bluuebunny/crossref_metadata_2025_split huggingface dataset:
MetaPro: a scalable and reproducible data processing and analysis pipeline for metatranscriptomic investigation of microbial communities
Authors: Taj Billy , Adeolu Mobolaji , Xiong Xuejian , Ang Jordan , Nursimulu Nirvana , Parkinson John 
Published: June 2023

Abstract
Background
Whole microbiome RNASeq (metatranscriptomics) has emerged as a powerful technology to functionally interrogate microbial communities. A key challenge is how best to process, analyze, and interpret these complex datasets. In a typical application, a single metatranscriptomic dataset may comprise from tens to hundreds of millions of sequence reads. These reads must first be processed and filtered for low quality and potential contaminants, before being annotated with taxonomic and functional labels and subsequently collated to generate global bacterial gene expression profiles.

Results
Here, we present MetaPro, a flexible, massively scalable metatranscriptomic data analysis pipeline that is cross-platform compatible through its implementation within a Docker framework. MetaPro starts with raw sequence read input (single-end or paired-end reads) and processes them through a tiered series of filtering, assembly, and annotation steps. In addition to yielding a final list of bacterial genes and their relative expression, MetaPro delivers a taxonomic breakdown based on the consensus of complementary prediction algorithms, together with a focused breakdown of enzymes, readily visualized through the Cytoscape network visualization tool. We benchmark the performance of MetaPro against two current state-of-the-art pipelines and demonstrate improved performance and functionality.

Conclusions
MetaPro represents an effective integrated solution for the processing and analysis of metatranscriptomic datasets. Its modular architecture allows new algorithms to be deployed as they are developed, ensuring its longevity. To aid user uptake of the pipeline, MetaPro, together with an established tutorial that has been developed for educational purposes, is made freely available at https://github.com/ParkinsonLab/MetaPro. The software is freely available under the GNU general public license v3.
Applying 4IRs in education technology to science pedagogy: effects and students’ experience
Authors: Ojetunde Segun Michael , Ramnarain Umesh 
Published: June 2023

AbstractEducation, technology, and economic growth are not only linked but synchronised to achieve holistic global development. An instance is the adoption of online platforms for learning and promoting economic activities during the COVID-19 pandemic lockdown. However, the lingering question among education stakeholders in Nigeria borders on what constitutes students’ experiences and how teaching in an online platform can foster basic learning outcomes in science. The study used a mixed method of explanatory concurrent design to investigate the innovation of online platforms for learning during the COVID-19 lockdown. The idea was to compare the innovation’s effects on participant and non-participant respondents. Of the 120 students studied, sixty students were selected from schools that adopted online learning platforms. They were comparatively paired with their contemporaries that did not adopt a similar innovation for analysis of their skills in problem-solving and critical thinking. Ten students who learned via online platforms were interviewed. Fallibilities associated with teaching–learning using online platforms were observed, coupled with the fact that the efficacy of online platforms in enhancing basic learning outcomes in science does not embrace critical thinking, but problem-solving. Therefore, actionable strategies by education stakeholders to design responsive and strictly academic online learning platforms were recommended.
Barriers and facilitators to implementation of nutrition-related actions in school settings in low- and middle-income countries (LMICs): a qualitative systematic review using the Consolidated Framework for Implementation Research (CFIR)
Authors: Meshkovska Biljana , Gebremariam Mekdes Kebede , Atukunda Prudence , Iversen Per Ole , Wandel Margareta , Lien Nanna 
Published: June 2023

Abstract
Background
Low- and middle-income countries (LMICs) are particularly vulnerable to the double burden of malnutrition: co-existence of underweight, overweight, obesity, and/or diet-related non-communicable diseases. Nutrition-related double-duty actions in school settings have been identified as one of the ways to address this challenge. However, to be able to take full advantage of the potential impact, it is important to understand their implementation as well. The aim of this paper is to systematically review qualitative research on barriers and facilitators to the implementation of nutrition-related actions in the school settings in LMICs.

Methods
The following databases were searched: EMBASE, ERIC, MEDLINE, Global Health and PsycInfo (all on Ovid), Scopus (Elsevier), the Web of Science Social Sciences Citation Index, and Global Index Medicus from the World Health Organization. Of the 4253 identified records, 4030 were excluded after the abstract and title screen, leaving 223 for the full-text screen. A final 36 papers were included in this review. The consolidated framework for implementation research (CFIR) was used in the analysis.

