Miracle-dz/UniFAR-FTUs huggingface dataset:
Antibiotic resistance pattern and spa types of Staphylococcus aureus strains isolated from food business and hospital kitchen employees in Çanakkale, Turkey

Background/aim The aim of this study was to determine antibiotic resistance profiles and spa types of Staphylococcus aureus strains isolated from food business employees in Çanakkale, Turkey. Materials and methods S. aureus isolates were collected from hand and nasal swabs of 300 individuals working in 17 food businesses and 9 hospital kitchens. All S. aureus isolates obtained from each carrier were typed by staphylococcal protein A (spa) typing method.Staphylococcal cassette chromosome mec (SCCmec) and multilocus sequence typing (MLST) of MRSA were performed by sequencing method. Results Of the 300 individuals, 125 (41.6%) were found to be carriers of S. aureus, 215 isolates of which were obtained in total. Three (1.4%) of 215 isolates were identified as MRSA. Sixty spa types were identified among the 121 MSSA isolates, the most common being t084 (9%). A novel spa type was discerned and added to the Ridom SpaServer database as t14963. The MLST type of the MRSA strains identified as spa type t786 was ST88 and as spa type t223 was ST22. All MRSA were determined to be SCCmec type IVa. Conclusion spa typing can be performed to screen for transmission of S. aureus. t786, ST88, and SCCmec IVa MRSA strains were identified for the first time in Turkey.
Chemical, nutritional and microbiological characterization of organic Fontina PDO cheese.

Chemical, microbiological and nutritional characteristics of organic Fontina, an Italian Protected Designation of Origin (PDO) raw cow's milk cheese, and of bulk milk used for its production, were studied. Organic winter-indoor and summer-pasture productions were compared; organic summer samples were compared to conventional summer ones. The organic and conventional summer samples from fresh grass-fed cows showed better lipid-ic compositions than the winter ones. The hypercholesterolemic saturated fatty acids content was lower while the unsaturated fatty acids and rumenic acid contents were higher. No significant chemical and microbiological differences were observed between the organic and conventional summer milk and the cheese samples.
ADVANCED JOURNAL OF EMERGENCY MEDICINE. 2018; 2(2): e21

Introduction: Appendicitis is a common condition that almost always requires emergency surgery. The diagnosis is clear when the patient presents with classic symptoms. However, presentation may be variable due to variations in the position and length of the appendix. Case presentation: Here, we report a 32-year-old man who presented with diarrhea and lower abdominal pain. Physical examination revealed a generalized abdominal tenderness, more prominent in the lower abdomen, including the right and left quadrants. Abdominal ultrasound failed to show any findings supportive of the diagnosis of appendicitis. Further investigation with abdominopelvic computed tomography (CT) with intravenous and oral contrast revealed retrocecal appendicitis. The patient was discharged home after a non-complicated appendectomy. Conclusion: Emergency physicians should be aware that appendicitis may not always show up with a typical presentation and they should consider the possibility of appendicitis when evaluating an acute abdomen to prevent any delay in diagnosis of atypical presentations.
Scrub Typhus – An Overlooked Aetiology for Acute Febrile Illness in Bangladesh: A Case Report

Rickettsial fevers are a heterogeneous group of illness characterized by fever, headache, myalgia and rash. Rickettsia has a wide global distribution and regional species specificity. In spite of significant serosurveillance reports, rickettsial fevers are occasionally reported in Bangladesh. Here, we report a case of scrub typhus occurring in a young girl who presented with fever and had a typical eschar. We emphasize rickettsial fever should be a differential diagnosis in acute fever without localizing symptoms and signs in Bangladesh. Birdem Med J 2019; 9(1): 80-81
Assessment of autonomic dysfunction in bronchial asthma patients

