bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiplexed RNA-FISH-guided Laser Capture Microdissection RNA Sequencing Improves Breast Cancer Molecular Subtyping, Prognostic Classification, and Predicts Response to Antibody Drug Conjugates
Authors: Paul Evan D. , Huraiová Barbora , Valková Natália , Birknerova Natalia , Gábrišová Daniela , Gubova Sona , Ignačáková Helena , Ondris Tomáš , Bendíková Silvia , Bíla Jarmila , Buranovská Katarína , Drobná Diana , Krchnakova Zuzana , Kryvokhyzha Maryna , Lovíšek Daniel , Mamoilyk Viktoriia , Mančíková Veronika , Vojtaššáková Nina , Ristová Michaela , Comino-Méndez Iñaki , Andrašina Igor , Morozov Pavel , Tuschl Thomas , Pareja Fresia , Čekan Pavol 
Published: December 2023

AbstractOn a retrospective cohort of 1,082 FFPE breast tumors, we demonstrated the analytical validity of a test using multiplexed RNA-FISH-guided laser capture microdissection (LCM) coupled with RNA-sequencing (mFISHseq), which showed 93% accuracy compared to immunohistochemistry. The combination of these technologies makes strides in i) precisely assessing tumor heterogeneity, ii) obtaining pure tumor samples using LCM to ensure accurate biomarker expression and multigene testing, and iii) providing thorough and granular data from whole transcriptome profiling. We also constructed a 293-gene intrinsic subtype classifier that performed equivalent to the research based PAM50 and AIMS classifiers. By combining three molecular classifiers for consensus subtyping, mFISHseq alleviated single sample discordance, provided near perfect concordance with other classifiers (κ > 0.85), and reclassified 30% of samples into different subtypes with prognostic implications. We also use a consensus approach to combine information from 4 multigene prognostic classifiers and clinical risk to characterize high, low, and ultra-low risk patients that relapse early (< 5 years), late (> 10 years), and rarely, respectively. Lastly, to identify potential patient subpopulations that may be responsive to treatments like antibody drug-conjugates (ADC), we curated a list of 92 genes and 110 gene signatures to interrogate their association with molecular subtype and overall survival. Many genes and gene signatures related to ADC processing (e.g., antigen/payload targets, endocytosis, and lysosome activity) were independent predictors of overall survival in multivariate Cox regression models, thus highlighting potential ADC treatment-responsive subgroups. To test this hypothesis, we constructed a unique 19-feature classifier using multivariate logistic regression with elastic net that predicted response to trastuzumab emtansine (T-DM1; AUC = 0.96) better than eitherERBB2mRNA or Her2 IHC alone in the T-DM1 arm of the I-SPY2 trial. This test was deployed in a research-use only format on 26 patients and revealed clinical insights into patient selection for novel therapies like ADCs and immunotherapies and de-escalation of adjuvant chemotherapy.
SARS-CoV-2 Infection is Associated with an Increase in New Diagnoses of Schizophrenia Spectrum and Psychotic Disorder: A Study Using the US National COVID Cohort Collaborative (N3C)
Authors: Rahman Asif , Russell Michael , Zheng Wanhong , Eckrich Daniel , Ahmed Imtiaz 
Published: December 2023

AbstractAmid the ongoing global repercussions of SARS-CoV-2, it’s crucial to comprehend its potential long-term psychiatric effects. Several recent studies have suggested a link between COVID-19 and subsequent mental health disorders. Our investigation joins this exploration, concentrating on Schizophrenia Spectrum and Psychotic Disorders (SSPD). Different from other studies, we took acute respiratory distress syndrome (ARDS) and COVID-19 lab negative cohorts as control groups to accurately gauge the impact of COVID-19 on SSPD. Data from 19,344,698 patients, sourced from the N3C Data Enclave platform, were methodically filtered to create propensity matched cohorts: ARDS (n = 222,337), COVID-positive (n = 219,264), and COVID-negative (n = 213,183). We systematically analyzed the hazard rate of new-onset SSPD across three distinct time intervals: 0-21 days, 22-90 days, and beyond 90 days post-infection. COVID-19 positive patients consistently exhibited a heightened hazard ratio (HR) across all intervals [0-21 days (HR: 4.6; CI: 3.7-5.7), 22-90 days (HR: 2.9; CI: 2.3 -3.8), beyond 90 days (HR: 1.7; CI: 1.5-1.)]. These are notably higher than both ARDS and COVID-19 lab-negative patients. Validations using various tests, including the Cochran Mantel Haenszel Test, Wald Test, and Log-rank Test confirmed these associations. Intriguingly, our data indicated that younger individuals face a heightened risk of SSPD after contracting COVID-19, a trend not observed in the ARDS and COVID-negative groups. These results, aligned with the known neurotropism of SARS-CoV-2 and earlier studies, accentuate the need for vigilant psychiatric assessment and support in the era of Long-COVID, especially among younger populations.
Socio-economic disparities and predictors of fertility among adolescents aged 15 to 19 in Zambia: Evidence from the Zambia demographic and health survey (2018)
Authors: Shumba Samson , Moonga Vanessa , Miyoba Thomas O. , Jere Stephen , Nkonde Jessy M. , Mumba Peter 
Published: December 2023

