complications can be achieved following early recognition and early open surgical ligamentous complex repair.
Water models for biomolecular simulations

Modern simulation and modeling approaches to investigation of biomolecular structure and function rely heavily on a variety of methods—water models—to approximate the influence of solvent. We give a brief overview of several distinct classes of available water models, with the emphasis on the conceptual basis at each level of approximation. The main focus is on classes of models most widely used in atomistic simulations, including popular implicit and explicit solvent models. Among the latter, nonpolarizable N‐point models are covered in most detail, including some recent methodological advances and nuances. Notes on practical availability and usage in biomolecular simulations are included. Atomistic simulations that were hardly possible only a short while ago have revealed significant problems that can be traced to deficiencies of most commonly used N‐point water models. Recently developed models of this class approximate experimental properties of liquid water much closer than before, and show promise in practical biomolecular simulations. Obstacles to wider adoption of these more accurate water models, both technical and conceptual, are discussed. It is argued that verifying robustness of simulation results to the choice of water model can be of immediate benefit even in the absence of a clear replacement for older models; a specific strategy is proposed. The review is concluded with a discussion on how force‐field development efforts can benefit from better solvent models, and vice versa. WIREs Comput Mol Sci 2018, 8:e1347. doi: 10.1002/wcms.1347
Plucked hair follicles from patients with chronic discoid lupus erythematosus show a disease-specific molecular signature

Objective When faced with clinical symptoms of scarring alopecia—the standard diagnostic pathway involves a scalp biopsy which is an invasive and expensive procedure. This project aimed to assess if plucked hair follicles (HFs) containing living epithelial cells can offer a non-invasive approach to diagnosing inflammatory scalp lesions. Methods Lesional and non-lesional HFs were extracted from the scalp of patients with chronic discoid lupus erythematosus (CDLE), psoriasis and healthy controls. RNA was isolated from plucked anagen HFs and microarray, as well as quantitative real-time PCR was performed. Results Here, we report that gene expression analysis of only a small number of HF plucked from lesional areas of the scalp is sufficient to differentiate CDLE from psoriasis lesions or healthy HF. The expression profile from CDLE HFs coincides with published profiles of CDLE from skin biopsy. Genes that were highly expressed in lesional CDLE corresponded to well-known histopathological diagnostic features of CDLE and included those related to apoptotic cell death, the interferon signature, complement components and CD8+ T-cell immune responses. Conclusions We therefore propose that information obtained from this non-invasive approach are sufficient to diagnose scalp lupus erythematosus. Once validated in routine clinical settings and compared with other scarring alopecias, this rapid and non-invasive approach will have great potential for paving the way for future diagnosis of inflammatory scalp lesions.
Clinicophysiological and haematobiochemical effects of dexmedetomidine as preanesthetic in combination with thiopental sodium and ketamine in dogs

The objective of the study was to evaluate a safe anaesthetic protocol that could lead to fast and smoother recovery and to determine various clinicophysiological and haematobiochemical parameters before and after anaesthesia. Twenty four clinically healthy dogs of either sex were divided into four groups. Atropine sulphate was administered @0.04mg/kg IM in all the groups. In group 1 ketamine was administered intravenously @ 10 mg/kg body weight. In group 2, dexmedetomidine was administered @ 10 μg/kg body weight, intravenously followed by ketamine till effect. The animals of group 3 were subjected to the administration of thiopental sodium I.V till effect. In animals of the group 4 dexmedetomidine was administered @10 μg/kg I.V. and thiopental sodium given I.V till effect. Dexmedetomidine prior to administration of ketamine and thiopental sodium results in quicker induction, better analgesia for more duration and better muscle relaxation as compared to use of ketamine and thiopental sodium alone. Total dose of ketamine and thiopental sodium required to produce general anaesthesia was decreased in animals of group 2 and 4, with increase in duration of anaesthesia, prolonged recovery time and better muscle relaxation. The clinical efficacy of anaesthesia was determined by performing various surgical operation viz cystotomy, gastrotomy, spaying and entrotomy. Haematological and biochemical parameters showed variable changes at various time intervals.
Efficient Feature Extraction Using Apache Spark for Network Efficient Feature Extraction Using Apache Spark for Network Behavior Anomaly Detection Behavior Anomaly Detection

