bluuebunny/crossref_metadata_2025_split huggingface dataset:
Branch Retinal Artery Occlusion as a presenting sign of Acute Retinal Necrosis: a rare association
Authors: Agarwal Manisha , Gupta Chanda , Jain Abhishek , Kumar Brajesh 
Published: February 2020

Abstract
Background
Acute retinal necrosis (ARN) is a potentially blinding necrotizing viral retinitis. It starts with one or more foci and spreads circumferentially and involves the posterior pole in the later stages. Vascular occlusions such as branch retinal artery occlusion, central retinal artery occlusion, and central retinal vein occlusion may occur secondary to underlying infectious etiology such as ARN.

Findings
An elderly male patient with a history of coronary artery disease was diagnosed with branch retinal artery occlusion (BRAO) in the right eye and referred to the treating cardiologist. Few days later, he complained of diminution of vision in the left eye which made him seek another consultation when he was diagnosed to have ARN in the left eye, encroaching the posterior pole. He was investigated and treated for the same leading to minimal improvement of vision in the left eye possibly due to a delay in the starting of the anti-viral therapy.

Conclusion
We report this case to highlight that occlusive vasculopathy can be a presenting sign of an underlying infectious etiology in any age group. BRAO was a rare presenting sign of ARN in our patient. A thorough peripheral examination is recommended in order to avoid missing infectious pathologies such as ARN which starts from the retinal periphery, progresses fast, and if not managed on time may lead to permanent loss of vision.
GsmPlot: a web server to visualize epigenome data in NCBI
Authors: Li Jia , Yin Yue , Zhang Mutian , Cui Jie , Zhang Zhenhai , Zhang Zhiyong , Sun Deqiang 
Published: February 2020

Abstract
Background
Epigenetic regulation is essential in regulating gene expression across a variety of biological processes. Many high-throughput sequencing technologies have been widely used to generate epigenetic data, such as histone modification, transcription factor binding sites, DNA modifications, chromatin accessibility, and etc. A large scale of epigenetic data is stored in NCBI Gene Expression Omnibus (GEO). However, it is a great challenge to reanalyze these large scale and complex data, especially for researchers who do not specialize in bioinformatics skills or do not have access to expensive computational infrastructure.

Results
GsmPlot can simply accept GSM IDs to automatically download NCBI data or can accept user’s private bigwig files as input to plot the concerned data on promoters, exons or any other user-defined genome locations and generate UCSC visualization tracks. By linking public data repository and private data, GsmPlot can spark data-driven ideas and hence promote the epigenetic research.

Conclusions
GsmPlot web server allows convenient visualization and efficient exploration of any NCBI epigenetic data in any genomic region without need of any bioinformatics skills or special computing resources. GsmPlot is freely available at https://gsmplot.deqiangsun.org/.
Genetic diversity and population structure analysis based on the high density SNP markers in Ethiopian durum wheat (Triticum turgidum ssp. durum)
Authors: Alemu Admas , Feyissa Tileye , Letta Tesfaye , Abeyo Bekele 
Published: February 2020

AbstractBackgroundEthiopia has been considered as a center of diversity and the second possible center of domestication of durum wheat. Genetic diversity and population structure analysis in the existing Ethiopian durum wheat germplasm have enormous importance in enhancing breeding effort and for sustainable conservation. Hence, 192 Ethiopian durum wheat accessions comprising 167 landraces collected from major wheat-growing areas of the country and 25 improved varieties released from Debre Zeit and Sinana Agricultural Research Centers, Ethiopia in different years (1994–2010) were assembled for the current study.ResultsThe panel was genotyped with a High-density 90 K wheat SNP array by Illumina and generated 15,338 polymorphic SNPs that were used to analyze the genetic diversity and to estimate the population structure. Varied values of genetic diversity indices were scored across chromosomes and genomes. Genome-wide mean values of Nei’s gene diversity (0.246) and polymorphism information content (0.203) were recorded signifying the presence of high genetic diversity within this collection. Minor allele frequency of the genome varied with a range of 0.005 to 0.5 scoring a mean value of 0.175. Improved varieties clustered separately to landraces in population structure analysis resulted from STRUCTURE, PCA and neighbor joining tree. Landraces clustering was irrespective of their geographical origin signifying the presence of higher admixture that could arise due to the existence of historical exchanges of seeds through informal seed system involving regional and countrywide farming communities in Ethiopia.ConclusionsSustainable utilization and conservation of this rich Ethiopian durum wheat genetic resource is an irreplaceable means to cope up from the recurrent climate changes and biotic stresses happening widely and thereby able to keep meeting the demand of durum productivity for the ever-growing human population.
Characterization of plant growth-promoting rhizobacteria from perennial ryegrass and genome mining of novel antimicrobial gene clusters
Authors: Li Zhibo , Song Chunxu , Yi Yanglei , Kuipers Oscar P. 
Published: February 2020

