bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seq2Sat and SatAnalyzer toolkit: Towards comprehensive microsatellite genotyping from sequencing data
Authors: Liu Peng , Wilson Paul , Redquest Bridget , Keobouasone Sonesinh , Manseau Micheline 
Published: January 2024

AbstractAccurate and efficient microsatellite loci genotyping is an essential process in population genetics that is also used in various demographic analyses. Protocols for next‐generation sequencing of microsatellite loci enable high‐throughput and cross‐compatible allele scoring, common issues that are not addressed by conventional capillary‐based approaches. To improve this process, we have developed an all‐in‐one software, called Seq2Sat (sequence to microsatellite), in C++ to support automated microsatellite genotyping. It directly takes raw reads of microsatellite amplicons and conducts read quality control before inferring genotypes based on depth‐of‐read, read ratio, sequence composition and length. We have also developed a module for sex identification based on sex chromosome–specific locus amplicons. To allow for greater user access and complement autoscoring, we developed SatAnalyzer (microsatellite analyzer), a user‐friendly web‐based platform that conducts reads‐to‐report analyses by calling Seq2Sat for genotype autoscoring and produces interactive genotype graphs for manual editing. SatAnalyzer also allows users to troubleshoot multiplex optimization by analysing read quality and distribution across loci and samples in support of high‐quality library preparation. To evaluate its performance, we benchmarked our toolkit Seq2Sat/SatAnalyzer against a conventional capillary gel method and existing microsatellite genotyping software, MEGASAT, using two datasets. Results showed that SatAnalyzer can achieve >99.70% genotyping accuracy and Seq2Sat is ~5 times faster than MEGASAT despite many more informative tables and figures being generated. Seq2Sat and SatAnalyzer are freely available on github (https://github.com/ecogenomicscanada/Seq2Sat) and dockerhub (https://hub.docker.com/r/rocpengliu/satanalyzer).
Deciding which ‘developing’ country list to use: A practical guide
Authors: Farias Deborah Barros Leal 
Published: January 2024

AbstractResearchers, policymakers and organisations sometimes need to explicitly classify countries as ‘developing’ or ‘developed’. The problem is that there are too many possible solutions. This short piece explores the developing/developed binary from an empirical perspective. The goal is to provide practical advice for choosing which list to use. It compares seven lists frequently used as reference for this classification, all based on material from these international organisations: World Bank, International Monetary Fund, three separate United Nations lists, as well as membership to the Organization for Economic Cooperation and Development and the Group of 77. These lists are compared by focusing on four elements: Purpose, Numbers, Criteria and Stability. Then, it compares these lists by explicitly outlining how each one classifies all countries in the world, per region. The piece fills a crucial empirical gap for those using the binary development‐based division by providing practical and useful advice for their decision‐making process.
Implications of metabolism on multi‐systems healthy aging across the lifespan
Authors: Yao Shanshan , Colangelo Laura A. , Perry Andrew S. , Marron Megan M. , Yaffe Kristine , Sedaghat Sanaz , Lima Joao A. C. , Tian Qu , Clish Clary B. , Newman Anne B. , Shah Ravi V. , Murthy Venkatesh L. 
Published: January 2024

AbstractAging is increasingly thought to involve dysregulation of metabolism in multiple organ systems that culminate in decreased functional capacity and morbidity. Here, we seek to understand complex interactions among metabolism, aging, and systems‐wide phenotypes across the lifespan. Among 2469 adults (mean age 74.7 years; 38% Black) in the Health, Aging and Body Composition study we identified metabolic cross‐sectionally correlates across 20 multi‐dimensional aging‐related phenotypes spanning seven domains. We used LASSO‐PCA and bioinformatic techniques to summarize metabolome‐phenome relationships and derive metabolic scores, which were subsequently linked to healthy aging, mortality, and incident outcomes (cardiovascular disease, disability, dementia, and cancer) over 9 years. To clarify the relationship of metabolism in early adulthood to aging, we tested association of these metabolic scores with aging phenotypes/outcomes in 2320 participants (mean age 32.1, 44% Black) of the Coronary Artery Risk Development in Young Adults (CARDIA) study. We observed significant overlap in metabolic correlates across the seven aging domains, specifying pathways of mitochondrial/cellular energetics, host‐commensal metabolism, inflammation, and oxidative stress. Across four metabolic scores (body composition, mental‐physical performance, muscle strength, and physical activity), we found strong associations with healthy aging and incident outcomes, robust to adjustment for risk factors. Metabolic scores for participants four decades younger in CARDIA were related to incident cardiovascular, metabolic, and neurocognitive performance, as well as long‐term cardiovascular disease and mortality over three decades. Conserved metabolic states are strongly related to domain‐specific aging and outcomes over the life‐course relevant to energetics, host‐commensal interactions, and mechanisms of innate immunity.
Rapid response of nail psoriasis to secukinumab in patients with moderate to severe psoriasis after 12 weeks of treatment with a total of 24 weeks of follow‐up
Authors: Go Gang Min , Hong Yong Jun , Lee Hyun Ji , Kim Miri 
Published: January 2024

