bluuebunny/crossref_metadata_2025_split huggingface dataset:
Continuing evolution of H6N2 influenza A virus in South African chickens and the implications for diagnosis and control
Authors: Abolnik Celia , Strydom Christine , Rauff Dionne Linda , Wandrag Daniel Barend Rudolph , Petty Deryn 
Published: October 2019

Abstract
Background: The threat of poultry-origin H6 avian influenza viruses to human health emphasizes the importance of monitoring their evolution. South Africa’s H6N2 epidemic in chickens began in 2001 and two co-circulating antigenic sub-lineages of H6N2 could be distinguished from the outset. The true incidence and prevalence of H6N2 in the country has been difficult to determine, partly due to the continued use of an inactivated whole virus H6N2 vaccine and the inability to distinguish vaccinated from non-vaccinated birds on serology tests. In the present study, the complete genomes of twelve H6N2 viruses isolated from various farming systems between September 2015 and February 2019 in three major chicken-producing regions were analysed and a serological experiment was used to demonstrate the effects of antigenic mismatch in diagnostic tests.
Results: Genetic drift in H6N2 continued and antigenic diversity in sub-lineage I is increasing; no sub-lineage II viruses were detected. Reassortment patterns indicated epidemiological connections between provinces as well as different farming systems, but there was no reassortment with wild bird or ostrich influenza viruses. The sequence mismatch between the official antigens used for routine hemagglutination inhibition (HI) testing and circulating field strains has increased steadily, and we demonstrated that H6N2 field infections are likely to be missed. More concerning, sub-lineage I H6N2 viruses acquired three of the nine HA mutations associated with human receptor-binding preference (A13S, V187D and A193N) since 2002. Most sub-lineage I viruses isolated since 2015 acquired the K702R mutation in PB2 associated with the ability to infect humans, whereas prior to 2015 most viruses in sub-lineages I and II contained the avian lysine marker. All strains had an unusual HA0 motif of PQVETRGIF or PQVGTRGIF.
Conclusions: The H6N2 viruses in South African chickens are mutating and reassorting amongst themselves but have remained a genetically pure lineage since they emerged more than 18 years ago. Greater efforts must be made by government and industry in the continuous isolation and characterization of field strains for use as HI antigens, new vaccine seed strains and to monitor the zoonotic threat of H6N2 viruses.
Informing patients with progressive neurological disease of their health status, and their adaptation to the disease
Authors: Bužgová Radka , Kozáková Radka 
Published: October 2019

Abstract
Background

Progressive neurological diseases, such as multiple sclerosis, Parkinson's disease, Huntington's disease, significantly interfere with patients' lives, and those of their families. The aim of the research was to establish whether the extent of the information on patients' health conditions, and the way patients learn this information from doctors affect their adaptation to chronic and progressive diseases.Methods

Qualitative methodology was used for a total of 52 participants (patients with progressive neurological diseases, their family members, and health and social workers). Data were collected using individual, in-depth interviews and focus groups. Analysis of data for interpretation, conceptualization, and re-integration was performed by open, axial, and selective coding.Results

It was determined that adequate information about patients’ health status, and the use of coping strategies are related to their adaptation to their disease, and consequently, to their quality of life. The participants often considered the extent of the information provided, and the way they were informed to be inadequate. Receiving the diagnosis, the progression of the disease, and the end of life were found to be the most burdensome.Conclusion

Our results show that Czech neurologist should develop better communication skills, particularly for informing patients with progressive neurological diseases. Open communication, emotional support, and support in selecting effective coping strategies can help patients adapt more readily to their disease, and improve their quality of life.
New Insights into Mammalian Sex Chromosome Structure and Evolution from High-quality Bovine X and Y Chromosome Sequences
Authors: Liu Ruijie , Low Wai Yee , Tearle Rick , Koren Sergey , Ghurye Jay , Rhie Arang , Phillippy Adam M. , Rosen Benjamin D. , Bickhart Derek M. , Smith Timothy P.L. , Hiendleder Stefan , Williams John Lewis 
Published: October 2019

