bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of different microbiological procedures for the diagnosis of Pneumocystis jirovecii pneumonia on bronchoalveolar-lavage fluid
Authors: Franconi Iacopo , Leonildi Alessandro , Erra Gianluca , Fais Roberta , Falcone Marco , Ghelardi Emilia , Lupetti Antonella 
Published: May 2022

Abstract
Background
The current diagnostic gold standard for Pneumocystis jirovecii is represented by microscopic visualization of the fungus from clinical respiratory samples, as bronchoalveolar-lavage fluid, defining “proven” P. jirovecii pneumonia, whereas qPCR allows defining “probable” diagnosis, as it is unable to discriminate infection from colonization. However, molecular methods, such as end-point PCR and qPCR, are faster, easier to perform and interpret, thus allowing the laboratory to give back the clinician useful microbiological data in a shorter time. The present study aims at comparing microscopy with molecular assays and beta-D-glucan diagnostic performance on bronchoalveolar-lavage fluids from patients with suspected Pneumocystis jirovecii pneumonia. Bronchoalveolar-lavage fluid from eighteen high-risk and four negative control subjects underwent Grocott-Gomori’s methenamine silver-staining, end-point PCR, RT-PCR, and beta-D-glucan assay.

Results
All the microscopically positive bronchoalveolar-lavage samples (50%) also resulted positive by end-point and real time PCR and all, but two, resulted positive also by beta-D-glucan quantification. End-point PCR and RT-PCR detected 10 (55%) and 11 (61%) out of the 18 samples, respectively, thus showing an enhanced sensitivity in comparison to microscopy. All RT-PCR with a Ct < 27 were confirmed microscopically, whereas samples with a Ct ≥ 27 were not.

Conclusions
Our work highlights the need of reshaping and redefining the role of molecular diagnostics in a peculiar clinical setting, like P. jirovecii infection, which is a rare but also severe and rapidly progressive clinical condition affecting immunocompromised hosts that would largely benefit from a faster diagnosis. Strictly selected patients, according to the inclusion criteria, resulting negative by molecular methods could be ruled out for P. jirovecii pneumonia.
Regulation mechanisms of flavonoids biosynthesis of Hancheng Dahongpao peels (Zanthoxylum bungeanum Maxim) at different development stages by integrated metabolomics and transcriptomics analysis
Authors: Zheng Tao , Han Jun , Su Ke-xing , Sun Bing-yin , Liu Shu-ming 
Published: May 2022

Abstract
Background
Flavonoids have strong free radical scavenging and antioxidant capacity. The high abundance of flavonoids in Chinese prickly ash peels have many benefits to human health. In this study, ‘Hancheng Dahongpao’, a main cultivar, was taken as materials to investigate the flavonoids biosynthesis mechanism of Zanthoxylum bungeanum Maxim at three key development stages by integration of metabolomics and transcriptomics analysis.

Results
A total of 19 differentially accumulated metabolites were identified, the key flavonoids compounds were kaempferol, quercetin and their glycoside derivatives, and two major anthocyanins (peonidin O-hexoside and peonidin 3-O-glucoside). 5 gene networks/modules including 15 important candidate genes were identified, which was highly correlated with flavonoids. Among these genes, ZM-163828 and ZM-184209 were strongly correlated with kaempferol and quercetin, and ZM-125833 and ZM-97481 were controlled the anthocyanins biosynthesis. Moreover, it was shown that MYB-ZM1, MYB-ZM3, MYB-ZM5, MYB-ZM6 and MYB-ZM7 coordinately controlled flavonoids accumulation through regulating the structural genes.

Conclusions
Generally, this study systematically revealed the flavonoids metabolic pathways and candidate genes involved in flavonoids biosynthesis and laid a foundation for the potential targets for the breeding of new valuable Chinese prickly ash cultivars.
Quantifying human mixing patterns in Chinese provinces outside Hubei after the 2020 lockdown was lifted
Authors: Zhao Yining , O’Dell Samantha , Yang Xiaohan , Liao Jingyi , Yang Kexin , Fumanelli Laura , Zhou Tao , Lv Jiancheng , Ajelli Marco , Liu Quan-Hui 
Published: May 2022

