bluuebunny/crossref_metadata_2025_split huggingface dataset:
A retrospective genomic analysis of drug-resistant strains of M. tuberculosis in a high-burden setting, with an emphasis on comparative diagnostics and reactivation and reinfection status.
Authors: Wollenberg Kurt , Harris Michael , Gabrielian Andrei , Ciobanu Nelly , Chesov Dumitru , Long Alyssa , Taaffe Jessica , Hurt Darrell , Rosenthal Alex , Tartakovsky Michael , Crudu Valeriu 
Published: November 2019

Abstract
Background Recurrence of drug-resistant tuberculosis (DR-TB) after treatment occurs through relapse of the initial infection or reinfection by a new drug-resistant strain. Outbreaks of DR-TB in high burden regions present unique challenges in determining recurrence status for effective disease management and treatment. In the Republic of Moldova the burden of DR-TB is exceptionally high, with many cases presenting as recurrent.Methods We performed a retrospective analysis of Mycobacterium tuberculosis from Moldova to better understand the genomic basis of drug resistance and its effect on the determination of recurrence status in a high DR-burden environment. To do this we analyzed genomes from 278 isolates collected from 189 patients, including 87 patients with longitudinal samples. These pathogen genomes were sequenced using Illumina technology, and SNP panels were generated for each sample for use in phylogenetic and network analysis. Discordance between genomic resistance profiles and clinical drug-resistance test results was examined in detail to assess the possibility of mixed infection.Results There were clusters of multiple patients with 10 or fewer differences among DR-TB samples, which is evidence of person-to-person transmission of DR-TB. Analysis of longitudinally collected isolates revealed that many infections exhibited little change over time, though 35 patients demonstrated reinfection by divergent (number of differences > 10) lineages. Additionally, several same-lineage sample pairs were found to be more divergent than expected for a relapsed infection. Network analysis of the H3/4.2.1 clade found very close relationships among 61 of these samples, making differentiation of reactivation and reinfection difficult. There was discordance between genomic profile and clinical drug sensitivity test results in twelve samples, and four of these had low level (but not statistically significant) variation at DR SNPs suggesting low-level mixed infections.Conclusions Whole-genome sequencing provided a detailed view of the genealogical structure of the DR-TB epidemic in Moldova, showing that reinfection may be more prevalent than currently recognized. We also found increased evidence of mixed infection, which could be more robustly characterized with deeper levels of genomic sequencing.
A systematic review of the overlap of fluid biomarkers in delirium and advanced cancer-related syndromes.
Authors: Amgarth-Duff Ingrid , Hosie Annmarie , Caplan Gideon , Agar Meera 
Published: November 2019

Abstract
Delirium is a serious and distressing neurocognitive disorder of physiological aetiology that is common in advanced cancer. Understanding of delirium pathophysiology is largely hypothetical, with some evidence for involvement of inflammatory systems, neurotransmitter alterations and glucose metabolism. To date, there has been limited empirical consideration of the distinction between delirium pathophysiology and that of the underlying disease, for example, cancer where these mechanisms are also common in advanced cancer syndromes such as pain and fatigue. This systematic review explores biomarker overlap in delirium, specific advanced cancer-related syndromes and prediction of cancer prognosis.Methods A systematic literature search was conducted, using MEDLINE, PubMed, Embase, CINAHL, CENTRAL and Web of Science, to identify body fluid biomarkers in delirium, cancer prognosis and advanced cancer-related syndromes of interest. Studies were excluded if they reported delirium tremens only; did not measure delirium using a validated tool; the sample had less than 75% of participants with advanced cancer; measured tissue, genetic or animal biomarkers, or were conducted post-mortem. Articles were screened for inclusion independently by two authors, and data extraction and an in-depth quality assessment conducted by one author, and checked by two others.Results The 151 included studies were conducted in diverse settings in 32 countries between 1985 and 2017, involving 28130 participants with a mean age of 69.3 years. Seventy-one studies investigated delirium biomarkers, and 80 studies investigated biomarkers of an advanced cancer-related syndrome or cancer prognosis. Overall, 41 biomarkers were studied in relation to both delirium and either an advanced cancer-related syndrome or prognosis; and of these, 24 biomarkers were positively associated with either delirium or advanced cancer syndromes/prognosis in at least one study. The quality assessment showed large inconsistency in reporting.Conclusion There is considerable overlap in the biomarkers in delirium and advanced cancer-related syndromes. Improving the design of delirium biomarker studies and considering appropriate comparator/controls will help to better understanding the discrete pathophysiology of delirium in the context of co-existing illness.
Building research capacity in musculoskeletal health: qualitative evaluation of a graduate Nurse and Allied Health Professional internship programme
Authors: Wright David , Fry Mary , Adams Jo , Bowen Catherine 
Published: November 2019

