bluuebunny/crossref_metadata_2025 huggingface dataset:
RNA fold prediction by Monte Carlo in graph space and the statistical mechanics of tertiary interactions
Authors: Phan Ethan N.H. , Mak Chi H.
Published: October 2024

Using a graph representation of RNA structures, we have studied the ensembles of secondary and tertiary graphs of two sets of RNA with Monte Carlo simulations. The first consisted of 91 target ribozyme and riboswitch sequences of moderate lengths (<150 nt) having a variety of secondary, H-type pseudoknots and kissing loop interactions. The second set consisted of 71 more diverse sequences across many RNA families. Using a simple empirical energy model for tertiary interactions and only sequence information for each target as input, the simulations examined how tertiary interactions impact the statistical mechanics of the fold ensembles. The results show that the graphs proliferate enormously when tertiary interactions are possible, producing an entropic driving force for the ensemble to access folds having tertiary structures even though they are overall energetically unfavorable in the energy model. For each of the targets in the two test sets, we assessed the quality of the model and the simulations by examining how well the simulated structures were able to predict the native fold, and compared the results to fold predictions from ViennaRNA. Our model generated good or excellent predictions in a large majority of the targets. Overall, this method was able to produce predictions of comparable quality to Vienna, but it outperformed Vienna for structures with H-type pseudoknots. The results suggest that while tertiary interactions are predicated on real-space contacts, their impacts on the folded structure of RNA can be captured by graph space information for sequences of moderate lengths, using a simple tertiary energy model for the loops, the base pairs, and base stacks.
Different faces of Mycoplasma pneumoniae in children - cardiological and skin complications- case reports and literature review
Authors: Piasecka Zuzanna , Knop-Chodyła Kinga , Wesołek- Bielaska Ewelina , Kochanowska- Mazurek Anna , Głaz Aneta , Pliszka Marzena , Kuzio Agnieszka , Cieplińska Aleksandra , Ziojła-Lisowska Kinga , Jama Grzegorz
Published: October 2024

Mycoplasma pneumoniae is one of the main pathogens responsible for atypical pneumonia, especially in children over the age of 5, where it accounts for about 40% of cases of extramedullary pneumonia. In addition to respiratory-related symptoms, it can lead to a variety of extrapulmonary manifestations associated with involvement of other organs. In this article, we present case reports of two pediatric patients with detected M. pneumoniae infection with associated cardiac and skin complications. The first case report describes an 11.5-year-old boy who was admitted to the Department of Pediatrics because of chest pain, fever and moist cough for several days, who was diagnosed with myocarditis during M. pneumoniae infection. The second case report describes a 17-year-old girl with a recent respiratory infection who was admitted to the hospital for pain, swelling, blistering of the lips and oral mucosa. Mycoplasma pneumoniae infection can lead to extrapulmonary complications in children, which can produce nonspecific symptoms, so clinical vigilance and early recognition are important to minimize the risk of complications.
The role of physical activity, diet, and stress management in maternal and infant health during pregnancy
Authors: Pawłowski Bartosz , Madej Aleksandra , Haczkur-Pawłowska Karolina , Jasiński Kacper , Kowal Alicja , Malczewska Julia , Fiszer Kornelia , Łomża-Łaba Aleksandra , Dziurda Stanisław , Jama Grzegorz
Published: October 2024

Introduction and aim of the study: During pregnancy, significant physiological, hormonal and circulatory changes occur that affect both the health of the mother and the child. Therefore, it is important for the mother to maintain physical activity, a healthy diet, and reduce stress to prevent complications and health problems for the mother and the child.
Material and Methods: The Pubmed database was searched. The criteria for qualifying the article for the review were the following keywords: pregnancy, exercise, rehabilitation, nutrition during pregnancy, postpartum depression, atopy, stress, asthma. 30 articles from 2002-2023 were analyzed.
Description of the state of knowledge: Regular physical activity during pregnancy brings many benefits such as reducing the risk of complications during childbirth, postpartum depression and helps to maintain a healthy body weight. Diet also has an impact on the health of both mother and baby. It should be balanced, providing the necessary nutrients and taking into account the mother's caloric needs. It is very important to reduce stress due to its negative impact on the mother and child.
Summary: Physical activity and a healthy diet directly affect the course of pregnancy and the health of the fetus and baby. Exercise prevents pregnancy complications and other diseases, and maternal nutritional status is critical for fetal growth. During pregnancy, women are exposed to stress, which can be the cause of chronic mental disorders. Depression is the most common mental illness that occurs during pregnancy, which is influenced by various factors. In addition, maternal stress has a negative impact on the child's health, potentially increasing the risk of a number of atopic and non-atopic diseases.
Sodium Butyrate as Gut Microbiota Modulators: Mechanisms of Action and Potential Clinical Applications - Literature Review and New Perspectives
Authors: Głąbień Marta , Miłkowski Paweł , Kuśnierz Anna , Kusiak Karolina , Aleksandrowicz Daria , Wieczorek Olga , Jakubczak Zofia , Zimniak Maria Weronika , Śliwiak Patryk , Kondratowicz Aneta
Published: October 2024