AbstractBackgroundContact patterns play a key role in the spread of respiratory infectious diseases in human populations. During the COVID-19 pandemic, the regular contact patterns of the population have been disrupted due to social distancing both imposed by the authorities and individual choices. Many studies have focused on age-mixing patterns before the COVID-19 pandemic, but they provide very little information about the mixing patterns in the COVID-19 era. In this study, we aim at quantifying human heterogeneous mixing patterns immediately after lockdowns implemented to contain COVID-19 spread in China were lifted. We also provide an illustrative example of how the collected mixing patterns can be used in a simulation study of SARS-CoV-2 transmission.Methods and resultsIn this work, a contact survey was conducted in Chinese provinces outside Hubei in March 2020, right after lockdowns were lifted. We then leveraged the estimated mixing patterns to calibrate a mathematical model of SARS-CoV-2 transmission. Study participants reported 2.3 contacts per day (IQR: 1.0–3.0) and the mean per-contact duration was 7.0 h (IQR: 1.0–10.0). No significant differences in average contact number and contact duration were observed between provinces, the number of recorded contacts did not show a clear trend by age, and most of the recorded contacts occurred with family members (about 78%). The simulation study highlights the importance of considering age-specific contact patterns to estimate the COVID-19 burden.ConclusionsOur findings suggest that, despite lockdowns were no longer in place at the time of the survey, people were still heavily limiting their contacts as compared to the pre-pandemic situation.
Diarrhoeal outcomes in young children depend on diarrhoeal cases of other household members: a cross-sectional study of 16,025 people in rural Uganda
Authors: Shaaban Farina L. , Kabatereine Narcis B. , Chami Goylette F. 
Published: May 2022

AbstractBackgroundThere is a limited understanding of how diarrhoeal cases across other household members influence the likelihood of diarrhoea in young children (aged 1–4 years).MethodsWe surveyed 16,025 individuals from 3421 households in 17 villages in Uganda. Using logistic regressions with standard errors clustered by household, diarrhoeal cases within households were used to predict diarrhoeal outcomes in young children. Regressions were adjusted for socio-demographic, water, sanitation, and hygiene (WASH), and ecological covariates. Selection bias for households with (1632/3421) and without (1789/3421) young children was examined.ResultsDiarrhoeal prevalence was 13.7% (2118/16,025) across all study participants and 18.5% (439/2368) in young children. Young children in households with any other diarrhoeal cases were 5.71 times more likely to have diarrhoea than young children in households without any other diarrhoeal cases (95% CI: 4.48–7.26), increasing to over 29 times more likely when the other diarrhoeal case was in another young child (95% CI: 16.29–54.80). Diarrhoeal cases in older household members (aged ≥ 5 years) and their influence on the likelihood of diarrhoea in young children attenuated with age. School-aged children (5–14 years) had a greater influence on diarrhoeal cases in young children (Odds Ratio 2.70, 95% CI: 2.03–3.56) than adults of reproductive age (15–49 years; Odds Ratio 1.96, 95% CI: 1.47–2.59). Diarrhoeal cases in individuals aged ≥ 50 years were not significantly associated with diarrhoeal outcomes in young children (P > 0.05). These age-related differences in diarrhoeal exposures were not driven by sex. The magnitude and significance of the odds ratios remained similar when odds ratios were compared by sex within each age group. WASH factors did not influence the likelihood of diarrhoea in young children, despite influencing the likelihood of diarrhoea in school-aged children and adults. Households with young children differed from households without young children by diarrhoeal prevalence, household size, and village WASH infrastructure and ecology.ConclusionsOther diarrhoeal cases within households strongly influence the likelihood of diarrhoea in young children, and when controlled, removed the influence of WASH factors. Future research on childhood diarrhoea should consider effects of diarrhoeal cases within households and explore pathogen transmission between household members.
Relationship between Helicobacter pylori infection and white matter lesions in patients with migraine
Authors: Öcal Serkan , Öcal Ruhsen , Suna Nuretdin 
Published: May 2022

Abstract
Background/aim
White matter lesions (WML) are more frequently observed in migraine patients than in the average population. Associations between Helicobacter pylori (H. pylori) infection and different extraintestinal pathologies have been identified. Here, we aimed to investigate the association between H. pylori infection and WML in patients diagnosed with episodic migraine.