AbstractBackground/ObjectivesNail psoriasis, a subtype of psoriasis, can cause significant pain, disability, and reduced quality of life. Despite the established efficacy of anti‐IL17 secukinumab in improving skin psoriasis, there is a lack of clinical trials focusing on nail psoriasis as primary endpoint. This study aims to investigate the efficacy of secukinumab in treating nail psoriasis in patients with moderate to severe psoriasis.MethodsWe prospectively recruited patients newly diagnosed with moderate to severe psoriasis in single centre from January 2021 to January 2022 who were treated with secukinumab.ResultsA total of 16 patients consisting of 9 males and 7 females were included. Their mean age was 38.88 ± 10.29 years. They had an average initial Nail Psoriasis Severity Index (NAPSI) score of 45.06 ± 20.39 and an average NAPSI score at 12 weeks of 8.94 ± 13.50, showing a significant (p < 0.05) decrease of NAPSI score after 12 weeks of secukinumab treatment. After 24 weeks of treatment, NAPSI score was decreased to 5.12 ± 8.52.ConclusionSecukinumab rapidly improved nail psoriasis after 12 weeks of treatment, with further enhancement at 24 weeks, suggesting its potential as a potent therapeutic option for nail psoriasis.
Isolation and characterization of tannin‐degrading bacteria from the rumen of wild Hokkaido sika deer (Cervus nippon yezoensis)
Authors: Sawabe Yoshihiko , Yamano Hidehisa , Koike Satoshi , Kobayashi Yasuo 
Published: January 2024

AbstractWe isolated tannin‐degrading bacteria from the rumen of wild Hokkaido sika deer and characterized their phylogeny and tannase activity in relation to sample sources. The condensed tannin level was higher in all deer rumen samples (n = 20) than in forage‐fed cattle rumen samples (n = 6), whereas no hydrolyzable tannins were detected in any of the rumen samples. Rumen bacteria were enumerated on nonselective brain heart infusion (BHI) agar medium and then transferred onto tannic acid‐containing BHI agar plates to screen for bacteria only showing growth (tannin‐resistant bacteria) and those showing both growth and a clear zone (tannin‐degrading bacteria). Summer samples provided only tannin‐resistant bacteria, none of which showed tannin‐degrading activity. Although winter samples also provided tannin‐resistant bacteria, most isolates exhibited tannin‐degrading activity. A total of 70 isolates exhibiting tannin‐degrading activity were classified as Streptococcus bovis group based on 16S rRNA gene sequencing and further classified into two groups, either group A or group B. Group A consisted of isolates showing weak tannase activity, whereas group B included a majority of the isolates exhibiting high tannase activity. These results suggest that wild Hokkaido sika deer develop tannin‐degrading Streptococcus in the rumen during winter, which allows access to woody food materials rich in tannins.
A phase II study of ibrutinib in combination with ixazomib in patients with Waldenström macroglobulinaemia
Authors: Parrondo Ricardo D. , Dutta Navnita , LaPlant Betsy R. , Elliott Jamie , Fernandez Andre , Zimmerman Ashley , Cicco Gina , Han Bing , Heslop Keisha , Chapin Dustin , Sher Taimur , Roy Vivek , Rasheed Ahsan , Das Saurav , Chanan‐Khan Asher A. , Paulus Aneel , Ailawadhi Sikander 
Published: January 2024

