bluuebunny/crossref_metadata_2025 huggingface dataset:
Plywood Cores as a Foundation for Good Woodwork
Authors: Knight E. Vernon , Perry Thomas D.
Published: January 2024

Plywood consists of laminated sheets of wood. The core supports the interlocking layers and the face veneer. Various manufacturing problems of plywood are discussed in this paper. The various woods used are selected for their strength, artistic figure, and workability. Some of the physical characteristics of the more usual species of woods are given. The various types of joints and the methods of matching and gluing are described, and department layouts for two plants are given to illustrate routing procedure and the types of woodworking tools used.
Protorheology
Authors: Hossain Mohammad Tanver , Ewoldt Randy H.
Published: January 2024

We all instinctively poke, bounce, scoop, and observe materials to understand rheological properties quickly. Yet, these observations are rarely analyzed quantitatively. To address this, here we introduce the paradigm of protorheology: approximate quantitative inference from simple observations. Several case studies demonstrate how protorheology is an inclusive entry to rheology for a broad range of practitioners and strengthens the confidence and interpretation of accurate laboratory measurements. We survey a range of creative tests according to which rheological phenomenon is revealed. Some new working equations are derived, and all working equations are summarized for convenient reference and comparison across different methods. This establishes a framework to enable increased use of photos, videos, and quantitative inference and to support the increasing interest in digital image analysis, inverse methods, and high-throughput characterization being applied to rheological properties.
Correlates of Motor Competence in Primary School Students: A Cross-Sectional Study From a Portuguese Municipality
Authors: Carvalho Francisco , Onofre Marcos , Mota João , Peralta Miguel , Marques Adilson , Quitério Ana , Rodrigues António , Alves Pedro , O’Brien Wesley , Martins João
Published: January 2024

Children’s motor competence (MC) levels tend to be low, and the investigation of variables that facilitate skillfulness is an important concern. The socioecological model is a useful framework to explore factors that influence MC and to inform the development of targeted interventions. This cross-sectional study aimed to perform an exploratory analysis of MC correlates among children. The sample comprised 267 second- and fourth-grade children (120 female; Mage = 102 months, SD = 14 months) from six primary schools. The children’s legal guardian questionnaire collected sociodemographic, behavioral, and family variables. MC was assessed with the Motorische Basiskompetenzen battery. Data analysis involved simple and multiple regression models. The mean total Motorische Basiskompetenzen score was 8.9 (3.4) out of a maximum score of 16. Sex, age, body mass index, and physical activity and sports clubs were significantly related to total MC in all models (p < .05). The final model predicted a variance of 24.5%, adjusted R2 = .245, F(20, 246) = 5.32, p < .001, with male sex (B = 2.03) and organized physical activity (B = 0.35) being positively associated with total MC. Fourth grade (B = −3.6) and body mass index (B = −0.23) were negatively associated with MC. The study provides provisional evidence for the role of some sociodemographic and behavioral factors in MC development, which are important to design future MC interventions.
Influence of Graft Type and Meniscal Involvement on Short-Term Outcomes Following Anterior Cruciate Ligament Reconstruction
Authors: Moler Casey , Cross Kevin M. , Kaur Mandeep , Bruce Leicht Amelia , Hart Joe , Diduch David
Published: January 2024

Context: The purpose of this study was to compare short-term clinical outcomes between meniscus procedures performed with anterior cruciate ligament reconstruction (ACLR), ACLR (ACLR-only), ACLR with meniscectomy/resection (ACLR-resect), and ACLR with meniscal repair (ACLR-repair) for bone patellar tendon bone grafts (BPTB) and hamstring tendon grafts, separately. Design: This was a cross-sectional study conducted in a controlled laboratory setting as part of a large point-of-care collaborative research program. Methods: This study included 314 participants (168 females; mean [SD]: age, 19.7 [4.8]) with primary unilateral ACLR with a BPTB or hamstring tendon. Patients were divided into 3 groups depending on meniscal procedure (ACLR-only, ACLR-resect, and ACLR-repair). Postsurgical testing included: isokinetic assessment of knee extension and flexion, single-leg hop tests, and patient-reported outcomes. Multivariate analysis of covariance compared differences between meniscal procedures on the battery of tests, and for each statistically significant variable an analysis of covariance assessed the effect of meniscal procedure within each graft type. Chi-square analysis assessed the influence of meniscal procedure on tests’ pass rates defined as 90% of limb symmetry index. Results: BPTB: ACLR-only had greater hamstring strength than ACLR-resect (P = .05) and ACLR-repair (P = .005). ACLR-only had the highest proportion of participants to pass the hamstring strength test (P = .02). Hamstring tendon: ACLR-only (P = .03) and ACLR-resect (P = .003) had higher International Knee Documentation Committee scale scores than ACLR-repair. There was a significant difference in the proportion of participants who scored >90% limb symmetry index on the timed hop test (P = .05). Conclusions: The influence of meniscal repair on clinical outcomes is dependent on the graft choice. Following an ACLR with BPTB and a meniscal procedure, hamstring function should be more closely monitored for optimal short-term recovery.
Can partial-cut harvesting be used to extend the availability of terrestrial forage lichens in late-seral pine-lichen woodlands? Evidence from the Lewes Marsh (southern Yukon) silvicultural systems trial
Authors: Coxson Darwyn , Sharples Robin
Published: January 2024