Materials and methods
A retrospective study was conducted with 526 subjects with a diagnosis of episodic migraine. Hyperintensity of WML had been previously evaluated in these patients with brain magnetic resonance imaging (MRI) examinations. Previous endoscopic gastric biopsy histopathological examination of the same patients and reports on H. pylori findings were recorded. The demographic characteristics of the patients, such as age, gender and chronic systemic diseases such as hypertension and diabetes mellitus (DM) were recorded. Statistical evaluation was made.

Results
Evaluation was made among 526 migraine patients who met the inclusion criteria, comprising 397 (75.5%) females and 129 (24.5%) males with a mean age of 45.57 ± 13.46 years (range, 18–69 years). WML was detected on brain MRI in 178 (33.8%) patients who were also positive for H. pylori (p <  0.05). Subjects who are H. pylori-positive with migraine, WML were observed at a 2.5-fold higher incidence on brain MRI (odds ratio: 2.562, 95% CI 1.784–3.680). WML was found to be more significant in patients with hypertension and migraine than those without (p <  0.001). Older age was also found to be associated with WML (OR = 1.07, 95% CI: 0.01–0.04, p <  0.001). The age (p <  0.001), H. pylori (p <  0.001), hypertension (p <  0.001), and hypertension + DM (p <  0.05), had significant associations in predicting WML according to the multivariate logistic regression analysis. The presence of hypertension had a higher odds ratio value than the other variables.

Conclusion
It was concluded that H. pylori infection, as a chronic infection, can be considered a risk factor in developing WML in subjects with migraine.
Characteristics and co-admissions of mothers and babies admitted to residential parenting services in the year following birth in NSW: a linked population data study (2000–2012)
Authors: Dahlen Hannah Grace , Schmied Virginia , Fowler Cathrine , Peters Lilian L. , Ormsby Simone , Thornton Charlene 
Published: May 2022

Abstract
Background
There is a tiered healthcare system in Australia to support maternal and child health, including, non-psychiatric day stay and residential parenting services (RPS) such as Tresillian and Karitane (in New South Wales [NSW]). RPS are unique to Australia, and currently there is limited information regarding the healthcare trajectory of women accessing RPS and if they are more likely to have admissions to other health facilities within the first-year post-birth. This study aimed to examine differences in hospital co-admissions for women and babies admitted to RPS in NSW in the year following birth compared to non-RPS admitted women.

Methods
A linked population data study of all women giving birth in NSW 2000–2012. Statistical differences were calculated using chi-square and student t-tests.

Results
Over the 12-year timeframe, 32,071 women and 33,035 babies were admitted to RPS, with 5191 of these women also having one or more hospital admissions (7607 admissions). The comparator group comprised of 99,242 women not admitted to RPS but having hospital admissions over the same timeframe (136,771 admissions). Statistically significant differences between cohorts were observed for the following parameters (p ≤ .001). Based upon calculated percentages, women who were admitted to RPS were more often older, Australian born, socially advantaged, private patients, and having their first baby. RPS admitted women also had more multiple births and labour and birth interventions (induction, instrumental birth, caesarean section, epidural, episiotomy). Their infants were also more often male and admitted to Special Care Nursery/Neonatal Intensive Care. Additionally, RPS admitted women had more admissions for mental health and behavioural disorders, which appeared to increase over time. There was no statistical difference between cohorts regarding the number of women admitted to a psychiatric facility; however, women attending RPS were more likely to have mood affective, or behavioural and personality disorder diagnoses.

Conclusion
Women accessing RPS in the year post-birth were more socially advantaged, had higher birth intervention and more co-admissions and treatment for mental health disorders than those not accessing RPS. More research is needed into the impact of birth intervention and mental health issues on subsequent parenting difficulties.
Role of CDH23 as a prognostic biomarker and its relationship with immune infiltration in acute myeloid leukemia
Authors: Yang Jiao , Lu Fei , Ma Guangxin , Pang Yihua , Zhao Yanan , Sun Tao , Ma Daoxin , Ye Jingjing , Ji Chunyan 
Published: May 2022

Abstract
Background
Cadherin-23 (CDH23) plays an important role in intercellular adhesion and is involved in the progression of several types of cancer. However, the biological functions and effect of CDH23 expression on the prognosis of patients with acute myeloid leukemia (AML) are unexplored. Herein, we aim to characterize the role and molecular functions of CDH23 in AML.

