bluuebunny/crossref_metadata_2025_split huggingface dataset:
Imputation method for single-cell RNA-seq data using neural topic model
Authors: Qi Yueyang , Han Shuangkai , Tang Lin , Liu Lin 
Published: November 2023

Abstract
Single-cell RNA sequencing (scRNA-seq) technology studies transcriptome and cell-to-cell differences from higher single-cell resolution and different perspectives. Despite the advantage of high capture efficiency, downstream functional analysis of scRNA-seq data is made difficult by the excess of zero values (i.e., the dropout phenomenon). To effectively address this problem, we introduced scNTImpute, an imputation framework based on a neural topic model. A neural network encoder is used to extract underlying topic features of single-cell transcriptome data to infer high-quality cell similarity. At the same time, we determine which transcriptome data are affected by the dropout phenomenon according to the learning of the mixture model by the neural network. On the basis of stable cell similarity, the same gene information in other similar cells is borrowed to impute only the missing expression values. By evaluating the performance of real data, scNTImpute can accurately and efficiently identify the dropout values and imputes them accurately. In the meantime, the clustering of cell subsets is improved and the original biological information in cell clustering is solved, which is covered by technical noise. The source code for the scNTImpute module is available as open source at https://github.com/qiyueyang-7/scNTImpute.git.
Evaluating long-read de novo assembly tools for eukaryotic genomes: insights and considerations
Authors: Cosma Bianca-Maria , Shirali Hossein Zade Ramin , Jordan Erin Noel , van Lent Paul , Peng Chengyao , Pillay Stephanie , Abeel Thomas 
Published: November 2023

Abstract

Background
Assembly algorithm choice should be a deliberate, well-justified decision when researchers create genome assemblies for eukaryotic organisms from third-generation sequencing technologies. While third-generation sequencing by Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) has overcome the disadvantages of short read lengths specific to next-generation sequencing (NGS), third-generation sequencers are known to produce more error-prone reads, thereby generating a new set of challenges for assembly algorithms and pipelines. However, the introduction of HiFi reads, which offer substantially reduced error rates, has provided a promising solution for more accurate assembly outcomes. Since the introduction of third-generation sequencing technologies, many tools have been developed that aim to take advantage of the longer reads, and researchers need to choose the correct assembler for their projects.

Results
We benchmarked state-of-the-art long-read de novo assemblers to help readers make a balanced choice for the assembly of eukaryotes. To this end, we used 12 real and 64 simulated datasets from different eukaryotic genomes, with different read length distributions, imitating PacBio continuous long-read (CLR), PacBio high-fidelity (HiFi), and ONT sequencing to evaluate the assemblers. We include 5 commonly used long-read assemblers in our benchmark: Canu, Flye, Miniasm, Raven, and wtdbg2 for ONT and PacBio CLR reads. For PacBio HiFi reads , we include 5 state-of-the-art HiFi assemblers: HiCanu, Flye, Hifiasm, LJA, and MBG. Evaluation categories address the following metrics: reference-based metrics, assembly statistics, misassembly count, BUSCO completeness, runtime, and RAM usage. Additionally, we investigated the effect of increased read length on the quality of the assemblies and report that read length can, but does not always, positively impact assembly quality.

Conclusions
Our benchmark concludes that there is no assembler that performs the best in all the evaluation categories. However, our results show that overall Flye is the best-performing assembler for PacBio CLR and ONT reads, both on real and simulated data. Meanwhile, best-performing PacBio HiFi assemblers are Hifiasm and LJA. Next, the benchmarking using longer reads shows that the increased read length improves assembly quality, but the extent to which that can be achieved depends on the size and complexity of the reference genome.
Military music and society during the French wars, 1793–1815
Authors: O’Keeffe Eamonn 
Published: November 2023

