bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antibiotic resistance pattern of Staphylococcus aureus with reference to MRSA isolates from pediatric patients
Authors: Gurung Raja Ram , Maharjan Prashanna , GC Ganga 
Published: July 2019

Abstract
Background: Staphylococcus aureus is one of the important superbugs distributed throughout the world. It causes minor skin infections to severe complications including nosocomial infections in both hospitals and community settings. These strains have multi-drug resistant property. Hence, they are difficult to manage which increase health-related costs and simultaneously intensifying the need for new antibiotics. The extent of Methicillin-Resistant Staphylococcus aureus (MRSA) in children is largely unknown. The study determines the current status of S. aureus and MRSA causing various infections in pediatric patients visiting International Friendship Children’s Hospital (IFCH).
Methods: A cross-sectional study was conducted among patients visiting a hospital. Various clinical specimens were aseptically collected and processed according to standard microbiological procedures. Isolation and identification of S. aureus were done by microscopy, mannitol fermentation, and coagulase positivity. All identified S. aureus isolates subjected to in-vitro antibiogram by Kirby-Bauer disc diffusion technique adopting Clinical and Laboratory Standards Institute (CLSI) guideline. Isolates resistant to cefoxitin were considered to be MRSA. Whereas, isolates produced D-shaped inhibition zone around clindamycin when kept near erythromycin were considered to be Inducible Clindamycin Resistant (ICR).
Results: 672 various types of clinical samples were processed from the microbiology laboratory from June and November 2015. Out of 300 culture positive samples, 52 (17.3%) were S. aureus isolates, among them 39 (75.0%) were found to be MRSA. The D-test showed that Macrolide-Lincosamide-Streptogramin-B (MLSB) phenotype was 15.4%.
Conclusion: The study shows the MRSA occurrence is prevalent in pediatric patients and newer classes’ drugs are found more effective than β-lactam drugs to treat S. aureus infection. However, restriction on the indiscriminate use of such drugs may be an effective strategy to control the drug resistance.

Keywords: Methicillin-Resistant Staphylococcus aureus (MRSA), Macrolide-Lincosamide-Streptogramin B (MLSB) phenotype, Inducible Clindamycin Resistant (ICR) test or D-zone test, Antibiotic resistance, Nepal
How methodological frameworks are being developed: Evidence from a scoping review
Authors: McMeekin Nicola , Wu Olivia , Germeni Evi , Briggs A 
Published: July 2019

Abstract
Background

A methodological framework is a structured guide to completing a process or procedure. Although the benefits of using methodological frameworks are increasingly recognised, to date, there is no formal definition of what constitutes a ‘methodological framework’, nor is there any published guidance on how to develop one. This study sought to: (a) map the existing landscape on the use of methodological frameworks; (b) identify approaches used for the development of methodological frameworks; and (c) recommend guidance for developing future methodological frameworks. We took a broad view and did not limit our study to methodological frameworks in research and academia.

Methods

A scoping review was conducted, drawing on Arksey and O’Malley’s methodological framework and more recent guidance. We systematically searched two major electronic databases (MEDLINE and Web of Science), as well as grey literature sources and the reference lists of key papers. Study characteristics and approaches used for development of methodological frameworks were extracted from included studies. Descriptive analysis was conducted.

Results

We included a total of 28 studies, representing a wide range of subject areas. The most commonly reported approach for developing a methodological framework was ‘Based on existing methods and guidelines’ (64.3%), followed by ‘Refined and validated’ (35.7%), ‘Experience and expertise’ (32.1%), ‘Literature review’ (28.6%), ‘Data synthesis and amalgamation’ (25.0%), ‘Data extraction’ (10.7%), ‘Iteratively developed’ (7.1%) and ‘Lab work results’ (3.6%). There was no consistent use of terminology; the studies included a range of terms for ‘methodological framework’, which were also used interchangeably within studies.

