bluuebunny/crossref_metadata_2025 huggingface dataset:
LETRAMENTOS E ENSINO REMOTO NA PANDEMIA:
Authors: De Araújo Santos Marques Ivoneide Bezerra , De Oliveira Carlos Moisés , Gomes de Souza Rudson Edson
Published: December 2023

A situação emergencial decorrente da pandemia que enfrentamos recentemente exigiu de todos os segmentos sociais e de nós que atuamos na área de formação docente um planejamento estratégico que pudesse oferecer respostas às necessidades urgentes que surgiram nesse contexto de crise humanitária. Neste artigo, temos por objetivo, analisar, em uma abordagem qualitativa, dados gerados no projeto "Formação docente para uma situação emergencial: letramentos para o ensino remoto de língua portuguesa durante a pandemia", investigados em uma pesquisa-ação desenvolvida no contexto de formação continuada, refletindo sobre o(s) letramento(s) do professor durante a pandemia da Covid 19. Os resultados apontam que os processos formativos do professor devem contemplar, situadamente, os letramentos que são exigidos desse profissional no local de trabalho.
A POLÍTICA DE ASSISTÊNCIA ESTUDANTIL DA UEM E OS IMPACTOS NO PROCESSO DE FORMAÇÃO DE PROFESSORES DO CAMPUS REGIONAL DO VALE DO IVAÍ
Authors: Viana Gabriela da Silva , Francisco Marcos Vinicius
Published: December 2023

Esta pesquisa teve como objetivo analisar o impacto da Política de Assistência Estudantil (PAE) no processo de formação inicial de estudantes do curso de Licenciatura em Educação Física do Campus Regional do Vale do Ivaí (CRV) vinculado à Universidade Estadual de Maringá (UEM). A investigação assenta-se nos pressupostos do materialismo histórico-dialético tendo como recursos metodológicos a análise documental e a revisão bibliográfica. Os resultados revelaram que, apenas as dimensões da alimentação e da inclusão digital foram direcionadas aos estudantes do curso de formação de professores/as de Educação Física do CRV, sendo que ao estratificar aqueles/as que se enquadravam em condição de vulnerabilidade social, a evasão se fez intensa nessa realidade.
ESTRATÉGIAS E HABILIDADES PARA A COMPREENSÃO LEITORA EM LÍNGUA MATERNA
Authors: Royes Schardosim Chris , Braga Tomitch Lêda Maria
Published: December 2023

Este texto tem por objetivo discutir os termos estratégias e habilidades para compreensão leitora, bem como apresentar uma compilação de estratégias para o ensino da compreensão leitora em português como língua materna com base em estudos recentes, especialmente os realizados no Brasil, preenchendo a lacuna de poucas pesquisas na área. Sugere quinze estratégias para a compreensão leitora a serem utilizadas antes, durante e após a leitura, compiladas e adaptadas para o ensino de português como língua materna. Por fim, este estudo considera que o ensino de estratégias pode contribuir para a melhoria da compreensão leitora em português como língua materna.
ALFALETRAR E A FORMAÇÃO DE PROFESSORES
Authors: Silva-Antunes Paula Tatiana , Silva Oliveira Nágila Maria
Published: December 2023

Nesta pesquisa, compartilhamos uma experiência formativa vivenciada na disciplina “Alfabetização, Leitura e Escrita”, ofertada no Curso de Pós-Graduação lato sensu “Saberes e Práticas Pedagógicas no Ensino Fundamental”, na Universidade Federal do Acre, em 2022. Na referida Especialização, os alunos-professores puderam tecer reflexões sobre as próprias práticas pedagógicas, problematizando os saberes linguísticos acionados na aquisição da língua materna de seus alunos nas escolas onde atuam. Partindo de formulários online, respondidos no início da disciplina, os professores foram levados a refletir sobre suas práticas com base no eixo leitura-oralidade-escrita (SOARES, 2003; 2018; 2021; MAGALHÃES; ALVIM, 2019). A disciplina culminou com a produção de sequências didáticas (DOLZ; NOVERRAZ; SCHNEUWLY, 2004) envolvendo variados gêneros discursivos para o ensino de práticas de línguas/linguagens.
LETRAMENTO CIENTÍFICO
Authors: Tavares Mari Inez
Published: December 2023

Este artigo mapeia dissertações e teses em Educação em Ciências de 2007 a 2016 que utilizam letramento científico com a finalidade de compreender os temas e sentidos atribuídos a essa expressão no Brasil. A pesquisa bibliográfica foi a metodologia adotada. O referencial teórico se fundamenta na filosofia bakhtiniana da linguagem e na teoria crítica da educação. A variedade temática no campo dos estudos do letramento científico revela que é um campo profícuo para estudos de temas que afetam ensino e aprendizagem das ciências. Confirma que letramento científico não é o termo adequado, devido ao fato de letramento estar vinculado à ideologia de alfabetização instrumental e propõe o uso de educação para a ciência para nominar reflexões, metodologias e práticas que envolvem o pensar e falar sobre ciência no campo da educação.
POLÍTICA NACIONAL DE ALFABETIZAÇÃO- DECRETO Nº 9.765, DE 11 DE ABRIL DE 2019:
Authors: Alencar Maria Fernanda dos Santos , Melo Cinthya  Torres
Published: December 2023