Abstract
Background
Plant growth-promoting rhizobacteria (PGPR) are good alternatives for chemical fertilizers and pesticides, which cause severe environmental problems worldwide. Even though many studies focus on PGPR, most of them are limited in plant-microbe interaction studies and neglect the pathogens affecting ruminants that consume plants. In this study, we expand the view to the food chain of grass-ruminant-human. We aimed to find biocontrol strains that can antagonize grass pathogens and mammalian pathogens originated from grass, thus protecting this food chain. Furthermore, we deeply mined into bacterial genomes for novel biosynthetic gene clusters (BGCs) that can contribute to biocontrol.

Results
We screened 90 bacterial strains from the rhizosphere of healthy Dutch perennial ryegrass and characterized seven strains (B. subtilis subsp. subtilis MG27, B. velezensis MG33 and MG43, B. pumilus MG52 and MG84, B. altitudinis MG75, and B. laterosporus MG64) that showed a stimulatory effect on grass growth and pathogen antagonism on both phytopathogens and mammalian pathogens. Genome-mining of the seven strains discovered abundant BGCs, with some known, but also several potential novel ones. Further analysis revealed potential intact and novel BGCs, including two NRPSs, four NRPS-PKS hybrids, and five bacteriocins.

Conclusion
Abundant potential novel BGCs were discovered in functional protective isolates, especially in B. pumilus, B. altitudinis and Brevibacillus strains, indicating their great potential for the production of novel secondary metabolites. Our report serves as a basis to further identify and characterize these compounds and study their antagonistic effects against plant and mammalian pathogens.
Implementation of the Goal-directed Medication review Electronic Decision Support System (G-MEDSS)© into home medicines review: a protocol for a cluster-randomised clinical trial in older adults
Authors: Kouladjian O’Donnell Lisa , Sawan Mouna , Reeve Emily , Gnjidic Danijela , Chen Timothy F. , Kelly Patrick J. , Bell J. Simon , Hilmer Sarah N. 
Published: February 2020

Abstract
Background
Older people living in the community have a high prevalence of polypharmacy and are vulnerable to adverse drug events. Home Medicines Review (HMR) is a collaborative medication review service involving general practitioners (GPs), accredited clinical pharmacists (ACPs) and patients, which aims to prevent medication-related problems. This study aims to evaluate the implementation of a Computerised Clinical Decision Support System (CCDSS) called G-MEDSS© (Goal-directed Medication Review Electronic Decision Support System) in HMRs to deprescribe anticholinergic and sedative medications, and to assess the effect of deprescribing on clinical outcomes.

Methods
This study consists of 2 stages: Stage I – a two-arm parallel-group cluster-randomised clinical trial, and Stage II – process evaluation of the CCDSS intervention in HMR. Community-dwelling older adults living with and without dementia who are referred for HMR by their GP and recruited by ACPs will be included in this study. G-MEDSS is a CCDSS designed to provide clinical decision support for healthcare practitioners when completing a medication review, to tailor care to meet the patients’ goals and preferences. The G-MEDSS contains three tools: The Goals of Care Management Tool, The Drug Burden Index (DBI) Calculator©, and The revised Patients’ Attitudes Towards Deprescribing (rPATD) questionnaire. The G-MEDSS produces patient-specific deprescribing reports, to be included as part of the ACPs communication with the patient’s GP, and patient-specific reports for the patient (or carer). ACPs randomised to the intervention arm of the study will use G-MEDSS to create deprescribing reports for the referring GP and for their patient (or carer) when submitting the HMR report. ACPs in the comparison arm will provide the usual care HMR service (without the G-MEDSS).

