bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metacell-2: a divide-and-conquer metacell algorithm for scalable scRNA-seq analysis
Authors: Ben-Kiki Oren , Bercovich Akhiad , Lifshitz Aviezer , Tanay Amos 
Published: April 2022

AbstractScaling scRNA-seq to profile millions of cells is crucial for constructing high-resolution maps of transcriptional manifolds. Current analysis strategies, in particular dimensionality reduction and two-phase clustering, offer only limited scaling and sensitivity to define such manifolds. We introduce Metacell-2, a recursive divide-and-conquer algorithm allowing efficient decomposition of scRNA-seq datasets of any size into small and cohesive groups of cells called metacells. Metacell-2 improves outlier cell detection and rare cell type identification, as shown with human bone marrow cell atlas and mouse embryonic data. Metacell-2 is implemented over the scanpy framework for easy integration in any analysis pipeline.
Epimutations in both the TESK2 and MMACHC promoters in the Epi-cblC inherited disorder of intracellular metabolism of vitamin B12
Authors: Oussalah Abderrahim , Siblini Youssef , Hergalant Sébastien , Chéry Céline , Rouyer Pierre , Cavicchi Catia , Guerrini Renzo , Morange Pierre-Emmanuel , Trégouët David , Pupavac Mihaela , Watkins David , Pastinen Tomi , Chung Wendy K. , Ficicioglu Can , Feillet François , Froese D. Sean , Baumgartner Matthias R. , Benoist Jean-François , Majewski Jacek , Morrone Amelia , Rosenblatt David S. , Guéant Jean-Louis 
Published: April 2022

AbstractBackgroundepi-cblCis a recently discovered inherited disorder of intracellular vitamin B12metabolism associating hematological, neurological, and cardiometabolic outcomes. It is produced by an epimutation at the promoter common toCCDC163PandMMACHC, which results from an aberrant antisense transcription due to splicing mutations in the antisensePRDX1gene neighboringMMACHC. We studied whether the aberrant transcription produced a second epimutation by encompassing the CpG island of theTESK2gene neighboringCCDC163P.MethodsWe unraveled the methylome architecture of theCCDC163P–MMACHCCpG island (CpG:33) and theTESK2CpG island (CpG:51) of 17 epi-cblCcases. We performed an integrative analysis of the DNA methylome profiling, transcriptome reconstruction of RNA-sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-Seq) of histone H3, and transcription expression ofMMACHCandTESK2.ResultsThePRDX1splice mutations and activation of numerous cryptic splice sites produced antisense readthrough transcripts encompassing the bidirectionalMMACHC/CCDC163Ppromoter and theTESK2promoter, resulting in the silencing of both theMMACHCandTESK2genes through the deposition of SETD2-dependent H3K36me3 marks and the generation of epimutations in the CpG islands of the two promoters.ConclusionsThe antisense readthrough transcription of the mutatedPRDX1produces an epigenetic silencing ofMMACHCandTESK2. We propose using the term 'epi-digenism' to define this epigenetic disorder that affects two genes. Epi-cblCis an entity that differs fromcblC.Indeed, thePRDX1 and TESK2altered expressions are observed in epi-cblCbut not incblC, suggesting further evaluating the potential consequences on cancer risk and spermatogenesis.
Use of dental drill handpiece to remove steel nut causing penile strangulation: a case report and review of the literature
Authors: Nguyen Tuan Thanh , Ngo Xuan Thai , Chau Quy Thuan , Hoang Khac Chuan , Dinh Le Quy Van , Ly Hoai Tam , Hoang Tien Dat , Dobbs Ryan W. , Thai Minh Sam 
Published: April 2022

Abstract
Background
Penile strangulation is an uncommon urological emergency that requires prompt intervention to avoid potentially serious sequelae including loss of the distal penis secondary to ischemia and subsequent gangrene. We present a case report of a patient who presented to the hospital with penile strangulation injury of 10-hour duration secondary to the presence of a thick hexagonal steel nut. This case is presented in accordance with Consensus Surgical Case Report guidelines.