AbstractBackgroundAnnually, 12 million girls aged 15-19 give birth globally, with Africa hosting 19% of the youth aged 15-24. Zambia sees 29% of adolescents experiencing childbirth, with notable variations among age groups. Predictors of adolescent fertility include age, residential area, education, contraceptive use, and socioeconomic status. Studies emphasize increased health risks for adolescent mothers, including eclampsia and systemic infections, while infants face elevated risks such as low birth weight and severe neonatal conditions. Projections anticipate a continued rise in these trends by 2030.MethodThe analysis utilized the 2018 Zambia Demographic Health Survey (ZDHS). The association between dependent and independent variables was assessed using the Rao–Scott Chi-square test. Determinants of adolescent fertility were identified through a multilevel ordinal logistic regression conducted at a significance level of 5%. Graphs were generated using Excel, and the analysis was carried out using Stata version 14.2.ResultsA total of 3,112 adolescents were involved in the study, revealing that 75.88% had not given birth, 21.14% had one child, and 2.98% had at least two children. The findings revealed that education played a protective role, with adjusted odds ratios (AOR) of 0.47 (95% CI, 0.23 – 0.97), 0.21 (95% CI, 0.10 – 0.47), and 0.03 (95% CI, 0.00 – 0.54) for primary, secondary, and tertiary education, respectively. On the other hand, certain factors were associated with an elevated risk of fertility. These included the age of adolescents, educational attainment, marital status, wealth index, contraceptive use, exposure to family planning (FP) messages, being educated about FP at health facilities, and age at first sexual encounter. Among contextual factors, only community age at first birth was identified as a predictor of fertility, AOR, 1.59 (95% CI, 1.01 – 2.52).ConclusionThe study highlights sociodemographic disparities in adolescent fertility, emphasizing the need for targeted sexual reproductive health policies. Education protects against having more than one child, while marital status significantly influences fertility, particularly for married adolescents. The research provides valuable insights into the complex factors shaping adolescent fertility in Zambia, offering guidance for interventions and policies to support this vulnerable demographic.
Improved coherence measure for EEG-based speech tracking in hearing impaired listeners
Authors: Keding Oskar , Alickovic Emina , Skoglund Martin , Sandsten Maria 
Published: December 2023

AbstractIn the literature, auditory attention is explored through neural speech tracking, primarily entailing modeling and analyzing electroencephalography (EEG) responses to natural speech via linear filtering. Our study takes a novel approach, introducing an enhanced coherence estimation technique that employs multitapers to assess the strength of neural speech tracking. This enables effective discrimination between attended and ignored speech. To mitigate the impact of colored noise in EEG, we address two biases – overall coherence-level bias and spectral peak-shifting bias. In a listening study involving 32 participants with hearing impairment, tasked with attending to competing talkers in background noise, our coherence-based method effectively discerns EEG representations of attended and ignored speech. We comprehensively analyze frequency bands, individual frequencies, and EEG channels. Frequency bands of importance are shown to be delta, theta and alpha, as well as the central EEG channels. Lastly, we showcase coherence differences across different noise reduction settings implemented in hearing aids, underscoring our method’s potential to objectively assess auditory attention and enhance hearing aid efficacy.
Mesenchymal Wnts are required for morphogenetic movements of calvarial osteoblasts during apical expansion
Authors: Polsani Nikaya , Yung Theodora , Thomas Evan , Phung-Rojas Melissa , Gupta Isha , Denker Julie , Feng Xiaotian , Ibarra Beatriz , Hopyan Sevan , Atit Radhika P. 
Published: December 2023