: Extracting and analyzing network trafﬁc feature is fundamental in the design and implementation of network behavior anomaly detection methods. The traditional network trafﬁc feature method focuses on the statistical features of trafﬁc volume. However, this approach is not sufﬁcient to reﬂect the communication pattern features. A different approach is required to detect anomalous behaviors that do not exhibit trafﬁc volume changes, such as low-intensity anomalous behaviors caused by Denial of Service/Distributed Denial of Service (DoS/DDoS) attacks, Internet worms and scanning, and BotNets. We propose an efﬁcient trafﬁc feature extraction architecture based on our proposed approach, which combines the beneﬁt of trafﬁc volume features and network communication pattern features. This method can detect low-intensity anomalous network behaviors and conventional trafﬁc volume anomalies. We implemented our approach on Spark Streaming and validated our feature set using labelled real-world dataset collected from the Sichuan University campus network. Our results demonstrate that the trafﬁc feature extraction approach is efﬁcient in detecting both trafﬁc variations and communication structure changes. Based on our evaluation of the MIT-DRAPA dataset, the same detection approach utilizes trafﬁc volume features with detection precision of 82.3% and communication pattern features with detection precision of 89.9%. Our proposed feature set improves precision by 94%.
A description of gamification in teaching second language pharmacy technician students

Introduction: Students whose first language is not the language of instruction struggle to master health science terminology in their first few years in higher education. In addition, the funding available to higher education institutions is diminishing. Educators have had to become creative in their teaching techniques to assist learners with low proficiency in the language of instruction. Description of innovation: A cost effective board game was developed to assist learners in a pharmacy technician programme to master pharmacy practice terminology. Evaluation: The game kept students engaged and motivated and several observations were made with respect to further game development. Recommendations: A five step process was developed to guide further development of low cost games for use in the classroom that can be used regardless of the learning objective. The five steps are: Plan, Prepare, Pilot, Play, and Perform.
A Corpus Driven Computational Intelligence Framework for Deception Detection in Financial Text

i PREAMBLE . ii TABLE OF CONTENTS . v APPENDICES . viii LIST OF FIGURES . ix LIST OF TABLES . xiii ACKNOWLEDGEMENTS . xiv DECLARATION . xv GLOSSARY OF ABBREVIATIONS AND DEFINITIONS . xvi Chapter One .
Epidemiological and Clinical Characteristics of Human Hepegivirus 1 Infection in Patients With Hepatitis C

Abstract Background Transmission of human hepegivirus 1 (HHpgV-1), a novel human pegivirus, is closely associated with hepatitis C virus (HCV). The impact of HHpgV-1 viremia on HCV infection is unknown. This study aimed to (a) evaluate the impact of HHpgV-1 viremia on HCV viral load and liver injury and (b) elucidate the clinical and molecular epidemiology of HHpgV-1 infection. Methods Individuals with HHpgV-1 viremia (cases) were identified by screening plasma from 655 HCV-infected adults. HHpgV-1 isolates were sequenced for phylogenetic analysis, and viral load was quantified. Cases were age- and sex-matched to HCV-infected individuals without HHpgV-1 viremia (controls) in a 1:3 ratio. A retrospective case–control analysis was performed to identify differences in HCV viral load and parameters of liver injury. Results Among HCV-infected adults, 16/655 (2.4%) had HHpgV-1 viremia. Risk groups for HHpgV-1 infection included intravenous drug users, blood product recipients, tattoo recipients, and men who have sex with men. Viral sequences clustered into 2 distinct HHpgV-1 genogroups. Cases had a higher mean HCV viral load than controls, with difference between means of 0.58 log10 IU/mL (P = .009). Cases were more likely to have an HCV viral load >5 log10 IU/mL (P = .028). Multiple regression demonstrated the impact of HHpgV-1 viral load and infection status on HCV viral load. HHpgV-1 infection was not associated with higher liver function tests, fibrosis scores, or imaging abnormalities. Conclusions HHpgV-1 viremia is associated with a higher HCV viral load in co-infected patients. HHpgV-1 infection does not affect progression of HCV-related liver disease.
Investigation into the Possible Risk Effects Associated with Drug and Alcohol-induced Gastrointestinal Ulcer in Wistar Albino Rats