Outcomes
The primary outcome is reduction in DBI exposure 3 months after HMR ± G-MEDSS intervention between comparison and intervention groups. The secondary outcomes include changes in clinical outcomes (physical and cognitive function, falls, institutionalisation, GP visits, medication adherence and mortality) 3-months after HMR.

Discussion
This study is expected to add to the evidence that the combination of CCDSS supporting medication review can improve prescribing and clinical outcomes in older adults.

Trial registration
The trial was registered on the Australian New Zealand Clinical Trials Registry ACTRN12617000895381 on 19th June 2017.
Annual and seasonal patterns in etiologies of pediatric community-acquired pneumonia due to respiratory viruses and Mycoplasma pneumoniae requiring hospitalization in South Korea
Authors:   Pneumonia and Respiratory Disease Study Group of Korean Academy of Pediatric Allergy and Respiratory Disease, Lee Eun , Kim Chul-Hong , Lee Yong Ju , Kim Hyo-Bin , Kim Bong-Seong , Kim Hyung Young , Kim Yunsun , Kim Sangyoung , Park Chorong , Seo Ju-Hee , Sol In Suk , Sung Myongsoon , Song Min Seob , Song Dae Jin , Ahn Young Min , Oh Hea Lin , Yu Jinho , Jung Sungsu , Lee Kyung Suk , Lee Ju Suk , Jang Gwang Cheon , Jang Yoon-Young , Chung Eun Hee , Chung Hai Lee , Choi Sung-Min , Choi Yun Jung , Han Man Yong , Shim Jung Yeon , Kim Jin Tack , Kim Chang-Keun , Yang Hyeon-Jong 
Published: February 2020

Abstract
Background
Community–acquired pneumonia (CAP) is one of the leading worldwide causes of childhood morbidity and mortality. Its disease burden varies by age and etiology and is time dependent. We aimed to investigate the annual and seasonal patterns in etiologies of pediatric CAP requiring hospitalization.

Methods
We conducted a retrospective study in 30,994 children (aged 0–18 years) with CAP between 2010 and 2015 at 23 nationwide hospitals in South Korea. Mycoplasma pneumoniae (MP) pneumonia was clinically classified as macrolide-sensitive MP, macrolide-less effective MP (MLEP), and macrolide-refractory MP (MRMP) based on fever duration after initiation of macrolide treatment, regardless of the results of in vitro macrolide sensitivity tests.

Results
MP and respiratory syncytial virus (RSV) were the two most commonly identified pathogens of CAP. With the two epidemics of MP pneumonia (2011 and 2015), the rates of clinical MLEP and MRMP pneumonia showed increasing trends of 36.4% of the total MP pneumonia. In children < 2 years of age, RSV (34.0%) was the most common cause of CAP, followed by MP (9.4%); however, MP was the most common cause of CAP in children aged 2–18 years of age (45.3%). Systemic corticosteroid was most commonly administered for MP pneumonia. The rate of hospitalization in intensive care units was the highest for RSV pneumonia, and ventilator care was most commonly needed in cases of adenovirus pneumonia.

Conclusions
The present study provides fundamental data to establish public health policies to decrease the disease burden due to CAP and improve pediatric health.
Factors associated with Salmonella infection in patients with gastrointestinal complaints seeking health care at Regional Hospital in Southern Highland of Tanzania
Authors: Ngogo Fadhili A. , Joachim Agricola , Abade Ahmed M. , Rumisha Susan F. , Mizinduko Mucho M. , Majigo Mtebe V. 
Published: February 2020

Abstract
Background
Salmonellosis remains an important public health problem globally. The disease is among the leading causes of morbidity and mortality in developing countries that experience poor hygiene and lack of access to clean and safe water. There was an increase in reported cases of Salmonellosis in Njombe Region, Southern Highland of Tanzania between 2015 and 2016 based on clinical diagnosis. Nevertheless, little is known about the factors contributing to the transmission of this disease in the region. This study was conducted to determine the prevalence, antimicrobial susceptibility, and factors associated with Salmonella infection among patients who report gastrointestinal complaints.