In northern British Columbia and southern Yukon woodland, caribou forage extensively on terrestrial lichens, predominately mat-forming Cladina species in late-successional pine-lichen woodlands. Many of these stands are now reaching a point in their development where lichen abundance declines as feather-moss mats increase. We evaluated the response of forest floor plant communities in pine-lichen woodlands from the southern Yukon Lewes Marsh partial-cutting trial 8 years after harvesting. Photoplot results documented a major decline (>60% ± 5.6% SE) in the mean surface area of existing large clumps of C. mitis in control (unharvested) treatments, whereas the mean surface area of large C. mitis clumps declined by 28% (±15% SE) in the one-third basal-area removal and showed an increase of 13.5% (±25% SE) in the two-thirds basal-area removal. Line intercept transects documented no changes in overall stand-level lichen abundance between pre-harvest (2012) and post-harvest (2021) measurements, while feather-moss mats and dwarf shrubs showed declines and increases, respectively, in partial-cutting harvest plots. Stand thinning may provide a bridging strategy to extend the period of forage lichen availability in late-seral pine-lichen woodlands, an important consideration in landscapes where increasing severity and frequency of fires are changing the seral-state distribution of caribou habitat.
Utility of Lissajous Plots for Electrochemical Impedance Spectroscopy Measurements: Detection of Non-Linearity and Non-Stationarity
Authors: Zabara M. A. , Goh J. M. , Gaudio V. M. , Zou L. , Orazem M. E. , Ulgut B.
Published: January 2024

Correct interpretation of Electrochemical Impedance Spectroscopy (EIS) data is bound to the linearity and stationarity of the measurement. Current-Potential traces, also known as Lissajous figures for EIS measurements, contain valuable information regarding the linearity and the stationarity of the obtained data. Here, the behavior of the Lissajous figures is analyzed for various scenarios. The Lissajous analysis is shown to be helpful in the determination of the linearity and the stationarity of the data, especially for situations where Kramers-Kronig compatibility tests fail. The averaging of the Lissajous plots is shown to change the EIS results for non-linear and non-stationary systems. Further, the analysis of the Lissajous figures in the frequency domain by means of Fourier transforms is found to be very useful in differentiating between the non-linear and the non-stationary behaviors in the obtained data. The effect of averaging the Lissajous figures is also shown to make a difference when the system is non-stationary.
Supplementary Information from Gain-of-Function p53 Mutation Acts as a Genetic Switch for TGFβ Signaling–Induced Epithelial-to-Mesenchymal Transition in Intestinal Tumors
Authors: Wang Dong , Nakayama Mizuho , Hong Chang Pyo , Oshima Hiroko , Oshima Masanobu
Published: January 2024

Supplementary Video legends, and Primer sequences
Table S8 from Genomic and Evolutionary Characterization of Concurrent Intraductal Carcinoma and Adenocarcinoma of the Prostate
Authors: Zhao Jinge , Xu Nanwei , Zhu Sha , Nie Ling , Zhang Mengni , Zheng Linmao , Cai Diming , Sun Xiaomeng , Chen Junru , Dai Jindong , Ni Yuchao , Wang Zhipeng , Zhang Xingming , Liang Jiayu , Chen Yuntian , Hu Xu , Pan Xiuyi , Yin Xiaoxue , Liu Haoyang , Zhao Fengnian , Zhang Bei , Chen Hao , Miao Jiashun , Qin Cong , Zhao Xiaochen , Yao Jin , Liu Zhenhua , Liao Banghua , Wei Qiang , Li Xiang , Liu Jiyan , Gao Allen C. , Huang Haojie , Shen Pengfei , Chen Ni , Zeng Hao , Sun Guangxi
Published: January 2024

Table S8
Table S5 from Genomic and Evolutionary Characterization of Concurrent Intraductal Carcinoma and Adenocarcinoma of the Prostate
Authors: Zhao Jinge , Xu Nanwei , Zhu Sha , Nie Ling , Zhang Mengni , Zheng Linmao , Cai Diming , Sun Xiaomeng , Chen Junru , Dai Jindong , Ni Yuchao , Wang Zhipeng , Zhang Xingming , Liang Jiayu , Chen Yuntian , Hu Xu , Pan Xiuyi , Yin Xiaoxue , Liu Haoyang , Zhao Fengnian , Zhang Bei , Chen Hao , Miao Jiashun , Qin Cong , Zhao Xiaochen , Yao Jin , Liu Zhenhua , Liao Banghua , Wei Qiang , Li Xiang , Liu Jiyan , Gao Allen C. , Huang Haojie , Shen Pengfei , Chen Ni , Zeng Hao , Sun Guangxi
Published: January 2024

Table S5
Supplementary Figure S3 from Targeting Transcriptional Regulation with a CDK9 Inhibitor Suppresses Growth of Endocrine- and Palbociclib-Resistant ER+ Breast Cancers
Authors: Soosainathan Arany , Iravani Marjan , El-Botty Rania , Alexander John , Sourd Laura , Morisset Ludivine , Painsec Pierre , Orha Rebecca , Nikitorowicz-Buniak Joanna , Pancholi Sunil , Haider Syed , Dowsett Mitch , Marangoni Elisabetta , Martin Lesley-Ann , Isacke Clare M.
Published: January 2024

Supplementary Figure S3
Figure 2 from Targeting Transcriptional Regulation with a CDK9 Inhibitor Suppresses Growth of Endocrine- and Palbociclib-Resistant ER+ Breast Cancers
Authors: Soosainathan Arany , Iravani Marjan , El-Botty Rania , Alexander John , Sourd Laura , Morisset Ludivine , Painsec Pierre , Orha Rebecca , Nikitorowicz-Buniak Joanna , Pancholi Sunil , Haider Syed , Dowsett Mitch , Marangoni Elisabetta , Martin Lesley-Ann , Isacke Clare M.
Published: January 2024