ABSTRACTApical expansion of calvarial osteoblast progenitors from the cranial mesenchyme (CM) above the eye is integral for calvarial growth and enclosure of the brain. The cellular behaviors and signals underlying the morphogenetic process of calvarial expansion are unknown. During apical expansion, we found that mouse calvarial primordia have consistent cellular proliferation, density, and survival with complex tissue scale deformations, raising the possibility that morphogenetic movements underlie expansion. Time lapse light sheet imaging of mouse embryos revealed that calvarial progenitors intercalate in 3D to converge supraorbital arch mesenchyme mediolaterally and extend it apically. In contrast, progenitors located further apically exhibited protrusive and crawling activity. CM cells express non-canonical Wnt/Planar Cell Polarity (PCP) core components and calvarial osteoblasts are bidirectionally polarized. We found non-canonical ligand,Wnt5a-/-mutants have less dynamic cell rearrangements, protrusive activity, and a flattened head shape. Loss of cranial mesenchyme-restrictedWntless (CM-Wls),a gene required for secretion of all Wnt ligands, led to diminished apical expansion of OSX+calvarial osteoblasts in the frontal bone primordia in a non-cell autonomous manner without perturbing proliferation or survival. Calvarial osteoblast polarization, progressive cell elongation and enrichment for actin cytoskeleton protein along the baso-apical axis were dependent on CM-Wnts. Thus, CM-Wnts regulate cellular behaviors during calvarial morphogenesis and provide tissue level cues for efficient apical expansion of calvarial osteoblasts. These findings also offer potential insights into the etiologies of calvarial dysplasias.
Optimal capital structure with supplier market power
Authors: Cui Xue , Sarkar Sudipto , Zhang Chuanqian 
Published: December 2023

AbstractWe use a real‐option model to study the effect of input supplier's market power on a firm's capital structure, and identify the Nash equilibrium outcome (firm's investment and financing policies and its supplier's pricing policy). When its supplier has market power, the firm will reduce leverage ratio and delay investment. This can help explain why observed leverage ratios are lower than in traditional capital‐structure models (without supplier market power). Firm value can be increased by the vertical acquisition of the supplier, which would also result in a higher leverage ratio. This helps explain the observed increase in leverage ratios after acquisitions.
Corporate transparency among government suppliers: Implications for firm valuation
Authors: Esqueda Omar A. , Ngo Thanh N. 
Published: December 2023

AbstractCorporate transparency has a positive impact on firm valuation, as predicted by agency theory; however, the transparency of strategically important government suppliers is not rewarded with higher valuations as the market expects politically sensitive firms to be inherently more transparent. The association between transparency and valuation among politically sensitive firms is consistent with the political cost hypothesis. We address endogeneity concerns using propensity score matching, Heckman's self‐selection models and entropy balancing. Our findings offer novel insights, suggesting that the influence of transparency on corporate valuation varies with political sensitivity – a significant consideration for both finance professionals and scholars.
let‐7g sensitized liver cancer cells to 5‐fluorouracil by downregulating ABCC10 expression
Authors: Chen Yun , Zhang Bocheng , Zhong Cui , Zhou Yuqing , Xue Lei , Luo Chenhui , Yi Liang , Gong Qian , Long Ying 
Published: December 2023

