bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical impact of minimal residual disease in blood and bone marrow of children with acute myeloid leukemia
Authors: Karol Seth E. , Coustan-Smith Elaine , Pounds Stanley , Wang Lei , Inaba Hiroto , Ribeiro Raul C. , Pui Ching-Hon , Klco Jeffery M. , Rubnitz Jeffrey E. 
Published: April 2023

AbstractThe prognostic significance of bone marrow minimal residual disease (MRD) in pediatric patients with acute myeloid leukemia (AML) is well characterized, but the impact of blood MRD is not known. We, therefore, used flow cytometric assessment of leukemia-specific immunophenotypes to measure levels of MRD in both the blood and bone marrow of patients treated in the AML08 (NCT00703820) clinical trial. Blood samples were obtained on days 8 and 22 of therapy, whereas bone marrow samples were obtained on day 22. Among patients who tested as having MRD-negative bone marrow on day 22, neither day-8 nor day-22 blood MRD was significantly associated with the outcome. However, day-8 blood MRD was highly predictive of the outcome among patients who tested as having MRD-positive bone marrow on day 22. Although the measurement of blood MRD on day 8 cannot be used to identify patients who have day-22 MRD–negative bone marrow who are likely to relapse, our findings suggest that day-8 blood MRD results can identify patients with MRD-positive bone marrow who have a dismal prognosis and may be candidates for the early use of experimental therapy.
Draft genome and transcriptome of Nepenthes mirabilis, a carnivorous plant in China
Authors: Gao Yuan , Liao Hao-Bin , Liu Ting-Hong , Wu Jia-Ming , Wang Zheng-Feng , Cao Hong-Lin 
Published: April 2023

Abstract
Objectives
Nepenthes belongs to the monotypic family Nepenthaceae, one of the largest carnivorous plant families. Nepenthes species show impressive adaptive radiation and suffer from being overexploited in nature. Nepenthes mirabilis is the most widely distributed species and the only Nepenthes species that is naturally distributed within China. Herein, we reported the genome and transcriptome assemblies of N. mirabilis. The assemblies will be useful resources for comparative genomics, to understand the adaptation and conservation of carnivorous species.

Data description
This work produced ~ 139.5 Gb N. mirabilis whole genome sequencing reads using leaf tissues, and ~ 21.7 Gb and ~ 27.9 Gb of raw RNA-seq reads for its leaves and flowers, respectively. Transcriptome assembly obtained 339,802 transcripts, in which 79,758 open reading frames (ORFs) were identified. Function analysis indicated that these ORFs were mainly associated with proteolysis and DNA integration. The assembled genome was 691,409,685 bp with 159,555 contigs/scaffolds and an N50 of 10,307 bp. The BUSCO assessment of the assembled genome and transcriptome indicated 91.1% and 93.7% completeness, respectively. A total of 42,961 genes were predicted in the genome identified, coding for 45,461 proteins. The predicted genes were annotated using multiple databases, facilitating future functional analyses of them. This is the first genome report on the Nepenthaceae family.
Identification of priority pathogens for aetiological diagnosis in adults with community-acquired pneumonia in China: a multicentre prospective study
Authors: Zhang Lulu , Xiao Yan , Zhang Guoliang , Li Hongru , Zhao Jianping , Chen Mingwei , Chen Fuhui , Liu Ling , Li Yalun , Peng Liping , Zhao Feng , Yang Donghong , Wen Zhongmei , Wu Lei , Wu Shuo , Sun Yajiao , Wang Ying , Chen Lan , Wang Xinming , Wang Lihui , Li Weimin , Qiu Haibo , Chen Yusheng , Gao Zhancheng , Ren Lili , Wang Jianwei 
Published: April 2023

Abstract
Background
Community-acquired pneumonia (CAP) is a major public health challenge worldwide. However, the aetiological and disease severity-related pathogens associated with CAP in adults in China are not well established based on the detection of both viral and bacterial agents.