Three-dimensional kinase inhibitor screens in LTED and palbociclib-resistant breast cancer cell line models. Three-dimensional assays were performed at 250 nmol/L final drug concentration (see Materials and Methods). Compounds with a robust Z-score ≤1.65 were classified as hits. A, Venn diagram illustrating the number of hits common to three or four of the cell line groups indicated. B, Comparison of hits in palbociclib-sensitive MCF7 LTED and HCC1428 LTED breast cancer cell lines and their palbociclib-resistant (PalboR) derivatives. C, Comparison of the hits in the palbociclib-resistant cell lines MCF7 LTEDPalboR and HCC1428 LTEDPalboR.
Data from Targeting MTHFD2 to Exploit Cancer-Specific Metabolism and the DNA Damage Response
Authors: Ramos Louise , Henriksson Martin , Helleday Thomas , Green Alanna C.
Published: January 2024

Abstract
The one-carbon folate enzyme methylenetetrahydrofolate dehydrogenase/cyclohydrolase 2 (MTHFD2) is a promising therapeutic target in cancer. MTHFD2 is upregulated across numerous cancer types, promotes growth and metastasis of cancer, and correlates with poorer survival. Recent studies have developed small-molecule inhibitors to the isozymes MTHFD2 and MTHFD1 that show promise as anticancer agents through different mechanisms. This review discusses the current understanding of the function of MTHFD2 in cancer and the status of inhibitors for treating MTHFD2-overexpressing cancers.
Figure S7 from Metabolic Hallmarks for Purine Nucleotide Biosynthesis in Small Cell Lung Carcinoma
Authors: Tabata Sho , Umemura Shigeki , Narita Miyu , Udagawa Hibiki , Ishikawa Takamasa , Tsuboi Masahiro , Goto Koichi , Ishii Genichiro , Tsuchihara Katsuya , Ochiai Atsushi , Kobayashi Susumu S. , Soga Tomoyoshi , Makinoshima Hideki
Published: January 2024

Body weights of lometrexol-treated mice
Supplementary Figure 2 from Distinct microRNA Signature and Suppression of ZFP36L1 Define ASCL1-Positive Lung Adenocarcinoma
Authors: Enokido Takayoshi , Horie Masafumi , Yoshino Seiko , Suzuki Hiroshi I. , Matsuki Rei , Brunnström Hans , Micke Patrick , Nagase Takahide , Saito Akira , Miyashita Naoya
Published: January 2024

PCR analyses in VMRC-LCD cells following ASCL1 knockdown
Supplementary Figure 4 from RNF185 Control of COL3A1 Expression Limits Prostate Cancer Migration and Metastatic Potential
Authors: Van Espen Benjamin , Oo Htoo Zarni , Collins Colin , Fazli Ladan , Molinolo Alfredo , Yip Kevin , Murad Rabi , Gleave Martin , Ronai Ze'ev A.
Published: January 2024

S4. RT-qPCR validation of RNF185, COL3A1 and COL5A2 expression in RNF185 and COL3A1 KD PC3 cells.
Cortical Gray Matter Thickness and Volume Changes and Their Association with Memory Functions in Hyperthyroid Patients
Authors: Kumar Mukesh , Singh Sadhana , Modi Shilpi , Rana Poonam , D’souza Maria , Sekhri Tarun , Khushu Subash
Published: January 2024

Introduction: Hyperthyroidism, characterized by excessive thyroid hormone production, is a common endocrine disorder that affects various physiological processes, including brain function. Recent advancements in neuroimaging techniques have enabled researchers to investigate structural alterations in the brain associated with hyperthyroidism. This study aimed to examine regional cortical thickness and cortical volume differences across the brain between hyperthyroid patients and control subjects. Methods: We examined localized cortical thicknesses and volumes in 34 hyperthyroid patients and 35 control subjects with high-resolution T1-weighted images using FreeSurfer software and assessed group differences with analysis of covariance (covariates: age, sex, education, and total intracranial volume). Spearman and partial correlations were performed between clinical variables and cortical thicknesses/volumes and between neuropsychological scores and cortical thicknesses/volumes, respectively. Results: Hyperthyroid patients exhibited significantly increased cortical thickness in bilateral superior temporal and superior frontal gyri, along with higher cortical volumes in various regions, including the right superior temporal gyrus, right superior parietal gyrus, right rostral and caudal middle frontal gyrus, and left superior frontal gyrus. Notably, thyroid hormones (fT3, fT4) correlated positively with cortical thicknesses and volumes in the superior temporal gyrus and superior frontal gyrus. Additionally, recognition memory scores negatively correlated with the right superior temporal gyrus and right superior frontal gyrus cortical thickness. Conclusion: The observed cortical thickening and increased cortical volume in specific brain areas provide new insights into the pathophysiological mechanism associated with brain impairment in hyperthyroidism.
Um percurso de ensino-aprendizagem retórico-interacionista a partir da obra Auto da Compadecida
Authors: Capitani Camila Alderete
Published: January 2024

Situada na dimensão das práticas sociais, a argumentação é uma atividade humana não coerciva que se enquadra no domínio da controvérsia, da polêmica e conserva o diálogo como sua matriz relacional. Seu ensino amplia a competência argumentativa do discente, composta pelas capacidades de dialogar, pensar, optar e comprometer-se, essenciais à formação do cidadão, segundo Grácio (2016). O espaço escolar torna-se, em vista disso, apropriado à promoção de práticas docentes esteadas em conhecimentos teórico-práticos que favoreçam o planejamento de aulas voltadas a esse fim. O presente artigo instala-se, portanto, neste contexto, e visa a responder como uma proposta didática retórico-interacionista baseada na obra Auto da Compadecida poderia ser desenvolvida em sala de aula a fim de criar situações de ensino-aprendizagem que viabilizem a ampliação das competências argumentativas dos discentes no ensino básico. A obra Auto da Compadecida é apropriada a tal intento porque João Grilo corporifica o poder do discurso persuasivo e revela toda sua competência argumentativa ao lutar pela própria vida contra o cangaceiro Severino no episódio da gaita benta.
O ensino da escrita-argumentativa voltada para a redação do Enem no canal digital do Youtube Luma e Ponto: textualidades seriadas e discurso
Authors: Leandro Michel Luís da Cruz Ramos , Pacífico Soraya Maria Romano
Published: January 2024