Results
We identified barriers and facilitators to implementation linked to the following CFIR constructs/sub-constructs: design quality and packaging, cost (intervention characteristics); target group needs and resources, cosmopolitanism, external policy and incentives (outer setting); structural characteristics, readiness for implementation (inner setting); knowledge and beliefs (characteristics of individuals) and engaging, executing (process). All identified constructs apart from target group needs and resources, knowledge and beliefs, and engaging were predominantly barriers. Available resources were the most prevalent barriers across studies.

Conclusion
This review identified barriers and facilitators to the implementation of nutrition-related actions based on qualitative articles in the school setting in LMICs, using the CFIR. Schools face continuous challenges in regard to funding and the government sector may have a role to play not only by offering financial assistance, but also through policy-making that would support healthy eating practices on school grounds.

Registration
PROSPERO ID: CRD42022296159.
Enfortumab Vedotin With or Without Pembrolizumab in Cisplatin-Ineligible Patients With Previously Untreated Locally Advanced or Metastatic Urothelial Cancer
Authors: O'Donnell Peter H. , Milowsky Matthew I. , Petrylak Daniel P. , Hoimes Christopher J. , Flaig Thomas W. , Mar Nataliya , Moon Helen H. , Friedlander Terence W. , McKay Rana R. , Bilen Mehmet A. , Srinivas Sandy , Burgess Earle F. , Ramamurthy Chethan , George Saby , Geynisman Daniel M. , Bracarda Sergio , Borchiellini Delphine , Geoffrois Lionnel , Maroto Rey Jose Pablo , Ferrario Christiano , Carret Anne-Sophie , Yu Yao , Guseva Maria , Homet Moreno Blanca , Rosenberg Jonathan E. 
Published: June 2023

PURPOSE Patients with locally advanced or metastatic urothelial cancer (la/mUC) who are ineligible for cisplatin-based therapy have limited first-line (1L) treatment options and significant need for improved therapies. Enfortumab vedotin (EV) and pembrolizumab (Pembro) individually have shown a survival benefit in urothelial cancer in second-line + la/mUC settings. Here, we present data from the pivotal trial of EV plus Pembro (EV + Pembro) in the 1L setting. PATIENTS AND METHODS In Cohort K of the EV-103 phase Ib/II study, cisplatin-ineligible patients with previously untreated la/mUC were randomly assigned 1:1 to receive EV as monotherapy or in combination with Pembro. The primary end point was confirmed objective response rate (cORR) per blinded independent central review. Secondary end points included duration of response (DOR) and safety. There were no formal statistical comparisons between treatment arms. RESULTS The cORR was 64.5% (95% CI, 52.7 to 75.1) and 45.2% (95% CI, 33.5 to 57.3) for patients treated with EV + Pembro (N = 76) and EV monotherapy (N = 73), respectively. The median DOR was not reached for the combination and was 13.2 months for monotherapy; 65.4% and 56.3% of patients who responded to the combination and monotherapy, respectively, maintained a response at 12 months. The most common grade 3 or higher treatment-related adverse events (TRAEs) in patients treated with the combination were maculopapular rash (17.1%), fatigue (9.2%), and neutropenia (9.2%). EV TRAEs of special interest (any grade) in the combination arm included skin reactions (67.1%) and peripheral neuropathy (60.5%). CONCLUSION EV + Pembro showed a high cORR with durable responses as 1L treatment in cisplatin-ineligible patients with la/mUC. Patients who received EV monotherapy had a response and safety profile consistent with previous studies. Adverse events for EV + Pembro were manageable, with no new safety signals observed.
Superior Hypophyseal Artery Intraoperative Indocyanine Green Angiogram as a Predictor of Postoperative Visual Function After Endoscopic Endonasal Surgery
Authors: Osorio Robert C. , Aabedi Alexander A. , El-Sayed Ivan H. , Gurrola Jose , Goldschmidt Ezequiel 
Published: June 2023

BACKGROUND AND OBJECTIVES:
To date, there are no tools to intraoperatively predict postoperative visual function after endoscopic endonasal surgery (EES) for suprasellar lesions. The objective of this study was to retrospectively evaluate the utility of indocyanine green (ICG) angiography as an intraoperative tool to measure optic chiasm perfusion and determine its relationship with postoperative visual function.

