bluuebunny/crossref_metadata_2025_split huggingface dataset:
dbGaPCheckup: pre-submission checks of dbGaP-formatted subject phenotype files
Authors: Heinsberg Lacey W. , Weeks Daniel E. 
Published: March 2023

Abstract
Background
Data archiving and distribution are essential to scientific rigor and reproducibility of research. The National Center for Biotechnology Information’s Database of Genotypes and Phenotypes (dbGaP) is a public repository for scientific data sharing. To support curation of thousands of complex data sets, dbGaP has detailed submission instructions that investigators must follow when archiving their data.

Results
We developed dbGaPCheckup, an R package which implements a series of check, awareness, reporting, and utility functions to support data integrity and proper formatting of the subject phenotype data set and data dictionary prior to dbGaP submission. For example, as a tool, dbGaPCheckup ensures that the data dictionary contains all fields required by dbGaP, and additional fields required by dbGaPCheckup; the number and names of variables match between the data set and data dictionary; there are no duplicated variable names or descriptions; observed data values are not more extreme than the logical minimum and maximum values stated in the data dictionary; and more. The package also includes functions that implement a series of minor/scalable fixes when errors are detected (e.g., a function to reorder the variables in the data dictionary to match the order listed in the data set). Finally, we also include reporting functions that produce graphical and textual descriptives of the data to further reduce the likelihood of data integrity issues. The dbGaPCheckup R package is available on CRAN (https://CRAN.R-project.org/package=dbGaPCheckup) and developed on GitHub (https://github.com/lwheinsberg/dbGaPCheckup).

Conclusion
dbGaPCheckup is an innovative assistive and timesaving tool that fills an important gap for researchers by making dbGaP submission of large and complex data sets less error prone.
Patterns of home care and community support preferences among older adults with disabilities in China: a latent class analysis
Authors: Xiao Feng , Cao Songmei , Xiao Mingzhao , Xie Liling , Zhao Qinghua 
Published: March 2023

Abstract
Background
Ageing in place is the preferred choice for most older adults worldwide. The role of the family as a core care resource has diminished as a result of changes in family structure, thus extending the responsibility for caring for older adults from within the family to outside it and requiring considerably more support from society. However, there is a shortage of formal and qualified caregivers in many countries, and China has limited social care resources. Therefore, it is important to identify home care patterns and family preferences to provide effective social support and reduce government costs.

Methods
Data were obtained from the Chinese Longitudinal Healthy Longevity Study 2018. Latent class analysis models were estimated using Mplus 8.3. Multinomial logistic regression analysis was adopted to explore the influencing factors with the R3STEP method. Lanza’s method and the chi-square goodness-of-fit test were used to explore community support preferences among different categories of families of older adults with disabilities.

Results
Three latent classes were identified based on older adults with disabilities’ characteristics (degree of disability, demand satisfaction), caregivers’ characteristics (length of providing care, care performance) and living status: Class 1- mild disability and strong care (46.85%); Class 2- severe disability and strong care (43.92%); and Class 3- severe disability and incompetent care (9.24%). Physical performance, geographic region and economic conditions jointly influenced home care patterns (P < 0.05). Home visits from health professionals and health care education were the top two forms of community support that were most preferred by the older adults with disabilities’ families (residual > 0). Families in the Class 3 subgroup preferred personal care support more than those in the other two subgroups (P < 0.05).

Conclusion
Home care is heterogeneous across families. Older adults’ degrees of disability and care needs may be varied and complex. We classified different families into homogeneous subgroups to reveal differences in home care patterns. The findings can be used by decision-makers in their attempts to design long-term care arrangements for home care and to adjust the distribution of resources for the needs of older adults with disabilities.
Assessment of Autologous Blood marker localIzation and intraoperative coLonoscopy localIzation in laparoscopic colorecTal cancer surgery (ABILITY): a randomized controlled trial
Authors: Zhang Ke-hui , Li Jing-ze , Zhang Hai-bin , Hu Ren-hao , Cui Xi-mao , Du Tao , Zheng Liang , Zhang Shun , Song Chun , Xu Mei-dong , Jiang Xiao-hua 
Published: March 2023

Abstract
Background
Laparoscopic colorectal surgery has been proved to have similar oncological outcomes with open surgery. Due to the lack of tactile perception, surgeons may have misjudgments in laparoscopic colorectal surgery. Therefore, the accurate localization of a tumor before surgery is important, especially in the early stages of cancer. Autologous blood was thought a feasible and safe tattooing agent for preoperative endoscopic localization but its benefits remain controversial. We therefore proposed this randomized trial to the accuracy and safety of autogenous blood localization in small, serosa-negative lesion which will be resected by laparoscopic colectomy.