Methods
A multicentre, prospective study was conducted involving 10 hospitals located in nine geographical regions in China from 2014 to 2019. Sputum or bronchoalveolar lavage fluid (BALF) samples were collected from each recruited CAP patient. Multiplex real-time PCR and bacteria culture methods were used to detect respiratory pathogens. The association between detected pathogens and CAP severity was evaluated.

Results
Among the 3,403 recruited eligible patients, 462 (13.58%) had severe CAP, and the in-hospital mortality rate was 1.94% (66/3,403). At least one pathogen was detected in 2,054 (60.36%) patients, with two or more pathogens were co-detected in 725 patients. The ten major pathogens detected were Mycoplasma pneumoniae (11.05%), Haemophilus influenzae (10.67%), Klebsiella pneumoniae (10.43%), influenza A virus (9.49%), human rhinovirus (9.02%), Streptococcus pneumoniae (7.43%), Staphylococcus aureus (4.50%), adenovirus (2.94%), respiratory syncytial viruses (2.35%), and Legionella pneumophila (1.03%), which accounted for 76.06–92.52% of all positive detection results across sampling sites. Klebsiella pneumoniae (p < 0.001) and influenza viruses (p = 0.005) were more frequently detected in older patients, whereas Mycoplasma pneumoniae was more frequently detected in younger patients (p < 0.001). Infections with Klebsiella pneumoniae, Staphylococcus aureus, influenza viruses and respiratory syncytial viruses were risk factors for severe CAP.

Conclusions
The major respiratory pathogens causing CAP in adults in China were different from those in USA and European countries, which were consistent across different geographical regions over study years. Given the detection rate of pathogens and their association with severe CAP, we propose to include the ten major pathogens as priorities for clinical pathogen screening in China.
Evidence gaps on weight gain in people living with HIV: a scoping review to define a research agenda
Authors: Guaraldi Giovanni , Bonfanti Paolo , Di Biagio Antonio , Gori Andrea , Milić Jovana , Saltini Paola , Segala Francesco V. , Squillace Nicola , Taramasso Lucia , Cingolani Antonella 
Published: April 2023

Abstract
Background
Combined antiretroviral therapy (cART) dramatically improved survival in people living with HIV (PLWH) but is associated with weight gain (WG), raising concern for a possible obesity epidemic in PLWH. This scoping review aims to identify the gaps in the existing evidence on WG in PLWH and generate a future research agenda.

Methods
This review was conducted according to the methodology for scoping studies and reported according to the PRISMA Extension for Scoping Review checklist. Articles published in English in the last 10 years indexed in Pubmed, WHO Global Index Medicus, or Embase were searched using specific queries focused on WG in PLWH.

Results
Following the selection process, 175 included articles were reviewed to search for the available evidence on four specific topics: (I) definition of WG in PLWH, (II) pathogenesis of WG in PLWH, (III) impact of ART on WG, (IV) correlation of WG with clinical outcomes. A summary of the data enabled us to identify gaps and clearly define the following research agenda: (I) develop a data-driven definition of WG in PLWH and define noninvasive assessment methods for body weight and fat composition; (II) further investigate the interaction between HIV/cART and immunity, metabolism, and adipose tissue; (III) establish the specific role of individual drugs on WG; (IV) clarify the independent role of WG, cART, HIV, and metabolic factors on clinical events.

Conclusions
The proposed research agenda may help define future research and fill the knowledge gaps that have emerged from this review.
Segmentation of thyroid glands and nodules in ultrasound images using the improved U-Net architecture
Authors: Zheng Tianlei , Qin Hang , Cui Yingying , Wang Rong , Zhao Weiguo , Zhang Shijin , Geng Shi , Zhao Lei 
Published: April 2023