Conclusions

Although no formal guidance exists on how to develop a methodological framework, this scoping review found an overall consensus in approaches used, which can be broadly divided into three phases: (a) identifying data to inform the methodological framework; (b) developing the methodological framework; and (c) validating, testing and refining the methodological framework. Based on these phases, we provide recommendations to facilitate the development of future methodological frameworks.
RNA 3D structure prediction using multiple sequence alignment information
Authors: Magnus Marcin , Kappel Kalli , Das Rhiju , Bujnicki Janusz 
Published: July 2019

Abstract
Background
The understanding of the importance of RNA has dramatically changed over recent years. As in the case of proteins, the function of an RNA molecule is encoded in its tertiary structure, which in turn is determined by the molecule's sequence. The prediction of tertiary structures of complex RNAs is still a challenging task.
Results
Using the observation that RNA sequences from the same RNA family fold into conserved structure, we test herein whether parallel modeling of RNA homologs can improve ab initio RNA structure prediction method. EvoClustRNA is a multi- step modeling process, in which homologous sequences for the target sequence are selected using the Rfam database. Subsequently, independent folding simulations using Rosetta FARFAR and SimRNA are carried out. The model of the target sequence is selected based on the most common structural arrangement of the common helical fragments. As a test, on two blind RNA-Puzzles challenges, EvoClustRNA predictions ranked as the first of all submissions for the L-glutamine riboswitch and as the second for the ZMP riboswitch.
Conclusion
Through a benchmark of known structures, we discovered several cases in which particular homologs were unusually amenable to structure recovery in folding simulations compared to the single original target sequence.
Selecting behaviour change techniques to reduce sedentary behaviour in people with stroke using the Behaviour Change Wheel
Authors: Wondergem Roderick , Hendrickx Wendy , Wouters Eveline , Bie Rob de , Visser Johanna , Veenhof Cindy , Pisters Martijn 
Published: July 2019

Abstract
Background

Research has shown that sedentary behaviour increases the risk of stroke, cardiovascular disease and mortality. People with stroke are highly sedentary. Therefore, reducing sedentary behaviour might reduce the risk of secondary events and death. Personalized strategies using behavioural change techniques directed at reducing sedentary behaviour in people with stroke are currently lacking.

Purpose

To systematically determine the behaviour change techniques (BCTs) for a behavioural change intervention, directed at reducing sedentary behaviour in community-dwelling people with stroke, using the Behaviour Change Wheel (BCW).

Method

To complete the stages of the BCW, information on understanding the behaviour, identifying intervention functions, identifying BCTs and modes of delivery were needed. To acquire this information, per stage a literature search was conducted and nominal group technique (NGT) sessions were conducted to identify BCTs. The NGT sessions were conducted with professionals working with people with stroke and with international researchers working in the stroke or sedentary behaviour field. Participants made their choice by rating the BCTs, starting from most important (eight points) down to zero points.

Results

In total, 75 eligible BCTs were identified. Five BCTs should always be included: ‘goal setting’, ‘action planning’, ‘social support’, ‘problem solving’ and ‘restructuring of the social environment’. For patients without cognitive impairments, ‘self-monitoring’, ‘feedback on behaviour’, ‘information about health consequences’ and ‘goal setting on outcome’ were advised to be included, while for patients with cognitive impairments, ‘prompts/cues’, ‘graded tasks’, ‘restructuring the physical environment’ and ‘social support practical’ should be considered.

Conclusion

Behaviour change techniques were identified for a behavioural change intervention aiming to reduce sedentary behaviour in community-dwelling people with first-ever stroke. BCTs recommendations depend on the presence of physical and cognitive impairments, although ‘goal setting’, ‘action planning’, ‘social support’, ‘problem solving’ and ‘restructuring of the social environment’ are recommended in all people with first-ever stroke. The identified BCTs serve as the basis for further development of a personalized blended care intervention to reduce sedentary behaviour in people with stroke.
The characteristics of antimicrobial resistance and treatment of carbapenem-resistant Enterobacteriaceae infections in children from 2013 to 2018 in a chinese tertiary hospital
Authors: Jia Xiu-Qin , Pang Feng , Luo Xin , Zhang Jian 
Published: July 2019

Abstract
Background

The aim of this study was to performe a retrospective analysis of prevalence and treatment of carbapenem-resistant Enterobacteriaceae (CRE) infections in children in a tertiary hospital.