Methods
We downloaded the transcriptomic profiles and clinical data from the Cancer Genome Atlas and Beat AML trial. The expression level of CDH23 was assessed using Gene Expression Profiling Interactive Analysis (GEPIA). Kaplan-Meier survival analysis was used to assess prognostic value of CDH23. Correlation and biological function analyses were performed using LinkedOmics and GeneMANIA. Relationship of CDH23 with immune infiltration level was determined using Tumor Immune Estimation Resource (TIMER).

Results
We found that the CDH23 expression was aberrantly upregulated in patients with AML and could be used as an independent risk factor of overall survival using Cox multivariate analysis. Notably, we observed a negative correlation between CDH23 expression and immune cell infiltration abundance by calculating the immune and stromal scores. In addition, functional enrichment analysis established that CDH23 plays a crucial role in tumor immunity.

Conclusions
Our findings indicate that upregulated CDH23 expression corresponds to decreased overall survival of patients with AML. CDH23 may be involved in mediating tumor immune environment, and this highlights the potential of CDH23 as a therapeutic target in AML.
Volasertib as a monotherapy or in combination with azacitidine in patients with myelodysplastic syndrome, chronic myelomonocytic leukemia, or acute myeloid leukemia: summary of three phase I studies
Authors: Platzbecker Uwe , Chromik Joerg , Krönke Jan , Handa Hiroshi , Strickland Stephen , Miyazaki Yasushi , Wermke Martin , Sakamoto Wataru , Tachibana Yoshifumi , Taube Tillmann , Germing Ulrich 
Published: May 2022

Abstract
Background
This report summarizes three phase I studies evaluating volasertib, a polo-like kinase inhibitor, plus azacitidine in adults with myelodysplastic syndromes (MDS), chronic myelomonocytic leukemia, or acute myeloid leukemia.

Methods
Patients received intravenous volasertib in 28-day cycles (dose-escalation schedules). In Part 1 of 1230.33 (Study 1; NCT01957644), patients received 250–350 mg volasertib on day (D)1 and D15; in Part 2, patients received different schedules [A, D1: 170 mg/m2; B, D7: 170 mg/m2; C, D1 and D7: 110 mg/m2]. In 1230.35 (Study 2; NCT02201329), patients received 200–300 mg volasertib on D1 and D15. In 1230.43 (Study 3; NCT02721875), patients received 110 mg/m2 volasertib on D1 and D8. All patients in Studies 1 and 2, and approximately half of the patients in Study 3, were scheduled to receive subcutaneous azacitidine 75 mg/m2 on D1–7.

Results
Overall, 22 patients were treated (17 with MDS; 12 previously untreated). Across Studies 1 and 2 (n = 21), the most common drug-related adverse events were hematological (thrombocytopenia [n = 11]; neutropenia [n = 8]). All dose-limiting toxicities were grade 4 thrombocytopenia. The only treated patient in Study 3 experienced 18 adverse events following volasertib monotherapy. Studies 1 and 2 showed preliminary activity (objective response rates: 25 and 40%).

Conclusions
The safety of volasertib with azacitidine in patients with MDS was consistent with other volasertib studies. All studies were terminated prematurely following the discontinuation of volasertib for non-clinical reasons by Boehringer Ingelheim; however, safety information on volasertib plus azacitidine are of interest for future studies in other diseases.
Effect of pre and post-transplant body mass index on pediatric kidney transplant outcomes
Authors: Abdelrahman Safaa M. , Samir Basma , Alazem Eman Abobakr Abd , Musa Noha 
Published: May 2022

Abstract
Introduction
Kidney transplantation (KT) has been established as an efficient treatment of end stage renal disease (ESRD) with the advantage of allowing the patient to live a nearly healthy life. We aimed to determine whether pre-transplant body mass index (BMI) affects renal allograft function and survival in pediatric KT recipients.

Methods
cross sectional cohort study included 50 post KT recipients (more than 3 years) with an age range of 10 to 15 years, regularly following at the Kidney Transplantation Outpatient Clinic, Cairo University Children’s Hospital, were subjected to a detailed history and physical examination, laboratory investigation in the form of fasting blood glucose (FBG),oral glucose tolerance test (OGTT), lipid profile, hemoglobin A1c (HbA1c) and microalbuminuria.

Results
Pre- post- kidney transplant BMI has significant positive correlation with graft rejection episodes, HbA1c, FBG, BMI post-KT, total cholesterol, triglycerides, and low-density lipoprotein (p < 0.01). There was a statistically significant negative correlation between the mean difference of BMI (post – pre) and graft survival in years (p = 0.036). Obese patients displayed lower survival compared with non-obese subjects at 5 years, but this was statistically not significant (p-value = 0.165).