este artigo aponta reflexões sobre a proposta de alfabetização centrada no método fônico de leitura e de aprendizagem da escrita, apresentada pelo Plano Nacional de Alfabetização (2019), do Ministério da Educação-Secretaria de Alfabetização, que orienta o ensino e a aprendizagem da leitura e da escrita de estudantes do ensino fundamental-anos iniciais e da EJA por meio do modelo fônico. Neste sentido, busca o diálogo com  discussões teóricas sobre alfabetização e o seu fazer pedagógico trazidas por Paulo Freire, compreendendo que os professores desenvolvem caminhos diversificados para o processo de alfabetização e que a leitura da palavra é a leitura da “palavramundo” (FREIRE, 2005).
A PROFESSORA COMO NEGOCIADORA DE SENTIDOS NA PRÁTICA DIALÓGICA DO PENSAR ALTO EM GRUPO
Authors: Oliveira Batista-Santos Dalve , Pereira de Assis Juliana
Published: December 2023

Este artigo busca investigar como a professora-pesquisadora se constitui mediadora na prática do Pensar Alto em Grupo (PAG) com o fito de formar leitores críticos. Para tanto, nos respaldamos na análise e interpretação de dados gerados a partir das interações e vivências de leituras do PAG com um grupo de participantes de um curso de extensão. A discussão proposta neste trabalho situa-se na área do conhecimento denominada Linguística Aplicada. As análises revelaram que a professora-mediadora ao negociar e mediar os sentidos, na atividade leitura, saia do seu lugar de ‘autoridade máxima’ interpretativa para exercer a escuta, bem como legitimar as vozes dos participantes durante a atividade de leitura.
Ambiente e subjetividades em estudos sobre paisagem no contexto da Covid-19
Authors: Neis Carelli Mariluci , Dalonso Fernanda , Barros Meira Roberta
Published: December 2023

A pandemia de Covid-19 propiciou novas relações entre ambiente e subjetividades, alterando como as pessoas se relacionam com seu território. Os objetivos do artigo foram levantar e discutir estudos já existentes sobre as relações ambiente e subjetividades em época de pandemia nos estudos acerca de paisagem cultural e Covid-19. A pesquisa foi guiada por questões que delimitam a amplitude da temática: a relação entre ambiente e subjetividades é uma discussão presente nos estudos sobre paisagem cultural e Covid-19? Quais são as contribuições desses estudos? Foi realizada uma pesquisa bibliográfica, qualitativa, exploratória e analítica em bases de dados. Nesse estudo, as categorias de análise emergentes foram: novas relações entre subjetividades e ambiente; o mundo pós-coronial; percepção da corresponsabilidade com o ambiente; e maneiras de memorar a pandemia de Covid-19 e expressões artísticas cotidianas. Uma possível contribuição ou inovação do estudo está no surgimento de uma abertura/categoria de discussão no campo do patrimônio: as paisagens vividas.
Carpoteca Imaginária
Authors: Villefort Teixeira Maria Cristina , Gouvêa Pimentel Lucia , Clemente de Oliveira Gabriela
Published: December 2023

Arte e alimento vegetal é o eixo que move uma pesquisa de doutorado com orientação pelo Programa de Pós-graduação em Ambiente Construído Patrimônio Sustentável (PACPS) da Escola de Arquitetura e coorientação pelo Programa de Pós-graduação em Artes da Escola de Belas Artes (PPGArtes), ambos ligados à Universidade Federal de Minas Gerais-(UFMG). Essa proposta de investigação é o desdobramento de um processo de produção em arte que se iniciou em 2017, durante uma ação cotidiana de preparar um almoço.
Virtual screening and molecular dynamics simulation to identify potential SARS-CoV-2 3CLpro inhibitors from a natural product compounds library
Authors: Gan Chunchun , Jia Xiaopu , Fan Shuai , Wang Shuqing , Jing Weikai , Wei Xiaopeng
Published: December 2023

Based on the crystal structure of the 3C-like protease/Nsp5 (PDB ID 6W63), virtual hits were screened from a natural product compounds database—containing 407270 natural products—by using the high-throughput virtual screening (HTVS) module of Discovery Studio software, and then filtering by “Lipinski’s rule of five” from the top 20 virtual hits. Two star-hits were selected by CDOCKER results and the protein-ligand interactions with the 3CLpro were analyzed. Finally, a 100 ns molecular dynamics simulation was carried out to verify the stability of the receptor-ligand complexes. We screened potent broad-spectrum non-covalent inhibitors that could bind to the SARS-CoV-2 3CLpro active binding site from the natural product compounds library through HTVS and molecular dynamics simulations methods. The LibDock scores and -CDOCKER energy value of the star-hits were higher than the original ligands (X77) bound to 3CLpro. CNP0348829 and CNP0474002, as star-hits, can bind stably to the active site of 3CLpro, which are promising candidate compounds for the treatment of SARS-CoV-2 and provide a theoretical basis for the development of antiviral drugs. The results of the present study may be useful in the prevention and therapeutic perspectives of COVID-19. However, further in vitro and in vivo validation tests are required in the future.
Efficient semi-supervised semantic segmentation of electron microscopy cancer images with sparse annotations
Authors: Pagano Lucas , Thibault Guillaume , Bousselham Walid , Riesterer Jessica L. , Song Xubo , Gray Joe W.
Published: December 2023