Abstract
Background: Evidence based practice enhances service planning and delivery, clinical decision making and patient care. However, health professionals often lack the time and opportunity to access or generate evidence. Research capacity building is thus an important mechanism for improving health service delivery. This study evaluates the effectiveness of a Nurse and Allied Health Professional musculoskeletal research internship programme and explores the experiences of interns and their mentors.
Methods: Sixteen new graduates completed the internship programme (September 2015 – August 2018). Twelve interns and thirteen mentors participated in the evaluation. The evaluation used qualitative asynchronous email-based interviews to explore the experiences of interns and mentors. Interpretive phenomenological analysis of coded transcripts identified principal themes.
Results: Early research outputs from the interns include three peer reviewed publications and 21 conference abstract presentations. Two interns were in full time research at the time of interview or had a research component in their clinical role. Nine interns in clinical posts disclosed plans to return to research in the near future. Seven themes were identified: the impact on interns’ careers; personal impact (for example, influence on self-confidence); impact on clinical practice; drivers for applying; intervention design (for example, attitudes concerning the timing and duration of the intervention); mentorship and networking (including general support provided and quality of career advice); challenges.
Conclusion: The internship programme is an effective model in building research capacity in musculoskeletal research for Nurses and Allied Health Professionals, influencing careers, building confidence and improving clinical practice. The internship programme has the potential to be replicable to other clinical contexts nationally and internationally.
Evaluating of the predictors of high blood pressure in children and adolescence: Findings from Iranian health care system reform plan
Authors: Taghizadeh Shahnaz , Farhangi Mahdieh Abbasalizad , Pourali Fathollah Pourali , jafarabadi mohammad asghari 
Published: November 2019

Abstract
Background: to evaluate the role of dietary pattern and life style associated factors in predicting hypertension among overweight and obese pediatrics. Methods : In the current cross-sectional study, 425 overweight and obese children and adolescents aged 6 to 18 years were enrolled. The predictors of blood pressure considering patterns of fruits, vegetables, dairy products, fast food or junk food intake and meal consumption and also life style habits including hours of watching TV and physical activity, anthropometric indices were included in the scoring algorithm. Results : The results of final model of hierarchical linear regression showed that SBP and DBP had directly significant correlation with age (p<0.001, p<0.001) and BMI (p<0.005, p<0.007) respectively. Moreover, DBP was in significant correlation with fruit consumption of less than 2 serving per day versus never consumption (p=0.014, B= 0.444), fruit consumption of more than 2 serving per day versus never consumption (p=0.014, B= 0.480), and vegetable consumption less than 3 serving per day versus never consumption (p=0.045, B= -0.374). Also, results showed that DBP had significant correlation with fast foods /junk foods consumption of 1-2 items per week versus almost every day consumption (p= 0.047, B=-0.177). This final model could predict 32.1% of hypertension by SBP and DBP (R2 =0.321). Conclusion : According to our findings, consumption of lower vegetables and fruits, higher amounts of fast foods, higher age and BMI could be potent predictors of high blood pressure among Iranian children and adolescents. Key words: hypertension, children, adolescents, Iranian health care reform system
Economic burden and mental health of primary caregivers of perinatally HIV infected adolescents from Kilifi, Kenya
Authors: Katana Patrick V , Abubakar Amina , Nyongesa Moses K. , Ssewanyana Derrick , Mwangi Paul , Newton Charles R , Jemutai Julie 
Published: November 2019