Case presentation
A 24-year-old Vietnamese man presented to the emergency room with urinary retention and decreased penile sensation following a 10-hour history of penile strangulation due to the presence of a thick hexagonal steel nut that he had placed around the shaft of the penis for the purpose of sexual enhancement during masturbation. The hexagonal nut was tightly entrapping the penile shaft, resulting in edema, congestion, and swelling of the distal 5 cm of the phallus. Given the thickness of the foreign body as well as the degree of penile swelling, we were unable to remove the hexagonal nut using traditional methods of alleviating penile strangulation injuries. Following consultation with a dental colleague, a dental diamond drill handpiece was utilized to cut the foreign body without injury to the underlying penile skin. Subsequent follow-up in clinic demonstrated no significant urinary or sexual sequalae from this episode.

Conclusion
We report a case of penile strangulation requiring novel instrumentation and collaboration for successful treatment.
What evidence exists on the impacts of large herbivores on climate change? A systematic map protocol
Authors: Ramsay Jennifer , Sandom Christopher , Ings Thomas , Wheeler Helen C. 
Published: April 2022

Abstract
Background
In recent years there has been an increased focus on the role of large herbivores in ecosystem restoration and climate change mitigation. There are multiple processes by which large herbivores could potentially influence climate feedback and forcing effects, but the evidence has not yet been synthesised in a systematic and accessible format. Grazing, browsing, trampling, defecation, and seed dispersal by large herbivores can influence vegetation and soils in ways that may directly or indirectly contribute to climate change or mitigation. For example, changes in vegetation could impact wildfire regimes, carbon storage, and albedo, with ultimate impacts on climate. These processes may be influenced by herbivore species composition, density, and functional traits.
The main aim of this systematic map is to synthesise the range of research on climate feedback and forcing effects from large herbivores (≥ 10 kg) in terrestrial ecosystems. We also aim to identify knowledge clusters and gaps in the research base, as well as assessing the potential for quantitative analyses.

Methods
A search of peer-reviewed and grey literature will be conducted using a range of bibliographic databases, search engines and websites. The search strategy will involve using a pre-defined search string with Boolean operators. All search results will be screened for relevance according to specific eligibility criteria. Screening will be conducted in two stages: all articles will initially be screened by title and abstract, then those that meet the eligibility criteria will be screened by full text. At both stages, articles will be excluded if they don’t meet all eligibility criteria or if they meet any exclusion criteria.
All articles included as eligible after full text screening will be coded. At each stage (of screening and coding) a proportion of articles will be processed independently by two reviewers to assess inter-reviewer reliability and resolve differences. The evidence will be presented in a searchable database with accompanying visual outputs. A narrative synthesis will be provided outlining the range and distribution of evidence, knowledge gaps and clusters, potential bias, and areas for further research.
The distribution and density of Huntingtin inclusions across the Huntington disease neocortex: regional correlations with Huntingtin repeat expansion independent of pathologic grade
Authors: Hickman Richard A. , Faust Phyllis L. , Marder Karen , Yamamoto Ai , Vonsattel Jean-Paul 
Published: April 2022