IntroductionSodium butyrate is an organic chemical compound belonging to sodium salts, which has the potential to be used in anticancer therapy. It reduces inflammation of the intestinal mucosa and promotes the development of beneficial intestinal flora, thanks to which it helps maintain homeostasis. Therefore, butyrate reduces the risk of developing colon cancer or reverses pathological changes occurring under the influence of this cancer. Scientific studies have also shown a beneficial effect of butyrate on the side effects of anticancer treatment - chemotherapy and radiotherapy. A proper diet also has a beneficial effect on the production of endogenous butyrate and reduces the risk of developing colon cancer. It is recommended to use a Mediterranean diet, rich in dietary fiber, highly unsaturated fatty acids and fresh vegetables and fruits. It is recommended to avoid highly processed products, rich in simple sugars and saturated fatty acids, and to limit the consumption of red meat.
Materials and methods
This article is based on the literature found in the PubMed and other scientific databases from the period of 1978-2023 with the use of key words such as “butyrate” “sodium butyrate” “colon cancer” “anticancer treatment” “intestinal microbiota” “Mediterranean diet”
Conclusion
Sodium butyrate is a potential substance that, through its properties, may support the treatment of colorectal cancer. Additionally, the use of an appropriate diet has a positive effect on the intestinal microflora, allowing the action of sodium butyrate and reducing the risk of colorectal cancer.
Analysis of environmental factors affecting the incidence of testicular cancer, with particular emphasis on testicular germ cell tumors (TGCTs). Literature review
Authors: Ptak Anita , Szyc Michał
Published: October 2024

Introduction: Testicular cancer is the most common malignancy among men in the 20-44 age group. Most of the incidence is testicular germ cell tumor. In recent years there has been a steady increase in the incidence of this cancer. For this reason, we analyzed available articles on environmental risk factors that may influence the incidence of increased testicular malignancies Material and methods: Review of the specialized literature in the field of urology and articles available on PubMed, searching by the keywords “testicular cancer,” “testicular cancer risk factors,” “germ cell tumor,” “tgct‘’Aim of the study: The purpose of the study is to review the available literature and research papers regarding risk factors for malignant tumors of the testis. Summary: In recent years, there has been an increase in the incidence of testicular cancer, especially among men aged 20-44 years. The vast majority of it is germ cell tumors (TGCT). This article discusses the influence of environmental factors on the development of testicular cancer, with particular emphasis on the induction of TGCT. Studies indicate an association between exposure to trichloroethylene and other solvents and the risk of TGCT induction. The role of exposure to pesticides (especially fungicides), organic chlorine compounds, and viruses was also indicated to increase the risk of developing TGCTs,. The association of neoplasia with marijuana and tobacco use has also been studied, but needs further research. There is a need for continued research regarding heavy metals, infertility and factors related to pregnancy and the perinatal period. It is necessary to know the mechanisms that induce the process of carcinogenesis in the testis, which will enable the use of prevention and prophylaxis.
Elements of an Undergraduate Agricultural Leadership Program: A Delphi Study
Authors: Morgan A. Christian , King Diana L. , Rudd Rick D. , Kaufman Eric K.
Published: October 2024

Programs in agricultural leadership are continuing to enjoy success in institutions around the country. To this point, there has been a lack of research conducted to (a) identify objectives for these programs, (b) identify courses that should be taught in these programs, (c) identify the need for and objectives of an internship requirement, or (d) determine future placements of program graduates. This study sought the opinions of 15 agricultural leadership experts from across the nation to address these questions. Although the panel came to consensus on these areas it was apparent that the experts in agricultural leadership must continue to work toward national goals and standards for agricultural leadership programs.
OM Forum—Operations Management Research: Relevance and Impact
Authors: Swaminathan Jayashankar M.
Published: October 2024

Problem definition: A fundamental issue faced by operations management researcher relates to striking the right balance between rigor and relevance in their work. Another important aspect of operations management research relates to influencing and positively impacting businesses and society at large. We constantly struggle to achieve these objectives. Methodology/results: This MSOM Fellow forum article discusses key opportunities for increasing the relevance and impact of Operations Management research. In particular, it highlights two major areas: technology enabled operations and society and operations where unique opportunities exist for the field to make lasting contributions to business and society. Managerial implications: It concludes with a menu of approaches to enhance practical impact of our research.
A ESCOLA VAI AO CINEMA: CONSIDERAÇÕES ACERCA DA PARCERIA ENTRE O SESC E O CINEDUC PARA FORMAÇÃO AUDIOVISUAL
Authors: Silveira Gusmão Milene de Cássia , Lopes Marcelo Costa
Published: October 2024

Resumo: As reflexões a seguir apresentadas resultam do percurso de pesquisa ancorado na linha Memória, Cultura e Educação, do Programa de Pós-Graduação em Memória: Linguagem e Sociedade, da Universidade Estadual do Sudoeste da Bahia. Tributário da pauta de investigações do projeto temático Memória, cinema e processos de formação cultural, o artigo toma como eixo analítico as ações do projeto A Escola Vai ao Cinema, realizado em parceria entre o SESC e o Cineduc, de 2001 a 2007, para compreender a proposição de formação cinematográfica e audiovisual que se desenvolveu mediante sessões de cinema e oficinas destinadas a professores e alunos de diversas escolas no país. Faz isto considerando a atualidade do debate acerca das relações entre cinema e educação, especialmente no que diz respeito à aprovação da Lei 13.006/2014.
A ESCOLA E O CINEMA: ALGUMAS REFLEXÕES E APREENSÕES FRENTE À LEI 13.006/14
Authors: Fresquet Adriana Mabel , Paes Bruno Teixeira
Published: October 2024