Electron microscopy (EM) enables imaging at a resolution of nanometers and can shed light on how cancer evolves to develop resistance to therapy. Acquiring these images has become a routine task.However, analyzing them is now a bottleneck, as manual structure identification is very time-consuming and can take up to several months for a single sample. Deep learning approaches offer a suitable solution to speed up the analysis. In this work, we present a study of several state-of-the-art deep learning models for the task of segmenting nuclei and nucleoli in volumes from tumor biopsies. We compared previous results obtained with the ResUNet architecture to the more recent UNet++, FracTALResNet, SenFormer, and CEECNet models. In addition, we explored the utilization of unlabeled images through semi-supervised learning with Cross Pseudo Supervision. We have trained and evaluated all of the models on sparse manual labels from three fully annotated in-house datasets that we have made available on demand, demonstrating improvements in terms of 3D Dice score. From the analysis of these results, we drew conclusions on the relative gains of using more complex models, and semi-supervised learning as well as the next steps for the mitigation of the manual segmentation bottleneck.
Analysis of morphological and quantitative changes in pathological myopia and perioperative changes in posterior scleral reinforcement using three-dimensional magnet resonance imaging
Authors: Liu Lin , Rong Hua , Wu Di , Xu He , He Qing , Du Bei , Zhang Xuejun , Wei Ruihua
Published: December 2023

Objective: To compare the morphological and quantitative changes in pathological myopia (PM) and the perioperative changes in posterior scleral reinforcement (PSR) using three-dimensional magnetic resonance images (3D MRI).

Methods: A total of 49 patients with high myopia (HM; 98 eyes), 15 with pathological myopia (PM; 19 eyes), and 10 without high myopia (NORM; 20 eyes) were recruited between September 2019 and July 2021. The patients underwent measurements of refractive error and axial length, as well as 3D MRI of the eyeball. Python was used to analyze the 3D MRI images, calculate the vitreous volume, establish a topography of the height of the eyeball posterior surface, and calculate the rate of change in height (H). For the PM group undergoing PSR, changes in vitreous volume and the highest point of the eyeball posterior surface in four quadrants (temporal, subtemporal, nasal, and subnasal) were compared before and after PSR.

Results: The vitreous volume was smaller in the NORM group compared to the HM and PM groups (p < 0.01). The PM group had a larger volume than the HM group (p < 0.01). The H for the PM group was higher than that of the NORM and HM groups (p < 0.01). After PSR in the PM group, the total vitreous volume, as well as the volume in the subnasal and supratemporal quadrants, decreased (p < 0.05). Additionally, the highest point of the eyeball’s posterior surface was generally shifted to the upper nasal side. Finally, the shape and position of the scleral band after PSR were plotted.

Conclusion: 3D MRI is capable of a quantitative description of the eyeball morphology in PM and PSR. It allows for precise calculations of changes in vitreous volume and the H of the posterior surface. It also facilitates a meticulous analysis of the specific details of the scleral band following PSR.
Recent advances in wearable iontronic sensors for healthcare applications
Authors: Choi Sung-Geun , Kang Se-Hun , Lee Ju-Yong , Park Joo-Hyeon , Kang Seung-Kyun
Published: December 2023

Iontronic sensors have garnered significant attention as wearable sensors due to their exceptional mechanical performance and the ability to maintain electrical performance under various mechanical stimuli. Iontronic sensors can respond to stimuli like mechanical stimuli, humidity, and temperature, which has led to exploration of their potential as versatile sensors. Here, a comprehensive review of the recent researches and developments on several types of iontronic sensors (e.g., pressure, strain, humidity, temperature, and multi-modal sensors), in terms of their sensing principles, constituent materials, and their healthcare-related applications is provided. The strategies for improving the sensing performance and environmental stability of iontronic sensors through various innovative ionic materials and structural designs are reviewed. This review also provides the healthcare applications of iontronic sensors that have gained increased feasibility and broader applicability due to the improved sensing performance. Lastly, outlook section discusses the current challenges and the future direction in terms of the applicability of the iontronic sensors to the healthcare.
Effects of indoor lighting environments on paper reading efficiency and brain fatigue: an experimental study
Authors: Zhou Anqi , Pan Younghwan
Published: December 2023

Introduction: This study investigated the influence of indoor lighting environments on paper reading efficiency and brain fatigue to explore lighting parameters that benefit users during various reading durations.

Methods: The study was conducted in the Smart Lighting Lab, where 12 participants were tested under different illuminance levels and correlated color temperatures (CCT) for three distinct reading durations. Reading efficiency during the task tests and objective measures of brain activity by monitoring participants’ electroencephalograms (EEGs) were used as key factors to assess participants’ fatigue levels.

Results: By analyzing the subjective and objective results, we found that paper reading efficiency was significantly affected by changes in the lighting environment. Also, based on the results of this study, we propose lighting recommendations for paper reading tasks of different durations. For a 15 min reading task, the lighting condition of 500 lux-6,500 K were the most efficient for reading; for a 30 min reading task, 500 lux-4,000 K lighting environments were found to be the most effective; and 750 lux-6,500 K was the best lighting environment for a 60 min reading duration.