SummaryThis phase II study evaluated time‐limited (24 cycles) treatment with ibrutinib and ixazomib in newly diagnosed (NDWM; n = 9) and relapsed/refractory (RRWM; n = 12) Waldenström macroglobulinaemia (WM). The overall response rate (ORR) was 76.2% (n = 16) in 21 evaluable patients with no patient achieving a complete response (CR). The median duration of treatment was 15.6 months, and after a median follow‐up time of 25.7 months, the median progression‐free survival (PFS) was 22.9 months. While the primary end‐point was not met (CR rate at any time) and 28.5% discontinued treatment due to toxicity, ibrutinib plus ixazomib led to a clinically meaningful ORR and PFS. Combined Bruton's tyrosine kinase (BTK) and proteasome inhibition merits further evaluation in WM.
Circular RNA circWNK1 inhibits the progression of gastric cancer via regulating the miR‐21‐3p/SMAD7 axis
Authors: Dai Ting , Qiu Shengkui , Gao Xuesong , Zhao Chengjin , Ge Zhenming , Yang Yanmei , Tang Chong , Feng Shichun 
Published: January 2024

AbstractGastric cancer (GC) is a highly aggressive malignancy with limited treatment options for advanced‐stage patients. Recent studies have highlighted the role of circular RNA (circRNA) as a novel regulator of cancer progression in various malignancies. However, the underlying mechanisms by which circRNA contributes to the development and progression of GC remain poorly understood. In this study, we utilized microarrays and real‐time quantitative polymerase chain reaction (qRT‐PCR) to identify and validate a downregulated circRNA, hsa_circ_0003251 (referred to as circWNK1), in paired GC and normal tissues. Through a series of in vitro and in vivo gain‐of‐function and loss‐of‐function assays, we demonstrated that circWNK1 exerts inhibitory effects on the proliferation, migration, invasion, and epithelial–mesenchymal transition (EMT) of GC cells. Additionally, we discovered that circWNK1 acts as a competitive endogenous RNA (ceRNA) for SMAD7 by sequestering miR‐21‐3p. Our findings were supported by comprehensive biological information analysis, as well as RNA pull‐down, luciferase reporter gene, and western blot assays. Notably, the downregulation of circWNK1 in GC cells resulted in reduced SMAD7 expression, subsequently activating the TGF‐β signaling pathway. Collectively, our study reveals that circWNK1 functions as a tumor suppressor in GC by regulating the miR‐21‐3p/SMAD7‐mediated TGF‐β signaling pathway. Furthermore, circWNK1 holds promise as a potential biomarker for the diagnosis and treatment of GC.
Inhibition of O6‐methylguanine‐DNA‐methyltransferase (MGMT) by lomeguatrib reduces multiple myeloma cell viability and impairs DNA repair in MGMT‐proficient cells
Authors: Akcora‐Yildiz Dilara , Ozkan Tulin , Cetintav Bekir , Yukselten Yunus , Calis Seyma , Sevim‐Nalkiran Hatice , Turkel Nezaket , Gunduz Mehmet , Ozen Mehmet , Beksac Meral , Sunguroglu Asuman 
Published: January 2024

AbstractThe function of direct DNA damage repair protein, namely MGMT in MM, and the impact of MGMT on melphalan treatment remains unclear. We showed a significantly higher MGMT mRNA expression in CD138+ myeloma cells than in matched CD138‐nontumorigenic cells derived from newly diagnosed and relapsed/refractory MM patients using qPCR. However, using gene expression databases, a similar expression of MGMT was observed during disease progression. MGMT depletion by its specific inhibitor lomeguatrib reduced myeloma cell viability, impaired S phase entry and DNA repair, and increased DNA damage and apoptosis. Apoptosis and DNA damage were further elevated by combined treatment with lomeguatrib and melphalan in RPMI 8226 cells. This is the first study demonstrating MGMT inhibition enhances DNA damage‐induced apoptosis and melphalan cytotoxicity in MGMT‐proficient MM cells and suggesting using lomeguatrib might have clinical importance in treating MM and overcoming melphalan resistance in MGMT‐proficient patients.
Further description of two individuals with de novo p.(Glu127Lys) missense variant in the ASCL1 gene
Authors: Malbos Marlène , Wakeling Emma , Gautier Thierry , Boespflug‐Tanguy Odile , Busby Louise , Taylor‐Miller Tashunka , Dudoignon Benjamin , Bokov Plamen , Govin Jérôme , Grisval Margot , Rega Adélaïde , Mourot De Rougemont Marie‐Gabrielle , Aubriot‐Lorton Marie‐Hélène , Darmency Véronique , Bensignor Candace , Houzel Anne , Huet Frédéric , Denommé‐Pichon Anne‐Sophie , Delanne Julian , Tran Mau‐Them Frédéric , Bruel Ange‐Line , Safraou Hana , Nambot Sophie , Garde Aurore , Philippe Christophe , Duffourd Yannis , Vitobello Antonio , Faivre Laurence , Thauvin‐Robinet Christel 
Published: January 2024

