bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs
Authors: Wolff Joachim , Backofen Rolf , Grüning Björn 
Published: May 2021

Abstract

Motivation
Hi-C technology provides insights into the 3D organization of the chromatin, and the single-cell Hi-C method enables researchers to gain knowledge about the chromatin state in individual cell levels. Single-cell Hi-C interaction matrices are high dimensional and very sparse. To cluster thousands of single-cell Hi-C interaction matrices, they are flattened and compiled into one matrix. Depending on the resolution, this matrix can have a few million or even billions of features; therefore, computations can be memory intensive. We present a single-cell Hi-C clustering approach using an approximate nearest neighbors method based on locality-sensitive hashing to reduce the dimensions and the computational resources.

Results
The presented method can process a 10 kb single-cell Hi-C dataset with 2600 cells and needs 40 GB of memory, while competitive approaches are not computable even with 1 TB of memory. It can be shown that the differentiation of the cells by their chromatin folding properties and, therefore, the quality of the clustering of single-cell Hi-C data is advantageous compared to competitive algorithms.

Availability and implementation
The presented clustering algorithm is part of the scHiCExplorer, is available on Github https://github.com/joachimwolff/scHiCExplorer, and as a conda package via the bioconda channel. The approximate nearest neighbors implementation is available via https://github.com/joachimwolff/sparse-neighbors-search and as a conda package via the bioconda channel.

Supplementary information
Supplementary data are available at Bioinformatics online.
Testicular localization of activating transcription factor 1 and its potential function during spermatogenesis
Authors: Tabara Masanori , Shiraishi Koji , Takii Ryosuke , Fujimoto Mitsuaki , Nakai Akira , Matsuyama Hideyasu 
Published: May 2021

AbstractActivating transcription factor 1 (ATF1), belonging to the CREB/ATF family of transcription factors, is highly expressed in the testes. However, its role in spermatogenesis has not yet been established. Here, we aimed to elucidate the impact of ATF1 in spermatogenesis by examining the expression pattern of ATF1 in mice and the effect of ATF1 knockdown in the mouse testes. We found that ATF1 is expressed in various organs, with very high levels in the testes. Immunohistochemical staining showed that ATF1 was localized in the nuclei of spermatogonia and co-localized with proliferating cell nuclear antigen. In ATF1-deficient mice, the seminiferous tubules of the testis contained cells at all developmental stages; however, the number of spermatocytes was decreased. Proliferating cell nuclear antigen expression was decreased and apoptotic cells were rare in the seminiferous tubules. These results indicate that ATF1 plays a role in male germ cell proliferation and sperm production.
Population preference for treatment of uncomplicated appendicitis
Authors: Bom W J , Scheijmans J C G , Gans S L , Van Geloven A A W , Boermeester M A 
Published: May 2021

Abstract

Background
Non-operative treatment of uncomplicated appendicitis is safe and increasing in popularity, but has other risks and benefits compared with appendicectomy. This study aimed to explore the preference of the general population regarding operative or antibiotic treatment of uncomplicated appendicitis.

Methods
In this prospective study, a clinical scenario and questionnaire were submitted to a panel comprising a sample of an average adult population. The survey was distributed by an independent, external research bureau, and included a comprehensive explanation of the risks and benefits of both treatment options. The primary outcome was the proportion of participants who would prefer antibiotics over surgery. Secondary outcomes were reasons for this preference and the accepted recurrence rate within 1 year when treated with antibiotics only. All outcomes were weighted for the average Dutch population.

Results
Of 254 participants, 49.2 per cent preferred antibiotic treatment for uncomplicated appendicitis, 44.5 per cent preferred surgery, and 6.3 per cent could not make a decision. About half of the participants preferring antibiotics would accept a recurrence risk of more than 50 per cent within 1 year. Avoiding surgery was their main reason. In participants preferring surgery, many tolerated a recurrence risk of no more than 10 per cent when treated with antibiotics. Removal of the cause of appendicitis was their main reason.