Este trabalho apresenta reflexões sobre a lei do audiovisual (lei 13.006/14) para a educação básica. A sua sanção no ano de 2014 mobilizou alguns setores interessados, movimentando debates entre distribuidores, cineastas, professores e especialistas da área de cinema e educação. A proposta é pensar que prioridades estão postas em cena. O interesse é fomentar o acesso, ou, explorar um nicho de mercado? Neste artigo apresentamos alguns dos pontos de vista de realizadores, produtores e educadores a respeito dos possíveis impactos, entraves e possibilidades do uso obrigatório do cinema nacional nas escolas brasileiras.
“AQUI NÃO É UMA COMUNIDADE TERAPÊUTICA”: ENTRE A DIVERSIDADE E NORMATIVIDADE EM TRATAMENTOS COM USUÁRIOS ABUSIVOS DE DROGAS
Authors: Brandão Beatriz , Carvalho Jonatas
Published: October 2024

Num cenário de complexidades, onde emerge uma gama de modos de tratamento para usuários abusivos de drogas, as comunidades terapêuticas vêm crescendo e tendo destaque. Por isso, a necessidade de uma normatização e enquadramento de legitimidade em meio às diversidades crescentes. O artigo objetiva articular as tentativas de regulação das CTs e os diversos meios pelos quais elas tentam se instaurar e se legitimar no espaço institucional, sem que respondam positivamente aos modelos impostos, como o médico-legal. Por meio do entendimento de seu histórico, seu lugar no cenário social e sua influência na formatação de toda uma rede de tratamento se analisará o caso de um centro de recuperação que, ainda que encontre pontos convergentes com a lógica das CTs, tenta se distanciar de sua formalidade, apresentando-se como um modo se operacionalizar formas de subjetivação e produções disciplinares.
Migração chinesa em Governador Valadares - MG: “primeira onda” e os desafios de deixar o país de origem em situações de conflito
Authors: Araújo e Pinto Franco Dani , Rial Carmen Silvia de Moraes , Siqueira Sueli
Published: October 2024

Governador Valadares, no leste de Minas Gerais, é conhecida como uma cidade de cultura emigratória, em especial para os Estados Unidos. Este artigo, no entanto, apresenta uma vertente que evidencia o outro lado desse fenômeno, que é o da presença de estrangeiros na cidade mineira. A pesquisa aqui apresentada é um recorte da tese de doutoramento em Ciências Humanas pela Universidade Federal de Santa Catarina (UFSC), que analisa a migração de chineses para o território de Governador Valadares, a partir das narrativas dos próprios imigrantes com base em suas experiências e trajetórias. A etnografia foi o método de pesquisa escolhido e a técnica de coleta de dados adotada foi a de entrevista de história oral. Neste artigo são apresentadas as duas grandes ondas migratórias de chineses para o Brasil e para Governador Valadares – a primeira, entre as décadas de 1950 e 1970; e a segunda, a partir da década de 1990. Para atender a proposta temática desta edição, optou-se por voltar as atenções para os chineses que migraram para a cidade mineira durante a chamada primeira grande onda, devido às suas particularidades. Nesse sentido, a pesquisa revela que entre os primeiros chineses que chegaram em Governador Valadares, os fatores que os levaram a deixar o país de origem estavam geralmente relacionados a contextos de guerra e conflitos políticos. Assim, para alguns, deixar a terra natal não era uma opção ou parte de um projeto previamente elaborado, mas uma alternativa de sobrevivência.
Nas diásporas e encruzilhadas do cotidiano escolar: as travessias dos currículos praticados de uma escola municipal de Manaus
Authors: Simões Ceane Andrade
Published: October 2024

O presente ensaio emerge de um processo de estudo iniciado a partir da busca de compreensão das experiências educativas de uma comunidade escolar situada na fissura entre a idealização da cidade modernizada e a cidade praticada por aqueles e aquelas que são jogados para as suas margens, oriundos e oriundas de diferentes movimentos diaspóricos, e que, a despeito de não serem convidados e convidadas a compor o clube da humanidade, nas palavras do líder indígena e pensador Ailton Krenak, ainda teimam em inventar e criar os seus saber[es]xistências. Diante da presença de filhos da comunidade haitiana, chegada à cidade de Manaus no fluxo migratório ocorrido nos anos de 2010 e, mais recentemente,  da comunidade venezuelana, cuja presença se intensificou a partir do ano de 2018, minha aposta é que o cerne das experiências curriculares produzidas na EMEF Prof. Waldir Garcia se adere a uma perspectiva fronteiriça, de encruzilhada, enredadas em diálogo com/nas diásporas vividas pelos seus sujeitos e que rasuram e desorganizam os limites e controles impostos à escola. Conhecer tais travessias, como recurso metafórico que permite entender os seus currículos praticados, exige considerar muito seriamente as gingas e as vozes dos sujeitos que a integram e o modo como atribuem significados, performatizam e narrativizam as práticas de educação, vida e arte no solo da escola, transcriando e (re)territorializando as suas múltiplas experiências existenciais e processos identitários.
Neutrophil-to-Lymphocyte Ratio, Platelet-to-Lymphocyte Ratio, and Prognostic Nutritional Index as Prognostic Markers for Lung Carcinoma
Authors: Mi Hai-li , Wei Wen-lu , Zhang Dong-hui , Liang Hua-ying , Yue Cai-feng , Xu Jing-ning
Published: October 2024

Aims/Background Lung cancer (LC) remains one of the most common malignant tumours worldwide, and assessment of its progression is important for ensuring better prognostic outcomes for patients. This study was designed to explore the prognostic role of certain indices, including the neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), and prognostic nutritional index (PNI) in patients with LC, to help clinics to better determine the prognosis of patients with LC, and to allow them to intervene in a timely manner.