Introduction: Many aspects of airway functions are controlled by autonomic nerves. Bronchospasm, airway edema and excessive mucus secretion may occur due to abnormality in autonomic regulation of airways. All these events lead to airway obstruction in bronchial asthma. Objective: The aim of the study was to compare the autonomic functions between bronchial asthma patients and normal controls. Materials and Methods: As per American Thoracic Society guidelines thirty bronchial asthma patients in the age group of 18-50 years were chosen. Thirty age and sex matched controls were chosen for comparison. Standardized autonomic function tests were done. Statistical analysis was done using students unpaired t’ test. Results: Significantly higher basal heart rate was found in asthmatics in comparison with controls. Parasympathetic function tests showed significantly higher values in asthmatics compared with controls. Statistically significant difference is also found in the sympathetic function tests between asthmatics and normal controls. Conclusion: Our study shows that autonomic dysfunction is present in asthmatic patients. Parasympathic activity is enhanced in asthmatics, thus supporting the hypothesis of enhanced parasympathetic reactivity as an integral factor in pathophysiology of bronchial asthma. Keywords: Bronchial asthma, Autonomic dysfunction, Parasympathetic tests, Sympathetic tests.
Feeding value of red clover-grass, Persian clover and common vetch for pigs

Red clover-grass, Persian clover, and common fetch that are generally grown for green manuring in organic cropping cycles, are also valuable forages for the feeding of pigs. They could substitute up to 30% of concentrates (on dry matter basis) in the feeding of growing pigs without negative impact on nitrogen (N) retention. This indicates that protein and amino acids of these legumes are well digested and utilised by the pigs. However, inclusion of roughage to pig diets shifts N utilisation so that N excretion to faeces is increased while N excretion to urine is decreased. Persian clover, in particular, is an intriguing roughage for pigs as its protein contains more amino acids that that of red clover-grass or common vetch. In addition, the digestibility of fibre is good in Persian clover, due to lower cellulose and lignin content in the fibre fraction. In practice, the voluntary feed intake of roughages remains lower, from 5% to 20% of pigs’ dry matter intake depending on the production phase.
Fungal Infections in Gastroenterology

Fungal infections are increasing in gastroenterology. Cirrhotic patients, liver transplantation recipients, and patients with inflammatory bowel disease (IBD) are vulnerable to these infections. The origin of these fungal infections is frequently the GI tract. The advent of sequencing technology can identify now previously unculturable fungi. Dysbiosis of the mycobiome and microbiome can uncheck normal commensal fungi and turn pathogenic by largely unknown mechanisms Resistance to antifungals is becoming a global problem. New antifungals are in development and they are badly needed. In this mini-review the enteric mycobiota and fungal infections in GI disease are discussed. DOI: 10.32474/CTGH.2018. 01.000114
Is Coral Bleaching due to the Instability of the Zooxanthellae Dark Reactions

Coral reefs are dominated by symbioses between marine invertebrates (e.g. corals, clams, sea anemones, sponges) and the dinoflagellate Symbiodinium. Increases in seawater temperature linked to global warming have lead to the phenomenon known as "bleaching", involving the disassociation of these symbioses and mass mortalities of the invertebrate host. Mass bleaching events have been linked to a thermal lesion in the photosynthesis of Symbiodinium, either at photosystem II or in the dark reactions of photosynthesis. Examination of two of the proposed lesion points, the carbon concentrating mechanism (CCM) and form II Rubisco, indicate that, over the temperature range examined, the CCM is not disrupted in Symbiodinium isolated from giant clams, however it was not possible to determine if Rubisco is the point of thermal lesion resulting in bleaching. Maximum photosynthetic rates were measured between 28 and 31°C and declined as temperature was increased. Despite a low correlation between Rubisco activity, oxygen evolution and temperature, Rubisco activity declined with increasing temperature.
Acute Myeloid Leukemia with t(8;21)(q22;q22) and Trisomy 4: A Rare Occurrence in a Female Child

Acute myeloid leukemia (AML) with balanced translocation t (8;21) is one of the most frequent chromosomal abnormalities and carries a favorable clinical outcome. However, according to a literature review, additional chromosomal aberrations can affect the overall disease prognosis. Trisomy 4 is a rare numerical abnormality in AML patients with t (8;21), which can be associated with c-KIT gene involvement. In adults, c-KIT mutation carries an unfavorable clinical outcome; however, its incidence and clinical importance in the pediatric population are still under scrutiny. Here, we report a case of AML with t(8;21) and trisomy 4 in an eight-year-old female child and the clinical course of the disease.
Phylogenetic Tree Based on Complete Genomes Using Fractal and Correlation Analyses without Sequence Alignment