Methods
A cross-sectional study was conducted from December 2017 to February 2018 among patients with gastrointestinal complaints at Kibena Regional Hospital. Stool samples were submitted for isolation of Salmonella spp. Identification was based on conventional biochemical tests and serotyping to differentiate typhoid and non-typhoid Salmonella (NTS). Antimicrobial susceptibility was performed using the Kirby-Bauer disc diffusion method. Multivariable logistic regression analysis was performed to examine the factors independently associated with Salmonella infection.

Results
The prevalence of Salmonella infection among participants with gastrointestinal complaints was 16.5% (95% CI: 12.7–21.1) of them, 83.7, 95% CI: 70.9–91.5 were NTS while 16.3, 95% CI: 8.5–29.0 were Typhoid Salmonella species.
All isolates were sensitive to ceftriaxone and ciprofloxacin, whereas 27.8 and 100% were resistant to co-trimoxazole and ampicillin respectively. The odd of Salmonella infection was fourfold higher among participants with formal employment (AOR 3.8, 95% CI, 1.53–9.40). Use of water from wells/rivers (AOR 2.2, 95% CI, 1.07–4.45), drinking untreated water (AOR 2.6, 95% CI, 1.21–5.48) and often eating at a restaurant (AOR 3.4, 95% CI, 1.28–8.93) had increased odds of Salmonella infection. Likewise, having abdominal pain (AOR 8.5, 95% CI, 1.81–39.78) and diarrhea (AOR 2.3, 95% CI, 1.12–4.68) were independent symptoms that predict Salmonella infection.

Conclusion
There is a high prevalence of Salmonella infection among people who report gastrointestinal complaints and it is clinically predicated by diarhoea and abdominal pain. Employed participants and those eating at restaurant and drinking unsafe water had higher risk of infection. Salmonella spp. causing gastroenteritis has developed resistance to commonly used antibiotics.
Rapid reduction of high-level pre-formed donor-specific antibodies after simultaneous liver-kidney transplantation: a report of two cases
Authors: Lai Christina , Newman Allyson , Mawson Jane , Abou-Daher Frederika , Watson Narelle , Majumdar Avik , Wyburn Kate , Chadban Steve , Gracey David 
Published: February 2020

Abstract
Background
Kidney transplantation performed in the presence of high-titre donor-specific antibodies (DSA) may result in hyper-acute or accelerated antibody-mediated rejection and rapid allograft loss. Previous studies have shown that this risk may be mitigated with simultaneous liver-kidney transplantation (SLKT); however, the mechanisms are not well defined. Here we report the evolution of pre-formed, high-level DSAs in two highly sensitised SLKT recipients peri-operatively and describe a profound sustained depletion of all DSAs from the time of liver anastomosis with no extra desensitisation therapy required.

Case presentation
Two patients underwent SLKT and received our centre’s standard renal transplant immunosuppression with basiliximab and methylprednisolone for induction therapy and prednisolone, mycophenolate and tacrolimus for maintenance therapy. HLA antibody samples were collected pre-operatively, and immediately post-liver and post-kidney revascularisation, and then regularly in the post-transplant period. Complement Dependant Cytotoxicity (CDC) crossmatches were also performed. Both patients were highly sensitised with a PRA over 97%. One patient had a positive B- and T-cell crossmatch pre-transplant. These positive CDC crossmatches became negative and the level of pre-formed DSAs reduced profoundly and rapidly, within 3 h post-liver revascularisation. The reduction in pre-formed DSAs, regardless of subclass, was seen immediately post-liver revascularisation, before implantation of the renal allografts. No significant reduction in non-donor specific HLA-antibodies was observed. Both patients maintained good graft function with no rejection on kidney allograft protocol biopsies performed at 10-weeks post-transplant.

Conclusions
These cases support the protective immunoregulatory role of the liver in the setting of SLKT, with no extra desensitisation treatment given pre-operatively for these highly sensitised patients.
The incidence, risk factors, and long-term outcomes of acute kidney injury in hospitalized diabetic ketoacidosis patients
Authors: Chen Junzhe , Zeng Honghui , Ouyang Xia , Zhu Mingsheng , Huang Qiuyan , Yu Wenjuan , Ling Li , Lan Hui-yao , Xu Anping , Tang Ying 
Published: February 2020

Abstract
Background
Emerging evidence has demonstrated that acute kidney injury (AKI) is an important risk factor associated with increased morbidity and mortality in diabetic ketoacidosis (DKA) patients. The current study aimed to investigate the incidence rate, risk factors, long-term renal outcomes, and mortality in DKA patients with AKI.

