AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data.

Detecting multiplets in single nucleus (sn)ATAC-seq data is challenging due to data sparsity and limited dynamic range. AMULET (ATAC-seq MULtiplet Estimation Tool) enumerates regions with greater than two uniquely aligned reads across the genome to effectively detect multiplets. We evaluate the method by generating snATAC-seq data in the human blood and pancreatic islet samples. AMULET has high precision, estimated via donor-based multiplexing, and high recall, estimated via simulated multiplets, compared to alternatives and identifies multiplets most effectively when a certain read depth of 25K median valid reads per nucleus is achieved

Operational Research: Methods and Applications

Throughout its history, Operational Research has evolved to include a variety of methods, models and algorithms that have been applied to a diverse and wide range of contexts. This encyclopedic article consists of two main sections: methods and applications. The first aims to summarise the up-to-date knowledge and provide an overview of the state-of-the-art methods and key developments in the various subdomains of the field. The second offers a wide-ranging list of areas where Operational Research has been applied. The article is meant to be read in a nonlinear fashion. It should be used as a point of reference or first-port-of-call for a diverse pool of readers: academics, researchers, students, and practitioners. The entries within the methods and applications sections are presented in alphabetical order

Endotracheal intubation practice from a pediatric emergency clinic of a tertiary hospital in Turkey

Aim: Airway management has primary importance to provide optimal ventilation and oxygenation in emergency services. Material and Methods: In the study, the resuscitation room records of patients aged 0-18 years in the pediatric emergency room of Healt Sciences University, Tepecik Education and Research Hospital between January 2017 and January 2020. We evaluated the patients who were admitted to the resuscitation room and underwent emergency or rapid sequential intubation. We compared the time elapsed from admission to the emergency room until the time of successful tracheal intubation in the resuscitation room.Results: The mean age of 111 patients in the study was 14.47 months (3.93-42.27), 65 (58.6%) of them were boys and 46 (41.1%) of them were girls. Nine (8.1%) patients were resuscitated outside the hospital and it continued in the resuscitation room. Successful tracheal intubation was achieved in 95 (85.5%) patients after the first attempt. Sedative or neuromuscular blocker agents were given to 71 (63.9%) patients before intubation and cardiopulmonary resuscitation was performed in only one of them. When the time elapsed from the time of admission until the patient was taken to the resuscitation room, vascular access was provided and successful intubation was achieved, there was no significant difference between working hours and out of working hours.Discussion: The intubation procedure, besides being a life-saving intervention, requires attention and care in terms of its risks and timing. It is very important to carry out the tracheal intubation procedure on time and the records should be kept properly and completely during the procedure

Murat production characteristics of Turkish native breeds: II. meat quality, fatty acid, and cholesterol profile of lambs

WOS: 000457421800001The study conducted a comparison of meat quality, fatty acid profile, and cholesterol amounts of longissimus dorsi (LD) and semitendinosus (ST) muscles of male lambs born to Turkish indigenous sheep breeds raised under intensive conditions. A total of 36 singleton male lambs were used as experimental animals of the Akkaraman (A), Morkaraman (M), Awassi (IW), Karayaka (KR), Kivircik (KV), and Middle Anatolian Merino (MAM) pure breeds. All lambs were fed the same diet until they reached a target weight of 40 kg weight. After the feeding period, all lambs were slaughtered and LD and ST muscle samples were collected to determine meat quality traits, fatty acid profile, and cholesterol amounts. Although there were no significant differences between lambs in terms of the fatty acid profile of LD and ST muscles, KR lambs had a higher cholesterol content in both muscles in comparison with the lambs born to other breeds (p < 0.05). While water-holding capacity, dripping loss, pH, color, dry matter, ash, and intramuscular fat values of ST muscles showed differences among breeds (p < 0.05), dripping loss, pH, cooking loss, color, dry matter, ash, protein, and intramuscular fat values of LD muscles differed between breeds (p < 0.05). The data of the current study indicated that meat quality characteristics and cholesterol contents of Turkish indigenous breeds showed differences, and these differences may be used for alternative lamb meat production for the consumer.General Directorate of Agricultural Researches and Policies of TurkeyGida Tarim Ve Hayvancilik Bakanligi [TAGEM 10/AR-GE/13]The authors wish to thank the General Directorate of Agricultural Researches and Policies of Turkey (project no: TAGEM 10/AR-GE/13) for their financial support for the present research

Antibiotic sensitivity of Stenotrophomonas maltophilia in a 5-year period and investigation of clonal outbreak with PFGE