O objetivo deste artigo é analisar algumas playlists do canal do Youtube Luma e Ponto e, também, um dos vídeos dessas playlists intitulado “Como escrever redação mais rápido”, a fim de interpretar de que modo esse site de compartilhamento produz significação, materializada por uma textualidade em série (Dias, 2019), transformando o olhar em trabalho (Bucci, 2021). Para isso, utilizou-se o referencial teórico da Análise de Discurso materialista, a partir do corpus selecionado, para fundamentar nossa interpretação de como a escrita-argumentativa, em especial, a redação do Enem, é discursivizada pelo sujeito-youtuber, sabendo que é na articulação da língua com a história que o discurso se materializa. Desse modo, observou-se que a organização das playlists do canal analisado leva a uma formação discursiva que sustenta a redação do Enem no ideário da técnica/modelo/rapidez em que a escrita é tida como mercadoria e o ensino se configura como capacitação (Orlandi, 2017), impedindo que a argumentação seja reconhecida como prática de linguagem (Piris, 2020) e direito (Pacífico, 2016).
A contribuição da argumentação para o letramento matemático de alunos do 1º ano do ensino fundamental
Authors: Oliveira Rosemeire da Silva Rio de , Sales Antonio
Published: January 2024

O presente estudo discute argumentação e seu uso no ensino da Matemática, para com alunos do 1º ano do Ensino Fundamental. Procurou-se responder à seguinte indagação: “o uso da argumentação matemática pode contribuir na aprendizagem dos alunos, tanto da matemática quanto da argumentação?”. A metodologia consistiu em utilizar a argumentação para analisar a sua influência na alfabetização matemática. Desenvolveu-se parte da pesquisa em um período de 60 dias, com foco nos estudos dos números em diversos contextos, propondo momentos de diálogos, discussões e reflexões por meio dos questionamentos feitos pela professora, instigando e analisando a expressão oral dos alunos durante o estudo dos conteúdos. Diante disso, foi possível observar nos relatos dos alunos uma maior interação no diálogo com a professora e com os colegas, a reorganização das ideias, após ouvir outras opiniões, e um pensamento racional dos alunos que indicava uma compreensão do conceito matemático em estudo.
Competencias de liderazgo intermedio para promover la argumentación en el aula de matemáticas
Authors: Solar Horacio , Peña-Rincón Pilar , Ortiz Andrés
Published: January 2024

Para fortalecer el desarrollo profesional docente, se requieren propuestas formativas de carácter colaborativo, que consideren competencias de liderazgo intermedio para monitorear, retroalimentar y modelar la práctica. En este artículo, se presenta una experiencia de formación dirigida a 27 líderes intermedios de 11 establecimientos educativos, en que se utiliza el modelo formativo “Mejoramiento de la Experiencia Docente” (MED) para que acompañen a docentes en el desarrollo de la argumentación en el aula de matemáticas. Mediante el análisis de esta experiencia se muestra de qué manera características y etapas del MED tales como problematizar la práctica del profesor, generar conflicto cognitivo en el docente, suscitar las ideas de los profesores y promover que los docentes analicen evidencias en el aula se relaciona con las tres competencias de un líder intermedio para monitorear, retroalimentar y modelar prácticas.
Formação de professores com foco no trabalho com a argumentação no ensino fundamental
Authors: Azevedo Isabel Cristina Michelan de , Santos Maristela Felix dos
Published: January 2024

O dinamismo das práticas de linguagem na vida e na escola exige dos professores contínua atualização do letramento docente. Assim, decidiu-se por uma modalidade de formação continuada de professores que possa complementar as lacunas observadas em cursos de Pedagogia e de Letras na formação inicial, desenvolvida no âmbito do projeto ENARE (Ensino de Argumentação na Escola), um projeto extensionista realizado em parceria com secretarias municipais de educação. Por assumir a argumentação como um processo interacional, complexo, multidimensional e discursivo, busca-se discutir as características de práticas pedagógicas que podem promover pontes entre os usos sociais da argumentação. Os resultados indicam que os professores: i. qualificam as ações quando partem das referências culturais dos estudantes implicados no processo de ensino-aprendizagem; ii. associam o processo formativo aos saberes docentes subjetivos, culturais e profissionais; iii. articulam a formação continuada à partilha de experiências quando isso é favorecido; iv. têm no diálogo e no estudo conceitual as bases para a construção de conhecimentos.
Blood Pressure Trajectories and Outcomes After Endovascular Thrombectomy for Acute Ischemic Stroke
Authors: Katsanos Aristeidis H. , Joundi Raed A. , Palaiodimou Lina , Ahmed Niaz , Kim Joon-Tae , Goyal Nitin , Maier Ilko L. , de Havenon Adam , Anadani Mohammad , Matusevicius Marius , Mistry Eva A. , Khatri Pooja , Arthur Adam S. , Sarraj Amrou , Yaghi Shadi , Shoamanesh Ashkan , Catanese Luciana , Psychogios Marios-Nikos , Tsioufis Konstantinos , Malhotra Konark , Spiotta Alejandro M. , Sandset Else Charlotte , Alexandrov Andrei V. , Petersen Nils H. , Tsivgoulis Georgios
Published: January 2024

BACKGROUND:

Data on systolic blood pressure (SBP) trajectories in the first 24 hours after endovascular thrombectomy (EVT) in acute ischemic stroke are limited. We sought to identify these trajectories and their relationship to outcomes.