AbstractBackgroundIdentifying thyroid nodules’ boundaries is crucial for making an accurate clinical assessment. However, manual segmentation is time-consuming. This paper utilized U-Net and its improved methods to automatically segment thyroid nodules and glands.MethodsThe 5822 ultrasound images used in the experiment came from two centers, 4658 images were used as the training dataset, and 1164 images were used as the independent mixed test dataset finally. Based on U-Net, deformable-pyramid split-attention residual U-Net (DSRU-Net) by introducing ResNeSt block, atrous spatial pyramid pooling, and deformable convolution v3 was proposed. This method combined context information and extracts features of interest better, and had advantages in segmenting nodules and glands of different shapes and sizes.ResultsDSRU-Net obtained 85.8% mean Intersection over Union, 92.5% mean dice coefficient and 94.1% nodule dice coefficient, which were increased by 1.8%, 1.3% and 1.9% compared with U-Net.ConclusionsOur method is more capable of identifying and segmenting glands and nodules than the original method, as shown by the results of correlational studies.
How do patients and families evaluate attitude of psychiatrists in Japan?: quantitative content analysis of open-ended items of patient responses from a large-scale questionnaire survey
Authors: Natsukari Ikuko , Higuchi Mari , Tsujimoto Tai 
Published: April 2023

Abstract
Background
Patient and Public Involvement (PPI) has been widely advocated in psychiatric fields. In Japan, however, PPI has not been implemented in clinical practice. In order to improve quality of psychiatric service in Japan, it is essential to understand psychiatrists’ attitudes from the patients’ perspective as a first step in practicing PPI. This study aimed to investigate the patients’ evaluation of psychiatrists’ attitudes by illustrating themes appeared in the questionnaire survey.

Methods
This study used the data obtained from the questionnaire survey responded by 2,683 patients with family members who belong to the family associations for psychiatric patients in Japan. Three open-ended question items in this survey, "criteria for selecting a psychiatrist (784 patient responses, response rate 29.2%),” “attitude of the psychiatrist in charge (929 patient responses, response rate 34.6%)," and "communication skills of the psychiatrist in charge (739 patient responses, response rate 27.5%)" were analyzed by co-occurrence network using KH Coder software.

Results
The common theme observed in all three items was whether psychiatrist took sufficient consultation time. The criteria for selecting a psychiatrist were summarized whether psychiatrist provided appropriate advices for patients’ problems, whether psychiatrist cared about patients’ demands and whether psychiatrist informed to patients about diseases and medications. The attitudes of the psychiatrists in charge that patients had most wanted their psychiatrists to improve were: psychiatrists only watch the computer, make diagnosis according to the patients’ individual condition, and try to build a relationship of trust with the patient. The patients’ demands regarding communication skills of the psychiatrist in charge included: whether the psychiatrist communicated in a way that improves the patient's psychological state, whether the psychiatrist was attentive to the patients’ family, and whether the psychiatrist could control his/her own mood during the consultation.

Conclusion
The results reflected the patients’ demands that do not appear in closed-ended items. It was suggested that patients’open-ended responses to questionnaires and their involvement in the psychiatric research (PPI) may provide more insight into improving pshchiaric care in Japan.
Pooled prevalence of depressive symptoms among medical students: an individual participant data meta-analysis
Authors:   Depression in Medical Students Research Group, Pacheco João Pedro Gonçalves , Bunevicius Adomas , Oku Afiong , Shindel Alan , Torres Albina Rodrigues , Bassols Ana Margareth Siqueira , de Abreu Ramos-Cerqueira Ana Teresa , Fernando Antonio , Katkute Arune , Mayda Atilla Senih , Nair Balakrishnan , Breyer Benjamin N. , Bakir Bilal , Kelly Brian , Angkurawaranon Chaisiri , Sreeramareddy Chandrashekhar , Samaranayake Chinthaka , Saravanan Coumaravelou , Del-Ben Cristina Marta , Hinic Darko , Goebert Deborah , Ristic-Ignjatovic Dragana , Al-faris Eiad , Chang Elaine , Venkatarao Epari , Mojs Ewa Helena , Youssef Farid Fayez , Huang Gan , Buneviciene Inesa , Gold Jessica Ashley , Smith Jim , Berner Juan Enrique , Warchol-Biedermann Katarzyna , Wilkins Kirsten Matthews , Walkiewicz Maciej , Lima Maria Cristina Pereira , Wolf Megan , Bore Miles , Yusoff Muhamad Saiful Bahri , Karaoglu Nazan , Mousa Omar , Bellodi Patricia Lacerda , Rohrbaugh Robert , Singh Ruchi , Gupta Sandhya , Baldassin Sergio , Mohd-Sidik Sherina , Peleg-Sagy Tal , Tin Tan Siew , Quince Thelma , Wahed Wafaa Yousif Abdel , Hu Xinran , Liu Zhening , Zatt Wilson Baldin , Lo Kenneth , Tam Wilson 
Published: April 2023