The complete genomes of living organisms have provided much information on their phylogenetic relationships. Similarly, the complete genomes of chloroplasts have helped resolve the evolution of this organelle in photosynthetic eukaryotes. In this review, we describe two algorithms to construct phylogenetic trees based on the theories of fractals and dynamic language using complete genomes. These algorithms were developed by our research group in the past few years. Our distance-based phylogenetic tree of 109 prokaryotes and eukaryotes agrees with the biologists’ “tree of life” based on the 16S-like rRNA genes in a majority of basic branchings and most lower taxa. Our phylogenetic analysis also shows that the chloroplast genomes are separated into two major clades corresponding to chlorophytes s.l. and rhodophytes s.l. The interrelationships among the chloroplasts are largely in agreement with the current understanding on chloroplast evolution.
Analysis of Oocyte Quality in the Rhesus Macaque (Macaca mulatta)

This Dissertation is protected by copyright and/or related rights. It has been brought to you by ScholarWorks@UNO with permission from the rights-holder(s). You are free to use this Dissertation in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s) directly, unless additional rights are indicated by a Creative Commons license in the record and/ or on the work itself.
Cloning, Expression, and Characterization of Ara h 3, a Major Peanut Allergen

This Thesis is protected by copyright and/or related rights. It has been brought to you by ScholarWorks@UNO with permission from the rights-holder(s). You are free to use this Thesis in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rightsholder(s) directly, unless additional rights are indicated by a Creative Commons license in the record and/or on the work itself.
Acute responses of high-intensity circuit training in women: Low physical fitness levels show higher muscle damage

High-intensity intermittent exercise (HIIE) elicits large improvements in health and cardiorespiratory fitness (CRF). HIIE can be applied with calisthenics exercises to improve strength and endurance. The acute effects of high-intensity circuit training (HICT) considering different CRF on myological variables are unknown. The aim was measure acute effects of HICT in young women considering different levels of CRF. Twelve women were allocated in two groups, who achieve 41mLO2•kg-1•min-1 or more= High Physical Fitness (HPF, n=5) and who achieve less than 41mLO2•kg-1•min-1= Low Physical Fitness (LPF,n=7). Protocol: 2x4 sets of 20 seconds at maximum intensity (all-out fashion) interspersed with 10 seconds of passive rest (jumping jacks, squat and thrust using 2kg dumbbells, mountain climber, and burpees). Blood samples were collected before, immediately after, 15minutes, 30minutes, one hour and 24 hours after. Heart rate, serum myoglobin, lactate, and creatine kinase (CK) concentration were analyzed. The HR achieved 94.1±3.7% of HRmax for LPF and 104.5±20.3% for HPF, p=0.03. The mean of delta lactate was similar between groups. The highest myoglobin has reached at 1h after the exercise protocol, with 50.0±30.2 ng/mL for LPF and 36.9±9.25 ng/mL for HPF. The delta of total CK before and after the exercise protocol shows that the serum CK level in LPF was significantly higher than HPF group (p=0.042). HICT composed by calisthenic protocol produced elevated and similar effects on HRmax, serum lactate and myoglobin in the woman with HPF and LPF. However, LPF group presented higher muscle damage inferred by serum CK concentrations.
Quality of Life of Patients Using the Hemodialysis Reliable Outflow (HeRO) Graft in Hemodialysis