METHODS:

We combined individual-level data from 5 studies of patients with acute ischemic stroke who underwent EVT and had individual blood pressure values after the end of the procedure. We used group-based trajectory analysis to identify the number and shape of SBP trajectories post-EVT. We used mixed effects regression models to identify associations between trajectory groups and outcomes adjusting for potential confounders and reported the respective adjusted odds ratios (aORs) and common odds ratios.

RESULTS:

There were 2640 total patients with acute ischemic stroke included in the analysis. The most parsimonious model identified 4 distinct SBP trajectories, that is, general directional patterns after repeated SBP measurements: high, moderate-high, moderate, and low. Patients in the higher blood pressure trajectory groups were older, had a higher prevalence of vascular risk factors, presented with more severe stroke syndromes, and were less likely to achieve successful recanalization after the EVT. In the adjusted analyses, only patients in the high-SBP trajectory were found to have significantly higher odds of early neurological deterioration (aOR, 1.84 [95% CI, 1.20–2.82]), intracranial hemorrhage (aOR, 1.84 [95% CI, 1.31–2.59]), mortality (aOR, 1.75 [95% CI, 1.21–2.53), death or disability (aOR, 1.63 [95% CI, 1.15–2.31]), and worse functional outcomes (adjusted common odds ratio,1.92 [95% CI, 1.47–2.50]).

CONCLUSIONS:

Patients follow distinct SBP trajectories in the first 24 hours after an EVT. Persistently elevated SBP after the procedure is associated with unfavorable short-term and long-term outcomes.
New species and record of Diplosmittia Sæther, 1981 (Diptera: Chironomidae, Orthocladiinae) from Brazil and Colombia
Authors: DANTAS GALILEU P.S. , AMAT EDUARDO , HAMADA NEUSA
Published: January 2024

Chironomidae is a diverse Diptera family found worldwide. The genus Diplosmittia Sæther, 1981, currently with 11 valid species, has been found exclusively in the New World, mainly in the Caribbean and in the northern parts of South America; only three species are recorded from Brazil and none from Colombia so far. In the present study a new species of Diplosmittia is described and illustrated based on material collected in northeastern Brazil. It appears to be most closely related to Diplosmittia beluina Andersen, 1996, but can be distinguished by morphological differences in the virga and gonostylus. Diplosmittia harrisoni Sæther, 1981 is documented for the first time from Colombia, and D. carinata Sæther, 1985 is formally placed as a junior synonym of D. harrisoni. In addition, an update identification key to all known species of the genus has been provide.
Optimized Allogenic Decellularized Meniscal Scaffold Modified by Collagen Affinity Stromal Cell–Derived Factor SDF1α for Meniscal Regeneration: A 6- and 12-Week Animal Study in a Rabbit Model
Authors: Zhang Tao , Shi Xin , Li Muzhi , Hu Jianzhong , Lu Hongbin
Published: January 2024

Background:

Total meniscectomy for treating massive meniscal tears may lead to joint instability, cartilage degeneration, and even progressive osteoarthritis. The meniscal substitution strategies for advancing reconstruction of the meniscus deserve further investigation.

Hypothesis:

A decellularized meniscal scaffold (DMS) modified with collagen affinity stromal cell–derived factor (C-SDF1α) may facilitate meniscal regeneration and protect cartilage from abrasion.

Study Design:

Controlled laboratory study.

Methods:

The authors first modified DMS with C-SDF1α to fabricate a new meniscal graft (DMS-CBD [collagen-binding domain]). Second, they performed in vitro studies to evaluate the release dynamics, biocompatibility, and differentiation inducibility (osteogenic, chondrogenic, and tenogenic differentiation) on human bone marrow mesenchymal stem cells. Using in vivo studies, they subjected rabbits that received medial meniscectomy to a transplantation procedure to implement their meniscal graft. At postoperative weeks 6 and 12, the meniscal regeneration outcomes and chondroprotective efficacy of the new meniscal graft were evaluated by macroscopic observation, histology, micromechanics, and immunohistochemistry tests.

Results:

In in vitro studies, the optimized DMS-CBD graft showed notable biocompatibility, releasing efficiency, and chondrogenic inducibility. In in vivo studies, the implanted DMS-CBD graft after total meniscectomy promoted the migration of cells and extracellular matrix deposition in transplantation and further facilitated meniscal regeneration and protected articular cartilage from degeneration.

Conclusion:

The new meniscal graft (DMS-CBD) accelerated extracellular matrix deposition and meniscal regeneration and protected articular cartilage from degeneration.

Clinical Relevance:

The results demonstrate that the DMS-CBD graft can serve as a potential meniscal substitution after meniscectomy.
Age-, season- and gender-specific reference intervals of serum 25-hydroxyvitamin D3 for healthy children (0 ~ 18 years old) in Nanning area of China
Authors: Zhou Dong-yi , Wei Shang-mou , Zhu Chun-ling , Wei Yu-hong , Wang Xiao-mei , Yi Li-ling , Yang Si-tao , Peng Qi-liu
Published: January 2024