WOS: 000487585400007Introduction: Stenotrophomonas maltophilia, which is able to form a biofilm, has mostly been related to catheters when it is the agent in hospital infections; these infections generally present as bacteremia and pneumonia, which may progress with complications and result in death. Methodology: The study included 153 S. maltophilia strains isolated from clinical samples sent to our hospital laboratory between 1 January 2014 and 30 June 2018. The bacteria were identified and their antibiotic sensitivity was determined using the VITEK-2 automated system. PFGE (Pulsed Field Gel Electrophoresis): The strains isolated from 34 patient clinical samples and from 1 patient bedcover were taken for PFGE examination. Results: The TMP/SXT and levofloxacin sensitivity of 153 S. maltophilia strains was examined. TMP/SXT resistance was determined to be 39% and levofloxacin resistance at 5%. Among 35 S. maltophilia strains, seven genotypes were identified using the PFGE method. While three strains showed a specific genotype profile, the other 32 were determined to consist of four clusters. The cluster rate was therefore 91.4% (32/35). Conclusions: There was a clonal relationship between the vast majority of the 35 S. maltophilia isolates, which suggests that there was a cross-contamination problem in the hospital. One strain (#4) was identified by dendrogram analysis showed a high rate of similarity to the other strains and was determined to be the common source of the cross-contamination

The relationship between muscle fiber characteristics and some meat quality parameters in Turkish native sheep breeds

WOS: 000402217900008This research was conducted to determine muscle fiber characteristics and its relationship with some meat quality traits in Longissimus dorsi (LD) and Semitendinosus (ST) muscles from lambs of some Turkish native sheep breeds. A total of 36 singleton male lambs were used as experimental pure breed animals of Karayaka (n = 6), Kivircik (n = 6), Middle Anatolian Merino (n = 6), Awassi (n = 6), Morkaraman (n = 6) and Akkaraman (n = 6) breeds. All experimental animals were fed the same diet until they reach to a target weight of 40 kg weight. After the feeding period all lambs were slaughtered and LD and ST muscle samples were collected for determination of some meat quality traits (tenderness, pH, water holding capacity, and colour) and ATPase staining of muscle fibers. Type IIB muscle fiber numbers of Morkaraman sheep were higher than those of other breeds in LD muscle (P < 0.05). Awassi lambs had higher number of (P < 0.05) type IIA fibers and total fiber numbers in ST muscle compared to other breeds. Diameter of type I muscle fiber of ST muscle from Kivircik lambs was higher than those of other breeds (P < 0.05). There were positive correlations between diameters of type I (r = 0.513; P<0.05), type ILIA (r = 0.476; P < 0.05) and tenderness in LD and ST muscles of all breeds. Results of the present study showed that muscle fiber characteristics of lambs of different Turkish native sheep breeds differ and muscle fiber characteristics influence some meat quality traits. (C) 2017 Elsevier B.V. All rights reserved.TAGEMGida Tarim Ve Hayvancilik Bakanligi [TAGEM/10/AR-GE/13]The authors acknowledge the financial support by TAGEM (TAGEM/10/AR-GE/13) to carry out this study

The relationship between muscle fiber characteristics and some meat quality parameters in Turkish native sheep breeds

WOS: 000402217900008This research was conducted to determine muscle fiber characteristics and its relationship with some meat quality traits in Longissimus dorsi (LD) and Semitendinosus (ST) muscles from lambs of some Turkish native sheep breeds. A total of 36 singleton male lambs were used as experimental pure breed animals of Karayaka (n = 6), Kivircik (n = 6), Middle Anatolian Merino (n = 6), Awassi (n = 6), Morkaraman (n = 6) and Akkaraman (n = 6) breeds. All experimental animals were fed the same diet until they reach to a target weight of 40 kg weight. After the feeding period all lambs were slaughtered and LD and ST muscle samples were collected for determination of some meat quality traits (tenderness, pH, water holding capacity, and colour) and ATPase staining of muscle fibers. Type IIB muscle fiber numbers of Morkaraman sheep were higher than those of other breeds in LD muscle (P < 0.05). Awassi lambs had higher number of (P < 0.05) type IIA fibers and total fiber numbers in ST muscle compared to other breeds. Diameter of type I muscle fiber of ST muscle from Kivircik lambs was higher than those of other breeds (P < 0.05). There were positive correlations between diameters of type I (r = 0.513; P<0.05), type ILIA (r = 0.476; P < 0.05) and tenderness in LD and ST muscles of all breeds. Results of the present study showed that muscle fiber characteristics of lambs of different Turkish native sheep breeds differ and muscle fiber characteristics influence some meat quality traits. (C) 2017 Elsevier B.V. All rights reserved.TAGEMGida Tarim Ve Hayvancilik Bakanligi [TAGEM/10/AR-GE/13]The authors acknowledge the financial support by TAGEM (TAGEM/10/AR-GE/13) to carry out this study