AbstractPatients with advanced liver cancer may benefit from 5‐fluorouracil (5‐FU) therapy. However, most of them eventually faced drug resistance, resulting in a poor prognosis. The present study aims to explore the potential mechanism of let‐7g/ABCC10 axis in the regulation of 5‐FU resistance in liver cancer cells. Huh‐7 cells were used to construct 5‐FU resistant Huh‐7/4X cells. CCK8, flow cytometry, and TUNEL staining were used to detect the characterization of Huh‐7 cells and Huh‐7/4X cells. Double luciferase report, PCR, and western blot analyses were used to detect the regulatory effects between let‐7g and ABCC10. The levels of biomarkers related to cell cycle progression and apoptosis were detected by western blot assays. The role of let‐7g in 5‐FU sensitivity of liver cancer cells was evaluated in nude mice. Compared with LX‐2 cells, the expression of let‐7g was decreased in Hep3B, HepG2, Huh‐7, and SK‐Hep1 cells, with the lowest expression in Huh‐7 cells. The sensitivity of Huh‐7 cell to 5‐FU was positively correlated with let‐7g expression. Transfection of let‐7g mimics inhibited the viability of Huh‐7/4X cells by prolonging the G1 phase, with the downregulation of ABCC10, PCNA, Cyclin D1, and CDK4. Meanwhile, let‐7g promoted apoptosis to increase 5‐FU sensitivity of Huh‐7/4X by downregulating ABCC10, Bcl‐XL as well as upregulating Bax, C‐caspase 3, and C‐PARP. Dual‐luciferase assay further confirmed that let‐7g inhibited ABCC10 expression by binding to the ABCC10 3’‐UTR region. Furthermore, let‐7g increased the sensitivity of Huh‐7/4X to 5‐FU in vitro and in vivo, which can be reversed by ABCC10 overexpression. In conclusion, let‐7g sensitized liver cancer cells to 5‐FU by downregulating ABCC10 expression.
A Perceptual Shape Loss for Monocular 3D Face Reconstruction
Authors: Otto C. , Chandran P. , Zoss G. , Gross M. , Gotardo P. , Bradley D. 
Published: December 2023

AbstractMonocular 3D face reconstruction is a wide‐spread topic, and existing approaches tackle the problem either through fast neural network inference or offline iterative reconstruction of face geometry. In either case carefully‐designed energy functions are minimized, commonly including loss terms like a photometric loss, a landmark reprojection loss, and others. In this work we propose a new loss function for monocular face capture, inspired by how humans would perceive the quality of a 3D face reconstruction given a particular image. It is widely known that shading provides a strong indicator for 3D shape in the human visual system. As such, our new ‘perceptual’ shape loss aims to judge the quality of a 3D face estimate using only shading cues. Our loss is implemented as a discriminator‐style neural network that takes an input face image and a shaded render of the geometry estimate, and then predicts a score that perceptually evaluates how well the shaded render matches the given image. This ‘critic’ network operates on the RGB image and geometry render alone, without requiring an estimate of the albedo or illumination in the scene. Furthermore, our loss operates entirely in image space and is thus agnostic to mesh topology. We show how our new perceptual shape loss can be combined with traditional energy terms for monocular 3D face optimization and deep neural network regression, improving upon current state‐of‐the‐art results.
Introduction: Perceiving and conceiving the Asian city1
Authors: Holwitt Pablo 
Published: December 2023

AbstractAsian cities are the setting of a vast agglomeration of transportation devices and services. These means of transport are inseparable from distinct concepts and images of the city. Interventions into modes of urban transport are inspired by visions for the future of urban life and quotidian practices of traversing urban space foster particular experiences that produce distinct ideas about the city. This special issue takes the multiplicity of mobility practices in Asian cities as a point of departure to interrogate connections between embodied experiences and collective representations. Drawing on three bodies of literature that deal with the topics of urban imaginaries, infrastructures as well as the body and the city, this introduction provides a theoretical framework for the study of connections between perception and conception of cities that informs the contributions to this special issue. It sets the stage for a set of three interconnected questions that guide the contributions: How do people affectively engage with urban spaces through practices of bodily movement? How are these practices of movement related to and generative of specific ideas and representations of the city? How do these practices of movement transform, challenge, subvert, or conform to dominant ideas and representations of the city?
The becoming of worker mothers: The untold narratives of an identity transition
Authors: Garcia‐Lorenzo Lucia , Carrasco Lorena , Ahmed Zehra , Morgan Alice , Sznajder Kim , Eggert Leonie 
Published: December 2023