Abstract
Background Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y chromosomes are smaller, have undergone substantial evolutionary changes and accumulated male specific genes and genes involved in sex determination. The PAR is conserved on the X and Y and pair during meiosis. The structure, evolution and function of mammalian sex chromosomes is still poorly understood because few species have high quality sex chromosome assemblies. Results Here we report the first bovine sex chromosome assemblies that include the complete pseudoautosomal region (PAR) spanning 6.84 Mb and three Y chromosome X-degenerate (X-d) regions. We show that the ruminant PAR comprises 31 genes and is similar to the PAR of pig and dog but extends further than those of human and horse. Differences in the pseudoautosomal boundaries are consistent with evolutionary divergence times. Conclusions A bovidae-specific expansion of members of the lipocalin gene family in the PAR may reflect immune-modulation and anti-inflammatory responses that contribute to parasite resistance in ruminants. Comparison of the X-d regions of Y chromosomes across species reveal five conserved X-Y gametologs, which are global regulators of gene activity, and may have a fundamental role in mammalian sexual dimorphism.
Remote ischemic preconditioning in prevention of contrast induced nephropathy: A Randomised control trial
Authors: Roy Debajyoti , Pande Shrikant D , Aw TARCHOON , Hausenloy Derek , Walsh Stewart , Morris Julie , Tang TY 
Published: October 2019

Abstract
Background: Contrast induced nephropathy (CIN) following angiography is one of the leading causes of in-hospital acute kidney injury (AKI). The aim of this study was to investigate the renoprotective effect of remote ischemic preconditioning (RIPC) to prevent CIN in patients with peripheral arterial disease (PAD) undergoing lower limb angioplasty with standard preventative measures. Methods: 40 adult patients (eGFR >45 ml/min) undergoing peripheral arterial angioplasty received either: (1) Control: standard preventative measures comprising intravenous (IV) hydration with 0.9% normal saline (1ml/kg/hour) or (2) RIPC: four-5 min inflations and deflations of a pneumatic cuff placed on the upper arm in addition to IV hydration prior to the angiographic procedure. Serial measurements of serum creatinine, serum cystatin and urinary NGAL were taken at baseline and 2, 24, 48- and 72-hours post-procedure. The primary outcome was CIN as defined by a rise of creatinine by 25% above baseline. Other outcome measures included the rise in urine NGAL and serum cystatin from base line at 2 hours, as an early marker of acute kidney injury (AKI). Results: Both groups had similar baseline characteristics. All recruited patients had eGFR >45 ml/min, and RIPC had no renoprotective effect. AKI occurred in five (13%) patients. Changes in serum creatinine at 2 hours post-procedure did not correlate with changes in urine NGAL or serum Cystatin C. Conclusion: In stable PAD patients (eGFR >45ml) undergoing lower limb angioplasty with standard preventative measures, RIPC did not offer any protection against development of CIN. This study is registered on ClinicalTrials.gov (Clinical Trials No. NCT02516072)
Adaptive Immune Responses Mediated Age-related Plasmodium yoelii 17XL and 17XNL Infections in 4 and 8-week-old BALB/c Mice
Authors: Wang Qiu-bo , Du Yun-ting , Liu Fei , Sun Xiao-dan , Sun Xun , Chen Guang , Pang Wei , Cao ya-ming 
Published: October 2019