Methods
The current study is a single-center, open-label, non-inferiority, randomized controlled trial. Eligible participants would be aged 18–80 years and diagnosed with large lateral spreading tumors that could not be treated endoscopically, malignant polyps treated endoscopically that required additional colorectal resection, and serosa-negative malignant colorectal tumors (≤ cT3). A total of 220 patients would be randomly assigned (1:1) to autologous blood group or intraoperative colonoscopy group. The primary outcome is the localization accuracy. The secondary endpoint is adverse events related to endoscopic tattooing.

Discussion
This trial will investigate whether autologous blood marker achieves similar localization accuracy and safety in laparoscopic colorectal surgery compared to intraoperative colonoscopy. If our research hypothesis is statistically proved, the rational introduction of autologous blood tattooing in preoperative colonoscopy can help improve identification of the location of tumors for laparoscopic colorectal cancer surgery, performing an optimal resection, and minimizing unnecessary resections of normal tissues, thereby improving the patient’s quality of life. Our research data will also provide high quality clinical evidence and data support for the conduction of multicenter phase III clinical trials.

Trial registration
This study is registered with ClinicalTrials.gov, NCT05597384. Registered 28 October 2022
Diagnostic aid to subepidermal calcified nodule with dermoscopy and reflectance confocal microscopy: a case report
Authors: Zhu Xiaomei , Zhang Xiaoyan , Yang Kun 
Published: March 2023

Abstract
Background
Subepidermal calcified nodule (SCN) is a type of calcinosis cutis that usually occurs in children. The lesions in the SCN resemble those of other skin diseases, such as pilomatrixoma, molluscum contagiosum, and juvenile xanthogranuloma, leading to a high rate of misdiagnoses. Noninvasive in vivo imaging techniques, represented by dermoscopy and reflectance confocal microscopy (RCM), have dramatically accelerated skin cancer research over the past decade, and their applications have greatly expanded into other skin disorders. However, the features of an SCN in dermoscopy and RCM have yet to be reported previously. Combining these novel approaches with conventional histopathological examinations is a promising method for increasing diagnostic accuracy.

Case presentation
We report on a case of SCN of the eyelid diagnosed with the aid of dermoscopy and RCM. A 14-year-old male patient who presented with a painless yellowish-white papule on his left upper eyelid was previously diagnosed with a common wart. Unfortunately, treatment with recombinant human interferon gel was not effective. To achieve a correct diagnosis, dermoscopy and RCM were performed. The former showed closely grouped multiple yellowish-white clods surrounded by linear vessels, and the latter exhibited hyperrefractile material nests at the dermal–epidermal junction level. The alternative diagnoses were, therefore, excluded because of in vivo characterizations. Subsequent surgical excision, histological examination, and von Kossa staining were performed. Pathology showed hyperkeratosis of the epidermis, a downward-directed basal-layer expansion, and small amorphous basophilic deposits scattered throughout the papillary dermis. The von Kossa staining confirmed calcium deposits in the lesion. An SCN was then diagnosed. During the 6-month follow-up, no relapse was observed.

Conclusions
Patients with SCN could benefit from dermoscopy and RCM, which help achieve an accurate diagnosis. Clinicians should consider the possibility of an SCN for an adolescent patient with painless yellowish-white papules.
The advantages of domestic ear molding system in molding bilateral neonatal congenital auricular deformities
Authors: Li Jie , Tan Junlong , Yang Denghua , Chen Liyan 
Published: March 2023

Abstract
Background
There are different types of ear molding devices on the market. However, due to high cost, the wide application of the ear molding is hindered, especially for children with bilateral congenital auricular deformities (CAD). This study is designed to correct the bilateral CAD with the flexible use of Chinese domestic ear molding system.

Methods
Newborns diagnosed with bilateral CAD were recruited in our hospital from September 2020 to October 2021. For each subject, one ear wore a set of domestic ear molding system, while the contralateral ear used only matching Retractor and Antihelix Former. Medical charts were reviewed to collect data on the types of CAD, the incidence of complications, the initiation and duration of treatment, as well as the satisfaction after treatment. Treatment outcomes were graded into three levels: excellent, good, and poor, according to the improvement of auricular morphology evaluated by both doctors and parents, respectively.

Results
A total of 16 infants (32 ears) were treated with the Chinese domestic ear molding system, which contains 4 cases with Stahl’s ear (8 ears), 5 cases with Helical rim deformity (10 ears), 3 cases with Cup ear (6 ears), 4 cases with Lop ear (8 ears). All infants accomplished the correction completely. Both parents and doctors were satisfied with the outcomes. No obvious complication was observed.