Conclusion
Around half of the average population sample preferred antibiotics over surgical treatment of uncomplicated appendicitis and were willing to accept a high recurrence risk to avoid surgery initially. Participants who preferred surgery tolerated only a very low recurrence risk with antibiotic treatment.
Analysis of Machine Learning and Deep Learning Frameworks for Opinion Mining on Drug Reviews
Authors: Youbi Fatiha , Settouti Nesma 
Published: May 2021

AbstractOpinion mining from medical forums such as health check-ups is sparking growing interest and a stimulating area for natural language processing. This allows for a better understanding of patient health status and drug reactions while generating new knowledge for health care professionals and drug manufacturers, which helps improve the quality of service and produce more effective treatments. In this paper, the researchers present a framework of opinions classification of drug reviews. The objective of this work is to find the best model for analyzing patients’ emotions about drugs. In this sense, the researchers oppose classical text vectorization methods (bag of words, term frequency-inverse document frequency) and word embedding methods (Word2vec, GloVe) for classical opinion mining face to modern machine learning tools with the Convolutional Neural Network (CNN), the Recurrent Neural Networks (Long Short-term Memory and Bidirectional Long Short-Term Memory). Experiments results show that the best model for drug reviews was achieved by CNN based on the Skip-gram model (85% accuracy). Experiments have led to conclude that the performance of a given model will depend on the type of dataset used, on feature representation and better collaboration between classifiers and feature extraction methods.
Left ventricular function, strain, and infarct characteristics in patients with transient ST-segment elevation myocardial infarction compared to ST-segment and non-ST-segment elevation myocardial infarctions
Authors: Demirkiran Ahmet , van der Hoeven Nina W , Janssens Gladys N , Lemkes Jorrit S , Everaars Henk , van de Ven Peter M , van Pouderoijen Nikki , van Cauteren Yvonne J M , van Leeuwen Maarten A H , Nap Alexander , Teunissen Paul F , Hopman Luuk H G A , Bekkers Sebastiaan C A M , Smulders Martijn W , van Royen Niels , van Rossum Albert C , Robbers Lourens F H J , Nijveldt Robin 
Published: May 2021

Abstract

Aims
This study aims to explore cardiovascular magnetic resonance (CMR)-derived left ventricular (LV) function, strain, and infarct size characteristics in patients with transient ST-segment elevation myocardial infarction (TSTEMI) compared to patients with ST-segment and non-ST-segment elevation myocardial infarctions (STEMI and NSTEMI, respectively).

Methods and results
In total, 407 patients were enrolled in this multicentre observational prospective cohort study. All patients underwent CMR examination 2–8 days after the index event. CMR cine imaging was performed for functional assessment and late gadolinium enhancement to determine infarct size and identify microvascular obstruction (MVO). TSTEMI patients demonstrated the highest LV ejection fraction and the most preserved global LV strain (longitudinal, circumferential, and radial) across the three groups (overall P ≤ 0.001). The CMR-defined infarction was less frequently observed in TSTEMI than in STEMI patients [77 (65%) vs. 124 (98%), P &lt; 0.001] but was comparable with NSTEMI patients [77 (65%) vs. 66 (70%), P = 0.44]. A remarkably smaller infarct size was seen in TSTEMI compared to STEMI patients [1.4 g (0.0–3.9) vs. 13.5 g (5.3–26.8), P &lt; 0.001], whereas infarct size was not significantly different from that in NSTEMI patients [1.4 g (0.0–3.9) vs. 2.1 g (0.0–8.6), P = 0.06]. Whilst the presence of MVO was less frequent in TSTEMI compared to STEMI patients [5 (4%) vs. 53 (31%), P &lt; 0.001], no significant difference was seen compared to NSTEMI patients [5 (4%) vs. 5 (5%), P = 0.72].