Abstract
Background As the quest to eradicate malaria continues, it is important to clarify the opposite clinical outcomes between childhood and adulthood. The relationship between adaptive immune response and age-related malaria infection remains unknown. Methods 4 and 8-week-old mice were used to mimic childhood and adulthood, respectively. Parasitemia and the survival rate were monitored. The proportion and function of Th1 and Th2 cells were detected by FACS. The levels of IFN-γ, IL-4, total IgG, IgG1, IgG2a and Plasmodium yoelii MSP-1-special IgG were measured by ELISA. Results Infant mice were more susceptible to P. yoelii 17XNL infection, with lower survival rate and higher parasitemia. The adult group showed greater resistance to P. yoelii 17XL infection, with lower parasitemia. Compared with 4-week-old mice, the percentage of CD4 + T-bet + IFN-γ + Th1 cells as well as IFN-γ production were significantly increased on day 5 p.i. in the 8-week-old mice after P. yoelii 17XNL infection. The percentage of CD4 + GATA3 + IL-4 + Th2 cells and CD4 + CXCR5 + Tfh cells, and IL-4 production in the 8-week-old mice obviously increased on day 5 and day 10 after P. yoelii 17XNL infection. Notably, the levels of total IgG, IgG1, IgG2a and P. yoelii MSP-1-special IgG were also significantly increased in the 8-week-old mice. PD-1, a marker of exhaustion, was up-regulated on CD4 + or activated CD4 + T cells in the 8-week-old mice as compared to the 4-week-old group. Conclusion We consider that enhanced cellular and humoral adaptive immunity might contribute to rapid clearance of malaria among adults, likely in a PD-1-dependent manner due to induction of CD4 + T cells exhaustion.
Genome-wide identification and characterization of multiple C2 domains and transmembrane region proteins in Gossypium hirsutum
Authors: Hao Pengbo , Wang Hantao , Ma Liang , Wu Aimin , Chen Pengyun , Cheng Shuaishuai , Wei Hengling , Yu Shuxun 
Published: October 2019

Abstract
Background Multiple C2 domains and transmembrane region proteins ( MCTPs ) may act as transport mediators of other regulators. Although increased number of MCTPs in higher plants implies their diverse and specific functions in plant growth and development, only a few plant MCTPs have been studied and no study on the MCTPs in cotton has been reported.Results In this study, we identified 31 MCTPs in G. hirsutum , which were classified into five subfamilies according to the phylogenetic analysis. GhMCTPs from subfamily V exhibited pIs less than 7, whereas GhMCTPs from subfamily I, II, III and IV exhibited pIs more than 7.5, implying their distinct biological functions. In addition, GhMCTPs within subfamily III, IV and V exhibited more diverse physicochemical properties, domain architectures and expression patterns than GhMCTPs within subfamily I and II, suggesting that GhMCTPs within subfamily III, IV and V diverged to perform more diverse and specific functions. Analyses of conserved motifs and pIs indicated that the N-terminus was more divergent than the C-terminus and GhMCTPs’ functional divergence might be mainly contributed by the N-terminus. Furthermore, yeast two-hybrid assay indicated that the N-terminus was responsible to interact with target proteins. Phylogenetic analysis classified multiple N-terminal C2 domains into four subclades, suggesting that these C2 domains performed different molecular functions in mediating the transport of target proteins.Conclusions Our systematic characterization of MCTPs in G. hirsutum will provide helpful information to further research GhMCTPs’ molecular roles in mediating other regulators’ transport to coordinate growth and development of various cotton tissues.
Assessing Quality of Newborn Care at District Facilities in Malawi
Authors: Kawaza Kondwani , Kinshella Mai-Lei Woo , Hiwa Tamanda , Njirammadzi Jenala , Banda Mwai , Vidler Marianne , Newberry Laura , Nyondo-Mipando Alinane Linda , Dube Queen , Molyneux Elizabeth , Goldfarb David M. 
Published: October 2019

Abstract
Background: Malawi is celebrated as one of the few countries in sub-Saharan Africa to meet the Millennium Development Goal of reducing under-5 mortality by two-thirds between 1990 and 2015. However, within this age range neonatal mortality rates are the slowest to decline, even though rates of facility births are increasing. Examining the quality of neonatal care at district level facilities where most deliveries occur is warranted. Objective: The objective of this paper is to evaluate the quality of neonatal care in three district hospitals and one primary health centre in southern Malawi as well as to report the limitations and lessons learned on using the WHO integrated quality of care assessment tool. Methodology: These facility assessments were part of the “Integrating a neonatal healthcare package for Malawi” project, a part of the Innovating for Maternal and Child Health in Africa (IMCHA) initiative. The WHO integrated quality of care assessment tool was used to comprehensively assess quality of care in addition to availability and quantity of supplies and resources. Because this study focused on neonatal care, the modules on infrastructure, neonatal care and labour and delivery were included. Facility assessments were administered in November 2017. Results: The continuum of labour, delivery and neonatal care were all assessed and areas that required improvements to meet standards of care were identified. Critical areas for improvements included the facilities for delivery, including operations and newborn care; for equipment and supplies; for neonatal case management, including sick newborns and routine monitoring and follow-up. Only one of the 12 domains, laboratory, met the standards of care with only minor improvements needed. Conclusion: The WHO integrated quality of care assessment tool is a validated tool that can shed light on the complex quality of care challenges faced by district level health facilities. The results reveal that the quality of care needs improvement, particularly for sick and vulnerable newborns.
Prevalence and factors associated with cancellation of elective procedures on surgical wards at Mulago hospital, Uganda
Authors: ogwal alfred , oyania felix , nkonge emmanuel , makumbi timothy kabanda , galukande fred moses 
Published: October 2019