Aim: The study investigated the possible risks associated with gastrointestinal ulcer disease by evaluating the biochemical response of three body organs; heart, kidney and liver, in gastric ulcerated rats. Methodology: Twenty male wistar albino rats were used in the study. Gastric ulcer was induced in rats with single oral dose of 400 mg/kg body weight (b.w.) aspirin, 80 mg/kg b.w. indomethacin and 5 ml/kg b.w. acidified ethanol (40:60 v/v). Blood samples were collected into heparinized bottle and centrifuged at 4000 rpm for 10 mins to obtain the plasma. Gastric tissue, liver, kidney and heart were also collected. Results: Oral administration of 400 mg/kg b.w. aspirin, 80 mg/kg b.w. indomethacin and 5 ml/kg b.w. acidified ethanol caused a remarkable increase in ulcer index. There was observed a significant (p<0.05) reduction in AST and ALT activities in gastric ulceration caused by aspirin (Asp), with no significant (p<0.05) change in total protein (TP) concentration, lactate dehydrogenase and creatine kinase activity. However, there was increase in creatinine and urea concentration. Acidified ethanol and Indomethacin-induced ulcerated rats showed significant (p<0.05) reduction in all other parameters except ALT and lactate dehydrogenase activities which did not show any significant (p<0.05) change. There was also observed a significant (p<0.05) increase in creatine kinase activity in indomethacin-induced ulcerated rats. Conclusion: Overall, the result indicates a link between gastric ulcer and organ toxicity. The use of NSAIDs above the therapeutic doses in the treatment of pains and related illness as well as excess consumption of alcohol is shown to negatively impact the stomach and cause serious damage to different body organs of wistar rats.
Prognostic value of chloride channel accessory mRNA expression in colon cancer

Chloride channel accessory (CLCA) is a gene family that encode Ca2+ activated chloride channels, which make a substantial contribution to various diseases. The aim of the present study was to investigate the prognostic value of CLCA expression in colon cancer. In an attempt to elucidate the value of CLCA mRNA expression in the prognosis of patients with colon cancer, the gene expression data of 438 patients with colon cancer were analyzed. The source of the data was The Cancer Genome Atlas, and it was identified that high expression levels of CLCA1 and CLCA2 were associated with a favorable overall survival (OS) time in patients with colon cancer. As revealed by joint effects analysis, the co-occurrence of high expression levels of CLCA1 and CLCA2 was associated with a favorable OS time in patients with colon cancer. CLCA genes were investigated using gene set enrichment analysis. The results of the bioinformatics analysis demonstrated that high expression levels of CLCA1 and CLCA2 were associated with the prognosis of colon cancer. These findings suggest that CLCA1 and CLCA2 are potential prognostic biomarkers for patients with colon cancer. Furthermore, combining CLCA1 and CLCA2 can enhance the sensitivity of the prediction of the OS time of patients with colon cancer.
STAPHYLOCOCCUS AUREUS BAKTERİYEMİLERİNDE MORTALİTE RİSK FAKTÖRLERİNİN ANALİZİ: SEFAZOLİN DAHA İYİ SONUÇLA İLİŞKİLİ

Objective: Methicillin-sensitive Staphylococcus aureus (MSSA) is frequent cause of bacteraemias and associated with substantial mortality. We defined risk factors for mortality among patients with either community-acquired (CA) or healthcare-associated (HCA) MSSA bacteraemia with special emphasis on treatment options including cefazolin and other antimicrobials (mainly ampicillin-sulbactam). Material and Method: All adult patients who were hospitalized and whose blood cultures were positive for MSSA between 2009 and 2014 were included. Patients with CA and HCA MSSA bacteraemia were compared. Results: 83% of the 127 patients with MSSA bacteraemia had HCA. The mortality rate of patients was 20.5% and this did not differ between patients with either CA or HCA MSSA bacteraemia. In the multivariate analysis, higher comorbidity index (HR 1.557), presence of metastatic foci (HR 2.883), and requirement for ICU support (HR 16.239) were found as independent risk factors for mortality, and cefazolin use was found to be protective against mortality (HR 0.178). Conclusion: Patients with MSSA bacteraemia should be treated with cefazolin instead of other antimicrobial options, especially in countries where anti-staphylococcal penicillins are not available or in patients who cannot tolerate anti-staphylococcal penicillins, as cefazolin was found to be protective against mortality.
Experience in radiofrequency ablation of hepatic focal lesions in a fourth-level institution.