AbstractHuntington disease is characterized by progressive neurodegeneration, especially of the striatum, and the presence of polyglutamine huntingtin (HTT) inclusions. Although HTT inclusions are most abundant in the neocortex, their neocortical distribution and density in relation to the extent of CAG repeat expansion in the HTT gene and striatal pathologic grade have yet to be formally established. We immunohistochemically studied 65 brains with a pathologic diagnosis of Huntington disease to investigate the cortical distributions and densities of HTT inclusions within the calcarine (BA17), precuneus (BA7), motor (BA4) and prefrontal (BA9) cortices; in 39 of these brains, a p62 immunostain was used for comparison. HTT inclusions predominate in the infragranular cortical layers (layers V-VI) and layer III, however, the densities of HTT inclusions across the human cerebral cortex are not uniform but are instead regionally contingent. The density of HTT and p62 inclusions (intranuclear and extranuclear) in layers V-VI increases caudally to rostrally (BA17 < BA7 < BA4 < BA9) with the median burden of HTT inclusions being 38-fold greater in the prefrontal cortex (BA9) than in the calcarine cortex (BA17). Conversely, intranuclear HTT inclusions prevail in the calcarine cortex irrespective of HTT CAG length. Neocortical HTT inclusion density correlates with CAG repeat expansion, but not with the neuropathologic grade of striatal degeneration (Vonsattel grade) or with the duration of clinical disease since motor onset. Extrapolation of these findings suggest that HTT inclusions are at a regionally-contingent, CAG-dependent, density during the advanced stages of HD. The distribution and density of HTT inclusions in HD therefore does not provide a measure of pathologic disease stage but rather infers the degree of pathogenic HTT expansion.
Thoracic endovascular aortic repair for avulsion of aortic branches in a trauma patient requiring resuscitative thoracotomy: a case report
Authors: Tanikawa Atsushi , Sato Takeaki , Fujita Motoo , Tsuchiya Chieri , Katsuta Ken , Suzuki Yusuke , Kumagai Kiichiro , Saiki Yoshikatsu , Kushimoto Shigeki 
Published: April 2022

Abstract
Background
Resuscitative thoracotomy is a lifesaving procedure for trauma patients that are hemodynamically unstable. Cross-clamping of the descending thoracic aorta is an essential procedure performed during resuscitative thoracotomy in patients with impending cardiac arrest. Although complications related to resuscitative thoracotomy have been reported, there is no report on avulsion of aortic branches related to cross-clamping of the descending aorta and its appropriate management.

Case presentation
We present the case of a 42-year-old woman who sustained blunt trauma due to an accidental fall. The patient was hemodynamically unstable and required resuscitative thoracotomy with cross-clamping of the thoracic aorta. However, hemorrhage from avulsion of aortic branches related to aortic cross-clamping was identified. Initially, transcatheter arterial embolization was attempted to achieve hemostasis; however, when that proved ineffective, thoracic endovascular aortic repair was performed, which resulted in successful hemorrhage control without any sequelae.

Conclusions
Thoracic endovascular aortic repair may be a management option for aortic branch avulsion due to cross-clamping of the descending aorta during resuscitative thoracotomy.
A pilot study investigating the safety and feasibility of endoscopic dilation using a radial incision and cutting technique for benign strictures of the small intestine: a study protocol
Authors: Moroi Rintaro , Shiga Hisashi , Nochioka Kotaro , Shimoyama Yusuke , Kuroha Masatake , Kakuta Yoichi , Kinouchi Yoshitaka , Masamune Atsushi 
Published: April 2022

Abstract
Background
Small benign intestinal stenosis is usually treated by endoscopic balloon dilation (EBD) or surgery. Although EBD and surgery are able to resolve the stenosis in most cases, they are associated with several problems such as insufficient dilation and surgical stress, respectively. On the contrary, a novel approach called radial incision and cutting (RIC) is reported to have several benefits when compared to EBD and surgery. We can currently adopt RIC only for the strictures in the colon or terminal ileum and not for those stenotic lesions present further in the small intestine where balloon-assisted endoscopy is utilized, because the long-type electric knife is currently not approved for use in Japan. We will herein conduct a pilot study to investigate the safety and feasibility of RIC for treating the benign stenoses of the small intestine using the long-type electric knife.

Methods
This will be a single-center, single-arm, interventional trial. The major criteria for inclusion will be age ranging from 20 to 80 years and the presence of benign stenosis in the small intestine. We will perform RIC on 10 participants. The primary outcome is the safety of this procedure, which will be assessed by measuring the frequency of adverse events of special interest. The secondary outcomes will be technical success rate, improvement in subjective symptoms, procedure time, and duration of hospitalization.

Discussion
This pilot study will provide useful information that will aid in adopting RIC for treating the benign strictures present in the small intestine.