Discussion: These suggestions can serve as a reference for designing indoor lighting environment. In addition, they provide guidance to researchers and reviewers conducting similar studies.
Applications of CRISPR screening to lung cancer treatment
Authors: Shen Wanying , Hu Fangli , Lei Pan , Tang Yijun
Published: December 2023

Lung cancer is an extremely aggressive and highly prevalent disease worldwide, and it is one of the leading causes of cancer death. Deciphering intrinsic genetic mechanism, finding new targets, and overcoming drug resistance are the key to lung cancer treatment. High-throughput CRISPR screening has been extensively used to obtain the genes related to cancers including lung cancer. This review describes CRISPR/Cas9 or CRISPR/dCas9-based technologies for high-throughput screening. We summarize the applications of CRISPR screening technology in exploring the mechanism of lung cancer development in vivo or in vitro, overcoming drug resistance, improving the effect of immunotherapy, and discovering new therapeutic targets. This review highlights the potential of CRISPR screening in combination with tumor barcoding and high-throughput sequencing (Tuba-seq) to precisely quantify the impact of alterations in many tumor suppressor genes on lung cancer.
Causal effects of gut microbiota on appendicitis: a two-sample Mendelian randomization study
Authors: Wang Zehui , Bao Lijie , Wu Lidong , Zeng Qi , Feng Qian , Zhou Jinchuan , Luo Zhiqiang , Wang Yibing
Published: December 2023

Background

Previous research has posited a potential correlation between the gut microbiota and the onset of appendicitis; however, the precise causal connection between appendicitis and the gut microbiota remains an unresolved and contentious issue.

Methods

In this investigation, we performed a Mendelian randomization (MR) analysis employing publicly accessible summary data extracted from genome-wide association studies (GWAS) to elucidate the potential causal nexus between the gut microbiota and the development of appendicitis. We initially identified instrumental variables (IVs) through a comprehensive array of screening methodologies, subsequently executing MR analyses using the Inverse Variance Weighted (IVW) technique as our primary approach, supplemented by several alternative methods such as MR Egger, weighted median, simple mode, and weighted mode. Additionally, we implemented a series of sensitivity analysis procedures, encompassing Cochran’s Q test, MR-Egger intercept test, Mendelian Randomized Polymorphism Residual and Outlier (MR-PRESSO) test, and a leave-one-out test, to affirm the robustness and validity of our findings.

Results

Our investigation indicates that an elevated prevalence of Deltaproteobacteria, Christensenellaceae, Desulfovibrionaceae, Eubacterium ruminantium group, Lachnospiraceae NK4A136 group, Methanobrevibacter, Desulfovibrionales, and Euryarchaeota is inversely associated with the risk of appendicitis. Conversely, we observed a positive correlation between an increased abundance of Family XIII, Howardella, and Veillonella and the susceptibility to appendicitis. Sensitivity analyses have corroborated the robustness of these findings, and Mendelian randomization analyses provided no indications of reverse causality.

Conclusion

Our Mendelian randomization (MR) analysis has unveiled potential advantageous or detrimental causal associations between the gut microbiota and the occurrence of appendicitis. This study offers novel theoretical and empirical insights into the understanding of appendicitis pathogenesis, along with its implications for preventive and therapeutic strategies.
Mitochondrial transplantation: the advance to therapeutic application and molecular modulation
Authors: McCully James D. , del Nido Pedro J. , Emani Sitaram M.
Published: December 2023

Mitochondrial transplantation provides a novel methodology for rescue of cell viability and cell function following ischemia-reperfusion injury and applications for other pathologies are expanding. In this review we present our methods and acquired data and evidence accumulated to support the use of mitochondrial transplantation.
Bivalirudin-hydrogel coatings of polyvinyl chloride on extracorporeal membrane oxygenation for anticoagulation
Authors: Gao Wenqing , Shen Hechen , Chang Yun , Tang Qin , Li Tong , Sun Di
Published: December 2023

Introduction

Thromboembolic events associated with extracorporeal membrane oxygenation (ECMO) in clinical treatment are typical. Heparin coating has been widely employed as a surface modification strategy for ECMO tubes. However, its clinical application is often accompanied by unavoidable complications due to its mechanism of action. As a direct thrombin inhibitor with a single target, Bivalirudin (BV) has exhibited a lower incidence of adverse events and superior pharmacokinetic performance compared to heparin.

Methods

A gelatin methacrylate hydrogel (GelMA) coating layer with BV was successfully synthesized on polyvinyl chloride, and the drug release ratio was close to complete release within 7 days.

Results and discussion

Simulated extracorporeal circulation experiments using roller pumps in vitro and jugular arteriovenous bypass experiments in rabbits demonstrated its outstanding anticoagulant efficacy. The systemic anticoagulant assay proved that BV hydrogel coating does not affect the coagulation level, and reduces the risk of complications such as systemic bleeding compared to intravenous injection. BV-Coating GelMA hydrogel tube has exhibited good biocompatibility and significantly improved anticoagulant performance, making it an optimal choice for surface materials used in blood-contacting medical devices.
Receptor-interacting protein 1 and 3 kinase activity are required for high-fat diet induced liver injury in mice
Authors: Wu Xiaoqin , Arya Rakesh K. , Huang Emily , McMullen Megan R. , Nagy Laura E.
Published: December 2023

Background

The RIP1-RIP3-MLKL-mediated cell death pathway is associated with progression of non-alcohol-associated fatty liver/steatohepatitis (NAFL/NASH). Previous work identified a critical role for MLKL, the key effector regulating necroptosis, but not RIP3, in mediating high fat diet-induced liver injury in mice. RIP1 and RIP3 have active N-terminus kinase domains essential for activation of MLKL and subsequent necroptosis. However, little is known regarding domain-specific roles of RIP1/RIP3 kinase in liver diseases. Here, we hypothesized that RIP1/RIP3 kinase activity are required for the development of high fat diet-induced liver injury.