Conclusion
TSTEMI yielded favourable cardiac LV function, strain, and infarct-related scar mass compared to STEMI and NSTEMI. LV function and infarct characteristics of TSTEMI tend to be more similar to NSTEMI than STEMI.
Facial asymmetry assessment in skeletal Class III patients with spatially-dense geometric morphometrics
Authors: Fan Yi , He Wei , Chen Gui , Song Guangying , Matthews Harold , Claes Peter , Jiang Ruoping , Xu Tianmin 
Published: May 2021

SummaryObjectiveQuantification and visualization of the location and magnitude of facial asymmetry is important for diagnosis and treatment planning. The objective of this study was to analyze the asymmetric features of the face for skeletal Class III patients using spatially-dense geometric morphometrics.MethodsThree-dimensional facial images were obtained for 86 skeletal Class III patients. About 7160 uniformly sampled quasi-landmarks were automatically identified on each face using template mapping technique. The pointwise surface-to-surface distance between original and mirror face was measured and visualized for the whole face after robust Procrustes superimposition. The degree of overall asymmetry in an individual was scored using a root-mean-squared-error. Automatic partitioning of the face was obtained, and the severity of the asymmetry compared among seven facial regions.ResultsFacial asymmetry was mainly located on, but not limited to, the lower two-thirds of the face in skeletal Class III patients. The lower cheek and nose asymmetry were detected to have more extensive and of a greater magnitude of asymmetry than other facial anatomical regions but with various individual variations. The overall facial asymmetry index and the regional facial asymmetry indices were higher in males and patients with chin deviation.ConclusionsSoft tissue asymmetry is predominately presented in the lower-third of the face in skeletal Class III patients and with various variations on other facial anatomical regions. Morphometric techniques and computer intensive analysis have allowed sophisticated quantification and visualization of the pointwise asymmetry on the full face.
Poverty as Misrecognition: What Role for Antidiscrimination Law in Europe?
Authors: Ganty Sarah 
Published: May 2021

Abstract
It is widely agreed that victims of discrimination on traditional status grounds such as gender and race are overrepresented among the poor and undereducated. People living in poverty also face discrimination because of their socioeconomic situation. Many national, European and international antidiscrimination provisions prohibit discrimination on grounds that are related to a person’s socioeconomic situation. It is striking, however, that this is hardly applied in practice. On the basis of domestic—Belgian, French and British—and European material, this paper argues that the prohibition of discrimination on grounds of social condition is an empowering legal tool in the protection of disadvantaged people, especially regarding issues of misrecognition. Four reasons for this are considered: the determining role of the prohibition of discrimination on grounds of social condition in applying a direct scrutiny of the socioeconomic underprivileged situation of the applicants, its role in combating stereotypes and stigma against poor people, its important cross-cutting function in cases of multiple discrimination, and its exclusive applicability in some occurrences of discrimination.
Mind the gap: Analyzing the divergence between constitutional text and constitutional reality
Authors: Voigt Stefan 
Published: May 2021

Abstract
Constitutional economics—the analysis of constitutions drawing on the economic approach—has made important progress over the last two decades. The factors determining whether a constitution is complied with, however, have received only little attention. This is surprising, as a huge gap between constitutional text and constitutional reality seems to exist in many countries. In this article, this gap is referred to as the de jure/de facto gap. The article discusses ways in which the gap can be researched systematically and surveys the scant available literature that has tried to do so thus far.
Circumstances, Postmortem Findings, Blood Concentrations and Metabolism in a Series of Methoxyacetylfentanyl-Related Deaths
Authors: Kronstrand Robert , Åstrand Anna , Watanabe Shimpei , Gréen Henrik , Vikingsson Svante 
Published: May 2021