AbstractAchaete‐Scute Family basic‐helix–loop–helix (bHLH) Transcription Factor 1 (ASCL1) is a proneural transcription factor involved in neuron development in the central and peripheral nervous system. While initially suspected to contribute to congenital central hypoventilation syndrome‐1 (CCHS) with or without Hirschsprung disease (HSCR) in three individuals, its implication was ruled out by the presence, in one of the individuals, of a Paired‐like homeobox 2B (PHOX2B) heterozygous polyalanine expansion variant, known to cause CCHS. We report two additional unrelated individuals sharing the same sporadic ASCL1 p.(Glu127Lys) missense variant in the bHLH domain and a common phenotype with short‐segment HSCR, signs of dysautonomia, and developmental delay. One has also mild CCHS without polyalanine expansion in PHOX2B, compatible with the diagnosis of Haddad syndrome. Furthermore, missense variants with homologous position in the same bHLH domain in other genes are known to cause human diseases. The description of additional individuals carrying the same variant and similar phenotype, as well as targeted functional studies, would be interesting to further evaluate the role of ASCL1 in neurocristopathies.
Textile printing: An integrated view of processes, properties, and future prospects
Authors: Rainert Karine Thaise , de Oliveira Carlos Rafael Silva , Felipe Brenno Henrique Siva , Herpich Heiderose , Valle Rita de Cássia Siqueira Curto , Valle José Alexandre Borges 
Published: January 2024

AbstractTextile printing processes consist of the localised application of colour on textile substrates to obtain well‐defined designs and patterns. Currently, there are many textile printing techniques; however, the limitations and selectivity of these techniques still keep the printing method of rotary screen printing the most important and used among them. One of the advantages of rotary printing is its excellent application versatility, which can be used for any fabric and non‐wovens, fibre, or mixtures, with high production speed, quality, colour fastness, and definition. However, due to its high complexity, rotary printing requires great technical knowledge. Rotary printing requires specific application care depending on the fabric structure, fibrous composition, grammage, and type of intended effect. Regardless of the technique used, printed articles need to ensure that the colour remains attached to the substrate, either by direct dye–fibre or indirect pigment–binder–fibre bonding, to resist the conditions of use, that is, light, abrasion, stretching, and washing. The rise in recent publications reflects the search for economic and sustainable textile printing alternatives, focusing on screen printing variables. Based on this, this review aimed to present a comprehensive guide containing all the care and essential technical information for processes based on rotary printing.
Neurological assessment tool for screening infants during the first year after birth: The Brief‐Hammersmith Infant Neurological Examination
Authors: Romeo Domenico M. , Velli Chiara , Sini Francesca , Pede Elisa , Cicala Graziamaria , Cowan Frances M. , Ricci Daniela , Brogna Claudia , Mercuri Eugenio 
Published: January 2024

AbstractAimTo develop a short version of the original Hammersmith Infant Neurological Examination (HINE) to be used as a screening tool (Brief‐HINE) and to establish if the short examination maintains good accuracy and predictive power for detecting infants with cerebral palsy (CP).MethodEleven items were selected from the original HINE (‘visual response’; ‘trunk posture’; ‘movement quantity’; ‘movement quality’; ‘scarf sign’; ‘hip adductor angles’; ‘popliteal angle’; ‘pull to sit’; ‘lateral tilting’; ‘forward parachute reaction’; ‘tendon reflexes’) identifying those items previously found to be more predictive of CP in both low‐ and high‐risk infants. In order to establish the sensitivity of the new module, the selected items were applied to existing data, previously obtained using the full HINE at 3, 6, 9, and 12 months, in 228 infants with typical development at 2 years and in 82 infants who developed CP.ResultsBrief‐HINE scores showed good sensitivity and specificity, at each age of assessment, for detecting infants with CP. At 3 months, a score of less than 22 was associated with CP with a sensitivity of 0.88 and a specificity of 0.92; at 6, 9, and 12 months, the cut‐off scores were less than 25 (sensitivity 0.93; specificity 0.87), less than 27 (sensitivity 0.95; specificity 0.81), and less than 27 (sensitivity 1; specificity 0.86) respectively. The presence of more than one warning sign, or items that are not optimal for the age of assessment, imply the need for a full examination reassessment.InterpretationThese findings support the validity of the Brief‐HINE as a routine screening method and the possibility of its use in clinical practice.
Neo‐Confucianism and the rise of science and technology in Medieval China
Authors: Dong Baomin , Cheng Bowen 
Published: January 2024