Methods

Rip1K45A/K45A and Rip3K51A/K51A kinase-dead mice on a C57BL/6J background and their littermate controls (WT) were allowed free access to a diet high in fat, fructose and cholesterol (FFC diet) or chow diet.

Results

Both Rip1K45A/K45A and Rip3K51A/K51A mice were protected against FFC diet-induced steatosis, hepatocyte injury and expression of hepatic inflammatory cytokines and chemokines. FFC diet increased phosphorylation and oligomerization of MLKL and hepatocyte death in livers of WT, but not in Rip3K51A/K51A, mice. Consistent with in vivo data, RIP3 kinase deficiency in primary hepatocytes prevented palmitic acid-induced translocation of MLKL to the cell surface and cytotoxicity. Additionally, loss of Rip1 or Rip3 kinase suppressed FFC diet-mediated formation of crown-like structures (indicators of dead adipocytes) and expression of mRNA for inflammatory response genes in epididymal adipose tissue. Moreover, FFC diet increased expression of multiple adipokines, including leptin and plasminogen activator inhibitor 1, in WT mice, which was abrogated by Rip3 kinase deficiency.

Discussion

The current data indicate that both RIP1 and RIP3 kinase activity contribute to FFC diet-induced liver injury. This effect of RIP1 and RIP3 kinase deficiency on injury is consistent with the protection of Mlkl-/- mice from high fat diet-induced liver injury, but not the reported lack of protection in Rip3-/- mice. Taken together with previous reports, our data suggest that other domains of RIP3 likely counteract the effect of RIP3 kinase in response to high fat diets.
Gut microbiota and metabolites in estrus cycle and their changes in a menopausal transition rat model with typical neuroendocrine aging
Authors: Dai Ruoxi , Huang Jianqin , Cui Liyuan , Sun Ruiqi , Qiu Xuemin , Wang Yan , Sun Yan
Published: December 2023

Background

Neuroendocrine alterations in the mid-life hypothalamus coupled with reproductive decline herald the initiation of menopausal transition. The certain feature and contribution of gut microflora and metabolites to neuroendocrine changes in the menopausal transition remain largely unknown.

Methods

Fecal samples of rats experiencing different reproductive stages were collected and processed for 16S rRNA and liquid chromatography–mass spectrometry sequencing. The differences of gut microbiota and metabolites between young and middle-aged rats during proestrus and diestrus were analyzed, and their relationships to neuroendocrine aging were then examined.

Results

At the genus level, Anaeroyorax, Rikenella, Tyzzerella_3, and Atopostipes were abundant at proestrus, while Romboutsia, Turicibacter, Clostridium_sensu_stricto_1, Ruminococcaceae_NK4A214_group, CHKCI002, Ruminococcaceae_UCG-010, Staphylococcus, Family_XII_AD3011_group, Ruminococcaceae UCG-011, and Christensenellaceae_R_7_group were enriched in the diestrus of middle-aged rats. DNF00809, Phocea, and Lachnospiraceae_UCG-006 were found abundant during proestrus instead, while Bacteroides, Lactobacillus, Erysipelatoclostridium, Anaeroplasma, Anaerofustis, Parasutterella, and Enterococcus were enriched at the diestrus of young female individuals. Discriminatory metabolites were identified involving 90 metabolic pathways among the animal sets, which were enriched for steroid hormone biosynthesis, arachidonic metabolism, primary bile acid synthesis, and ovarian steroidogenesis. A total of 21 metabolites lacking in hormone-associated changes in middle-aged female individuals presented positive or negative correlations with the circulating luteinizing hormone, bile acid, fibroblast growth factor 19, and gut hormones. Moreover, close correlations were detected between the intestinal bacteria and their metabolites.

Conclusion

This study documents specific gut microbial composition changes and concomitant shifting trends of metabolites during menopausal transition, which may initiate the gut–brain dysfunction in neuroendocrine aging.
A surface-tunnel frequency domain electromagnetic method for mineral exploration in Tajikistan area
Authors: Wang Hongyu , Liu Jianxin , Guo Wenbo , Tian Shengqi
Published: December 2023

For old mines, numerous mining tunnels exist, which can potentially bring us closer to the deep ore-bearing structures. Therefore, we propose a surface-tunnel frequency domain electromagnetic (EM) method to utilize these mining tunnels for geophysical exploration. In this method, the transmitter is placed on the Earth’s surface, while the receiver is positioned within the tunnel space, providing higher resolution due to its proximity to the target body. This paper presents the derived analytical solution for the electric field in the surface-tunnel configuration. We also propose a survey system for our surface-tunnel frequency domain electromagnetic method and provide a field example of lead-zinc deposits in Tajikistan. Synthetic cases demonstrate a significant enhancement of the EM signal when the receiver is moved into the tunnel. The field application validates the practicality of our surface-tunnel frequency domain EM method for deep mineral exploration in active mines.
A landscape-based ecological hazard evaluation and characterization of influencing factors in Laos
Authors: Ma Jun , Khromykh Vadim , Wang Jinliang , Zhang Jianpeng , Li Wenjuan , Zhong Xuzheng
Published: December 2023