Abstract
Background: Eighty per cent of perinatally HIV infected (PHI) adolescents live in sub-Saharan Africa (SSA), a setting also characterized by huge economic disparities. Caregiving is crucial to the management of chronic illness such as HIV/AIDS, but the economic costs and mental disorders borne by caregivers of PHI adolescents often go unnoticed. In this study, we evaluated economic costs, coping strategies and association between economic cost and mental health functioning of caregivers of perinatally HIV infected adolescents in Kilifi, Kenya. Methods: We used a cost of illness descriptive analysis approach and mental health was assessed using the Patient Health Questionnaire (PHQ-9). Cross-sectional data were collected from 121 primary caregivers of PHI adolescents in Kilifi using a structured cost questionnaire. Economic costs (direct costs and indirect costs) were measured from primary caregivers’ perspective. We used descriptive statistics in reporting the results of this study. Results: Average monthly direct and indirect costs per primary caregiver was Ksh 2,784.51 (USD 27.85). Key drivers of direct costs were transportation (66.5%) and medications (13.8%). Total monthly costs represented 28.8% of the reported caregiver monthly earnings. Majority of the caregivers borrowed resources to cope with high economic burden. About 10.7% of primary caregivers reported depressive symptoms. Caregivers with positive depression screen (PHQ-9 score ≥10) had high average monthly direct and indirect costs. However, this was not statistically different compared to costs incurred by caregivers who screened negative for depressive symptoms. Conclusion: Our study indicates that HIV/AIDS is associated with a significant economic burden for caregivers of adolescents living with HIV. These high economic burdens seem to negatively influence the mental health of caregivers of adolescents living with HIV. Results underscore the need for developing economic empowerment and social support programmes that reduce the economic burden of caring for perinatally infected adolescent. These efforts may improve the mental health and quality of life of caregivers of adolescents living with HIV.
Characterization of lumbar lymph node, a CNS-specific draining lymph node, after spinal cord injury in rats
Authors: Askarifirouzjaei Hadi , Khajoueinejad Leila , Fazeli Mehdi , Tiraihi Taki , Pourfathollah Ali Akbar 
Published: November 2019

Abstract
Regional tissue-draining lymph nodes are the major active site after inflammation that generate primary immune responses according to lymphatic system pathways. However, CNS specific draining lymph nodes have not characterized individually after spinal cord injury (SCI). Therefore, we examined the morphofunctional state of the Lumbar lymph node, the closest CNS-draining lymph node adjacent to the lesion site in thoracic spinal cord injury. Findings: Lumbar lymph nodes isolated 7 days after low thoracic spinal cord injury were compared with sham control and intact control rats. The significant enlargement was observed in lumbar lymph nodes in SCI group accompanied by increased total cell number, while there was a significantly higher cell death rate. Besides, the proliferation test performed on lymphocytes lumbar lymph nodes one week after SCI revealed accelerated proliferation rate compared to sham and intact control groups, which was associated with significant elevation of IFN-γ/IL4 ratio, which confirms adaptive immunity is biased towards the Th1 pro-inflammatory responses. Conclusions: Accordingly, we conclude that the lumbar lymph node is an important CNS-draining lymph node for understanding the immunopathology of SCI, which needs to be considered as a major active lymphoid organ adjacent to the lesion site.
Differential Activation of Neuroinflammatory Pathways in Children with Seizures: A Cross-Sectional Study
Authors: Bartolini Luca , Moran Michael P. , Norato Gina , Thomas Bobbe , Dick Alexander D. , Wells Elizabeth , Suslovic William , Bumbut Adrian , Chamberlain James M. , Theodore William H. , Gaillard William D. , Jacobson Steven 
Published: November 2019