Methods A retrospective analysis of 116 initially diagnosed patients with LC in China from 2018 to 2020 was conducted. The counts of neutrophils (NEU), lymphocytes (LYM), and monocytes (MON), as well as albumin levels, were obtained from laboratory databases. The PNI was calculated using a specific formula. The progression-free survival (PFS) curves were plotted using the Kaplan–Meier method, and the Log-rank test was used to compare survival among different groups. The potential prognostic role of these indicators was assessed with univariate and multivariate regression analysis.

Results Multivariate Cox regression demonstrated that the PNI (hazard ratio (HR): 0.513, 95% confidence interval (CI): 0.288–0.917, p = 0.024), NLR (HR: 2.038, 95% CI: 1.128–3.682, p = 0.018), and tumour type (small cell lung cancer vs. non-small cell lung cancer) (HR: 2.145, 95% CI: 1.308–3.520, p = 0.003) were significantly associated with PFS. The median PFS for patients with low and high PNI was 10 and 11.5 months, respectively.

Conclusion The NLR, PLR, and PNI are all significantly associated with the prognostic survival of LC patients.
Family care in Germany and its gender-(un)specific patterns: an analysis using novel data from the German Socio-Economic Panel Innovation Sample
Authors: Kelle Nadiya , Ehrlich Ulrike
Published: October 2024

This article examines how the characteristics of people needing care determine the provision of family care and the time intensity of caring for men and women. Using novel data, we conduct linear (probability) regression models and find that women face family care demands as often as men but tend to provide more (time-intensive) care. When of retirement age, men are more likely than women to meet care needs for partners and support individuals with lower-severity care needs. Women invest more time caring for (adult) children and co-residents and on higher-severity care than men, particularly when they are of working age.
T. Pomponius Atticus, M. Vipsanius Agrippa, and the Marriage Between Caecilia Attica And Agrippa
Authors: Zhang Xiaoxi
Published: October 2024

Abstract: This article examines the marriage between Atticus’ daughter Caecilia Attica and Agrippa, with a focus on why Atticus and Agrippa agreed upon it. I argue that political considerations were the major driving force for both men. More specifically, Atticus accepted this match in order to establish/deepen ties with powerful figures without abandoning his neutral policy, and Agrippa accepted it so as to advance his own career while minimizing the risks that might arise from his ambition. Meanwhile, I contend that intellectual considerations also played a role, since Atticus, Attica, and Agrippa shared scholarly interests.
Simple but efficient polarization-entangled photon sources
Authors: Fazili Riza , Chauhan Purujit Singh , Chandrashekara Uday , Kržič Andrej , Gómez Rodrigo , Gräfe Markus , Steinlechner Fabian
Published: October 2024

We report on the design and characterization of polarization-entangled photon sources at NIR and telecom wavelengths, based on spontaneous parametric downconversion in a linear interferometric arrangement with beam displacers. The sources demonstrate state-of-the-art performance with respect to detected brightness, heralding efficiency, and entanglement visibility. Featuring a stable and compact profile with simple alignment, they hold great promise for future development of field- and space-ready prototypes, alongside serving as a practical guide for researchers interested in designing efficient entangled photon sources.
Sputtered aluminum nitride waveguides for the telecommunication spectrum with less than 0.16 dB/cm propagation loss
Authors: Singh Radhakant , Raghuwanshi Mohit , Sundarapandian Balasubramanian , Thomas Rijil , Kirste Lutz , Suckow Stephan , Lemme Max C.
Published: October 2024

We report the fabrication and characterization of photonic waveguides from sputtered aluminum nitride (AlN). The AlN films were deposited on 6” silicon substrates with a 3 µm buried silicon oxide layer using reactive DC magnetron sputtering at a temperature of 700°C. The resulting uncladded polycrystalline waveguides exhibit propagation losses of 0.137 ± 0.005 dB/cm at wavelengths of 1310 nm and 0.154 ± 0.008 dB/cm at a wavelength of 1550 nm in the TE polarization. These results are the best reported for sputtered AlN waveguides in the C-band and the first report in the O-band. These performances are comparable to those of the best-reported AlN waveguides, which are epitaxially grown by metal-organic chemical vapor deposition (MOCVD) on sapphire substrates. Our findings highlight the potential of sputtered AlN for photonic platforms working in the telecom spectrum.
Improving the performance of depth estimation with the rising edge fitting method
Authors: Ding Ding , Shen Haoran , Lu Zheng , Li Jian , Wang Qin
Published: October 2024

High-resolution detection of optical surfaces is crucial for enhancing the performance of light detection and ranging (LiDAR) systems. Single-photon LiDAR has emerged as a leading technology for precise depth estimation, which is indispensable in application fields such as biological imaging, autonomous navigation, and virtual reality. However, most existing depth estimation algorithms heavily rely on peak position information in single-photon LiDAR data, making them significantly affected by peak jitter. In this work, a time-correlated single-photon counting (TCSPC) LiDAR system has been built, and what we believe to be a new depth estimation method based on the rising edge of the instrument response function has been proposed. Experimental results show that the proposed method is less subject to peak jitter and can achieve much lower errors and faster convergence speed under the same conditions, comparing with several existing methods.
Superconducting nanowire single-photon detector enhanced near-infrared II portable confocal microscopy for tissue imaging with indocyanine green
Authors: Liu Yifan , Yao Cheng-You , Rambo Timothy M. , Li Bo , Juhong Aniwat , Doredla Jeremy S. , Luker Gary D. , Han Ming , Miller Aaron J. , Qiu Zhen
Published: October 2024