Conclusions
Ear molding is an effective nonsurgical treatment for CAD. Molding with Retractor and Antihelix Former is simple and effective. Domestic ear molding system can be flexibly used in correcting bilateral CAD. With this approach, infants with bilateral CAD will benefit more in the near future.
Perceptions of friendship, peers and influence on adolescent smoking according to tobacco control context: a systematic review and meta-ethnography of qualitative research
Authors: Littlecott H. J. , Moore G. F. , Evans R. E. , Melendez-Torres G. J. , McCann M. , Reed H. , Mann M. , Dobbie F. , Jennings S. , Donaldson C. , Hawkins J. 
Published: March 2023

Abstract
Background
A relationship between smoking and interpersonal influences has been well established within the literature. There have been cultural shifts in denormalisation and a reduction in tobacco smoking in many countries. Hence there is a need to understand social influences on adolescents’ smoking across smoking normalisation contexts.

Methods
The search was conducted in July 2019 and updated in March 2022 within 11 databases and secondary sources. Search terms included schools, adolescents, smoking, peers, social norms and qualitative research. Screening was conducted by two researchers independently and in duplicate. Study quality was assessed using the eight-item Evidence for Policy and Practice Information and Co-ordinating Centre (EPPI-centre) tool for the appraisal of qualitative studies. Results were synthesised using a meta-narrative lens for meta-ethnography and compared across smoking normalisation contexts.

Results
Forty one studies were included and five themes were developed, mapping onto the socio ecological model. The social processes by which adolescents take up smoking differed according to a mixture of school type, peer group structure and the smoking culture within the school, as well as the wider cultural context. Data available from smoking denormalised contexts, described changes in social interactions around smoking to cope with its stigmatisation. This was manifested through i) direct peer influence, whereby subtle techniques were employed, ii) group belonging whereby smoking was less likely to be seen as a key determinant of group membership and smoking was less commonly reported to be used as a social tool, and iii) popularity and identity construction, whereby smoking was perceived more negatively in a denormalised context, compared with a normalised context.

Conclusions
This meta-ethnography is the first study to demonstrate, drawing on international data, that peer processes in adolescent smoking may undergo changes as smoking norms within society change. Future research should focus on understanding differences across socioeconomic contexts, to inform the adaptation of interventions.
High-pressure balloon dilatation of primary obstructive megaureter in children: a systematic review
Authors: Ripatti Liisi , Viljamaa Hanna-Reeta , Suihko Anna , Pakkasjärvi Niklas 
Published: March 2023

Abstract
Objective
We aimed to evaluate the effectiveness and complication rates of endoscopic high-pressure balloon dilatation (HPBD) in treating primary obstructive megaureter (POM) in children based on current literature. Specifically, we wanted to clarify the evidence on the use of HPBD in children under one year of age.

Methods
A systematic search of the literature was performed via several databases. The preferred reporting items for systematic reviews and meta-analyses guidelines were followed. The primary outcomes studied in this systematic review were the effectiveness of HBPD in relieving obstruction and reducing hydroureteronephrosis in children. The secondary outcome was to study the complication rate of endoscopic high-pressure balloon dilatation. Studies that reported one or both of these outcomes (n = 13) were considered eligible for inclusion in this review.

Results
HPBD significantly decreased both ureteral diameter (15.8 mm [range 2–30] to 8.0 mm [0–30], p = 0.00009) and anteroposterior diameter of renal pelvis (16.7 mm [0–46] to 9.7 mm [0–36], p = 0.00107). The success rate was 71% after one HPBD and 79% after two HPBD. The median follow-up time was 3.6 years (interquartile range 2.2–6.4 years). A complication rate of 33% was observed, but no Clavien–Dindo grade IV–V complications were reported. Postoperative infections and VUR were detected in 12% and 7.8% of cases, respectively. For children under one year of age, outcomes of HPBD seem to be similar to those in older children.

Conclusions
This study indicates that HPBD appears to be safe and can be used as the first-line treatment for symptomatic POM. Further comparative studies are needed addressing the effect of treatment in infants, and also long-term outcomes of the treatment. Due to the nature of POM, identifying those patients who will benefit from HPBD remains challenging.
Under- and post-graduate training to manage the acutely unwell patient: a scoping review
Authors: Church Helen R. , Murdoch-Eaton Deborah , Sandars John 
Published: March 2023

AbstractBackgroundJunior doctors are often the first responders to acutely unwell patients and yet frequently report feeling under-prepared to do so. To understand whether this is consequential of how medical students and doctors are trained to manage acutely unwell patients, a scoping review was conducted using a systematic approach.MethodsThe review, informed by the Arksey and O’Malley and PRISMA-ScR guidelines, identified educational interventions targeting the management of acutely unwell adults. Seven major literature databases were searched for journal articles published in English from 2005 to 2022, in addition to the Association of Medical Education in Europe (AMEE) conference proceedings from 2014 to 2022.ResultsSeventy-three articles and abstracts were eligible for the review, the majority of which were from the UK or USA, and demonstrated that educational interventions were more commonly targeted at medical students than qualified doctors. The majority of studies used simulation, but very few integrated complexities of the clinical environment within scenarios such as multidisciplinary working, distraction-handling techniques and other non-technical skills. A wide range of learning objectives pertaining to acute patient management were stated across studies, but few explicitly cited educational theory underpinning their study.ConclusionsThe results of this review encourages future educational initiatives to consider enhancing authenticity within simulation to promote transfer of learning to clinical practice, and use educational theory to augment the sharing of educational approaches within the community of clinical education practice. Additionally, increasing the focus on post-graduate learning, building upon undergraduate educational foundations, is essential to promoting lifelong learning within the ever-changing healthcare environment.
Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters
Authors: Richer Stephen , Tian Yuan , Schoenfelder Stefan , Hurst Laurence , Murrell Adele , Pisignano Giuseppina 
Published: March 2023