METHODS:
Videos of patients undergoing EES for resection of suprasellar lesions were reviewed, where 5 mg of ICG was diluted in 10 mL of saline and administered. Time between luminescence of the anterior cerebral artery and the superior hypophyseal artery branches supplying the optic chiasm was noted, and the percentage of optic chiasm vessels that luminesced was recorded. Postoperative examinations and imaging studies were used to assess visual function. Patients with and without new deficits were compared with examination of trends in ICG findings.

RESULTS:
A total of 7 trials were reviewed on 6 patients, with no complications occurring from ICG administration. Mean time to chiasm peak luminescence was 3.8 seconds, and 81.8% of chiasm vessels luminesced. Patients with stable or improved vision after resection demonstrated over 90% chiasm luminescence in every case, and mean chiasm time in these postresection ICG administrations was 4.0 seconds. One patient experienced new postoperative visual deficits; on review of their ICG administration, 11.5% of chiasm vessels luminesced, and the chiasm itself failed to display robust luminescence after 30 seconds of direct observation.

CONCLUSION:
This pilot study showed the capability of intraoperative ICG angiography to demonstrate perfusion of the optic chiasm during EES for resection of suprasellar lesions. While larger studies are required, preliminary results suggest chiasm times under 5 seconds and over 90% chiasm vessel illumination may reflect adequate chiasm perfusion, while those with delayed or absent chiasm luminescence may have compromised chiasm perfusion.
SIX1+PAX3+ identify a progenitor for myogenic lineage commitment from hPSCs
Authors: Jaime Olga G. , Arias Jessica , Pavani Shreya , Pyle April D. , Hicks Michael R. 
Published: June 2023

ABSTRACT
The earliest skeletal muscle progenitor cells (SMPCs) derived from human pluripotent stem cells (hPSCs) are often identified by factors expressed by a diverse number of progenitors. An early transcriptional checkpoint that defines myogenic commitment could improve hPSC differentiation to skeletal muscle. Analysis of several myogenic factors in human embryos and early hPSC differentiations found SIX1+PAX3+ co-expression was most indictive of myogenesis. Using dCas9-KRAB hPSCs, we demonstrate that early inhibition of SIX1 alone significantly decreased PAX3 expression, reduced PAX7+ SMPCs, and myotubes later in differentiation. Emergence of SIX1+PAX3+ precursors can be improved by manipulating seeding density, monitoring metabolic secretion and altering the concentration of CHIR99021. These modifications resulted in the co-emergence of hPSC-derived sclerotome, cardiac and neural crest that we hypothesized enhanced hPSC myogenic differentiation. Inhibition of non-myogenic lineages modulated PAX3 independent of SIX1. To better understand SIX1 expression, we compared directed differentiations to fetal progenitors and adult satellite cells by RNA-seq. Although SIX1 continued to be expressed across human development, SIX1 co-factor expression was dependent on developmental timing. We provide a resource to enable efficient derivation of skeletal muscle from hPSCs.
RBP-Tar – a searchable database for experimental RBP binding sites
Authors: Gresova Katarina , Racek Tomas , Martinek Vlastimil , Cechak David , Svobodova Radka , Alexiou Panagiotis 
Published: June 2023

Background: RNA-binding proteins (RBPs) play a critical role in regulating gene expression by binding to specific sites on RNA molecules. Identifying these binding sites is crucial for understanding the many functions of RBPs in cellular function, development and disease. Current experimental methods for identifying RBP binding sites, such as ultra-violet (UV) crosslinking and immunoprecipitation (CLIP), and especially the enhanced CLIP (eCLIP) protocol, were developed to identify authentic RBP binding sites experimentally. Methods: To make this data more accessible to the scientific community, we have developed RBP-Tar (https://ncbr.muni.cz/RBP-Tar), a web server and database that utilises eCLIP data for 167 RBPs mapped on the human genome. The web server allows researchers to easily search and retrieve binding site information by genomic location and RBP name. Use case: Researchers can produce lists of all known RBP binding sites on a gene of interest, or produce lists of binding sites for one RBP on different genomic loci. Conclusions: Our future goal is to continue to populate the web server with additional experimental datasets from CLIP experiments as they become available and processed, making it an increasingly valuable resource for the scientific community.
Comparative study on scenarios for rotating gantry mechanical structures
Authors: Piacentini Luca , Dassa Luca , Perini Diego , Ratkus Andris , Torims Toms , Uberti Stefano , Vilcans Janis , Vretenar Maurizio 
Published: June 2023