AbstractBackgroundThe methodological choice of aggregated estimates for meta-analysis may be notable for some common drawbacks, including variations in the cut-off values of depression, and lower statistical power for analyzing the associated factors. The study aimed to refine the precision of previous findings on the prevalence of depressive symptoms among medical students, through gathering individual participant data (IPD) as identified from our previous reviews.Material and methodsIn the present study, we searched MEDLINE, EMBASE, PsycINFO, WanFang, Scielo and LILACS to identify published systematic reviews and meta-analyses up to March 2018, then individual data was requested for further analysis (PROSPERO registration: CRD42018091917). The participants’ age, sex, year of study, scores for depressive symptoms, and other predictor variables were requested. To pool the prevalence from the included studies, random-effects model (two-step method) was used. Multiple linear regression was used to examine the associated factors on the depression z-scores (one-step method).ResultsOf the 249 studies, the datasets of 34 studies were included. The crude prevalence was 19.4% (95% CI: 18.8%, 19.9%) by one-step method and the pooled prevalence was 18.1% (95% CI: 14.1%, 22.1%) by two-step method. Multiple linear regression revealed that being a female, older age, and senior year of study were significantly associated with the z-score.ConclusionThe pooled prevalence of depressive symptoms from the Individual Participant Data (IPD) meta-analysis was lower than the previous meta-analyses using aggregated data. Age, sex, and year of study were significantly associated with the depression z-score. IPD meta-analysis may provide a more accurate estimation of disease burden, and allow verification of associated factors.
Assessment of vulnerability dimensions considering Family History and environmental interplay in Autism Spectrum Disorder
Authors: Brito Anita , Franco Felipe , Brentani Helena , Beltrão-Braga Patrícia Cristina Baleeiro 
Published: April 2023

Abstract
Background
Despite previous studies have recently shown Autism Spectrum Disorders (ASD) as having a strong genetics background, over a minimum environmental background, no study up to date has investigated the interplay between genetics and environment.

Methods
We have collected data regarding Family History (FH) and Environmental Factors (EF) from 2,141 individuals with ASD and their caretakers throughout Brazil, based on an online questionnaire. Most of the ASD individuals were males (81%) and the average age was 02 years minimum for males and females, and the maximum age was 41 years for males and 54 for females. People from all states in Brazil have answered the questionnaire. Genetic inheritance was obtained based on the declared FH of Psychiatric and Neurological diagnosis. As for EF, exposure to risk factors during pregnancy was considered, like infections, diabetes, drugs/chemicals exposure, socioeconomic, and psychological factors. Respondents were invited to answer the questionnaire in lectures given throughout Brazil, and by the social networks of the NGO “The Tooth Fairy Project”. A Multiple Correspondence Analysis (MCA) was conducted to search vulnerability dimensions, and a Cluster Analysis was conducted to classify and identify the subgroups.

Results
Regarding EF, social and psychological exposures contributed to the first two dimensions. Concerning FH, the first dimension represented psychiatric FH, while the second represented neurological FH. When analyzed together, EF and FH contributed to two new dimensions: 1. psychiatric FH, and 2. a psychosocial component. Using Cluster Analysis, it was not possible to isolate subgroups by genetic vulnerability or environmental exposure. Instead, a gradient of psychiatric FH with similar contributions of EF was observed.