In this Letter a novel, to our knowledge, approach for near-infrared
(NIR) fluorescence portable confocal microscopy is introduced, aiming
to enhance fluorescence imaging of biological samples in the NIR-II
window. By integrating a superconducting nanowire single-photon
detector (SNSPD) into a confocal microscopy, we have significantly
leveraged the detection efficiency of the NIR-II fluorescence signal
from indocyanine green (ICG), an FDA-approved dye known for its NIR-II
fluorescence capabilities. The SNSPD, characterized by its extremely
low dark count rate and optimized NIR system detection efficiency,
enables the excitation of ICG with 1 mW and the capture of
low-light fluorescence signals from deep regions (up to
512 µm). Consequently, our technique was able to produce
high-resolution images of bio samples with a superior signal-to-noise
ratio, making a substantial advancement in the field of fluorescence
microscopy and offering a promising opportunity for future clinical
study.
6.7–8.1 µm tunable single-frequency difference frequency generation in ZGP for high-resolution spectroscopy
Authors: Xu Ziang , Xing Suwan , Miao Yuxiu , Fu Zhizhuo , Yang Xuemei , He Linzhen , Li Wenlong , Liang Houkun , Hu Bo , Hou Yubin , Wang Pu , Wu Han
Published: October 2024

Difference frequency generation (DFG) based tunable single-frequency mid-infrared (MIR) light sources are desirable for high-resolution spectroscopy, sensing, and imaging. In this work, we demonstrate a continuous-wave (CW) single-frequency DFG in a ZnGeP2 (ZGP) crystal driven by all-fiber near-infrared (NIR) fiber lasers, for the first time to our knowledge. The all-fiber NIR laser sources consist of a 1.5 µm erbium-doped fiber amplifier seeded by a CW tunable fast scanning single-frequency laser and a 1.9 µm CW tunable single-frequency thulium-doped fiber laser. Taking advantage of the high nonlinear coefficient and large birefringence of the ZGP crystal, single-frequency DFG in ZGP achieves a broad spectral tuning range from 6.7 to 8.1 µm, with an output power at the 10 µW level. Precise detection of C2H2 gas by continuously scanning the DFG source across a spectral range of 1.1 THz (∼34 cm−1) is also presented, highlighting the potential of the tunable DFG source for high-resolution optical spectroscopy applications. We anticipate this work will provide what we believe to be a new platform for spectroscopy in the molecular fingerprint spectral region.
Design of mid/long-wave infrared dual-band panoramic optical system
Authors: chunyan wang , Chang Honglei , Sun Hao , Yao Xingzhi
Published: October 2024

A dual-band and confocal panoramic band optical system for infrared detection is designed to achieve 360° range warning. The working band covers the mid-infrared band (3 ~ 5μm) and the long infrared band (7 ~ 9.5μm), the field of view Angle is (28° ~ 80°) × 360°, and the head unit of the lens is composed of two mirrors and a Ge protection window. The aperture number of the system is 1.3. The symmetrical aspherical surface is introduced into the system to correct the aberration, and the passive athermalisation design is carried out by combining the aspherical surface with the lens material. To achieve good imaging quality in the working environment of -35 ~ 55℃.
On the identification of differentially-active transcription factors from ATAC-seq data
Authors: Gerbaldo Felix Ezequiel , Sonder Emanuel , Fischer Vincent , Frei Selina , Wang Jiayi , Gapp Katharina , Robinson Mark D. , Germain Pierre-Luc
Published: October 2024

ATAC-seq has emerged as a rich epigenome profiling technique, and is commonly used to identify Transcription Factors (TFs) underlying given phenomena. A number of methods can be used to identify differentially-active TFs through the accessibility of their DNA-binding motif, however little is known on the best approaches for doing so. Here we benchmark several such methods using a combination of curated datasets with various forms of short-term perturbations on known TFs, as well as semi-simulations. We include both methods specifically designed for this type of data as well as some that can be repurposed for it. We also investigate variations to these methods, and identify three particularly promising approaches (a chromVAR-limma workflow with critical adjustments, monaLisa and a combination of GC smooth quantile normalization and multivariate modeling). We further investigate the specific use of nucleosome-free fragments, the combination of top methods, and the impact of technical variation. Finally, we illustrate the use of the top methods on a novel dataset to characterize the impact on DNA accessibility of TRAnscription Factor TArgeting Chimeras (TRAFTAC), which can deplete TFs—in our case NFkB—at the protein level.
Adverse health outcomes in offspring of parents with alcohol-related liver disease: Nationwide Danish cohort study
Authors: Jepsen Peter , West Joe , Larsen Anna Kirstine Kjær , Kann Anna Emilie , Kraglund Frederik , Morling Joanne R. , Crooks Colin , Askgaard Gro
Published: October 2024

Background

Parental drinking can cause harm to the offspring. A parent’s diagnosis of alcohol-related liver disease (ALD) might be an opportunity to reach offspring with preventive interventions. We investigated offspring risk of adverse health outcomes throughout life, their association with their parent’s educational level and diagnosis of ALD.