End-stage renal disease (ESRD) is one of the most feared consequences of kidney disease. A large number of patients with ESRD require long-term hemodialysis. Vascular access options for hemodialysis include the placement of arteriovenous (AV) fistulas, AV grafts, and tunneled dialysis catheters (TDCs). An alternative to the TDC is the Hemodialysis Reliable Outflow (HeRO; Cryolife Inc., Eden Prairie, MN, USA) Graft. The HeRO Graft has been designed to overcome the development of central venous stenosis or occlusion. The objective is to evaluate the quality of life of patients using the HeRO Graft in end-stage renal disease for hemodialysis. We searched PubMed, Medical Literature Analysis and Retrieval System Online (MEDLINE), Excerpta Medica dataBASE (EMBASE), Cumulative Index to Nursing and Allied Health Literature (CINHAL), Directory of Open Access Journals (DOAJ), Pubpsych, and Google Scholar on October 30, 2018. We included published articles in the English language that used the HeRO Graft for ESRD. The adequacy of dialysis and bacteremia rates proved to be equal to those of conventional AV grafts. It turned out that 2.21 interventions per year were needed to maintain the patency of the HeRO Graft while only 1.17 interventions were needed to maintain the patency of the lower extremity graft. Mortality, ischemia, and infection rates were similar for both groups. The tunneled dialysis catheters have a higher incidence of infection as compared to the HeRO Graft. The initial device and placement costs for the HeRO Graft were higher than those for TDCs but savings from the lower incidence of device complications and longer effective device patency make it cost-effective. Based on the limited evidence, it has been discerned that the HeRO Graft is an optimal option for hemodialysis in patients of ESRD who have exhausted all means of upper extremity access. Though almost similar to the AV grafts in terms of complications and less functional than femoral grafts, it still outclasses them in improving the quality of life of such patients.
Estudio comparativo de la aplicación de 6 modelos de inventarios para decidir la cantidad y el punto de reorden de un artículo

espanolEste trabajo presenta la aplicacion de 6 modelos de inventarios para obtener la cantidad de pedido y el punto de reorden para el caso de cubetas de pintura con demanda y tiempos de entrega discretos, aleatorios, independientes y conocidos, considerando descuentos en el precio de compra por adquirir mayores volumenes. Los modelos utilizados han sido el de la cantidad economica de pedido (EOQ), el de un solo lote (USL), el metodo Hibrido (MH), el algoritmo Silver-Meal (SM), el Wagner-Within (WW) y Simulacion (S). Los mejores resultados se han obtenido con Simulacion y el metodo Hibrido, pues han resultado con los menores costos del inventario y llevan a la misma decision: de pedir 301 cubetas de pintura. El caso presentado es un buen ejemplo ilustrativo de la manera de administrar correctamente el inventario. EnglishThis paper presents the application of six inventory models for order quantity and reorder point related to paint buckets with discreet demand and delivery times, random, independent and known, considering wholesale discounts. The models used were: economic order quantity (EOQ), single batch (SB), hybrid method (HM), Silver-Meal algorithm (SM), Wagner-Within (WW) and Simulation (S). The best results were obtained with the Simulation and Hybrid methods, since they had the lowest inventory costs and lead to the same decision: order 301 paint buckets. This case is a good example illustrating properly inventory management.
ILK modulates stress-induced apoptosis in epidermal keratinocytes

ii Co-Authorship Statement . iii Acknowledgments . iv Table of Contents . vi List of Tables . ix List of Figures. x Chapter 1 – Introduction . 1 1.1 Architecture of the skin . 1 1.1.1 The epidermis . 1 1.2 Keratinocyte survival and programmed cell death . 4 1.2.1 Types of cell death. 4 1.2.2 Apoptosis in the epidermis . 6 1.2.3 Extrinsic vs. intrinsic apoptosis pathway . 6 1.3 Reactive oxygen species . 11 1.3.1 Sources of ROS. 13 1.3.2 ROS in keratinocytes . 13 1.3.3 Stress-induced apoptosis . 15 1.4 Integrins . 16 1.4. 1 Integrins and epidermal homeostasis. 18 1.5 Integrin-linked kinase. 18 1.5. 1 ILK as a pseudokinase. 19 1.5. 2 ILK in different cell types . 25 1.5. 3 ILK in the epidermis. 25 1.5. 4 The role of ILK in cell survival. 26 vii 1.6 Rationale and hypothesis. 27 Chapter 2 – Materials and Methods. 29 2.1 Reagents . 29 2.2 Antibodies . 31 2.3 Mouse strains and genotyping . 32 2.4 Isolation and culture of primary mouse epidermal keratinocytes . 34 2.5 Measurement of cell proliferation . 36 2.6 Measurement of DNA synthesis. 36 2.7 Apoptosis measurements . 37 2.8 Preparation of cell lysates for protein analysis . 38 2.9 Denaturing polyacrylamide gel electrophoresis and immunoblotting . 39 2.10 Preparation of glass coverslips . 40 2.11 Confocal and immunofluorescence microscopy . 41 2.12 Quantification of reactive oxygen species (ROS) . 42 2.13 Statistical analysis . 43 Chapter 3 – Results . 44 3.1 Proliferation of ILK-deficient keratinocytes . 44 3.2 Apoptosis in cultured ILK-deficient keratinocytes. 50 3.2.1 Role of the Akt pathway in increased apoptosis in ILK-deficient keratinocytes. 53 3.3 Role of the mitochondrial localization of Bax in apoptosis of ILK-deficient keratinocytes. 56 3.3.1 Activation of the MAPK pathway in ILK-deficient keratinocytes. 59 3.3.2 Activation of Bax-caspase pathway in apoptosis in ILK-deficient keratinocytes. 59 3.4 Reactive oxygen species in ILK-deficient cells . 69 3.5 DNA damage markers in ILK-deficient keratinocytes. 77
Steps in the process of DNA binding and entry in transformation. [Pneumococcus]