Establishing specific reference intervals (RIs) of serum 25-hydroxyvitamin D3 [25(OH)D] for children is essential for improving the accuracy of diagnosis and prognosis monitoring of diseases such as rickets and growth retardation. The study including 6,627 healthy children was conducted to establish specific RIs of 25(OH)D for children in Nanning area of China. The results showed that there were statistically significant differences among age, season, and gender of serum 25(OH)D levels, and the age-specific RIs of serum 25(OH)D were 20.3 ~ 53.6 ng/mL for 0 ~  ≤ 1 year and 18.9 ~ 49.6 ng/mL for 2 ~  ≤ 3 years. The age-, season-specific RIs of serum 25(OH)D for 4 ~  ≤ 6 years in spring–summer and autumn–winter were 15.8 ~ 42.6 ng/mL and 15.2 ~ 37.7 ng/mL, respectively. The age-, gender-specific RIs of serum 25(OH)D for 7 ~  ≤ 18 years for males and females were 12.1 ~ 36.1 ng/mL and 10.8 ~ 35.3 ng/mL, respectively. This study successfully established the RIs of serum 25(OH)D, which may help to improve disease diagnosis and monitoring for children in the Nanning area of China.
GCNFORMER: graph convolutional network and transformer for predicting lncRNA-disease associations
Authors: Yao Dengju , Li Bailin , Zhan Xiaojuan , Zhan Xiaorong , Yu Liyang
Published: January 2024

Background

A growing body of researches indicate that the disrupted expression of long non-coding RNA (lncRNA) is linked to a range of human disorders. Therefore, the effective prediction of lncRNA-disease association (LDA) can not only suggest solutions to diagnose a condition but also save significant time and labor costs.

Method

In this work, we proposed a novel LDA predicting algorithm based on graph convolutional network and transformer, named GCNFORMER. Firstly, we integrated the intraclass similarity and interclass connections between miRNAs, lncRNAs and diseases, and built a graph adjacency matrix. Secondly, to completely obtain the features between various nodes, we employed a graph convolutional network for feature extraction. Finally, to obtain the global dependencies between inputs and outputs, we used a transformer encoder with a multiheaded attention mechanism to forecast lncRNA-disease associations.

Results

The results of fivefold cross-validation experiment on the public dataset revealed that the AUC and AUPR of GCNFORMER achieved 0.9739 and 0.9812, respectively. We compared GCNFORMER with six advanced LDA prediction models, and the results indicated its superiority over the other six models. Furthermore, GCNFORMER's effectiveness in predicting potential LDAs is underscored by case studies on breast cancer, colon cancer and lung cancer.

Conclusions

The combination of graph convolutional network and transformer can effectively improve the performance of LDA prediction model and promote the in-depth development of this research filed.
Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs
Authors: Freitas Felipe André Oliveira , Brito Luiz F. , Fanalli Simara Larissa , Gonçales Janaína Lustosa , da Silva Bruna Pereira Martins , Durval Mariah Castro , Ciconello Fernanda Nery , de Oliveira Camila Sabino , Nascimento Lucas Echevarria , Gervásio Izally Carvalho , Gomes Julia Dezen , Moreira Gabriel Costa Monteiro , Silva-Vignato Bárbara , Coutinho Luiz Lehmann , de Almeida Vivian Vezzoni , Cesar Aline Silva Mello
Published: January 2024

Background

Mapping expression quantitative trait loci (eQTLs) in skeletal muscle tissue in pigs is crucial for understanding the relationship between genetic variation and phenotypic expression of carcass traits in meat animals. Therefore, the primary objective of this study was to evaluate the impact of different sets of single nucleotide polymorphisms (SNP), including scenarios removing SNPs pruned for linkage disequilibrium (LD) and SNPs derived from SNP chip arrays and RNA-seq data from liver, brain, and skeletal muscle tissues, on the identification of eQTLs in theLongissimus lumborumtissue, associated with carcass and body composition traits in Large White pigs. The SNPs identified from muscle mRNA were combined with SNPs identified in the brain and liver tissue transcriptomes, as well as SNPs from the GGP Porcine 50 K SNP chip array. Cis- and trans-eQTLs were identified based on the skeletal muscle gene expression level, followed by functional genomic analyses and statistical associations with carcass and body composition traits in Large White pigs.

Results

The number of cis- and trans-eQTLs identified across different sets of SNPs (scenarios) ranged from 261 to 2,539 and from 29 to 13,721, respectively. Furthermore, 6,180 genes were modulated by eQTLs in at least one of the scenarios evaluated. The eQTLs identified were not significantly associated with carcass and body composition traits but were significantly enriched for many traits in the “Meat and Carcass” type QTL. The scenarios with the highest number of cis- (n = 304) and trans- (n = 5,993) modulated genes were the unpruned and LD-pruned SNP set scenarios identified from the muscle transcriptome. These genes include 84 transcription factor coding genes.

Conclusions

After LD pruning, the set of SNPs identified based on the transcriptome of the skeletal muscle tissue of pigs resulted in the highest number of genes modulated by eQTLs. Most eQTLs are of the trans type and are associated with genes influencing complex traits in pigs, such as transcription factors and enhancers. Furthermore, the incorporation of SNPs from other genomic regions to the set of SNPs identified in the porcine skeletal muscle transcriptome contributed to the identification of eQTLs that had not been identified based on the porcine skeletal muscle transcriptome alone.
Single-cell and transcriptomic analyses reveal the influence of diabetes on ovarian cancer
Authors: Zhao Zhihao , Wang Qilin , Zhao Fang , Ma Junnan , Sui Xue , Choe Hyok Chol , Chen Peng , Gao Xue , Zhang Lin
Published: January 2024

Background

There has been a significant surge in the global prevalence of diabetes mellitus (DM), which increases the susceptibility of individuals to ovarian cancer (OC). However, the relationship between DM and OC remains largely unexplored. The objective of this study is to provide preliminary insights into the shared molecular regulatory mechanisms and potential biomarkers between DM and OC.