Conclusion
In this study, it was not possible to isolate groups of patients that correspond to only one component, but rather a continuum with different compositions of genetic and environmental interplay.
Heart rate monitoring to detect acute pain in non-verbal patients: a study protocol for a randomized controlled clinical trial
Authors: Kildal Emilie S. M. , Quintana Daniel S. , Szabo Attila , Tronstad Christian , Andreassen Ole , Nærland Terje , Hassel Bjørnar 
Published: April 2023

AbstractBackgroundAutism entails reduced communicative abilities. Approximately 30% of individuals with autism have intellectual disability (ID). Some people with autism and ID are virtually non-communicative and unable to notify their caregivers when they are in pain. In a pilot study, we showed that heart rate (HR) monitoring may identify painful situations in this patient group, as HR increases in acutely painful situations.ObjectivesThis study aims to generate knowledge to reduce the number of painful episodes in non-communicative patients’ everyday lives. We will 1) assess the effectiveness of HR as a tool for identifying potentially painful care procedures, 2) test the effect of HR-informed changes in potentially painful care procedures on biomarkers of pain, and 3) assess how six weeks of communication through HR affects the quality of communication between patient and caregiver.MethodsWe will recruit 38 non-communicative patients with autism and ID residing in care homes.Assessments: HR is measured continuously to identify acutely painful situations. HR variability and pain-related cytokines (MCP-1, IL-1RA, IL-8, TGFβ1, and IL-17) are collected as measures of long-term pain. Caregivers will be asked to what degree they observe pain in their patients and how well they believe they understand their patient’s expressions of emotion and pain.Pre-intervention:HR is measured 8 h/day over 2 weeks to identify potentially painful situations across four settings: physiotherapy, cast use, lifting, and personal hygiene.Intervention:Changes in procedures for identified painful situations are in the form of changes in 1) physiotherapy techniques, 2) preparations for putting on casts, 3) lifting techniques or 4) personal hygiene procedures.Design:Nineteen patients will start intervention in week 3 while 19 patients will continue data collection for another 2 weeks before procedure changes are introduced. This is done to distinguish between specific effects of changes in procedures and non-specific effects, such as caregivers increased attention.DiscussionThis study will advance the field of wearable physiological sensor use in patient care.Trial registrationRegistered prospectively at ClinicalTrials.gov (NCT05738278).
Life in a time of COVID: retrospective examination of the association between physical activity and mental well-being in western Australians during and after lockdown
Authors: Piggott Ben , Chivers Paola , Sarasjärvi Kiira Karoliina , Bhoyroo Ranila , Lambert Michelle , Millar Lynne , Bulsara Caroline , Codde Jim 
Published: April 2023

Abstract
Background
The aim of this study was to examine physical activity and sedentary behaviours during Western Australia’s COVID-19 lockdown and their association with mental well-being.

Methods
Participants completed activity related questions approximately two months after a three-month lockdown (which formed part of a larger cross-sectional study from August to October 2020) as part of a 25-minute questionnaire adapted from the Western Australia Health and Well-being Surveillance system. Open-ended questions explored key issues relating to physical activity behaviours.

Results
During the lockdown period, 463 participants (female, n = 347; 75.3%) reported lower number of active days (W = 4.47 p < .001), higher non-work-related screen hours per week (W = 11.8 p < .001), and higher levels of sitting time (χ2=28.4 p < .001). Post lockdown body mass index was higher (U = 3.0 p = .003), with obese individuals reporting the highest non-work-related screen hours per week (Wald χ2= 8.9 p = .012). Inverse associations were found for mental well-being where higher lockdown scores of Kessler-10 (p = .011), Dass-21 anxiety (p = .027) and Dass-21 depression (p = .011) were associated with lower physical activity levels. A key qualitative message from participants was wanting to know how to stay healthy during lockdown.

Conclusions
Lockdown was associated with lower physical activity, higher non-work-related screen time and more sitting time compared to post lockdown which also reported higher body mass index. Lower levels of mental well-being were associated with lower physical activity levels during lockdown. Given the known positive affect of physical activity on mental well-being and obesity, and the detrimental associations shown in this study, a key public health message should be considered in an attempt to maintain healthy activity behaviours in future lockdowns and similar emergency situations to promote and maintain positive well-being. Furthermore, consideration should be given to the isolation of a community due to infectious disease outbreaks and to recognise the important role physical activity plays in maintaining weight and supporting good mental health.