Methods and findings

We used nationwide health registries to identify offspring of parents diagnosed with ALD in Denmark 1996 to 2018 and age- and sex-matched comparators (20:1). We estimated the incidence rate ratios (IRRs) of hospital contacts with adverse health outcomes, overall and in socioeconomic strata. We used a self-controlled design to examine whether health outcomes were more likely to occur during the first year after the parent’s ALD diagnosis.

The 60,804 offspring of parents with ALD had a higher incidence rate of hospital contacts from age 15 to 60 years for psychiatric disease, poisoning, fracture or injury, alcohol-specific diagnoses, other substance abuse, and of death than comparators. Associations were stronger for offspring with low compared to high socioeconomic position: The IRR for admission due to poisoning was 2.2 versus 1.0 for offspring of an ALD parent with a primary level versus a highly educated ALD parent. Offspring had an increased risk for admission with psychiatric disease and poisoning in the year after their parent’s ALD diagnosis. For example, among offspring whose first hospital contact with psychiatric disease was at age 13 to 25 years, the IRR in the first year after their parent’s ALD diagnosis versus at another time was 1.29 (95% CI 1.13, 1.47). Main limitation was inability to include adverse health outcomes not involving hospital contact.

Conclusions

Offspring of parents with ALD had a long-lasting higher rate of health outcomes associated with poor mental health and self-harm that increased shortly after their parent’s diagnosis of ALD. Offspring of parents of low educational level were particularly vulnerable. This study highlights an opportunity to reach out to offspring in connection with their parent’s hospitalization with ALD.
Saudi Learner Translation Corpus: The design and compilation of an English–Arabic learner translation corpus
Authors: Al-Harthi Maha , Alsaif Amal , Al-Nafjan Eman , Alshihri Fatma , Saleh Mahmoud
Published: October 2024

This article introduces the Saudi Learner Translation Corpus (SauLTC), an innovative multi-version English–Arabic parallel corpus featuring part-of-speech tagging. We describe the corpus parameters and compilation process and explain how textual processing and sentence alignment are conducted. The participants include 366 student translators, 48 instructors, and 23 alignment verifiers. The corpus provides access to two target versions of every ST to allow the detection of the changes in the translation and revision processes from the initial to the final draft. The translations were collected over three years, yielding 5,160,386 tokens. The metadata of 23 sentence alignment verifiers were added to the analysis as a unique variable to investigate individual differences in the manual verification process. This unidirectional corpus can be used to identify student translators’ strategies and errors in translation and analyze the efficacy of instructors’ feedback. Furthermore, it is accessible via an application and a website. It provides translation teachers and researchers with a database that can help develop corpus-based and corpus-driven teaching materials.
News source bias and sentiment on social media
Authors: Knutson Brian , Hsu Tiffany W. , Ko Michael , Tsai Jeanne L.
Published: October 2024

As social media becomes a key channel for news consumption and sharing, proliferating partisan and mainstream news sources must increasingly compete for users’ attention. While affective qualities of news content may promote engagement, it is not clear whether news source bias influences affective content production or virality, or whether any differences have changed over time. We analyzed the sentiment of ~30 million posts (on twitter.com) from 182 U.S. news sources that ranged from extreme left to right bias over the course of a decade (2011–2020). Biased news sources (on both left and right) produced more high arousal negative affective content than balanced sources. High arousal negative content also increased reposting for biased versus balanced sources. The combination of increased prevalence and virality for high arousal negative affective content was not evident for other types of affective content. Over a decade, the virality of high arousal negative affective content also increased, particularly in balanced news sources, and in posts about politics. Together, these findings reveal that high arousal negative affective content may promote the spread of news from biased sources, and conversely imply that sentiment analysis tools might help social media users to counteract these trends.
ChatGPT as a prospective undergraduate and medical school student
Authors: Giunti Marco , Garavaglia Fabrizia Giulia , Giuntini Roberto , Sergioli Giuseppe , Pinna Simone
Published: October 2024

This article reports the results of an experiment conducted with ChatGPT to see how its performance compares to human performance on tests that require specific knowledge and skills, such as university admission tests. We chose a general undergraduate admission test and two tests for admission to biomedical programs: the Scholastic Assessment Test (SAT), the Cambridge BioMedical Admission Test (BMAT), and the Italian Medical School Admission Test (IMSAT). In particular, we looked closely at the difference in performance between ChatGPT-4 and its predecessor, ChatGPT-3.5, to assess its evolution. The performance of ChatGPT-4 showed a significant improvement over ChatGPT-3.5 and, compared to real students, was on average within the top 10% in the SAT test, while the score in the IMSAT test granted admission to the two highest ranked Italian medical schools. In addition to the performance analysis, we provide a qualitative analysis of incorrect answers and a classification of three different types of logical and computational errors made by ChatGPT-4, which reveal important weaknesses of the model. This provides insight into the skills needed to use these models effectively despite their weaknesses, and also suggests possible applications of our analysis in the field of education.
HIV-related perceived stigma and internalized stigma among people living with HIV/AIDS in Africa: A systematic review and meta-analysis
Authors: Tadesse Gebresilassie , Rtbey Gidey , Andualem Fantahun , Takelle Girmaw Medfu , Melkam Mamaru , Tadesse Abate Asnake , Wassie Yilkal Abebaw , Tekleslassie Alemayehu Tekletsadik , Geremew Gebremariam Wulie , Dires Eshetie Andargie , Tinsae Techilo , Fentahun Setegn , Nakie Girum
Published: October 2024

Background

HIV-related stigma has significant adverse impacts on people living with HIV/AIDS, such as psychological distress, decreased quality of life, a reluctance to get screened and treated, and a reluctance to disclose their status due to fear of stereotypes or rejection.