Background: This paper outlines a comparative study on scenarios of gantries mechanical design for ion-therapy of cancer, which is a crucial step toward the development of the next ion medical machine. Methods: Multiple scenarios were considered based on robustness of the design, size, weight and complexity, deformation and precision performances and costs, as well as environmental impact. Four prospective scenarios were identified, each of them capable of providing beam to at least 220° around the patient. One scenario is capable of providing treatment angles of 360°. This report will describe the unified methodology performed during the study in order to achieve unbiased results in a comprehensive manner. Results: Results show that in statically balanced scenarios, considerable improvements can be reached in terms of safety, deformation, precision performances, complexity and costs of implementation. Conclusions: All scenarios are deemed suitable for further gantry design development.
Pontine and extrapontine myelinolysis associated with rapid correction of hyponatremia - a review
Authors: Dominik Hanna , Pawęska Wojciech , Radwański Jan , Czudy Zuzanna , Polatowska Marika , Gadomska Anna , Kurek Justyna , Gorzyński Rafał , Garstka Michał , Molczyk-Sieńczak Justyna 
Published: June 2023

Pontine myelinolysis was first described in 1959 by Adams, Victor and Mancall and reported in alcoholic patients.[1] It is characterized, above all, by acute non-inflammatory symmetrical lesion of myelin sheath and apoptosis of oligodendrocytes affecting the central part of thebasis pontis.[5] Demyelination may also appear in other parts of central nervous system such as thalamus, basal nuclei and cerebellum. Involvement of the regions beyond pons is called extrapontine myelinolysis. These two manifestations- pontine and extrapontine myelinolysis are combined in one neurological entity- osmotic demyelination syndrome.Pontine and extrapontine myelinolysis are mainly caused by rapid increase in extracellular fluid osmolarity; usually in situation of iatrogenic correction of chronic hyponatremia.[7]The other causes include severe electrolyte disturbances other than hyponatremia (hypokalemia, hypophosphatemia, hypernatremia), anorexia nervosa, AIDS, acute alcoholic hepatitis, liver transplantation, Vernickes syndrome, chemotherapy, chronic renal failure. [11,12] Osmotic demyelination syndrome vary in clinical manifestations. The most common presentations include encephalopathies, pareses, dystonias. The method of choice in diagnostic process is MRI imaging. Treatment of osmotic demyelination syndrome is still in an experimental phase.
TRANSLATION: A FAMILY OF “MOVES” IN DISTINCT LANGUAGE-GAMES
Authors: Oliveira Paulo 
Published: June 2023

O interesse na obra de Wittgenstein nos estudos da tradução aumentou de modo significativo nos últimos anos, com contribuições de pesquisador@s eminentes (p. ex., TYMOCZKO, 2014 [2007]) e até mesmo uma abordagem declaradamente wittgensteiniana (WILSON, 2016). Tymoczko assume uma perspectiva "pós-positivista" semelhante à das ciências cognitivas, recorrendo às 'semelhanças de família' de Wittgenstein — compreendidas como cluster concepts. Isso ecoa um uso pioneiro de conceitos wittgensteinianos nos estudos da tradução (TOURY, 1980), mas a discussão ainda precisa ser aprofundada. Retomando e aprofundando a discussão de alguns tópicos, sustento aqui que 'concepção de linguagem' é logicamente anterior a qualquer 'teoria da tradução' que possamos elaborar, a primeira dimensão sendo, então, uma 'condição de possibilidade' para a segunda. Minha abordagem é informada pela Epistemologia do Uso de Arley Moreno, na compreensão de que a 'gramática' dos conceitos tem uma 'função transcendental', ainda que a 'descrição do uso' só possa ocorrer após o ato, ou a parte post, no sentido do epistemólogo francês G.-G. Granger. Nessa perspectiva, a proximidade de Toury com Wittgenstein é muito maior do que prima facie, o que pode ser útil no diálogo dos estudos da tradução com a filosofia.
ANOTHER STRAND IN THE RULE-FOLLOWING CONSIDERATIONS
Authors: Ianni Segatto Antonio 
Published: June 2023