Characteristics of Laboratory-Confirmed Positive Cases in the First Year of the COVID-19 Pandemic in a University Hospital

Introduction: The new coronavirus named SARS-CoV-2, emerged in Wuhan, China in December 2019 and caused a pandemic. Unusual clinic of viral pneumonia caused by this virus was named COVID-19 and pandemic was declared on 11 March 2020 by World Health Organization. In this study, it was aimed to investigate the epidemiological and clinical characteristics of pediatric and adult patients who were admitted to Ege University Faculty of Medicine (EUFM) Hospital, Izmir, Turkey with COVID-19 findings between March 2020 and February 2021 and whose diagnosis was confirmed by the SARS-CoV-2 RT-PCR test. Materials and Methods: Age and gender characteristics of the patients were screened according to the services and months they admitted to the hospital, and the severity of infection was evaluated in three groups as mild, moderate and severe. In the severe patient group, the relationship between the common comorbid diseases observed in the community and survival status of patients were also evaluated. All statistical analysis performed by SPSS V.26,0. Results: One year from the start of the pandemic, 75851 people applied to the EUFM Hospital with the suspicion of COVID-19. The age median of the patients who applied was 39 (age-range; 0-96) and 50.7% were male patients. SARS-CoV-2 were detected in a total of 7951 (10.5%, median age 39) patients, of them 4044 (10.5%) were male and 3907 (10.5%) were female (p= 0.796). All of the patients, 66577 (87.8%) were adults and 9274 (12.2%) were children. The rate of positivity for SARS-CoV2 in pediatric and adult groups were 7.7% (n= 716) and 10.9% (7235), respectively (p= 0.000). The percentage of patients who were classified as mild, moderate, and severe were 92.7%, 3.4%, and 3.9%, respectively. As a result of paired comparisons for all three level case groups, a statistically significant difference was found between mild cases and others (p= 0.000). However, there was no statistically significant difference between moderate and severe cases (p= 0.298). The mild-moderate-severe clinical level distributions were 3721 (50.4%),142 (52.7%), 181 (58.7%) in male, 3653 (49.5%), 127 (47.2%), 127 (41.2%) in female, respectively (p= 0.014). All severe clinical level patients, 234 (76%) were intensive care patients. Smoking, obesity, hypertension (HT), diabetes mellitus (DM), coronary artery disease (CAD), congestive heart failure (CHF), chronic renal failure (CRF), chronic obstructive pulmonary disease (COPD),malignancy, and chemotherapy p values were found 0.037, 0.001, 0.052, 0.025, 0.003, 0.004, 0.006, 0.558, 0.355, 0.056, respectively. Conclusion: As a result, in a one-year period, COVID-19 showed up a mild illness in both the pediatric and adult groups without the need for hospitalization. In the community, women and men were equally infected with COVID-19, but severe-clinical-level disease was more common in men and over 60 years of age. Mortality rates were found to be high, especially in patients treated in intensive care. Smoking, obesity, DM, CAD, CHF, CRF comorbidities and being >= 60 years old, associated with poor prognosis and death. Due to the Izmir earthquake at the end of October, COVID-19 peaked in Izmir, in November 2020

A Single Clone Acinetobacter baumannii Outbreak in a State Hospital in Turkey

ERTURK, AYSE/0000-0001-6413-9165WOS: 000320094900014PubMed: 23698489Acinetobacter baumannii is an important pathogen in hospitalized patients, particularly those in the intensive care unit (ICU). A total of 21 A. baumannii (6 from 5 patients and 15 from environmental samples) were isolated in the ICU and the isolation room of a state hospital in June 2011. The possible source of the outbreak was investigated. A. baumannii isolates were identified using conventional biochemical tests, BBL Crystal Identification Systems, OXA-51 specific PCR, and 16S rDNA sequencing. All the isolates were multidrug-resistant, showing resistance to cephalosporins, carbapenems, fluoroquinolones, and the aminoglycoside group of antibiotics. Pulsed-field gel electrophoresis suggested that all A. baumannii isolates were derived from a common source