Methods

The non-repeat clinical isolates of CRE in children were collected in Liaocheng People's Hospital from January, 2013 to December, 2018. The bacterial identification and antibiotic susceptibility was performed according to the standard methods. The isolated strains will be detected carbapenemases genotypes and homology analysis. All data on the culture-positive strains and associated clinical infection from different pediatric wards were reviewed.

Results

A total of 20 CRE strains isolated from pediatric patients, which derived from different infection sites and present a classification of multiple species of Enterobacteriaceae. And the production of IMP-type carbapenemase in these strains is the main reason of antimicrobial resistance. Most of the infected patients have severe comorbidities and invasive procedures, and use insensitive drugs due to the high resistance rates and medication restrictions. Nevertheless, most infected children have been treated despite the resistance of pathogens to multiple antimicrobial agents. In our follow-up survey, most children received adjuvant therapy such as human intravenous immunoglobulin, which may be an important factor in helping patients defeat pathogenic bacteria.

Conclusions

This study demonstrates a high prevalence of IMP-mediated CRE infection in pediatric patients with severe comorbidities and invasive procedures. Most children have been cured, which may be related to application of adjuvant therapy and weaker pathogenicity of the IMP-type Enterobacteriaceae.
RESPONSE TO NEOADYAVANT CHEMOTHERAPY WITH PLATINUM-BASED DRUGS IN BREAST CANCER PATIENTS WITH BRCA1 DELETION IN TUMOR
Authors: Tsyganov M. M. , Tarabanovskaya N. A. , Deryusheva I. V. , Ibragimova M. K. , Kazantseva P. V. , Pevzner A. M. , Slonimskaya E. M. , Litviakov N. V. 
Published: July 2019

Currently, the presence of the germinal mutation BRCA1 5382insC in breast cancer patients is one of the determining factors for prescribing platinum-based drugs. However, this type of mutation is found in no more than 10 % of patients, thus limiting the feasibility of administering platinum-based drugs. Various somatic changes in the BRCA1 gene in breast tumors, in particular the deletions of this gene, can play an important role in the tumor sensitivity to platinum drugs.Case description. We present the case of a 42-year-old woman diagnosed with breast cancer. The deletion of the BRCA1 gene was detected in the tumor. The patient had a complete response to preoperative chemotherapy according to the CP regimen.Conclusion. The frequency of the germline mutation of the BRCA1 gene does not exceed 10 %, and the deletion frequency of this gene can vary from 30 to 45 %, thus greatly increasing the feasibility of using platinum-based drugs in mutationnegative patients to achieve complete pathologic response and high survival rates.
COMPLICATIONS OF NEOADYAVANT THERAPY FOR CANCER OF THE HEAD OF THE PANCREAS
Authors: Rasulov R. I. , Zemko M. V. , Shelekhov A. V. , Zubrinckiy K. G. , Songolov G. I. 
Published: July 2019

Aim: to study complications of preoperative chemoembolization of the gastroduodenal artery and external beam radiation therapy in patients with pancreatic head cancer.Material and Methods. Sixty patients underwent chemoembolization of the gastroduodenal artery and external beam radiation therapy. Femoral artery angiography was performed using the Seldinger’s technique. Lipiodol 5–7 ml and gemcitabine 400 mg/m2 were used for transarterial chemoembolization. Radiation therapy was given at a total dose of 50 Gy (2 Gy/fraction, 5 times a week, over 5 weeks) using AGAT -R apparatus.Results. Complications after chemoembolization of the gastroduodenal artery were observed in 18.3 % of patients: abdominal pain in 3.3 % of patients; pain and nausea in 3.3 %; pain, nausea and fever in 6.7 %; pain, nausea and increased blood amylase in 1.7 %; pain, nausea and fever, blood amylase in 1.7 %; nausea, fever and blood amylase in 1.7 %. Radiation-induced injuries were observed in 23.3 % of patients: erythema in 18.3 %, grade 1 leukopenia in 1.7% and grade 2 leukopenia in 3.3 %.Conclusion. Complications of neoadjuvant therapy in terms of frequency and severity were consistent with literature data, were manageable with conservative treatment, and did not increase the duration of the preoperative period.
INFECTIONS CAUSED BY ACINETOBACTER BAUMANNII IN CANCER PATIENTS
Authors: Dmitrieva N. V. , Eidelshtein M. V. , Aginova V. V. , Grigorievskaya Z. V. , Petukhova I. N. , Tereshchenko I. V. , Bagirova N. S. , Dyakova S. A. , Kalinchuk T. A. , Dmitrieva A. I. , Shek E. A. , Skleenova E. Yu. 
Published: July 2019