Abstract
Background: Experimental and clinical findings suggest a crucial role of inflammation in epileptogenesis. We aimed to analyze levels of inflammatory cytokines in plasma and saliva from children with acute seizures and healthy controls and measure their associations with HHV6 and EBV infection.
Methods: We analyzed plasma from 36 children within 24 hours of acute seizures (cases) and 43 healthy controls and saliva from 44 cases and 44 controls with a multiplex immunoassay. Saliva from all controls and 65 cases and blood from 26 controls and 35 cases were also analyzed by ddPCR for viral DNA. Statistical analysis included Wilcoxon Rank Sum test, Fisher’s exact test, ANOVA and Spearman correlation.
Results: Compared to controls, children with breakthrough seizures (n=18) had higher levels of CCL11 (p<0.001), CCL26 (p<0.001), IL-8 (p=0.03), CCL4 (p=0.02) in plasma. Children with new onset seizures (n=13) showed higher levels of CCL11 (p=0.05) and IL-6 (p=0.01). Patients with febrile seizures (n=5) had higher levels of IFNg (p<0.001), IL-6 (p<0.001), IL-10 (p<0.001), CXCL10 (p=0.001). CCL11 was higher with 3 or more seizures (p=0.01), seizures longer than 10 minutes (p=0.001) and when EEG showed focal slowing (p=0.02).
In saliva, febrile seizures had higher levels of IL-1β (n=7, p=0.04) and new onset seizures had higher IL-6 (n=15, p=0.02). Plasma and saliva cytokine levels did not show correlation.
Frequency of HHV-6 and EBV detection was similar across seizure types and not different than controls. We found no correlation between viral load and cytokine levels
Conclusions: We showed differential activation of neuroinflammatory pathways in plasma from different seizure etiologies compared to controls, unrelated to HHV-6 infection.
Monitoring of selected parasites and other foodborne microorganisms in vegetable products at point of sale
Authors: Moravkova Monika , Vasickova Petra , Mikel Pavel , Slany Michal , Kolackova Ivana , Karpiskova Renata , Kralik Petr 
Published: November 2019

Abstract
It is supposed that epidemiological data linked to cases of alimentary infection from fresh produce are scarce and usually underestimated. The present study reveals data concerning the occurrence of less studied foodborne pathogens such as parasites ( Giardia intestinalis , Cryptosporidium parvum/hominis ) and viruses (norovirus, hepatitis A virus) in 175 samples of fresh-cut vegetables, frozen vegetables and sprouts. In addition, samples were also analyzed for the presence of bacterial indicators of production hygiene such as Escherichia coli and Staphylococcus aureus . Our results revealed that DNA of G. intestinalis was found in two samples (1.1%) of mixed fresh vegetable salads and mixed frozen vegetables at a level of 100 CFU/g. Norovirus was detected in two samples (1.1%) of rucola and frozen mixed vegetables. No sample was positive for C. parvum/hominis or hepatitis A virus. Our results highlight the need for microbial analysis of food of non-animal origin for specific parasitic and viral agents not generally monitored in these food category types, but their presence poses risks for alimentary infection.
Effects of Acute Peritoneal Dialysis in Extremely-Low-Birth-Weight Infants: A Retrospective Cohort Study
Authors: Noh Jihyun , Kim Chae Young , Jung Euiseok , Lee Joo Hoon , Park Young-Seo , Lee Byong Sop , Kim Ellen Ai-Rhan , Kim Ki-Soo 
Published: November 2019

Abstract
Background :Acute peritoneal dialysis (APD) is a first-line rescue therapy for neonatal acute kidney injury (AKI) refractory to conservative management, but its efficacy in preterm infants remains unclear. This study aimed to investigate the clinical outcomes of APD and APD efficiency in extremely-low-birth-weight (ELBW) infants. Methods : We reviewed the medical records of inborn ELBW infants who underwent APD in a tertiary center. We recorded perinatal characteristics, including the causes of AKI and clinical outcomes. Serial input and output data and laboratory parameters to assess ultrafiltration/dialysis efficiency were also obtained. Results : A total of 12 ELBW infants were included in the study. Mean gestational age and birth weight were 27.2 weeks and 706.5 g, respectively. Leading cause of AKI was sepsis (50%) followed by perinatal asphyxia. Mean age at the start of PD was 16.3 days. Mean ultrafiltration (UF) rate was 2.73 mL/kg/h. After a mean duration of 9.4 days, the mean reduction in serum BUN and Cr levels was 42.5% and 20.1%, respectively. Mean sodium level increased from 135.8 to 144.7 mg/mL, and mean potassium level decreased from 6.8 to 5.0 mg/mL. The most common complication was mechanical dysfunction of the catheter, including dialysate leakage via the insertion site (75%). Only two patients were successfully weaned off APD. The overall mortality rate was 92%. Conclusions : In ELBW infants with AKI, APD was an effective rescue therapy in terms of its ultrafiltration and dialysis efficiency, but not with respect to neonatal mortality. Indications for APD in ELBW infants should be individualized depending on the etiology of AKI.
IDentification of patients in need of general and specialised PALLiative care (ID-PALL©): item generation and content validity of a new interprofessional screening instrument.
Authors: Lüthi Fabienne Teike , Bernard Mathieu , Beauverd Michel , Gamondi Claudia , Ramelet Anne-Sylvie , Borasio Gian Domenico 
Published: November 2019