Abstract
The French Revolutionary and Napoleonic Wars were experienced by the ears as much as the eyes, yet the auditory dimensions of these conflicts have received limited attention from historians. This article interrogates the reach and reception of military music in wartime Britain and Ireland by drawing on a wealth of evidence from memoirs, diaries, press reports and regimental archives. It demonstrates that military bands provided sought-after entertainment at myriad public events and staged open-air concerts for socially diverse audiences. The article interprets martial music-making as an important civil-military interface and a potent form of cultural propaganda: a means of inculcating patriotism and asserting the sonic supremacy of the established order in a revolutionary age. But it also reveals that military music provoked irritation, controversy and distress, not least by generating noise complaints and exacerbating sectarianism in Ireland. The article concludes by considering the role of British regimental music-making in overseas colonies and foreign theatres of operations, arguing that it functioned as a form of soft power that underpinned imperial authority, aided diplomacy and eased relations with local inhabitants. An intrusive symptom of large-scale military mobilization, martial music shaped civilian attitudes and soundscapes while profoundly influencing broader musical culture.
(Re)Designing Security and War? Reflections on Transgressive Creativity and International Relations
Authors: Lacy Mark 
Published: November 2023

Abstract
In the discipline of IR, a growing number of academics work with artists, designers, architects, and filmmakers to explore a range of global political, economic, and security challenges. At the same time, there has been a concern—made powerfully by Dan Öberg—that there is a danger of what he terms “transgressive creativity” in the way that new approaches and methods are being used to respond to security challenges, especially in a military context. In this essay, I explore how the problem of this “transgressive creativity” is a concern shared by two groups working on the problems of security, war, technology, economy, and politics: critical designers and military designers (or the group that is becoming known as the Archipelago of Design). While the objectives of both communities are different, they both share a view that a sense of openness to collaboration is essential to go beyond traditional institutional approaches in order to make sense of complex and uncertain futures in a time of technological acceleration and geopolitical change. The essay concludes that we should be vigilant to the problems of transgressive creativity that Öberg alerts us to, but we also need to broaden the research agenda to understand how creative techniques are being used by a variety of actors and organizations to address the problems of international politics; academics in IR also need to see whether the “openness” to collaboration has broader disciplinary and methodological implications for researchers.
Double marginalization, market foreclosure, and vertical integration
Authors: Choné Philippe , Linnemer Laurent , Vergé Thibaud 
Published: November 2023

Abstract
Double marginalization is a robust phenomenon in procurement under asymmetric information when sophisticated contracts can be implemented. In this context, vertical integration causes merger-specific elimination of double marginalization but biases the make-or-buy decision against independent suppliers. If the buyer has full bargaining power over prices and quantities, a vertical merger benefits final consumers even when it results in the exclusion of efficient suppliers. If on the contrary the buyer’s bargaining power is reduced after she has committed to deal exclusively with a limited set of suppliers, exclusion of efficient suppliers may harm final consumers.
The art of rivalry
Authors: Hilker Anne 
Published: November 2023

Abstract
In the years just before the Wall Street Crash of 1929, the American banker and philanthropist Jules S. Bache (1861–1944) built a collection of European paintings and decorative art which, in the 1930s, was located at a crossroads in collecting practices and museum growth in the United States. His offer of the collection as a gift to the Metropolitan Museum of Art, made in 1936 on condition that it be separately named and housed, was at first rejected. He next opened his home to the public as a museum, burnishing his holdings with frequent exhibitions and publicity. In 1943 the Second World War forced Bache’s museum to close but brought the collection on loan to the Met, which had put its own masterworks into protective storage. Acquisition of Bache’s collection was now ‘imperative’, and the parties agreed on terms. At his death he contributed fifty-eight paintings together with items of sculpture, Georgian silver, enamel work, porcelain, tapestry, and furniture. Their transfer to the Met illustrates the competitive forces – personal, financial, institutional and geopolitical – that brought private collections to public museums in the USA before and during the years of global war.
Best practice guidelines for clinical and radiological assessment of patients with femoroacetabular impingement. Results from the ISHA International Delphi Consensus Project—Phase 2
Authors: Radha Sarkhell , Hutt Jonathan , Lall Ajay , Domb Benjamin , Lynch T Sean , Griffin Damian , Field Richard E , Chuck-Cakic Josip 
Published: November 2023