Abstract
Background: Cancellation of elective surgical procedures has been noted to waste resources and with potential to increase morbidity and mortality among patients. This study set out to determine the prevalence and factors associated with cancellation of elective surgical procedures at Mulago Hospital. Methods: A prospective cross-sectional study was conducted from 10 th January 2018 to 20 th February 2018. We recruited patients of all ages admitted on surgical wards and scheduled for elective surgery. Demographic data, diagnosis, specialty of surgery, proposed surgery, theatre and reasons for cancellation were extracted and analyzed using logistic regression. Results: There were 115 procedures canceled out of 400 cases, giving us a prevalence of cancellation of 28.8%. Neurosurgery had the highest cancellation rate at 46.8% (n=29), OR = 2.23, 95% CI (1.22, 4.06). UCI theatre was about two times more likely to have a procedure canceled (OR = 2.12, 95% CI, 0.91-4.96). Facility factors contributed 67.8% to overall cancellations. Commonest reason for case cancellations was theatre time run out. There was no procedure canceled due to lack of ICU bed. There was a significant association between specialty and surgical cancellation rate (p < 0.05). Conclusions: The prevalence of cancellation of elective surgical procedures in Mulago Hospital is 28.8% with Neurosurgery having the highest cancellation rate. Two thirds of the factors responsible for procedure cancellations were facility related with more than fifty percent of them being potentially preventable. Quality improvement strategies are necessary in those sub specialties susceptible to procedure cancellations due to facility factors. Keywords: cancellation; elective procedures; factors; prevalence
Antibiotic prescribing among inpatients with infectious and non-infectious indications in obstetrics and gynaecology departments at two tertiary care hospitals in Central India
Authors: Machowska Anna , Landstedt Kristoffer , Lundborg Cecilia Stålsby , Sharma Megha 
Published: October 2019

Abstract
Background : Patients in departments such as obstetrics and gynaecology (OBGY) are at high risk of life-threatening infections, thus are prescribed antibiotics extensively. Use of antibiotics leads to increasing antibiotic resistance. Antibiotic surveillance is one of the cornerstones to combat antibiotic resistance. However, hospital-based, department specific surveillance data of prescribed antibiotics are scarce, especially in low- and middle-income countries. Aim: To describe and compare antibiotic prescribing patterns among the inpatients at OBGY departments of two tertiary care hospitals, one teaching (TH) and one non-teaching (NTH), in Central India. Methods: Data of all inpatients was collected manually for three years and analysed using demographics, length of hospital stay, diagnoses and prescribed antibiotics including dose, duration, and frequency and defined daily dose per 1000 inpatients were calculated. The patients were divided into, infectious and non-infectious categories and further into surgical, non-surgical and possible surgical indications. The data was coded based on the Anatomical Therapeutic Chemical classification system and the International Classification of Disease system version-10. Results: Of the total 5558 admitted patients, 2044 (81%) in the TH and 2567 (85%) in the NTH received antibiotic treatment (p<0.001). In both hospitals, a majority of the patients with surgical indications were prescribed antibiotics (87% to 100%). Prescribing of the fixed-dose combinations of antibiotics (FDCs) and use of brand names was more common at the NTH then at the TH. A majority of the inpatients who neither had surgery nor had any confirmed bacterial infection also received antibiotic prescriptions (TH-71%, NTH-75%). Overall, higher DDD/1000 patients were prescribed in the TH compared to the NTH in both categories. Conclusions: More frequent prescribing of broad-spectrum antibiotics, including FDCs and higher brand-name prescribing at the NTH compared to the TH, is a point of concern. Antibiotics prescribed to the inpatients having non-bacterial infection indications is another point of concern and requires urgent action. Investigation of underlying reasons for prescribing antibiotics for unindicated diagnoses and the development and implementation of antibiotic stewardship programs are recommended measures to improve the prescribing of antibiotics.
Is There an Association Between Dietary Habits and Recurrent Deliberate Self-harm?
Authors: Berg Elizabeth , Wilhelm Kay , Handley Tonelle Elizabeth 
Published: October 2019