ABSTRACT: In this paper, I intend to show, first, that there is a misconception underlying two opposing readings of Wittgenstein’s rule-following considerations, notably Kripke’s sceptical reading and Baker and Hacker’s reading. I believe that the correct characterization of this misunderstanding is the first step towards the correct way to read the rule-following considerations, since these readings are still subject to a philosophical confusion that Wittgenstein wants to dissolve. Then I present a commentary on the rule-following considerations inspired by the so-called resolute reading, more precisely, by the idea that Wittgenstein’s main purpose is to undermine the philosophical illusion according to which we could contemplate our own practices from sideways on, that is, from a standpoint independent of all the human activities and reactions. In my reading I stress an often-neglected aspect of the rule-following considerations, namely the temporal aspect of language.
KEYWORDS: Rules; Scepticism; Agreement; Time.
RESUMO: Neste artigo, pretendo mostrar, em primeiro lugar, que há um equívoco subjacente a duas leituras opostas das considerações de Wittgenstein sobre seguir regras, a saber, a leitura cética de Kripke e a leitura de Baker e Hacker. Acredito que a caracterização correta desse mal-entendido é o primeiro passo em direção a uma maneira correta de compreender as considerações de seguir regras, uma vez que essas leituras estão sujeitas a uma confusão filosófica que Wittgenstein deseja dissolver. Em seguida, apresento um breve comentário das considerações sobre seguir regras inspirado na chamada leitura resoluta, mais precisamente, na ideia de que o principal objetivo de Wittgenstein é minar a ilusão filosófica segundo a qual poderíamos contemplar nossas próprias práticas de fora, isto é, de um ponto de vista independente de todas as atividades e reações humanas.
PALAVRAS-CHAVE: Regras; Ceticismo; Acordo; Tempo.
Duchenne muscular dystrophy in Italy: A systematic review of epidemiology, quality of life, treatment adherence, and economic impact
Authors: Orso Massimiliano , Migliore Antonio , Polistena Barbara , Russo Eleonora , Gatto Francesca , Monterubbianesi Mauro , d’Angela Daniela , Spandonaro Federico , Pane Marika 
Published: June 2023

Objective
This systematic review aims to update the evidence on Duchenne muscular dystrophy (DMD) in Italy, describing the epidemiology, quality of life (QoL) of patients and caregivers, treatment adherence, and economic impact of DMD.

Methods
Systematic searches were conducted in PubMed, Embase and Web of Science up to January 2023. Literature selection process, data extraction and quality assessment were performed by two independent reviewers. Study protocol was registered in PROSPERO (CRD42021245196).

Results
Thirteen studies were included. The prevalence of DMD in the general population is 1.7–3.4 cases per 100,000, while the birth prevalence is 21.7–28.2 per 100,000 live male births. The QoL of DMD patients and caregivers is lower than that of healthy subjects, and the burden for caregivers of DMD children is higher than that of caregivers of children with other neuromuscular disorders. The compliance of real-world DMD care to clinical guidelines recommendations in Italy is lower than in other European countries. The annual cost of illness for DMD in Italy is € 35,000–46,000 per capita while, adding intangible costs, the total cost amounts to € 70,000.

Conclusion
Although it is a rare disease, DMD represents a significant burden in terms of quality of life of patients and their caregivers, and economic impact.
Contemporary Art from Cyprus: Politics, Identities, and Cultures across Borders, Elena Stylianou, Evanthia Tselika and Gabriel Koureas (eds) (2021)
Authors: Markidou Tereza 
Published: June 2023

Review of: Contemporary Art from Cyprus: Politics, Identities, and Cultures across Borders, Elena Stylianou, Evanthia Tselika and Gabriel Koureas (eds) (2021)
London: Bloomsbury, 272 pp.,
ISBN 978-1-35019-864-7, h/bk, $108
An Extraordinary Cause of Colonic Obstruction: Merkel Cell Carcinoma of Unknown Primary
Authors: Ganjineh Brandon , Abel William , Reddy Shravani , Fagan Kiley , Grider Douglas 
Published: June 2023

ABSTRACT
Merkel cell carcinoma is an aggressive and rare neuroendocrine skin cancer with documented metastases to the liver, lungs, and, seldom, the gastrointestinal tract. Metastases to the colon are rare but are seen with primary skin lesions or recurrent disease. Presented is a patient with large bowel obstruction secondary to a large hepatic flexure mass. Pathologic workup revealed Merkel cell carcinoma, and a dermatologic evaluation did not identify a primary cutaneous lesion. This is the first reported case of Merkel cell carcinoma of unknown primary presenting as large bowel obstruction.