Methods
A total of 179 patients diagnosed with DKA at Sun Yat-sen Memorial Hospital from January 2012 to January 2018 were included in the analysis. AKI was diagnosed according to the 2012 KDIGO criteria. Risk factors, long-term renal outcomes, and mortality were analyzed by logistic regression and Cox proportional hazards models.

Results
Among 179 DKA patients, 98 patients (54.75%) were diagnosed as AKI. Aging; increased blood glucose, serum uric acid and white blood cells; decreased serum pH and albumin; coma; and preexisting chronic kidney disease (CKD) were risk factors of AKI in patients with DKA. During follow-up, DKA patients with AKI showed more than a two-fold decline in eGFR within 1 year after discharge from the hospital when compared with non-AKI DKA patients. Furthermore, AKI was also an independent risk factor for poor long-term renal outcomes and mortality in DKA patients.

Conclusions
Multiple risk factors contribute to the development of AKI in DKA patients. AKI and advanced AKI stage are associated with rapid progressive CKD and long-term mortality in patients with DKA.
Myotonic dystrophy type 1 accompanied with normal pressure hydrocephalus: a case report and literature review
Authors: Wang Junyang , Liu Ming , Shang Wenjie , Chen Zhongqin , Peng Guoping 
Published: February 2020

Abstract
Background
Myotonic dystrophy type 1 (DM1) is the most common disease that can cause muscle weakness and atrophy among adults. Normal pressure hydrocephalus (NPH) is characterized by the triad of gait disturbance, cognitive impairment and urinary incontinence. The association between DM1 and NPH is extremely rare. We report a Chinese female patient with DM1 in association with NPH.

Case presentation
The patient presented with a history of 3-year of walking instability and cognitive impairment. Her brain MRI showed ventriculomegaly with normal cerebrospinal fluid (CSF) pressure and the CSF tap-test was positive, which indicated the diagnosis of probable NPH. DM1 was confirmed by genetic testing.

Conclusions
Four patients with DM1-NPH association were found before. The association between NPH and DM1 may not be just a coincidence, NPH may occur in DM1 later in life and it is vital to recognize the association as a shunt surgery may improve patients’ quality of life.
A qualitative study of the factors influencing recruitment to a pilot trial on the prevention of striae gravidarum
Authors: Brennan Miriam , Clarke Mike , Devane Declan , Dowling Maura 
Published: February 2020

Abstract
Background
Striae gravidarum are a common occurrence in pregnancy and many women use a topical product to prevent their development or lessen their appearance if they do develop. There is a lack of evidence on the effectiveness of many of the products used by women. This study arose from challenges in recruitment to a pilot randomised trial (ISRCTN trial registration number:76992326) designed to evaluate the feasibility of a definitive trial to compare a moisturising oil to no treatment in the prevention and reduction in severity of striae gravidarum. The study reported here explored the factors influencing recruitment to that pilot trial.

Methods
A qualitative descriptive study was undertaken involving primigravid women attending an Irish maternity hospital. Data were collected by semi-structured telephone interviews over a four-week period and analysed using the framework method of analysis. Fifteen interview transcripts were included in the analysis.

Results
Four main themes consisting of twelve categories were identified from the interview data. The themes focused on women’s prevention of stretch marks and their choice of anti-stretch mark product, who and what influenced that choice and influences on trial participation. In relation to influences on trial participation, the possibility of being randomised to the non- intervention or control group was a deterrent for many women.

Conclusions
The prevention of stretch marks is important to pregnant women, as is their choice of product to prevent them. Offering women the opportunity to be part of a trial that would be of low burden and would test a well-known product may optimise recruitment. However, reluctance to be randomised because of the possibility of being allocated to the non-intervention control group suggests that further work is needed in this field on how best to communicate uncertainty to potential participants.