AbstractThe Song dynasty (960–1279 A.D.) witnessed a surge of scientific and technological development, notably in mechanical engineering, metallurgy, shipbuilding and nautics, civil engineering, manufacturing, etc. At the same time, Neo‐Confucianism, which advocated ‘upholding heavenly principle and annihilating human desire’, flourished in Song time. The rise of Neo‐Confucianism as a conservative movement appeared fundamentally at odds with the splendid technological achievements in Medieval China. To address the question, we dismantle the notion of Neo‐Confucianism in the Song dynasty context by constructing the indices of the Neo‐Confucian spirit characterized by the pursuit of principle (li), broad learning, and scepticism on the basis of Song Confucian works recorded in the Records of Song and Yuan scholarship (Song Yuan xue an). Our results show that the popularity of Neo‐Confucianism facilitated the development of science and technology during the Song period. Using historical Confucian academy data compiled from several extensive surveys, we show that the vigorous development of the Confucian academies served as a channel to propagate the Neo‐Confucian spirit in a locality, thereby influencing the scientific and technological output of the Song era.
Sensitivity and specificity of Yubi‐wakka (finger‐ring) screening method for sarcopenia among older Thai adults
Authors: Lawongsa Kasidid , Srisuwan Patsri , Tejavanija Sirakarn , Gesakomol Kulachade 
Published: January 2024

AimThe aim of this study was to validate a Yubi‐wakka (finger‐ring) test to identify older adults at risk for sarcopenia. Generally, measurements of muscle mass are considered to be a gold standard for testing for sarcopenia; such measurements are typically attained using bioelectrical impedance analysis (BIA) or dual‐energy X‐ray absorptiometry (DXA). However, the Yubi‐wakka test is a simple assessment that can also be used to screen for sarcopenia.MethodsAn analytic cross‐sectional study was conducted to determine the sensitivity and specificity of the Yubi‐wakka test. The study cohort included 230 adults older than 60 years who had no disabilities or handicaps and who visited the outpatient department of Phramongkutklao Hospital. Each participant underwent the Yubi‐wakka test, a handgrip strength test, the 5‐chair stand test, and BIA. We analyzed the associations between the Yubi‐wakka test results and sarcopenia. The findings were compared with diagnoses that followed from the Asian Working Group for Sarcopenia 2019.ResultsThe test results were statistically associated with sarcopenia (“just fits” odds ratio [OR]: 8.55, 95% confidence interval [CI]: 3.29–22.18, and “smaller” OR: 10.73, 95% CI: 4.31–26.73, relative to “bigger”). The sensitivity and specificity of the Yubi‐wakka test in men were 85.7% and 71.2% (area under the curve [AUC]: 0.785, 95% CI: 0.618–0.952), respectively. For women, the sensitivity and specificity of the test were 87.5% and 80.8% (AUC: 0.842, 95% CI: 0.764–0.919), respectively.ConclusionsThe Yubi‐wakka test is a practical way of identifying the risk of sarcopenia among the elderly; it exhibits promising sensitivity and specificity. Geriatr Gerontol Int 2024; 24: 263–268.
MotherHack: Creative coding as an artist‐mother
Authors: Putnam EL 
Published: January 2024

AbstractEnmeshed in the materiality of caregiving, becoming a mother changes how one relates to the world and others. These changes involve how a mother as subject is defined by others through cultural and societal idealizations of motherhood and parenting norms, but also through the leaking boundaries between the mother and other subjects as she is attuned to the needs of caregiving. In this analysis, I consider maternal subjectivity in terms of working as an artist‐mother, defined as an artist who is also a mother and whose practice does not distinguish between these roles. In particular, I focus on the process of my development of a creative coding project, Emergent, during the COVID‐19 pandemic. Through this analysis of the process of developing Emergent, I attend to the questions of maternal subjectivity that arose through its production, drawing from the embodied experiences of working as an artist‐mother, in order to understand maternal subjectivity through the practice of computation. Here the work of producing art becomes the means of considering maternal subjectivity differently through embodied experience, as the labor affiliated with care‐giving is entangled with the process of art making.