The purpose of the study was to evaluate the frequency of isolation of multi-resistant Acinetobacter baumannii in cancer patients and identify the mechanisms of resistance to carbapenems.Material and Methods. We analyzed 942 strains of A. baumannii isolated from clinical samples of cancer patients in the period 2014–16. The level of resistance to ampicillin-sulbactam, piperacillin-tazobactam, ceftazidime, cefepime, imipenem, meropenem, ciprofloxacin, amikacin, and to other antibiotics was determined. Carbapenem-resistant (Car-R) strains were examined for the presence of carbapenemases.Results. Between 2014 and 2016, the number of strains resistant to: ampicillin-sulbactam was 95.5–74.6 % (p≤0.0001), piperacillin – tazobactam 64.3–98.1 % (p<0.01), ceftazidime – 66.1–44.3 % (p≤0.0001), cefepime – 94.7–98.3 % (p≤0.01), ciprofloxacin – 95.8–91.8 % (p<0.05), amikacin – 77.7–91.0 % (p≤0.0001). An increase in the number of Car-R strains from 77.2 % in 2014 to 84.1 % in 2015 (p<0.05) and up to 90.0 % in 2016 (p<0.05) was observed. The resistance to imipenem was 100 %. The analysis of 6 strains in relation to acquired carbapenemases revealed the production of serine carbapenemases of the OXA-23 group in 100 % of cases.Conclusion. A. baumannii remains to be highly resistant to almost all classes of antibiotics, and the resistance to carbapenems is caused by the production of carbapenemases OXA-23.
MORPHOLOGIC AND MOLECULAR FEATURES OF PRIMARY GLIOBLASTOMA IN PATIENTS SURVIVING MORE THAN 3 YEARS
Authors: Matsko M. V. , Matsko D. E. , Volkov N. M. , Ulitin A. Yu. , Moiseenko V. M. , Imyanitov E. N. , Iyevleva A. G. 
Published: July 2019

Primary glioblastoma (GB) is a rapidly progressing central nervous system tumor with aggressive biological behavior. Long-term glioblastoma survival, defined as survival beyond 3 years, is a rare phenomenon. Various factors contributing to such prolonged lifespan have been proposed.Aim. This study aimed to compare demographic, clinical, morphologic, immunohistochemical and molecular features of primary GB in patients with different survival.Material andMethods. This prospective study included 69 patients, who were treated at A.L. Polenov Neurosurgery institute. The analysis considered clinical, morphologic, immunohistochemical (Ki67, P53, INA , EGFR) and genetic (MGMT, VEGF and PDGFRA gene expression; ID H1/2 mutational status, 1p/19q co-deletion) characteristics of the disease.Results. 11 (15.9 %) patients survived beyond 3 years. Prolonged survival was associated with younger patient age (p=0.002), use of more than 6 cycles of temozolomide in the 1st line therapy (p=0.016), use of the 2nd line therapy (p=0.017) and low level of MGMT expression in the tumor tissue (p=0.038). Other factors including patients’ gender, VEGF and PDGFRA mRNA expression levels, ID H1 mutation, 1p/19q deletion, and the immunohistochemical markers Ki67, p53, INA , EGFR, were not associated with prolonged survival (p>0.05).Conclusion. Prolonged survival in GB patients is a non-random event and can be explained by several clinical and biological factors. A high percentage of 3-year survival of GB patients in our study may be explained by an individual approach to treatment and intensive chemotherapeutic tactics (from 6 to 15 cycles of temozolomide in the 1st line therapy and use of the 2nd line therapy), as opposed to standard short treatment protocols.
THE ROLE OF EPITHELIAL-TO-MESENCHYMAL TRANSITION AND AUTOPHAGY IN ANTITUMORAL RESPONSE OF MELANOMA CELL LINES TO TARGET INHIBITION OF MEK AND mTOR KINASES
Authors: Lozhkomoev A. S. , Bakina O. V. , Fomenko A. N. , Avgustinovich A. V. , Afanasyev S. G. , Dobrodeev A. Yu. , Spirina L. V. , Tarasova A. S. , Urmonov U. B. 
Published: July 2019