ABSTRACT
In 2018, the International Society for Hip Preservation Surgery (ISHA) initiated a series of Delphi consensus studies to identify the global hip preservation community’s current opinion on best practices for different facets of hip preservation surgery. Arthroscopic procedures to treat hip pathologies, such as femoroacetabular impingement syndrome (FAIS) are now established in mainstream orthopaedic practice. This study establishes recommendations for the investigation of patients with suspected FAIS. The investigation has focused on the three phases of the diagnostic process—patient history, physical examination and special investigations. Our expert panel consisted of 174 international orthopaedic surgeons with expertise in hip preservation surgery, thereby making recommendations generalisable across the globe. After three rounds of survey and analysis with 174 participants per round, our study achieved consensus at a minimum agreement threshold of 80.0% on 55 statements pertaining to the assessment of patients with FAIS. We encourage our junior and senior hip arthroscopy colleagues internationally to consider these statements both to standardize the clinical and radiological assessment of patients with FAIS and to aid in the design of future research.
Highly efficient conversion of mouse fibroblasts into functional hepatic cells under chemical induction
Authors: Zhong Zhi , Du Jiangchuan , Zhu Xiangjie , Guan Lingting , Hu Yanyu , Zhang Peilin , Wang Hongyang 
Published: November 2023

Abstract
Previous studies have shown that hepatocyte-like cells can be generated from fibroblasts using either lineage-specific transcription factors or chemical induction methods. However, these methods have their own deficiencies that restrict the therapeutic applications of such induced hepatocytes. In this study, we present a transgene-free, highly efficient chemical-induced direct reprogramming approach to generate hepatocyte-like cells from mouse embryonic fibroblasts (MEFs). Using a small molecule cocktail (SMC) as an inducer, MEFs can be directly reprogrammed into hepatocyte-like cells, bypassing the intermediate stages of pluripotent and immature hepatoblasts. These chemical-induced hepatocyte-like cells (ciHeps) closely resemble mature primary hepatocytes in terms of morphology, biological behavior, gene expression patterns, marker expression levels, and hepatic functions. Furthermore, transplanted ciHeps can integrate into the liver, promote liver regeneration, and improve survival rates in mice with acute liver damage. ciHeps can also ameliorate liver fibrosis caused by chronic injuries and enhance liver function. Notably, ciHeps exhibit no tumorigenic potential either in vitro or in vivo. Mechanistically, SMC-induced mesenchymal-to-epithelial transition and suppression of SNAI1 contribute to the fate conversion of fibroblasts into ciHeps. These results indicate that this transgene-free, chemical-induced direct reprogramming technique has the potential to serve as a valuable means of producing alternative hepatocytes for both research and therapeutic purposes. Additionally, this method also sheds light on the direct reprogramming of other cell types under chemical induction.
Clinical outcomes of scalp or face angiosarcoma treatment with intensity-modulated radiotherapy: a multicenter study
Authors: Iwai Takahiro , Imagumbai Toshiyuki , Hiraoka Shinya , Kishi Takahiro , Okabayashi Shun , Ashida Ryo , Mitsuyoshi Takamasa , Matsuo Yukinori , Ishigaki Takashi , Mizowaki Takashi , Kokubo Masaki 
Published: November 2023