Abstract
Background
There is widespread interest in the three-dimensional chromatin conformation of the genome and its impact on gene expression. However, these studies frequently do not consider parent-of-origin differences, such as genomic imprinting, which result in monoallelic expression. In addition, genome-wide allele-specific chromatin conformation associations have not been extensively explored. There are few accessible bioinformatic workflows for investigating allelic conformation differences and these require pre-phased haplotypes which are not widely available.

Results
We developed a bioinformatic pipeline, “HiCFlow,” that performs haplotype assembly and visualization of parental chromatin architecture. We benchmarked the pipeline using prototype haplotype phased Hi-C data from GM12878 cells at three disease-associated imprinted gene clusters. Using Region Capture Hi-C and Hi-C data from human cell lines (1-7HB2, IMR-90, and H1-hESCs), we can robustly identify the known stable allele-specific interactions at the IGF2-H19 locus. Other imprinted loci (DLK1 and SNRPN) are more variable and there is no “canonical imprinted 3D structure,” but we could detect allele-specific differences in A/B compartmentalization. Genome-wide, when topologically associating domains (TADs) are unbiasedly ranked according to their allele-specific contact frequencies, a set of allele-specific TADs could be defined. These occur in genomic regions of high sequence variation. In addition to imprinted genes, allele-specific TADs are also enriched for allele-specific expressed genes. We find loci that have not previously been identified as allele-specific expressed genes such as the bitter taste receptors (TAS2Rs).

Conclusions
This study highlights the widespread differences in chromatin conformation between heterozygous loci and provides a new framework for understanding allele-specific expressed genes.
SRTsim: spatial pattern preserving simulations for spatially resolved transcriptomics
Authors: Zhu Jiaqiang , Shang Lulu , Zhou Xiang 
Published: March 2023

AbstractSpatially resolved transcriptomics (SRT)-specific computational methods are often developed, tested, validated, and evaluated in silico using simulated data. Unfortunately, existing simulated SRT data are often poorly documented, hard to reproduce, or unrealistic. Single-cell simulators are not directly applicable for SRT simulation as they cannot incorporate spatial information. We present SRTsim, an SRT-specific simulator for scalable, reproducible, and realistic SRT simulations. SRTsim not only maintains various expression characteristics of SRT data but also preserves spatial patterns. We illustrate the benefits of SRTsim in benchmarking methods for spatial clustering, spatial expression pattern detection, and cell-cell communication identification.
Loss of MLL3/4 decouples enhancer H3K4 monomethylation, H3K27 acetylation, and gene activation during embryonic stem cell differentiation
Authors: Boileau Ryan M. , Chen Kevin X. , Blelloch Robert 
Published: March 2023

AbstractBackgroundEnhancers are essential in defining cell fates through the control of cell-type-specific gene expression. Enhancer activation is a multi-step process involving chromatin remodelers and histone modifiers including the monomethylation of H3K4 (H3K4me1) by MLL3 (KMT2C) and MLL4 (KMT2D). MLL3/4 are thought to be critical for enhancer activation and cognate gene expression including through the recruitment of acetyltransferases for H3K27.ResultsHere we test this model by evaluating the impact of MLL3/4 loss on chromatin and transcription during early differentiation of mouse embryonic stem cells. We find that MLL3/4 activity is required at most if not all sites that gain or lose H3K4me1 but is largely dispensable at sites that remain stably methylated during this transition. This requirement extends to H3K27 acetylation (H3K27ac) at most transitional sites. However, many sites gain H3K27ac independent of MLL3/4 or H3K4me1 including enhancers regulating key factors in early differentiation. Furthermore, despite the failure to gain active histone marks at thousands of enhancers, transcriptional activation of nearby genes is largely unaffected, thus uncoupling the regulation of these chromatin events from transcriptional changes during this transition. These data challenge current models of enhancer activation and imply distinct mechanisms between stable and dynamically changing enhancers.ConclusionsCollectively, our study highlights gaps in knowledge about the steps and epistatic relationships of enzymes necessary for enhancer activation and cognate gene transcription.