Poster: "ECR 2018 / C-3040 / Experience in radiofrequency ablation of hepatic focal lesions in a fourth-level institution. " by: "A. S. Morales Cardenas, C. Aldana Silva, R. Martinez, J. M. PEREZ; Bogota/CO"
Longitudinal epidemiology of pain severity and interference among women with metastatic breast cancer

Background. Knowledge about risk factors for cancer pain over the course of disease in specific tumor types is limited. This study assesses pain hazards over time among patients with metastatic breast cancer. We identify risk factors for worse pain outcomes over time and explore the effect of using different intensity cutpoints on the Brief Pain Inventory (BPI) severity and interference with daily living 0-10 subscales, as related to baseline clinical and demographic characteristics. Methods. We conducted proportional hazards analyses of existing data from a clinical trial that assessed patient outcomes observed at 11 visits over 51 weeks using the BPI to measure pain among 1124 patients with metastatic breast cancer. Univariate (per-cutpoint) and multivariate (cutpoints 3, 4, 5, 6, and 7) models were used to estimate hazards for time to reach each outcome on the BPI severity and interference scales. The sets of clinical and demographic baseline explanatory variables were then compared among the models. Results. In multivariate analyses of the severity scale, compared with Caucasian race, non-Caucasian race was associated with 2.29 times the hazard of reaching severity cutpoint 7 versus 1.38 for cutpoint 3, all other covariates held constant. For the interference scale, compared with active baseline Eastern Cooperative Oncology Group (ECOG) status, restricted baseline ECOG status was associated with 2.97 times the hazard of reaching
Clinical and Radiographic Characteristics of Neuro-Behçet's Disease in South Korea

Background and Purpose Neurological involvement in Behçet's disease [neuro-Behçet's disease (NBD)] is uncommon, but it is worth investigating since it can cause substantial disability. However, difficulties exist in understanding the clinical features of NBD due to regional variations and the lack of studies utilizing well-established diagnostic criteria. We therefore analyzed the clinical features of patients with NBD based on the recent international consensus recommendation. Methods We retrospectively searched electronic databases for patients with Behçet's disease (BD) between 2000 and 2017, and reviewed their medical records. Based on the recent international consensus recommendation, patients with definite or probable NBD were included. Results Of 9,817 patients with the diagnosis code for BD, 1,682 (17.1%) visited the neurology clinic and 110 (1.1%) were classified as NBD. Ninety-eight patients exhibited parenchymal NBD and 12 exhibited nonparenchymal NBD. Their age at the onset of NBD was 37.6±10.6 years and the male-to-female ratio was 1.24:1. Brainstem syndrome (43.9%) was the most common condition in the 98 patients with parenchymal NBD, followed by multifocal (32.7%) and spinal cord (12.2%) syndromes. 72.4% exhibited acute NBD and 27.6% exhibited a progressive disease course. Frequent manifestations included pyramidal signs (52.0%), headache (45.9%), dysarthria (42.9%), and fever (31.6%). A frequent pattern in brain MRI was an upper brainstem lesion extending to the thalamus and basal ganglia. Conclusions Approximately 1% of the patients with suspected BD exhibited NBD. Neurologists must understand the clinical characteristics of NBD in order to perform the differential diagnosis and management of these patients.
Inferior survival after microbiota injury: A multicenter allo-HCT study.

7015 Background: Relationships between microbiota composition and clinical outcomes following allogeneic hematopoietic cell transplantation (allo-HCT) have been described in single-center studies. Geographic variations in human microbial communities and differences in clinical practices across institutions raise the question of whether these associations are generalizable. We report the first multi-center study of the intestinal microbiota in allo-HCT. Methods: Intestinal communities in 8,768 fecal samples from 1,362 allo-HCT patients at 4 centers on 3 continents were profiled by 16S sequencing. Associations between microbiota composition and clinical outcomes were analyzed with proportional-hazards analysis in an observational study. Results: We observed reproducible patterns of microbiota injury characterized by loss of diversity and domination by single taxa. Low diversity in the neutrophil engraftment period was reproducibly associated with increased risk of death (multivariate HR 0.48 [0.30-0.77] p = 0.002 in the largest cohort). These reductions in OS were in part due to an increased risk of transplant-related mortality and graft-vs-host disease. Baseline pre-HCT samples already bore evidence of microbiome disruption; low diversity prior to transplantation was associated with poor survival. A bacterial-composition risk score that was trained in one cohort predicted mortality in the other three cohorts (multivariate HR 1.42 [1.04-1.93] p = 0.03), indicating that not only a diversity metric but also a signature of specific bacterial abundances is informative about post-HCT mortality risk across independent institutions. Conclusions: We demonstrate a relationship between microbiota and survival after allo-HCT that is independent of transplant center and geographic location. The diversity of clinical practices across institutions imposed significant heterogeneity in the study, yet we observed reproducible microbiota injury patterns and associations with outcomes. This concordance suggests that approaches to manipulate the intestinal microbiota in allo-HCT may be generalizable.