Methods

Multiple datasets from the GEO database were utilized for bioinformatics analysis. Single cell datasets from the GEO database were analysed. Subsequently, immune cell infiltration analysis was performed on mRNA expression data. The intersection of these datasets yielded a set of common genes associated with both OC and DM. Using these overlapping genes and Cytoscape, a protein‒protein interaction (PPI) network was constructed, and 10 core targets were selected. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were then conducted on these core targets. Additionally, advanced bioinformatics analyses were conducted to construct a TF-mRNA-miRNA coregulatory network based on identified core targets. Furthermore, immunohistochemistry staining (IHC) and real-time quantitative PCR (RT-qPCR) were employed for the validation of the expression and biological functions of core proteins, including HSPAA1, HSPA8, SOD1, and transcription factors SREBF2 and GTAT2, in ovarian tumors.

Results

The immune cell infiltration analysis based on mRNA expression data for both DM and OC, as well as analysis using single-cell datasets, reveals significant differences in mononuclear cell levels. By intersecting the single-cell datasets, a total of 119 targets related to mononuclear cells in both OC and DM were identified. PPI network analysis further identified 10 hub genesincludingHSP90AA1, HSPA8, SNRPD2, UBA52, SOD1, RPL13A, RPSA, ITGAM, PPP1CC, and PSMA5, as potential targets of OC and DM. Enrichment analysis indicated that these genes are primarily associated with neutrophil degranulation, GDP-dissociation inhibitor activity, and the IL-17 signaling pathway, suggesting their involvement in the regulation of the tumor microenvironment. Furthermore, the TF-gene and miRNA-gene regulatory networks were validated using NetworkAnalyst. The identified TFs included SREBF2, GATA2, and SRF, while the miRNAs included miR-320a, miR-378a-3p, and miR-26a-5p. Simultaneously, IHC and RT-qPCR reveal differential expression of core targets in ovarian tumors after the onset of diabetes. RT-qPCR further revealed that SREBF2 and GATA2 may influence the expression of core proteins, including HSP90AA1, HSPA8, and SOD1.

Conclusion

This study revealed the shared gene interaction network between OC and DM and predicted the TFs and miRNAs associated with core genes in monocytes. Our research findings contribute to identifying potential biological mechanisms underlying the relationship between OC and DM.
Inferring single-cell copy number profiles through cross-cell segmentation of read counts
Authors: Liu Furui , Shi Fangyuan , Yu Zhenhua
Published: January 2024

Background

Copy number alteration (CNA) is one of the major genomic variations that frequently occur in cancers, and accurate inference of CNAs is essential for unmasking intra-tumor heterogeneity (ITH) and tumor evolutionary history. Single-cell DNA sequencing (scDNA-seq) makes it convenient to profile CNAs at single-cell resolution, and thus aids in better characterization of ITH. Despite that several computational methods have been proposed to decipher single-cell CNAs, their performance is limited in either breakpoint detection or copy number estimation due to the high dimensionality and noisy nature of read counts data.

Results

By treating breakpoint detection as a process to segment high dimensional read count sequence, we develop a novel method called DeepCNA for cross-cell segmentation of read count sequence and per-cell inference of CNAs. To cope with the difficulty of segmentation, an autoencoder (AE) network is employed in DeepCNA to project the original data into a low-dimensional space, where the breakpoints can be efficiently detected along each latent dimension and further merged to obtain the final breakpoints. Unlike the existing methods that manually calculate certain statistics of read counts to find breakpoints, the AE model makes it convenient to automatically learn the representations. Based on the inferred breakpoints, we employ a mixture model to predict copy numbers of segments for each cell, and leverage expectation–maximization algorithm to efficiently estimate cell ploidy by exploring the most abundant copy number state. Benchmarking results on simulated and real data demonstrate our method is able to accurately infer breakpoints as well as absolute copy numbers and surpasses the existing methods under different test conditions. DeepCNA can be accessed at: https://github.com/zhyu-lab/deepcna.

Conclusions

Profiling single-cell CNAs based on deep learning is becoming a new paradigm of scDNA-seq data analysis, and DeepCNA is an enhancement to the current arsenal of computational methods for investigating cancer genomics.
Genomic evaluation for breeding and genetic management in Cordia africana, a multipurpose tropical tree species
Authors: Ousmael Kedra M. , Cappa Eduardo P. , Hansen Jon K. , Hendre Prasad , Hansen Ole K.
Published: January 2024

Background

Planting tested forest reproductive material is crucial to ensure the increased resilience of intensively managed productive stands for timber and wood product markets under climate change scenarios. Single-step Genomic Best Linear Unbiased Prediction (ssGBLUP) analysis is a cost-effective option for using genomic tools to enhance the accuracy of predicted breeding values and genetic parameter estimation in forest tree species. Here, we tested the efficiency of ssGBLUP in a tropical multipurpose tree species,Cordia africana,by partial population genotyping. A total of 8070 trees from three breeding seedling orchards (BSOs) were phenotyped for height. We genotyped 6.1% of the phenotyped individuals with 4373 single nucleotide polymorphisms. The results of ssGBLUP were compared with pedigree-based best linear unbiased prediction (ABLUP) and genomic best linear unbiased prediction (GBLUP), based on genetic parameters, theoretical accuracy of breeding values, selection candidate ranking, genetic gain, and predictive accuracy and prediction bias.

Results

Genotyping a subset of the study population provided insights into the level of relatedness in BSOs, allowing better genetic management. Due to the inbreeding detected within the genotyped provenances, we estimated genetic parameters both with and without accounting for inbreeding. The ssGBLUP model showed improved performance in terms of additive genetic variance and theoretical breeding value accuracy. Similarly, ssGBLUP showed improved predictive accuracy and lower bias than the pedigree-based relationship matrix (ABLUP).