Trial registration
jRCT Identifier, jRCTs022200040. Registered on 1 March 2021.
Cloud economy and its relationship with China’s economy—a capital market-based approach
Authors: Lin Lichao , Cheung Adrian 
Published: April 2022

AbstractThrough the lens of the stock market, we examine whether and how the cloud economy affects China’s economy. We review the literature on cloud computing and related concepts and propose a definition of the cloud economy. Based on this new definition, we create a China Cloud Economy Index (CCEI) and its sub-indices. Using stock market data from 2012 to 2020, we analyze the basic characteristics of these indices, their validity, and their relationship with the overall stock market. The robustness of the new index is also examined. We find that the relationship between the CCEI and the stock market had been getting stronger but weakened somewhat after January 11, 2019 plausibly because of the availability of recent cloud-related policies that have widened the gap between the market performance of CCEI and that of the stock market.
Cognitive performance in systemic lupus erythematosus patients: a cross-sectional and longitudinal study
Authors: Langensee L. , Mårtensson J. , Jönsen A. , Zervides K. , Bengtsson A. , Nystedt J. , Cannerfelt B. , Nilsson P. , Mannfolk P. , Lätt J. , Rumetshofer T. , Sundgren P. C. 
Published: April 2022

Abstract
Background
Previous research has provided evidence for cognitive dysfunction as a common symptom of systemic lupus erythematosus (SLE). In light of this, the primary goal of this study was to investigate how cognitive impairment in this patient group develops over time. In addition, the present dataset contributes to delineating the specific abilities that are impaired in SLE patients as well as answering the question whether the disease affects the cognition of SLE patients with neuropsychiatric manifestations (NPSLE) and without (non-NPSLE) in distinct ways.

Methods
91 female participants (33 NPSLE, 29 non-NPSLE, 29 healthy controls (HC)) underwent standardized neurocognitive testing. A total of ten different cognitive abilities were assessed, among others executive function, memory, and attention. Some of the participants (30 NPSLE patients, 22 non-NPSLE, 13 HC) were tested twice (mean time between testing sessions: 50 months) to enable longitudinal tracking of cognitive abilities. Analyses of Variance (ANOVA) were conducted to determine whether cognitive performance differed cross-sectionally between the groups. Linear mixed effects models were fit to investigate performance differences between the groups over time.

Results
Cross-sectional analysis at follow-up demonstrated that the cognitive performance of both NPSLE and non-NPSLE was significantly lower than that of HC for the motor speed and the psychomotor speed domain. Additionally, NPSLE patients performed significantly weaker than HC in the complex attention domain. At the same time, the cross-sectional data did not yield any support for performance differences between NPSLE and non-NPSLE patients. Weak positive correlations between disease duration and psychomotor speed, motor speed and reaction time emerged. A temporal progression of cognitive dysfunction in SLE patients was not confirmed.

Conclusions
Cognitive performance is affected in both non-NPSLE and NPSLE patients. However, a linear decline in performance over time could not be verified. More in-depth longitudinal assessments of cognition in SLE patients are needed to establish how cognitive abilities in this patient population develop over time.
The use of technology in postgraduate medical education within radiology: a scoping review
Authors: Akoob Sakina , Akbar Khalida , Van Wyk Jacqueline 
Published: April 2022

AbstractPostgraduate radiology training has traditionally followed didactic approaches; however, complex reasoning skills and critical thinking are essential in the field of radiology. Therefore, the shortages of radiologists in Africa have necessitated the need to review the use of technology in postgraduate education to improve efficient training and service. This scoping review was conducted to map the evidence on the role of technology in postgraduate radiology education and practice. A systematic scoping review search strategy was undertaken to review material published between January 2005 and August 2020 on the use of technology in radiology education. Data from the included studies were extracted and analyzed for emerging themes and presented in response to the research question. Seven articles described studies from the African continent. The most popular technological intervention was telemedicine, and several niche areas of technology implementation were identified (blended learning, flipped learning, digital teaching files). Furthermore, the most challenging aspects relating to technology use remain fiscal and credentialing constraints. Technology plays a role in postgraduate radiology education through networks, synchronous and asynchronous applications. It has the potential to increase support to doctoral students in the African context and alleviate some stressors associated with traditional, face-to-face didactic programs.
Implementation of telepsychiatry in Kenya: acceptability study
Authors: Kaigwa Loice Cushny , Njenga Frank , Ongeri Linnet , Nguithi Anne , Mugane Maryanne , Mbugua Gathoni M. , Anundo Jacqueline , Kimari Margaret Zawadi , Onono Maricianah 
Published: April 2022

Background
COVID-19-related restrictions on in-person contact in healthcare, increasing psychiatric illness during the pandemic and pre-existing shortages of mental healthcare providers have led to the emergence of telepsychiatry as an attractive option for the delivery of care. Telepsychiatry has been promoted as economical and effective, but its acceptance in low- and middle-income countries is poorly understood.