Objectives

To determine the pooled prevalence and factors associated with HIV-related perceived stigma and internalized stigma among people living with HIV/AIDS in Africa.

Methods

Articles that assessed the prevalence and associated factors of HIV-related perceived stigma and internalized stigma were reviewed. PubMed, EMBASE, Google Scholar, African Journal Online, CINAHL, and Science Direct were the databases used to search the primary studies. The data was extracted through a Microsoft Excel spreadsheet and exported to STATA version 14 for further analysis. The I2 test was applied to test heterogeneity, whereas Egger’s test and funnel plot were used to check publication bias.

Results

In this study, the total sample size was 28,355 (for perceived stigma) and 22,732 (for internalized stigma). The overall pooled prevalence of HIV-related perceived stigma and internalized stigma was determined to be 41.23% and 35.68%, respectively. Based on the subgroup analysis results, the highest pooled prevalence of perceived stigma was observed in Nigeria (50.04%), followed by Ethiopia (41.72%), while the highest prevalence of internalized stigma was observed in Ethiopia (56.13%), followed by Cameroon (44.66%). Females (OR = 1.63: 1.31, 2.02) and rural dwellers (OR = 1.93: 1.36, 2.74) had more odds of experiencing HIV-related perceived stigma.

Conclusion and recommendation

This study concluded that four in ten and more than one-third of people living with HIV/AIDS suffered from perceived and internalized stigma. Thus, special considerations must be given to women and rural dwellers. It is recommended to implement multi-level interventions and foster empowerment and support for individuals living with HIV.
Investigating the effects of a daily multidisciplinary intensive outpatient rehabilitation program on innovative biomarkers in people with Parkinson’s disease: Study protocol for a phase III randomized controlled clinical trial
Authors: Saibene Francesca Lea , Agliardi Cristina , Salvatore Anna , Arcuri Pietro , Castagna Anna , Gobbo Silvia , Merlo Federico , Bowman Thomas , Anastasi Denise , Pagliari Chiara , Farina Elisabetta , Alberoni Margherita , Calabrese Elena , La Rosa Francesca , Arienti Chiara , Saresella Marina , Guerini Franca Rosa , Cattaneo Davide , Baglio Francesca , Clerici Mario , Navarro Jorge , Meloni Mario
Published: October 2024

Background

To date, there has been no medication that has prevented the progression of Parkinson’s disease (PD). Many benefits of intensive and multidisciplinary rehabilitation program for PD are supported by clinical, epidemiological, and experimental data. The main question is whether high-intensity motor and cognitive exercises have an effect on the disease’s biological mechanisms.

Objective

This study protocol is a Randomized Controlled Trial (RCT) designed to determine the efficacy of an experimental, intensive, and multidisciplinary treatment in comparison to a home-based self-treatment in improving biomolecular and functional parameters in PD.

Methods

A total of 72 participants will be randomly allocated to two different groups, experimental (n = 36) and control group (n = 36). The rehabilitation program will last 6 consecutive weeks and will involve the execution of a total of 30 sessions, one for each day of the week from Monday to Friday. Participants allocated to the control group will carry out a home-based self-treatment program that includes muscle-stretching and active mobilization exercises for 40’/day for 6 consecutive weeks. The primary outcome measure is the effects of both treatments on a new set of molecular biomarkers such as oligomeric alpha-synuclein and neurotrophic factors measured in peripheral neural derived extracellular vesicles (NDEVs). Secondary outcomes will include changes of motor and non-motor symptoms, balance and gait performance and cognitive functioning. This RCT has been registered as “Intensive Multidisciplinary Rehabilitation and Biomarkers in Parkinson’s Disease” on 30 May, 2022 to ClinicalTrials.gov with the Study ID number: NCT05452655.

Discussion

This rehabilitation program is believed to be crucial in modifying biomolecular and functional parameters in people with PD. We expect that this study will provide additional evidence to understand the impact of an aerobic and intensive rehabilitation program on brain plasticity in patients with PD.
Junior to senior transition of male elite junior tennis players: A retrospective study
Authors: Bozděch Michal , Zháněl Jiří
Published: October 2024

This study explores the intricate dynamics of the Junior-to-Senior (JTS) transition phase in elite tennis. Focusing on challenges faced by young talents, the research aims to unveil factors influencing successful transitions and the role of elite junior tournaments. In a retrospective analysis, male tennis players (n = 240) from national teams in the ITF World Junior Tennis Finals tournament (2012–2016) were analyzed using Chi-square tests, Cramer’s V, Bayesian statistics, and Multinomial Logistic Regression (MLR). Results revealed that 62.1% of elite junior participants were found in the Association of Tennis Professionals database, emphasizing the significance of team nominations and tournament results as important variables to monitor. Inferential and Bayesian statistics confirmed robustness, with MLR highlighting tournament results’ importance. The findings highlight the complexities of the JTS transition and underscore the pivotal roles of participation, national team nominations, and tournament results. The study recommends the implementation of comprehensive player development programs, urging strategic team selections by national federations and academies. Coaches, stakeholders, and organizations should prioritize monitoring these variables for early talent identification and support. These measures collectively aim to optimize success trajectories, navigating the critical JTS phase in junior tennis players’ sporting careers.
Exploring the influence of music on cognitive performance in female assembly line workers at a medical device manufacturing unit
Authors: Abbasi Melika , Esmaeili Reza , Pourabdian Siamak , Shakerian Mahnaz
Published: October 2024