AbstractWorker mothers still struggle to find a good balance between their care and work identities. Most research on motherhood at work focuses on how organizational structures can enable professional women to find a balance between caring and work identities neglecting their personal experiences and how they understand themselves in relation to both motherhood and work. We propose to use a liminal identity work perspective to explore the identity tensions that professional women experience during their transition into motherhood and how they manage it. To explore this question, we conducted a qualitative study over 2 years with worker mothers in Latin and North America, Europe, Asia Pacific, and Africa. The thematic and narrative analysis of 80 individual narrative interviews shows the emergence of two coexisting identity narratives. The first narrative understands motherhood as a linear process, where women experience liminality, uncertainty, and identity loss but eventually return to work after having aggregated their new worker mother identities during maternity leaves. The second coexisting narrative challenges this linear and finite view by highlighting the transition to motherhood as a continuous, liminoid, and never‐ending process. The two narratives are contextualized and managed differently according to the different cultural, historical, and social contexts where they are developed; the overall results present motherhood as a ‘liminoid’ experience that requires constant identity work to navigate the tensions emerging between potentially new and customary identities and behaviors in work contexts.
Disruption of a kasB homolog gene (kasB) causes attenuation of cell invasion and virulence of Nocardia seriolae
Authors: Zhou Su‐Ming , Shu Feng‐Ling , Liu Hao , Qian Dong , Xie Jia‐Song , Wang Ya‐Jun , Yin Fei 
Published: December 2023

AbstractNocardia seriolae is the primary aetiological agent of nocardiosis in fish, which causes mass mortality in freshwater and marine fish. β‐ketoacyl‐ACP synthase (KAS) is one of the essential enzymes in the synthesis of mycolic acids (MASs) in Mycobacterium spp. and has been chosen as the target for therapeutic intervention in mycobacterial diseases. In the present study, a kasB homologue gene (kasB) was identified in the genome of N. seriolae, and the gene‐deficient mutant (ΔkasB) was generated based on a clinical isolate, XSYC‐Ns. Compared to the wild‐type (WT) strain, the ΔkasB showed a measurably growth defect in vitro but retained the acid‐fastness in acid‐fast staining. Observation of the cell ultrastructure showed some alterations in the cell wall of the ΔkasB strain. Compared to its original strain, the cell wall lipid layer seemed sparser, and a wider electron‐transparent zone was observed in the cell wall of ΔkasB strain. Moreover, the ΔkasB strain showed impaired ability of cell invasion as well as intracellular survival in the cell line originating from the head‐kidney of the large yellow croaker (LYC‐hK), compared to its original strain. In addition, the deficiency of ΔkasB significantly attenuated the virulence of N. seriolae in largemouth bass. The present study suggested that the ΔkasB gene might be involved in the synthesis of extracellular cell‐wall lipids in N. seriolae and play a crucial role in its pathogenicity.
Randomized controlled trial of effects of a familiarization video and patient‐controlled Entonox inhalation on patient stress levels and clinical efficacy of flexible sigmoidoscopy without analgesia or sedation for investigation of fresh rectal bleeding
Authors: Bagshaw Philip , Cameron Christopher , Aramowicz Jaana , Frampton Christopher , Pretty Christopher 
Published: December 2023

AbstractBackground and AimFlexible sigmoidoscopy (FS) without analgesia or sedation can be unpleasant for patients, resulting in unsatisfactory examinations. Prior familiarization videos (FVs) and intra‐procedural Entonox inhalation have shown inconsistent effects. This study investigated their effects on undesirable participant factors (anxiety, stress, discomfort, pain, satisfaction, later unpleasant recall of procedure, and vasovagal reactions) and clinical effectiveness (extent of bowel seen, lesions detected, and procedural/recovery times).MethodsThis cluster‐randomized single‐center study evaluated 138 participants undergoing FS. There were 46 controls, 49 given access to FV, and 43 access to both FV and self‐administered Entonox. Participant factors were measured by self‐administered questionnaires, independent nurse assessments, and heart rate variability (HRV) metrics.ResultsQuestionnaires showed that the FV group was slightly more tense and upset before FS, but knowledge of Entonox availability reduced anxiety. Nonlinear HRV metrics confirmed reduced intra‐procedural stress response in the FV/Entonox group compared with controls and FV alone (P < 0.05). Entonox availability allowed more bowel to be examined (P < 0.001) but increased procedure time (P < 0.05), while FV alone had no effect. FV/Entonox participants reported 1 month after FS less discomfort during the procedure. Other comparisons showed no significant differences between treatment groups, although one HRV metric showed some potential to predict vasovagal reactions.ConclusionsEntonox availability significantly improved clinical effectiveness and caused a slight reduction in undesirable participant factors. The FV alone did not reduce undesirable participant factors or improve clinical effectiveness. Nonlinear HRV metrics recorded effects in agreement with stress reduction and may be useful for prediction of vasovagal events in future studies.