Conclusions

This study ofC. africana, a species in decline due to deforestation and selective logging, revealed inbreeding depression. The provenance exhibiting the highest level of inbreeding had the poorest overall performance. The use of different relationship matrices and accounting for inbreeding did not substantially affect the ranking of candidate individuals. This is the first study of this approach in a tropical multipurpose tree species, and the analysed BSOs represent the primary effort to breedC. africana.
A chromosome-level genome assembly of the Rhus gall aphid Schlechtendalia chinensis provides insight into the endogenization of Parvovirus-like DNA sequences
Authors: Ahmad Aftab , von Dohlen Carol , Ren Zhumei
Published: January 2024

The Rhus gall aphid, Schlechtendalia chinensis, feeds on its primary host plant Rhus chinensis to induce galls, which have economic importance in medicines and the food industry. Rhus gall aphids have a unique life cycle and are economically beneficial but there is huge gap in genomic information about this group of aphids. Schlechtendalia chinensis induces rich-tannin galls on its host plant and is emerging as a model organism for both commercial applications and applied research in the context of gall production by insects. Here, we generated a high-quality chromosome-level assembly for the S. chinensis genome, enabling the comparison between S. chinensis and non-galling aphids. The final genome assembly is 344.59 Mb with 91.71% of the assembled sequences anchored into 13 chromosomes. We predicted 15,013 genes, of which 14,582 (97.13%) coding genes were annotated, and 99% of the predicted genes were anchored to the 13 chromosomes. This assembly reveals the endogenization of parvovirus-related DNA sequences (PRDs) in the S. chinensis genome, which could play a role in environmental adaptations. We demonstrated the characterization and classification of cytochrome P450s in the genome assembly, which are functionally crucial for sap-feeding insects and have roles in detoxification and insecticide resistance. This genome assembly also revealed the whole genome duplication events in S. chinensis, which can be considered in comparative evolutionary analysis. Our work represents a reference genome for gall-forming aphids that could be used for comparative genomic studies between galling and non-galling aphids and provides the first insight into the endogenization of PRDs in the genome of galling aphids. It also provides novel genetic information for future research on gall-formation and insect-plant interactions.
Genome-wide association study of agronomic traits related to nitrogen use efficiency in Henan wheat
Authors: Zhang Zaicheng , Peng Chaojun , Xu Weigang , Li Yan , Qi Xueli , Zhao Mingzhong
Published: January 2024

Background

Nitrogen use efficiency (NUE) is closely related to crop yield and nitrogen fertilizer application rate. Although NUE is susceptible to environments, quantitative trait nucleotides (QTNs) for NUE in wheat germplasm populations have been rarely reported in genome-wide associated study.

Results

In this study, 244 wheat accessions were phenotyped by three NUE-related traits in three environments and genotyped by 203,224 SNPs. All the phenotypes for each trait were used to associate with all the genotypes of these SNP markers for identifying QTNs and QTN-by-environment interactions via 3VmrMLM. Among 279 QTNs and one QTN-by-environment interaction for low nitrogen tolerance, 33 were stably identified, especially, one large QTN (r2 > 10%), qPHR3A.2, was newly identified for plant height ratio in one environment and multi-environment joint analysis. Among 52 genes around qPHR3A.2, four genes (TraesCS3A01G101900, TraesCS3A01G102200, TraesCS3A01G104100, and TraesCS3A01G105400) were found to be differentially expressed in low-nitrogen-tolerant wheat genotypes, while TaCLH2 (TraesCS3A01G101900) was putatively involved in porphyrin metabolism in KEGG enrichment analyses.

Conclusions

This study identified valuable candidate gene for low-N-tolerant wheat breeding and provides new insights into the genetic basis of low N tolerance in wheat.
Comprehensive evaluation of morphological and physiological responses of seventeen Crassulaceae species to waterlogging and drainage under temperate monsoon climate
Authors: Zhang Jie , Song Feng , Xu Xiaolei , Xia Tiantian , Zhang Xu , Dong Li , Yin Dejie
Published: January 2024

Unpredictable rainfall frequently results in excess moisture, which is detrimental to the landscape because it interferes with the genetic, morphological, and physiological processes of plants, even though the majority of urban landscapes frequently experience moisture shortages. A study was conducted to analyze the effects of a 36-day waterlogging phase and a subsequent 12-day recovery period on the morpho-physiological responses of 17 Crassulaceae species with the goal of identifying those which were more tolerant of the conditions. Results revealed that waterlogging stress has an impact on all morpho-physiological parameters. Sensitive materials (S7, Hylotelephium telephium ‘Purple Emperor’ and S15, S. sexangulare) showed severe ornamental quality damage, mortality, decreases in total dry biomass, root-shoot ratio, and chlorophyll content, as well as higher MDA concentrations. Lower reductions in these parameters, along with improved antioxidant enzyme activities and greater recovery capabilities after drainage, were observed in the most tolerant materials S2 (H. spectabile ‘Brilliant’), S3 (H. spectabile ‘Carl’), and S5 (H. telephium ‘Autumn Joy’). Furthermore, with the exception of early death materials (S7 and S15), all materials showed varying intensities of adventitious root formation in response to waterlogging. The 17 species were divided into 4 clusters based on the comprehensive evaluation value. The first group included S1-S3, S5-S6, S8-S12, which were waterlogged tolerant with the highest values (0.63–0.82). S14 belongs to the intermediate waterlogging tolerant. S4, S13, S16, and S17 were clustered into the low waterlogging-tolerant group. S7 and S15 were the most susceptible to waterlogging. The survival and success of Crassulaceae species (especially, the first and second cluster), throughout this prolonged period of waterlogging (36 days) and recovery were attributed to a combination of physiological and morphological responses, indicating that they are an appealing species for the creation of rain gardens or obstructed drainage locations.