Abstract
Combined modality therapy, including radiotherapy (RT), is a common treatment for scalp or face angiosarcoma. Although intensity-modulated radiotherapy (IMRT) can deliver homogeneous doses to the scalp or face, clinical data are limited. This multicenter study aimed to evaluate scalp or face angiosarcoma treated with definitive or post-operative IMRT. We retrospectively analyzed data from patients who received IMRT for scalp or face angiosarcoma at three institutions between January 2015 and March 2020. Local control (LC) rate, overall survival (OS), progression-free survival (PFS), recurrence patterns and toxicity were evaluated. Fifteen patients underwent IMRT during the study period. Definitive RT was performed on 10 patients and post-operative RT was performed on 5 patients. The 1-year LC rate was 85.7% (95% confidence interval [CI], 53.9–96.2%). The 1-year OS and PFS rates were 66.7% (95% CI, 37.5–84.6%) and 53.3% (95% CI, 26.3%–74.4%), respectively. Univariate analysis revealed that a clinical target volume over 500 cm3 was associated with poor LC. Distant metastasis was the most common recurrence pattern. All patients experienced Grade 2 or 3 radiation dermatitis, and five patients experienced grade ≥ 3 skin ulceration. One patient who underwent maintenance therapy with pazopanib developed Grade 5 skin ulceration. Fisher’s exact test showed that post-operative RT was significantly associated with an increased risk of skin ulceration of grade ≥ 3. These results demonstrate that IMRT is a feasible and effective treatment for scalp or face angiosarcoma, although skin ulceration of grade ≥ 3 is a common adverse event in patients who receive post-operative RT.
Module 9: Managing Cognitive Difficulties and “Brain Fog”
Authors: Jaywant Abhishek , Oberlin Lauren E. , Cherestal Stephanie , Bueno Castellano Christina , Wilkins Victoria M. , Kanellopoulos Dora 
Published: November 2023

Abstract
This chapter focuses on how to handle common post-COVID-19 cognitive difficulties and symptoms of brain fog, using the cognitive behavioral model. While two or three sessions are recommended, clients can have more sessions if their main concern is their cognitive difficulties and brain symptoms. Therapists may also refer the client for a neuropsychological evaluation and administer self-report measures of cognitive functioning, such as the Patient-Reported Outcomes Measurement Information System (PROMIS) cognitive function scale. Monitoring cognitive lapses may help clients become aware of how often they occur in their daily lives. The chapter offers some cognitive strategies adapted from existing approaches and workbooks for attention-deficit/hyperactivity disorder, traumatic brain injury, and neurologic illness.
Module 12: Putting it all Together and Managing Uncertainty
Authors: Jaywant Abhishek , Oberlin Lauren E. , Cherestal Stephanie , Bueno Castellano Christina , Wilkins Victoria M. , Kanellopoulos Dora 
Published: November 2023

Abstract
This chapter covers how to consolidate and maintain the gains that the client made in treatment. Practicing can help clients to manage ongoing uncertainty, navigate setbacks, and prevent relapse into unhealthy cognitive and behavioral patterns. Clients must understand the nature of the gains they achieved in therapy and their agency as they transition into the later phases of treatment. Reflecting on the treatment helps build self-monitoring habits. Therapists should make clients aware of the difference between temporary setbacks (which are inevitable) and the persistent re-emergence of mood or anxiety symptoms (which need further treatment). The chapter emphasizes that successful completion of therapy does not preclude clients from experiencing difficulties.
Caregivers and Families
Authors: Jaywant Abhishek , Oberlin Lauren E. , Cherestal Stephanie , Bueno Castellano Christina , Wilkins Victoria M. , Kanellopoulos Dora 
Published: November 2023

Abstract
This chapter focuses on the importance of supporting family caregivers and involving them in the treatment of the client. Family members and friends of individuals with persisting sequelae of COVID-19 may find themselves temporarily or permanently involved in caregiving tasks, and as a result may experience sometimes dramatic changes in their usual roles. Caregivers are at risk for caregiver burden, which is associated with negative health outcomes. Family caregivers can positively impact the client’s adherence to medical and rehabilitation treatments. The chapter provides information about cultural factors that therapists need to consider when they are working with ethnoculturally diverse families.
Comparison of Theater Medical Data Store and Reportable Medical Event Records to Theater Animal Bite Reports Submissions, 2018–2019
Authors: Knobbe Marc G , Aden Brandon J , Ashbaugh Hayley R 
Published: November 2023

ABSTRACT

Introduction
This analysis evaluates potential reporting discrepancies of the DD2341 Form (Report of Animal Bite—Potential Rabies Exposure) submitted to a forward-deployed Rabies Advisory Board to the Theater Medical Data Store (TMDS) and Reportable Medical Event (RME) systems to identify reporting gaps that can lead to improved best practices that ensure documentation of Post Exposure Prophylaxis (PEP) of potential rabies exposures into service members (SMs) electronic medical records.