Abstract
Background Early identification of patients requiring palliative care is a major public health concern. A growing number of instruments exist to help professionals in identifying these patients, but thus far, none have been thoroughly assessed for criterion validity. In addition, no currently available instruments differentiate between patients in need of general vs. specialized palliative care, and most are primarily intended for physicians’ use. This study aims to develop a new interprofessional instrument allowing identification of patients in need of general vs specialized palliative care.Methods The instrument development consisted of four steps: i) literature review to determine the concept to measure; ii) generation of a set of items; iii) review of the initial set of items by experts to establish the content validity; iv) administration of the items to a sample of the target population to establish face validity. We conducted a Delphi process with experts in palliative care to accomplish step 3 and sent a questionnaire to nurses and physicians non-specialised in palliative care to achieve step 4. A committee of interdisciplinary clinical experts supervised all steps.Results The study was conducted in the French - and Italian-speaking regions of Switzerland. The literature review confirmed the necessity of distinguishing between general and specialised palliative care needs and of adapting clinical recommendations to these different needs. Thirty-six nurses and physicians participated in the Delphi process and 28 were involved in the face validity assessment. The Delphi process resulted in two item lists: a 7-items list to identify patients in need of general PC and an 8-items list for specialised PC needs. The content and face validity were deemed to be acceptable by both the expert and the target populations.Conclusion This instrument considers a new perspective in the identification of patients requiring palliative care as it has been designed to differentiate between general and specialised palliative care needs. Moreover, diagnostic data is not fundamental to the use of the instrument, thus facilitating its use by healthcare professionals other than physicians, in particular nurses. Internal and criterion validity assessments are ongoing and essential before further dissemination of the instrument.
Oral health status and associated lifestyle behaviors among Iranian adults: a population based household survey
Authors: Jahangiry Leila , Bagheri Raziollah , Darabi Fatemeh , Sarbakhsh Parvin , Sistani Mohammad Mehdi Naghibi , Ponnet Koen 
Published: November 2019

Abstract
Background: Poor oral hygiene can lead to serious diseases, like periodontitis, tooth decay, pain and discomfort in teeth or gums, infection, and loss of teeth. In Iran, particularly adults between 50 years and older experience oral health problems, and this age group will grow the next decades. Despite increasing attention into healthy aging, there is less emphasis on oral hygiene. This survey aimed to investigate oral health status among Iranian adults. This knowledge may provide vital information to those who are planning strategies of oral health care.
Method: A population-based household survey was conducted to recruit a representative sample of adults. This study was carried out among adults aged 18-65 years between May and October 2016 in Tabriz, Iran. The study population was sampled using a multi-stage cluster sampling design. The WHO’s oral health questionnaire (WHO’s OHQ) was used for measuring oral health status and oral health behavior.
Results: In total, 2310 respondents completed the survey. The mean age (SD) of the participants was 41.6(23.4) years. About 48.8% of participants were male and 51.2% were female. 187(8.1%) were edentulous, and 152 (20.7%) of those participants were aged 50 to 65 years. 72.3% of the sample were dentate in that they had 20 or more teeth. Half of adults aged 50-65 years said they had 20 or more teeth. In general, about one-third of the participants reported that they don’t brush their teeth daily (23% for 18-35-year-old adults, 35.9% for 36-50-year-old adults, and 44.6% for 51- to 65-year-old adults).
In our sample, 39.4% of 18-35-year-olds, 34.1% of 36-50-year-olds, and 26.6% of 51-65-year-olds had visited a dentist less than six months ago. One-third of participants eat sweets every day and frequently consume tea with sugar.
Conclusion: The oral health status indicates that even though the majority of Iranian people assess their dental health positively, only a minority of participants have regular dental visits. Visits to the dentist decline by increasing age, and oral health problems increase. The study findings underline the importance of dental visits and that poor oral health may increase the risk of adverse health outcomes, particularly as age increases.