The study of the spatiotemporal evolution of landscape ecological hazard and human and natural influences is essential for conservative management and regional sustainable development. This study applied a landscape pattern analysis method and geodetector to multi-source data for 2000, 2010, and 2020 to analyze changes in and drivers of landscape ecological hazard in Laos. The results indicated that: (1) There were more prominent changes in landscape types in Laos. Forest area decreased, whereas the areas of other landscape types increased. There was an overall steady change in the landscape patterns of Laos. Besides for significant changes in the artificial surface landscape index, landscape indices remained stable; (2) The cumulative high and extreme ecological hazard areas increased by 1,947.81 km2, whereas the cumulative areas of low and minimal ecological hazard decreased by 8,461.8 km2. Areas of low and moderate ecological hazard accounted for > 85% of the total area. Areas of low ecological hazard were mainly in the northwest and southeast. The area of high ecological hazard was concentrated in the central and northeastern regions. The distributions of different landscape ecological hazards in Laos during the study period were similar, with general patterns of decreasing hazard from north to south; (3) A positive Moran’s I of landscape ecological hazard in Laos was obtained. While the agglomeration effect was pronounced, it decreased over time, resulting in a weakening in spatial autocorrelation. A significant positive autocorrelation was observed in the spatial distribution of landscape ecological hazard in the study area. Agglomerated areas of high and low ecological hazard were mainly concentrated in the northeast and southeast, respectively; (4) The spatiotemporal evolution of landscape ecological hazard in Laos over the last 20 years could be attributed to interactions between natural and anthropogenic influences. Natural influences were a significant driver of changes to landscape ecological hazard in Laos, with annual precipitation and average temperature being the most significant. Anthropogenic influences, including socioeconomic factors and regional accessibility, significantly impacted local ecological deterioration in Laos.
Plant functional groups and soil properties vary with the restoration periods in Zoige desertification land
Authors: Wang Ruolan , Lou Yuanxin , He Li , Chen Juanli , Chen Yali , Yan Wuxian , Deng Dongzhou , Mu Junpeng
Published: December 2023

Desertification has a significant impact on the Zoige meadow. Research efforts are directed towards the rehabilitation of the Zoige desertified alpine meadow, specifically in understanding the soil’s physical and chemical characteristics and the functional groupings of plants. However, the relationships between plant functional groups and soil properties remains uncertain. The primary objective of this study is to investigate the correlation between plant functional groups and soil nutrients across various stages of restoration. This study examined important value of plant functional groups, as well as variations in several soil characteristics, such as soil total nitrogen, total carbon, total phosphorus, available nitrogen, available potassium, available phosphorus, and soil pH during the stages of recovery. The results showed that the relative significance of importance values differed across distinct functional groups during different stages of recovery. The important value of legumes was found to have a strong negative correlation with the levels of soil available nitrogen and potassium. In contrast, there was a substantial positive correlation between the important value of grass and both soil total carbon and available potassium. Conversely, there was a strong negative relationship between the importance value of sedges and both total soil carbon and phosphorus. These findings indicate that the linkages between soil properties and plant functional groups varied across different recovery periods. This study would shed new light on the restoration in the Zoige desertified alpine meadows.
Incorporating CNV analysis improves the yield of exome sequencing for rare monogenic disorders—an important consideration for resource-constrained settings
Authors: Louw Nadja , Carstens Nadia , Lombard Zané ,   for DDD-Africa as members of the H3Africa Consortium
Published: December 2023

Exome sequencing (ES) is a recommended first-tier diagnostic test for many rare monogenic diseases. It allows for the detection of both single-nucleotide variants (SNVs) and copy number variants (CNVs) in coding exonic regions of the genome in a single test, and this dual analysis is a valuable approach, especially in limited resource settings. Single-nucleotide variants are well studied; however, the incorporation of copy number variant analysis tools into variant calling pipelines has not been implemented yet as a routine diagnostic test, and chromosomal microarray is still more widely used to detect copy number variants. Research shows that combined single and copy number variant analysis can lead to a diagnostic yield of up to 58%, increasing the yield with as much as 18% from the single-nucleotide variant only pipeline. Importantly, this is achieved with the consideration of computational costs only, without incurring any additional sequencing costs. This mini review provides an overview of copy number variant analysis from exome data and what the current recommendations are for this type of analysis. We also present an overview on rare monogenic disease research standard practices in resource-limited settings. We present evidence that integrating copy number variant detection tools into a standard exome sequencing analysis pipeline improves diagnostic yield and should be considered a significantly beneficial addition, with relatively low-cost implications. Routine implementation in underrepresented populations and limited resource settings will promote generation and sharing of CNV datasets and provide momentum to build core centers for this niche within genomic medicine.
Small supernumerary marker chromosomes derived from human chromosome 11
Authors: Liehr Thomas , Ziegler Monika , Person Luisa , Kankel Stefanie , Padutsch Niklas , Weise Anja , Weimer Jörg Paul , Williams Heather , Ferreira Susana , Melo Joana B. , Carreira Isabel M.
Published: December 2023

Introduction: With only 39 reported cases in the literature, carriers of a small supernumerary marker chromosome (sSMC) derived from chromosome 11 represent an extremely rare cytogenomic condition.

Methods: Herein, we present a review of reported sSMC(11), add 18 previously unpublished cases, and closely review eight cases classified as ‘centromere-near partial trisomy 11’ and a further four suited cases from DECIPHER.