Materials and Methods
The project compares the number of Service Member animal exposure DD2341 reports submitted to the Camp Arifjan, Kuwait Rabies Advisory Board to in-theater treatment electronic records at the same forward deployed locations from January 1, 2018 to December 31, 2019 recorded in the TMDS and RME databases. Records included active duty and reserve SM deployed to six countries in the United States Central Command (USCENTCOM) area of responsibility. The analysis compared some demographic information, type of potential rabies exposure (e.g., whether a bite or scratch), and PEP to rabies with Human Rabies Immune Globulin (HRIG), Human Rabies Vaccine (HRV), or both between the reporting systems.

Results
There were 44 fewer records of PEP from the TMDS data records than reported from in theater written reports. Electronic record data showed 85 coded rabies exposure diagnoses. Twenty-two received HRV and no HRIG, while four received HRIG and HRV for PEP. Only seven of the 26 SM receiving rabies PEP had a confirmed RME associated with the electronic record. There were 116 SM animal exposure written reports, with 70 reporting PEP. There were 41 records indicating the SM received HRIG and HRV as part of PEP, while 29 reports indicated that the patient received only HRV PEP. Of the 41 SM receiving HRIG, 32 of the exposures were from cat scratches or bites. Seven records specified HRIG was indicated for treatment but not available at the location; therefore, HRV was the only treatment available. The most common reason indicated on the written report for not receiving rabies PEP was that treatment was not indicated based on the risk category of animal exposure.

Conclusions
This study is the first to compare the electronic medical record data to in theater reports for potential rabies exposure in a theater of operations. The analysis suggests that some written forms generated in the USCENTCOM theater are not entered into SM Military Health System electronic medical records, indicating that electronic medical records may be a less sensitive method than in-theatre reports for rabies program surveillance in a deployed setting. There is under-reporting in electronic medical records of rabies PEP in both TMDS and RME databases. Rabies PEP is an RME according to the Armed Forces Health Surveillance Division guidelines and case definitions. There needs to be better integration of the DD2341 into the electronic medical records system.
Raising the U.S. Army Height–Weight (Body Mass Index) Standards: Quantifying Metabolic Risk
Authors: Smith Maria , Cooper Alma , Hill James O , Yankovich Michael , Crofford Ira , Thomas Diana M 
Published: November 2023

ABSTRACT

Background & objectives
The U.S. Army fell 25% short of its recruitment goal in 2022 and therefore, increasing the eligibility pool for potential recruits is of interest. Raising the body mass index (BMI) standards for eligibility presents a path to increase the recruitable population; however, there may be additional costs incurred due to attendant health risks that may be present in individuals with higher BMI.

Methods
We filtered the 2017-2020 National Health and Nutrition Examination Survey by age (17-25 years) and BMI (up to 30 kg/m2). A k-means cluster analysis was performed on the filtered dataset for the variables used to determine metabolic syndrome. Metabolic syndrome Clusters were characterized through summary statistics and compared over clinical measurements and questionnaire responses.

Results
Five distinct clusters were identified and mean BMI in two clusters (Clusters1 and 3) exceeded the current U.S. Army BMI thresholds. Of these two clusters, Cluster 1 members had metabolic syndrome. Cluster 3 members were at higher risk for metabolic syndrome compared to members of Clusters 2, 4, and 5. Mean waist circumference was slightly lower in Cluster 3 compared to Cluster 1. None of the clusters had significant differences in depression scores, poverty index, or frequency of dental visits.

Conclusions
Potential recruits from Cluster 1 have excessive health risk and may incur substantial cost to the U.S. Army if enlisted. However, potential recruits from Cluster 3 appear to add little risk and offer an opportunity to increase the pool for recruiting.