Abstract
Methoxyacetylfentanyl is one of many fentanyl analogs available as new psychoactive substances. It have been encountered in both the European Union and the United States, and existing literature suggest that methoxyacetylfentanyl is around 3- to 5-fold less potent than fentanyl. The aim of the present work was to combine case information with blood concentrations and abundance of urinary metabolites to investigate the importance of these parameters for toxicological interpretation. Quantification of methoxyacetylfentanyl in femoral blood was performed by LC--MS-MS and urinary metabolites were analyzed by LC--QTOF-MS with and without hydrolysis with β-glucuronidase/arylsulfatase. For confirmation of identified metabolites, methoxyacetylfentanyl was incubated with hepatocytes for up to 5 hours and analyzed with the same method as the urine samples. In eleven postmortem cases (27 to 41 years old and including one female) methoxyacetylfentanyl was reported in femoral blood. The cause of death was intoxication by methoxyacetylfentanyl alone or in combination with other drugs in all but one case, where death was attributed to acute complications of an underlying heart disease but with possible contribution from methoxyacetylfentanyl. In total, 27 urinary metabolites were found, including eight glucuronides. Major biotransformations were O-demethylation, dealkylation to form the nor-metabolite, mono- and dihydroxylations of the phenethyl moiety, as well as combinations thereof. The most abundant metabolites in hydrolyzed urine included O-desmethyl-, O-desmethyl-phenethyl-hydroxy-, O-desmethyl-phenethyl-hydroxymethoxy- and nor-methoxyacetylfentanyl. Differences in the abundance of methoxyacetylfentanyl and its major metabolites could be interpreted to indicate fatal intoxications in abstinent or chronic users. We postulate that urinary concentrations of methoxyacetylfentanyl and two metabolites, in combination with the methoxyacetylfentanyl concentration in femoral blood, might be good indicators of the time between administration and death as well as prior use.
Consensus-based classification system for intra-operative management of labral tears during hip arthroscopy—aggregate recommendations from high-volume hip preservation surgeons
Authors: Lall Ajay C , Annin Shawn , Chen Jeff W , Diulus Samantha , Ankem Hari K , Rosinsky Philip J , Shapira Jacob , Meghpara Mitchell B , Maldonado David R , Hartigan David E , Krych Aaron J , Levy Bruce A , Domb Benjamin G 
Published: May 2021

Abstract
The purpose of this study was to survey high-volume hip preservation surgeons regarding their perspectives on intra-operative management of labral tears to improve decision-making and produce an effective classification system. A cross-sectional survey of high-volume hip preservation surgeons was conducted in person and anonymously, using a questionnaire that is repeated for indications of labral debridement, repair and reconstruction given the torn labra are stable, unstable, viable or non-viable. Twenty-six high-volume arthroscopic hip surgeons participated in this survey. Provided the labrum was viable (torn tissue that is likely to heal) and stable, labral debridement would be performed by 76.92% of respondents for patients &gt;40 years of age and by &gt;84% of respondents for stable intra-substance labral tears in patients without dysplasia. If the labrum was viable but unstable, labral repair would be performed by &gt;80% of respondents for patients ≤40 years of age and &gt; 80% of respondents if the labral size was &gt;3 mm and located anteriorly. Presence of calcified labra or the Os acetabuli mattered while deciding whether to repair a labrum. In non-viable (torn tissue that is unlikely to heal) and unstable labra, labral reconstruction would be performed by 84.62% of respondents if labral size was &lt;3 mm. The majority of respondents would reconstruct calcified and non-viable, unstable labra that no longer maintained a suction seal. Surgeons performing arthroscopic hip labral treatment may utilize this comprehensive classification system, which takes into consideration patient age, labral characteristics (viability and stability) and bony morphology of the hip joint. When choosing between labral debridement, repair or reconstruction, consensus recommendations from high-volume hip preservation surgeons can enhance decision-making.
Carios kelleyi (Acari: Ixodida: Argasidae) Infected With Rickettsial Agents Documented Infesting Housing in Kansas, United States
Authors: Nadolny Robyn M , Kennedy Ashley C , Rodgers James M , Vincent Zachary T , Cornman Hannah , Haynes Scott A , Casal Cory , Robbins Richard G , Richards Allen L , Jiang Ju , Farris Christina M 
Published: May 2021

Abstract
During September–December 2018, 25 live ticks were collected on-post at Fort Leavenworth, Kansas, in a home with a history of bat occupancy. Nine ticks were sent to the Army Public Health Center Tick-Borne Disease Laboratory and were identified as Carios kelleyi (Cooley and Kohls, 1941), a species that seldom bites humans but that may search for other sources of blood meals, including humans, when bats are removed from human dwellings. The ticks were tested for numerous agents of human disease. Rickettsia lusitaniae was identified by multilocus sequence typing to be present in two ticks, marking the first detection of this Rickettsia agent in the United States and in this species of tick. Two other Rickettsia spp. were also detected, including an endosymbiont previously associated with C. kelleyi and a possible novel Rickettsia species. The potential roles of C. kelleyi and bats in peridomestic Rickettsia transmission cycles warrant further investigation.
Mental Disorder and Suicide: What’s the Connection?
Authors: Maung Hane Htut 
Published: May 2021