Results and discussion: Based on these data, we deduced the borders of the pericentric regions associated with clinical symptoms into a range of 2.63 and 0.96 Mb for chromosome 11 short (p) and long (q) arms, respectively. In addition, the minimal pericentric region of chromosome 11 without triplo-sensitive genes was narrowed to positions 47.68 and 60.52 Mb (GRCh37). Furthermore, there are apparent differences in the presentation of signs and symptoms in carriers of larger sSMCs derived from chromosome 11 when the partial trisomy is derived from different chromosome arms. However, the number of informative sSMC(11) cases remains low, with overlapping presentation between p- and q-arm-imbalances. In addition, uniparental disomy (UPD) of ‘normal’ chromosome 11 needs to be considered in the evaluation of sSMC(11) carriers, as imprinting may be an influencing factor, although no such cases have been reported. Comprehensively, prenatal sSMC(11) cases remain a diagnostic and prognostic challenge.
Clinical application of single nucleotide polymorphism microarray analysis in pregnancy loss in Northwest China
Authors: Xue ShuYuan , Wang LiXia , Wei Jie , Liu YuTong , Ding GuiFeng , Dai PengGao
Published: December 2023

Background: Spontaneous abortion is the most common complication of early pregnancy. In this study, we aim to investigate the clinical application value of genetic diagnosis using single nucleotide polymorphism (SNP) microarray analysis on the products of conception and to characterize the types of genetic abnormalities and their prevalence in pregnancy loss in Northwest China.

Methods: Over 48 months, we selected 652 products of conception, which included chorionic villi, fetal tissues, germ cell samples, amniotic fluid samples, cord blood samples, and a cardiac blood sample. We analyzed the distribution of chromosomal abnormalities leading to fetal arrest or abortion using SNP array. The patients were then categorized divided into groups based on maternal age, gestational age, number of miscarriages, and maternal ethnic background. The incidences of various chromosomal abnormalities in each group were compared.

Results: Of the 652 cases, 314 (48.16%) exhibited chromosomal abnormalities. These included 286 cases with numerical chromosomal abnormalities, 24 cases with copy number variation, and four cases with loss of heterozygosity. Among them, there were 203 trisomy cases, 55 monosomy cases, and 28 polyploidy cases. In the subgroup analysis, significant differences were found in the frequency of numerical chromosomal abnormalities and copy number variation between the advanced and younger maternal age group as well as between the early and late abortion groups. Furthermore, we identified significant differences in the frequency of numerical chromosomal abnormalities between the first spontaneous abortion and recurrent miscarriage groups. However, there were no significant differences in the frequency of numerical chromosomal abnormalities between the Han and Uighur groups.

Conclusion: Our research highlights chromosomal abnormalities as the primary cause of spontaneous abortion, with a higher incidence in early pregnancy and among women of advanced age. The use of SNP array analysis emerges as an effective and reliable technique for chromosome analysis in aborted fetuses. This method offers a comprehensive and dependable genetic investigation into the etiology of miscarriage, establishing itself as a valuable routine selection for genetic analysis in cases of natural abortions.
DPred_3S: identifying dihydrouridine (D) modification on three species epitranscriptome based on multiple sequence-derived features
Authors: Ren Jinjin , Chen Xiaozhen , Zhang Zhengqian , Shi Haoran , Wu Shuxiang
Published: December 2023

Introduction: Dihydrouridine (D) is a conserved modification of tRNA among all three life domains. D modification enhances the flexibility of a single nucleotide base in the spatial structure and is disease- and evolution-associated. Recent studies have also suggested the presence of dihydrouridine on mRNA.

Methods: To identify D in epitranscriptome, we provided a prediction framework named “DPred_3S” based on the machine learning approach for three species D epitranscriptome, which used epitranscriptome sequencing data as training data for the first time.

Results: The optimal features were evaluated by the F-score and integration of different features; our model achieved area under the receiver operating characteristic curve (AUROC) scores 0.955, 0.946, and 0.905 for Saccharomyces cerevisiae, Escherichia coli, and Schizosaccharomyces pombe, respectively. The performances of different machine learning algorithms were also compared in this study.

Discussion: The high performances of our model suggest the D sites can be distinguished based on their surrounding sequence, but the lower performance of cross-species prediction may be limited by technique preferences.
Human VH4-34 antibodies derived from B1 cells are more frequently autoreactive than VH4-34 antibodies derived from memory cells
Authors: Ray Michelle E. , Rothstein Thomas L.
Published: December 2023

Human B1 cells produce natural antibodies characterized by overutilization of heavy chain variable region VH4-34 in comparison to other B cell populations. VH4-34-containing antibodies have been reported to be autoreactive and to be associated with lupus and other autoimmune dyscrasias. However, it has been unclear to what extent VH4-34 antibodies manifest autoreactivity in B1 cells or other B cell populations—in other words, are VH4-34 containing antibodies autoreactive wherever found, or mainly within the B1 cell population? To address this issue we sort purified single human B1 and memory B cells and then amplified, sequenced, cloned and expressed VH4-34-containing antibodies from 76 individual B cells. Each of these antibodies was tested for autoreactivity by HEp-2 IFA and autoantigen ELISA. Antibodies were scored as autoreactive if positive by either assay. We found VH4-34 antibodies rescued from B1 cells were much more frequently autoreactive (14/48) than VH4-34 antibodies rescued from memory B cells (2/28). Among B1 cell antibodies, 4 were HEp-2+, 6 were dsDNA+ and 4 were positive for both. Considering only HEp-2+ antibodies, again these were found more frequently among B1 cell VH4-34 antibodies (8/48) than memory B cell VH4-34 antibodies (1/28). We found autoreactivity was associated with greater CDR3 length, as expected; however, we found no association between autoreactivity and a previously described FR1 “hydrophobic patch”. Our results indicate that autoreactive VH4-34-containing antibodies tend to reside within the human B1 cell population.
New insights from integrated bioinformatics analysis: the role of circadian rhythm disruption and immune infiltration in obstructive sleep apnea disease
Authors: Zhang Xinyue , Wang Yixuan , Pan Zhou , Hu Ke
Published: December 2023

Background

Circadian rhythm disruption and immune infiltration are both closely associated with the development of Obstructive sleep apnea (OSA) disease and a variety of cardiovascular and neurological complications, but their interactions with OSA disease are not clear. In this study, we used bioinformatics to investigate the roles of circadian rhythm disruption and immune microenvironments in OSA.