Introduction. Cutaneous melanoma is a challenge to treat due to rapid progression of disease and acquired resistance to therapy. Autophagy and the epithelial-to-mesenchymal transition (EMT) are closely interrelated and play a key role in tumor progression. Targeted co-inhibition of MEK and mTOR kinases is a potential target for melanoma therapy by downregulatoin of the EMT.Objective: to study the effect of MEK and mTOR co-inhibition on cell viability, ability to form 3D-spheroids and migratory capacity of melanoma cell lines, and correlation of these changes with EMTand autophagy-related markers.Material and Methods. Melanoma cell lines Mel Z and Mel MTP were derived from patients, who were treated at the N.N. Blokhin National Medical Research Center of Oncology. The antiproliferative effect of binimetinib and/or rapamycin was studied by the MTT -test. 3D spheroids were formed using RGD peptides. Cell migration and invasion were assessed by a Boyden chamber migration assay. The expression levels of autophagy and EMT markers were investigated by immunocytochemistry or immunoblotting.Results. Rapamycin increased cytotoxicity of binimetinib in both 2D and 3D melanoma cell line cultures. At the same time, binimetinib and rapamycin reduced invasion, but not migration capacity of melanoma cells in vitro. The effectiveness of the combination was associated with a decrease in the EMT markers (N-cadherin and β-catenin) and autophagy markers (Beclin 1, p62/SQST M1 and LC3BII ) in melanoma cells.Conclusion. Inactivation of autophagy and EMT leads to overcoming the resistance to current anti-melanoma therapy and can be considered as a promising target for the treatment of melanoma.
MICROSURGICAL METHODS OF EX VIVO EXAMINATION OF THE LYMPHATIC SYSTEM IN BREAST CANCER PATIENTS
Authors: Gantsev S. K. , Tatunov M. A. , Gantsev K. S. , Kzyrgalin S. R. , Mukhamedyarov R. S. 
Published: July 2019

The purpose of the study was ex vivo examination of lymph node perfusion in patients with metastatic breast cancer.Material and Methods. Lymph nodes affected with metastatic breast cancer were examined. These nodes were subsequently subjected to microsurgical dissection with the isolation of the capsule, lymphatic vessels, parenchyma and stroma. All manipulations were performed after preliminary lymph node dissection using an axillary node sample, and the dissection of an isolated lymph node from this region was then performed. A total of 100 breast cancer patients underwent lymph node dissection and microsurgical lymph node dissection. The control group comprised samples taken from women who died in accidents and had no a history of cancer. Lymph nodes and vessels were isolated from the adipose tissue of the axillary region by the sonolipodestruction technique using LySonix 3000® ultrasonic device with PulseSelect™. A detailed examination of lymph nodes was carried out using OPTON microscope – OPMI 6 CFC and a set of microsurgical instruments. Color lymphography of isolated afferent lymphatic vessels with 0.5 % methylene blue solution was performed. Along with color lymphography, digital morphometry of the components of the lymphatic system (Image-Pro Plus 6.0) and microsurgical dissection of the lymph node capsule and lymphangion valves were performed.Results. Data on non-metastatic and metastatic lymph nodes were obtained and digitally recorded. When studying the metastatic blockade of the lymphoid lobule and afferent lymphatic vessels by the method of antegrade color lymphography, we revealed the compensatory development of lymphatic bypass – intracapsular neo-lymphatic microangiogenesis that was confirmed by histological studies.Conclusion. Color lymphography reliably determines the areas and the extent of functional perfusion. Post-radiation changes in tissues markedly change the logistics of lymph flow and regional metastasis. The lymph node capsule with metastases undergoes a pathological transformation characterized by the development of a network of lymphatic capillaries, the severity of which depends on the extent of metastatic block. Lymph node metastasis changes the lymphatic hydrodynamics by changing the number of lymphatic vessels and their diameter.