Abstract
This paper offers a philosophical analysis of the connection between mental disorder and suicide risk. In contemporary psychiatry, it is commonly suggested that this connection is a causal connection that has been established through empirical discovery. Herein, I examine the extent to which this claim can be sustained. I argue that the connection between mental disorder and increased suicide risk is not wholly causal but is partly conceptual. This in part relates to the way suicidality is built into the definitions of some psychiatric diagnoses. It also relates to the broader normative assumption that suicidal behavior is by definition mentally disordered behavior. The above has significant epistemological implications, which I explore. I propose that the claim that suicide is connected with mental disorder cannot be justified solely by appealing to empirical evidence but also warrants a justification on conceptual and normative grounds.
Discrimination of Minority Welfare Claimants in the Real World: The Effect of Implicit Prejudice
Authors: Assouline Michaela , Gilad Sharon , Ben-Nun Bloom Pazit 
Published: May 2021

AbstractExploiting rare access to doctors’ real-world judgments of incapacity benefits applications to an Israeli governmental program (2015–17), we examine the prevalence and underlying mechanisms of discrimination against Muslims versus Jews. To mitigate confounding explanations for unequal treatment, we restrict the analysis to claimants whose applications passed a strict medical-disability threshold so that their medical condition was undisputed. Theoretically, we offer a comprehensive theoretical framework for possible micro-mechanisms underlying bureaucratic discrimination of minorities, the decision-environment conditions that instigate them, and observational implications for their decoding. Findings indicate that despite organizational commitment to equality Jewish doctors were more likely to reject applications by Muslims and to recommend partial compensation for Jews. We find no differences with regard to full compensation. Further, we empirically illustrate how our proposed theoretical framework can be employed to analyze which micro-mechanism is most likely to underlie discrimination and to empirically decipher among alternative explanations, demonstrating that bureaucratic discrimination, in this case, is best explained by implicit prejudice triggered under conditions of complexity and ambiguity that undermined doctors’ systematic processing of information.
Effects of western juniper (Juniperus occidentalis) control on ecosystem nitrogen stocks in central Oregon, USA
Authors: Abdallah Mohamed A B , Mata-González Ricardo , Noller Jay S , Ochoa Carlos G 
Published: May 2021

Abstract

Aims
In the Oregon of USA, the control of western juniper (Juniperus occidentalis) is an accepted rangeland management practice to restore sagebrush steppe habitats of importance to wildlife and livestock. The effects of juniper cutting on ecosystem nitrogen, however, have not been well addressed although woody plant control has important implications for local watershed management and regional nitrogen pools.

Methods
We quantified ecosystem nitrogen stocks in two adjacent watersheds, comprised of a treated watershed (most juniper removed) and an untreated watershed (juniper not removed). Thirteen years after juniper removal, we measured aboveground nitrogen stocks for juniper trees, shrubs, grasses and litter in both watersheds. We also measured belowground nitrogen stocks (roots and soil) in both watersheds at two soil depths (0–25 and 25–50 cm).

Important Findings
Aboveground nitrogen stocks were 6.9 times greater in the untreated than in the treated watershed considering the much larger aboveground biomass. However, root nitrogen stocks were 3.1 times greater in the treated one due to the gain of understory root biomass associated with juniper cutting. Soil nitrogen stocks at both 0–25 and 25–50 cm depths were not affected by juniper removal. Overall, total ecosystem nitrogen stocks did not differ between the treated (9536 kg N ha−1) and untreated (9456 kg N ha−1) watersheds. The greatest ecosystem nitrogen accumulation (at least 95% total ecosystem nitrogen) resided belowground (soil 0–50 cm and roots) in both watersheds. This study provides evidence that the benefits of juniper removal can be attained without significantly affecting the capacity of ecosystem nitrogen storage.