The DNA uptake phase of genetic transformation in S. pheumoniae is reviewed with emphasis on molecular interactions at each step. An initial, reversible binding appears to be dependent on the molecular concentration of donor DNA. Subsequent irreversible binding, limited to the numbr of molecules corresponding to a fixed number of receptor sites, requires potassium ions and energy. Competition of different DNAs for uptake occurs at the initial step, but depends on the size of the DNA as well as its molecular concentration. Single-strand breakage accompanies irreversible binding of DNA. The frequency of breaks does not appear to depend on DNA concentration. Entry of DNA follows irreversible binding. The entry step, in which donor DNA is converted to single strands, requires action of a membrane nuclease. In the membrane this nuclease is part ofa specific multiprotein structure, which may function as a unit in DNA binding and entry.
SAT0480 Evaluation of standardised teaching of modified rodnan skin score assessment in systemic sclerosis

Background The modified Rodnan skin score (mRSS) is a standard outcome measure for skin involvement in systemic sclerosis (SSc) clinical trials. Training assessors reduces variability in mRSS measurement. Objectives Our objective is to report the inter- and intra-observer variability of mRSS scoring using newly developed standardised training guidelines by the Scleroderma Clinical Trials Consortium (SCTC). Methods Two SSc experts (DK/AL), 2 facilitators, 52 rheumatology trainees and 8 SSc patients fulfilling the 2013 American College of Rheumatology criteria participated in a SSc skin scoring workshop. Eight SSc patients were examined by 2 SSc experts and facilitators together and consensus scores reached. All trainees attended a talk on mRSS skin scoring by an SSc expert (DK), followed by a video and live demonstration by an expert examining a patient exhibiting different aspects of skin scoring. Each trainee subsequently performed mRSS scoring on 4 SSc patients independently. This concluded the teaching session for mRSS scoring. The mRSS scoring for each trainee was compared to the consensus expert mRSS, and a score of ≤5 in 3 out of 4 patients is considered acceptable inter-observer variability, as determined by SCTC guidelines. Two days after training, 12 trainees, 2 facilitators and 2 experts re-assessed independently the mRSS of 2 SSc patients whom they had examined previously. The repeat day 2 mRSS score for each trainee was compared to the baseline mRSS score, and a score of ≤3 is considered acceptable intra-observer variability. We computed the inter- and intra-observer variability using a linear mixed model with an intercept term and random effects for patient, rater and patient by rater with the following values representing the degrees of agreement:<0 –poor; 0–0.20 –slight; 0.21–0.40 –fair; 0.41–0.60 –moderate; 0.61–0.80 –substantial; and 0.81–1.00 –almost perfect agreement. Results For the first group of assessors involving 52 trainees, 65.4% of them achieved acceptable inter-observer variability, with inter-observer variability of 0.71, inter-observer mean of 8.64 and within-patient standard deviation (SD) of 4.25. For the second group of assessors who returned 2 days after training (n=14), compared to the experts’ scores, the inter-observer and intra-observer variability was 0.73 and 0.85 respectively. The inter-observer mean was 7.39 with a within-patient SD of 3.65. The intra-observer mean was 6.92 and within-patient SD was 2.73. Conclusions There was substantial inter-observer reliability and excellent intra-observer reliability. This is the first study examining the training of assessors using the SCTC training guidelines and our results support the importance of standardised teaching for mRSS. Disclosure of Interest None declared