Aims
To explore the acceptance, experiences and perspectives of patients and healthcare providers in the uptake of telepsychiatry services in a middle-income country.

Method
Focus group discussions were conducted on the WhatsApp platform with patients and care providers who have engaged in telepsychiatry. Data were analysed using a thematic approach.

Results
Three main themes emerged from the five focus groups: (a) technical access, (b) user experience and (c) perceived effectiveness compared with face-to-face (in-person) interactions. Care providers reported challenges establishing rapport with the patient, particularly for initial sessions, maintaining privacy during sessions and detecting non-verbal cues on video. Patients cited internet connectivity problems, difficulty finding private space to have their sessions and cost as major challenges. Patients also felt in-person sessions were better for initial visits. Both patients and providers reported difficulties making insurance payment claims for telepsychiatry services. Overall, participants were mostly positive about telepsychiatry, citing its convenience and overall perceived effectiveness compared with in-person sessions.

Conclusions
Telepsychiatry is an acceptable platform for delivery of out-patient psychiatric services in a middle-income country. Patients and providers appreciate the convenience it offers and would like it integrated as a routine mode of delivery of care.
Biomarkers for Adjuvant Endocrine and Chemotherapy in Early-Stage Breast Cancer: ASCO Guideline Update
Authors: Andre Fabrice , Ismaila Nofisat , Allison Kimberly H. , Barlow William E. , Collyar Deborah E. , Damodaran Senthil , Henry N. Lynn , Jhaveri Komal , Kalinsky Kevin , Kuderer Nicole M. , Litvak Anya , Mayer Erica L. , Pusztai Lajos , Raab Rachel , Wolff Antonio C. , Stearns Vered 
Published: April 2022

PURPOSE To update recommendations on appropriate use of breast cancer biomarker assay results to guide adjuvant endocrine and chemotherapy decisions in early-stage breast cancer. METHODS An updated literature search identified randomized clinical trials and prospective-retrospective studies published from January 2016 to October 2021. Outcomes of interest included overall survival and disease-free or recurrence-free survival. Expert Panel members used informal consensus to develop evidence-based recommendations. RESULTS The search identified 24 studies informing the evidence base. RECOMMENDATIONS Clinicians may use Onco type DX, MammaPrint, Breast Cancer Index (BCI), and EndoPredict to guide adjuvant endocrine and chemotherapy in patients who are postmenopausal or age > 50 years with early-stage estrogen receptor (ER)–positive, human epidermal growth factor receptor 2 (HER2)–negative (ER+ and HER2–) breast cancer that is node-negative or with 1-3 positive nodes. Prosigna and BCI may be used in postmenopausal patients with node-negative ER+ and HER2– breast cancer. In premenopausal patients, clinicians may use Onco type in patients with node-negative ER+ and HER2– breast cancer. Current data suggest that premenopausal patients with 1-3 positive nodes benefit from chemotherapy regardless of genomic assay result. There are no data on use of genomic tests to guide adjuvant chemotherapy in patients with ≥ 4 positive nodes. Ki67 combined with other parameters or immunohistochemistry 4 score may be used in postmenopausal patients without access to genomic tests to guide adjuvant therapy decisions. BCI may be offered to patients with 0-3 positive nodes who received 5 years of endocrine therapy without evidence of recurrence to guide decisions about extended endocrine therapy. None of the assays are recommended for treatment guidance in individuals with HER2-positive or triple-negative breast cancer. Treatment decisions should also consider disease stage, comorbidities, and patient preferences. Additional information is available at www.asco.org/breast-cancer-guidelines .