Conclusion
obesity is an independent risk factor for graft loss and patient death in kidney transplantation. Careful patient selection with pre-transplantation weight reduction is mandatory to reduce the rate of early post-transplantation complications and to improve long-term outcomes.
Impact of COVID-19 lockdown and link to women and children’s experiences of violence in the home in South Africa
Authors: Mahlangu P , Gibbs A , Shai N , Machisa M , Nunze N , Sikweyiya Y 
Published: May 2022

Abstract
Background
Evidence on the impact of COVID-19 and lockdown remains at an early stage. There is limited research about the impact of hard lockdown restrictions on families, specifically how these restrictions impact on women and children’s experiences of domestic violence, including intimate partner violence (IPV) and child abuse in South Africa. We conducted research among men and women in Gauteng province, South Africa to understand their experiences of the COVID-19 national lockdown and its impact and link to women and children’s experiences of domestic violence.

Methods
We conducted a qualitative study, using social media to recruit men and women who were 18 years and older, living with a spouse and/or children in Gauteng province, South Africa during the lockdown. To collect the data, we conducted telephone interviews, and analyzed data using the thematic approach.

Results
The lockdown had unprecedented negative economic impacts on families, and exacerbated some of the risk factors for violence against women and children in the home in South Africa. Some women reported experiences of emotional violence. Experiences of physical violence were mostly amongst children. The risk factors for women and children’s experiences of violence in the home differed by socio-economic class. Job losses and reduction in earnings resulted to food insecurity which was a key driver of violence in most low socio-economic status (SES) families. Confinement in the home with spouses was an unfamiliar and difficult experience, associated with conflict and perpetration of violence by men in high SES families. Participants across socio-economic groups reported high levels of stress with limited psychosocial support available during the lockdown.

Conclusions
Our finding showing a link between low-socio-economic status and increased risk for domestic violence during the lockdown in South Africa suggests the need for socio-economic interventions to mitigate these risks. Structural and social relief measures need to be strengthened to reduce the loss of jobs and income and to address food insecurity during pandemics. Psychosocial support should be provided to men and women to mitigate the mental health impacts of the pandemics and lockdown.
Estimating the public health impact had tobacco-free nicotine pouches been introduced into the US in 2000
Authors: Lee Peter N. , Fry John S. , Ljung Tryggve 
Published: May 2022

Abstract
Background
For smokers not intending to quit, switching to a reduced-risk nicotine product should be healthier than continuing smoking. We estimate the health impact, over the period 2000–2050, had the nicotine pouch ZYN hypothetically been introduced into the US in 2000. ZYN’s toxicant profile and method of use is like that for Swedish snus, a product with known health effects much less than smoking.

Methods
Our modelling approach is similar to others developed for estimating potential effects of new tobacco products. It starts with a simulated cohort of 100,000 individuals in the year 2000 subdivided by age, sex, and smoking status (including years since quitting). They are followed annually accounting for births, net immigrations, deaths and product use changes, with follow-up carried out in the Base Case (ZYN not introduced) and Modified Case (ZYN introduced). Using informed assumptions about initiation, quitting and switching rates, distributions of the population over time are then constructed for each Case, and used to estimate product mortality based on assumptions about the relative risk according to product use.

Results
Whereas in both Base and Modified Cases, the prevalence of any current product use is predicted to decline from about 22% to 10% during follow-up, in the Modified Case about 25% of current users use ZYN by 2050, about a quarter being dual users and the rest ZYN-only users. Over the 50 years, deaths at ages 35–84 from product use among the 100,000 are estimated as 249 less in the Modified than the Base Case, equivalent to about 700,000 less in the whole US. Sensitivity analyses varying individual parameter values confirm the benefits of switching to ZYN, which increase as either the switching rate to ZYN increases or the initiation rate of ZYN relative to smoking increases. Even assuming the reduction in excess mortality risk using ZYN use is 20% of that from smoking rather than the 3.5% assumed in the main analyses, the reduction in product-related deaths would still be 213, or about 600,000 in the US.

Conclusions
Although such model-based estimates involve uncertainties, the results suggest that introducing ZYN could substantially reduce product-related deaths.