Methods

We analyzed differential genes and their associated functional pathways in the circadian rhythm-associated OSA dataset, then regrouped OSA samples using the differential genes and explored differences in immune cell infiltration between the two different subgroups. Meanwhile, we used two machine learning algorithms to further define circadian rhythm-related signature genes and to explore the relationship between key genes and immune cell infiltration. Finally, we searched for the transcription factors of the key differential gene JUN.

Results

We screened 15 circadian rhythm-related differential genes in the OSA-related dataset and further defined 3 signature genes by machine learning algorithms. Immunoassays showed a significant increase in resting mast cell infiltration and a decrease in monocyte infiltration in the OSA group. The results of our animal experiments also confirmed that the expression of these 3 key genes, as well as the immune cell infiltration, showed a trend consistent with the results of the bioinformatics analysis.

Conclusions

In conclusion, this study reveals the interaction between circadian rhythm disruption and immune infiltration in OSA, providing new insights into the potential pathogenesis of OSA.
Characterization of young and aged ferrets as animal models for SARS-CoV-2 infection with focus on neutrophil extracellular traps
Authors: Pilchová Veronika , Gerhauser Ingo , Armando Federico , Wirz Katrin , Schreiner Tom , de Buhr Nicole , Gabriel Gülşah , Wernike Kerstin , Hoffmann Donata , Beer Martin , Baumgärtner Wolfgang , von Köckritz-Blickwede Maren , Schulz Claudia
Published: December 2023

Neutrophil extracellular traps (NETs) are net-like structures released by activated neutrophils upon infection [e.g., severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)] as part of the innate immune response that have protective effects by pathogen entrapment and immobilization or result in detrimental consequences for the host due to the massive release of NETs and their impaired degradation by nucleases like DNase-1. Higher amounts of NETs are associated with coronavirus disease 2019 (COVID-19) severity and are a risk factor for severe disease outcome. The objective of our study was to investigate NET formation in young versus aged ferrets to evaluate their value as translational model for SARS-CoV-2-infection and to correlate different NET markers and virological parameters. In each of the two groups (young and aged), nine female ferrets were intratracheally infected with 1 mL of 106 TCID50/mL SARS-CoV-2 (BavPat1/2020) and euthanized at 4, 7, or 21 days post-infection. Three animals per group served as negative controls. Significantly more infectious virus and viral RNA was found in the upper respiratory tract of aged ferrets. Interestingly, cell-free DNA and DNase-1 activity was generally higher in bronchoalveolar lavage fluid (BALF) but significantly lower in serum of aged compared to young ferrets. In accordance with these data, immunofluorescence microscopy revealed significantly more NETs in lungs of aged compared to young infected ferrets. The association of SARS-CoV-2-antigen in the respiratory mucosa and NET markers in the nasal conchae, but the absence of virus antigen in the lungs, confirms the nasal epithelium as the major location for virus replication as described for young ferrets. Furthermore, a strong positive correlation was found between virus shedding and cell-free DNA or the level of DNAse-1 activity in aged ferrets. Despite the increased NET formation in infected lungs of aged ferrets, the animals did not show a strong NET phenotype and correlation among tested NET markers. Therefore, ferrets are of limited use to study SARS-CoV-2 pathogenesis associated with NET formation. Nevertheless, the mild to moderate clinical signs, virus shedding pattern, and the lung pathology of aged ferrets confirm those animals as a relevant model to study age-dependent COVID-19 pathogenesis.
Targeting vascular normalization: a promising strategy to improve immune–vascular crosstalk in cancer immunotherapy
Authors: Qian Cheng , Liu Chaoqun , Liu Weiwei , Zhou Rui , Zhao Liang
Published: December 2023

Blood vessels are a key target for cancer therapy. Compared with the healthy vasculature, tumor blood vessels are extremely immature, highly permeable, and deficient in pericytes. The aberrantly vascularized tumor microenvironment is characterized by hypoxia, low pH, high interstitial pressure, and immunosuppression. The efficacy of chemotherapy, radiotherapy, and immunotherapy is affected by abnormal blood vessels. Some anti-angiogenic drugs show vascular normalization effects in addition to targeting angiogenesis. Reversing the abnormal state of blood vessels creates a normal microenvironment, essential for various cancer treatments, specifically immunotherapy. In addition, immune cells and molecules are involved in the regulation of angiogenesis. Therefore, combining vascular normalization with immunotherapy may increase the efficacy of immunotherapy and reduce the risk of adverse reactions. In this review, we discussed the structure, function, and formation of abnormal vessels. In addition, we elaborated on the role of the immunosuppressive microenvironment in the formation of abnormal vessels. Finally, we described the clinical challenges associated with the combination of immunotherapy with vascular normalization, and highlighted future research directions in this therapeutic area.