Abstract
Purpose Despite increasing awareness of high rates of physical illness and poor lifestyle behaviours among patients with a history of suicidality (suicidal ideation and behaviours), there is little research on specific lifestyle factors that are potentially problematic for this group. This paper aims to explore the relationship between frequency of deliberate self-harm and certain lifestyle factors, including balanced meals, eating breakfast, consumption of 'unhealthy' food, weight, exercise, substance and alcohol use, smoking and social support, in a cohort of patients who present to the Emergency Department (ED) with suicidality. Methods From 2007-2016, data from lifestyle and mental health measures were collected from 448 attenders at an outpatient clinic for suicidal behaviour following an ED presentation. Lifestyle behaviours (from Fantastic Lifestyle Checklist) and mental health (from Depression and Anxiety Stress Scale, clinical diagnosis and number of previous deliberate self-harm episodes) were measured on arrival. The associations between lifestyle variables and mental health outcome measures were examined. Results Gender, age, depression symptoms, poor diet, and smoking were all associated with a higher average number of DSH episodes. There were nonsignificant positive trends between all the other poor lifestyle behaviours and deliberate self-harm. There was no association between deliberate self-harm episodes and diagnosis of depression or anxiety disorder. In a multiple linear regression model the only factors that remained significant were age, smoking and eating balanced meals. Conclusion In this sample of patients with suicidal behaviour, balanced meals and smoking were the lifestyle behaviours that were found to have the strongest independent association with repeated deliberate self-harm. We suggest that asking two simple questions about current smoking and balanced meals has the potential to direct the focus on modifiable lifestyle behaviours with important long term implications for individuals and public health implications for the group of people presenting with suicidality.
Evaluation of retinal nerve fiber layer thickness in patients of pituitary adenomas with and without optic chiasmal compression
Authors: Lei Kun , Wang Lina , Wang Meizi , Wang Shuran , Qu Yuanzhen 
Published: October 2019

Abstract
Background: Numerous studies have demonstrated loss of circumpapillary retinal nerve fiber layer (cpRNFL) thickness in patients with chiasmal compression using optical coherence tomography (OCT). This study aimed to evaluate the cpRNFL and ganglion cell compound (GCC) thicknesses in patients suffering pituitary tumors with and without chiasmal compression. Methods: forty-four patients with pituitary adenoma (PA) (twenty-one without chiasmal compression and twenty-three with chiasmal compression) and eighteen controls were enrolled. cpRNFL and GCC thickness were measured in both patients and controls by SD-OCT. Results: three groups (PAs with optic chiasmal compression, PAs without optic chiasmal compression and controls) were closely matched in terms of mean age, sex and IOP (p=0.173, p=0.184 and P=0.343, respectively). The average cpRNFL and GCC thickness was significantly different among three groups (cpRNFL : 94.1±12.5µm, 106.4±7.3µm, 110.7±6.9µm, respectively; GCC: 85.8±6.9µm, 93.8±5.0µm, 97.2±5.6µm, respectively ). The cpRNFL was analyzed in different regions, and significant difference was found in nasal upper and nasal lower between PAs without optic chiasmal compression and controls. Conclusion: Even there is no evidence of compression at the chiasm on magnetic resonance imaging (MRI), GCC and cpRNFL thinning could still be detected in patients of pituitary tumor by SD-OCT. The loss of RNFL is more severe in patients with chiasmal compression.