The significance of enhancing working conditions for the physical health and performance of workers, particularly female workers, underscores the need for research in this domain and the examination of interventions such as music. Previous studies have yielded diverse outcomes regarding the influence of music on individuals’ performance; hence, further research in this area appears imperative. The aim of this study is to explore the impact of music on the cognitive and task performance of female assembly operation operators. This study is an interventional (quasi-experimental) study that involved 81 participants from the female workforce of the medical equipment assembly unit in Isfahan, Iran. The evaluation encompassed task performance, working memory using N-Back test, sustained attention using continues performance test (CPT), degree of sleepiness, and mental fatigue using Flicker Fusion test, along with physiological parameters such as heart rate and blood oxygen level. Participants underwent testing both in the presence of classical music and in a condition without music playback. The provision of background music enhanced the workers’ sustained attention and working memory. It led to improved task performance and a reduction in drowsiness. Concerning physiological parameters, it resulted in a slight decrease in heart rate at the end of the work shift and a marginal increase in participants’ blood oxygen levels. Background music enhanced working memory (p-value = 0.001), sustained attention (p-value = 0.001), and improved the task performance of workers(p-value = 0.005). Additionally, likely due to increased relaxation, it led to a decrease in heart rate (p-value = 0.001) and an increase in blood oxygen levels (p-value = 0.016). Music also played a role in reducing participants’ sleepiness (p-value = 0.001).
Phylogenetic and divergence analysis of Pentatomidae, with a comparison of the mitochondrial genomes of two related species (Hemiptera, Pentatomidae)
Authors: Jia Wang , Chen Jing , Ge Siyuan , Zhang Zhenhua , Xiao Yuliang , Qi Long , Zhao Qing , Zhang Hufang
Published: October 2024

Pentatomidae, the most diverse family of Pentatomoidea, is found worldwide. Currently, the phylogenetic relationships among Pentatomidae tribes remain unstable, and subfamily divergence has not been estimated. Here, we sequenced and analyzed the complete mitochondrial genomes of two species of Lelia, and studied the phylogenetic relationships among Pentatominae tribes. We also selected three available fossil as the calibration points in the family, and preliminarily discussed the divergence time of Pentatomidae. Trees of Pentatomidae were reconstructed using the Bayesian inference method. Divergence times of Pentatominae were estimated based on the nucleotide sequences of protein-coding genes with a relaxed clock log-normal model in BEASTv.1.8.2. The results showed that the gene arrangements, nucleotide composition, and codon preferences were highly conserved in Lelia. Further, a phylogenetic analysis recovered Eysarcorini, Strachiini, Phyllocephalini, and Menidini as monophyletic with strong support, however, the monophyly of Antestiini, Nezarini, Carpocorini, Pentatomini and Cappaeini were rejected. Moreover, Pentatominae diverged from Pentatomidae soon after the origin of the Cretaceous Period, at approximately 110.38 Ma. This study enriches the mitochondrial genome database of Pentatomidae and provides a reference for further phylogenetic studies, and provides a more accurate estimate of divergence time.
Variability of amylose content and its correlation with the paste properties of cassava starch
Authors: Ribeiro Natalia Rocha , Sousa Massaine Bandeira e , Oliveira Luciana Alves de , de Oliveira Eder Jorge
Published: October 2024

The amylose content can significantly impact the diverse industrial applications of cassava starch. This study aimed to assess the variability of cassava germplasm concerning amylose content and other attributes pertinent to root quality, alongside its correlation with paste properties. Starch extracted from 281 genotypes, obtained in germplasm evaluation trials, was evaluated for amylose content, with additional analysis of parameters such as pasting temperature, time to peak viscosity (TPV), viscosity breakdown (BrD), retrogradation tendency, and maximum, minimum, and final viscosities. The genotypes exhibited considerable variation in dry matter content (ranging from 27.06% to 41.02%), starch content (from 14.61% to 25.67%), cyanogenic compounds (1.77 to 7.81), and amylose content (0.05% to 33.23%). High phenotypic variability in paste properties was observed, alongside a low residual effect for most traits, resulting in high broad-sense heritabilities (>0.95). Strong correlations of significant magnitude (>0.80) were found between parameters such as peak viscosity × viscosity breakdown, minimum viscosity × final viscosity, and final viscosity × retrogradation tendency. Moderate correlations were also identified, such as between dry matter content × starch content (0.56). While positive, correlations between amylose content and paste properties were of low magnitude (ranging from 0.13 to 0.35), except for TPV and BrD. Principal component discriminant analysis clustered the germplasm into six distinct groups based on root quality and paste properties, with most improved genotypes falling into two clusters characterized by high starch and dry matter contents. This study underscores the necessity of simultaneous evaluation of amylose content and paste properties in the breeding pipeline. Additionally, clustering cassava genotypes proves beneficial in identifying those that fulfill specific requirements in industrial and breeding applications.