bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multidimensional quantitative phenotypic and molecular analysis reveals neomorphic behaviors of p53 missense mutants
Authors: Pal Anasuya , Gonzalez-Malerva Laura , Eaton Seron , Xu Chenxi , Zhang Yining , Grief Dustin , Sakala Lydia , Nwekwo Lilian , Zeng Jia , Christensen Grant , Gupta Chitrak , Streitwieser Ellen , Singharoy Abhishek , Park Jin G. , LaBaer Joshua 
Published: September 2023

AbstractMutations in the TP53 tumor suppressor gene occur in >80% of the triple-negative or basal-like breast cancer. To test whether neomorphic functions of specific TP53 missense mutations contribute to phenotypic heterogeneity, we characterized phenotypes of non-transformed MCF10A-derived cell lines expressing the ten most common missense mutant p53 proteins and observed a wide spectrum of phenotypic changes in cell survival, resistance to apoptosis and anoikis, cell migration, invasion and 3D mammosphere architecture. The p53 mutants R248W, R273C, R248Q, and Y220C are the most aggressive while G245S and Y234C are the least, which correlates with survival rates of basal-like breast cancer patients. Interestingly, a crucial amino acid difference at one position—R273C vs. R273H—has drastic changes on cellular phenotype. RNA-Seq and ChIP-Seq analyses show distinct DNA binding properties of different p53 mutants, yielding heterogeneous transcriptomics profiles, and MD simulation provided structural basis of differential DNA binding of different p53 mutants. Integrative statistical and machine-learning-based pathway analysis on gene expression profiles with phenotype vectors across the mutant cell lines identifies quantitative association of multiple pathways including the Hippo/YAP/TAZ pathway with phenotypic aggressiveness. Further, comparative analyses of large transcriptomics datasets on breast cancer cell lines and tumors suggest that dysregulation of the Hippo/YAP/TAZ pathway plays a key role in driving the cellular phenotypes towards basal-like in the presence of more aggressive p53 mutants. Overall, our study describes distinct gain-of-function impacts on protein functions, transcriptional profiles, and cellular behaviors of different p53 missense mutants, which contribute to clinical phenotypic heterogeneity of triple-negative breast tumors.
Human retinal ganglion cell neurons generated by synchronous BMP inhibition and transcription factor mediated reprogramming
Authors: Agarwal Devansh , Dash Nicholas , Mazo Kevin W. , Chopra Manan , Avila Maria P. , Patel Amit , Wong Ryan M. , Jia Cairang , Do Hope , Cheng Jie , Chiang Colette , Jurlina Shawna L. , Roshan Mona , Perry Michael W. , Rho Jong M. , Broyer Risa , Lee Cassidy D. , Weinreb Robert N. , Gavrilovici Cezar , Oesch Nicholas W. , Welsbie Derek S. , Wahlin Karl J. 
Published: September 2023

AbstractIn optic neuropathies, including glaucoma, retinal ganglion cells (RGCs) die. Cell transplantation and endogenous regeneration offer strategies for retinal repair, however, developmental programs required for this to succeed are incompletely understood. To address this, we explored cellular reprogramming with transcription factor (TF) regulators of RGC development which were integrated into human pluripotent stem cells (PSCs) as inducible gene cassettes. When the pioneer factorNEUROG2was combined with RGC-expressed TFs (ATOH7,ISL1,andPOU4F2) some conversion was observed and when pre-patterned by BMP inhibition, RGC-like induced neurons (RGC-iNs) were generated with high efficiency in just under a week. These exhibited transcriptional profiles that were reminiscent of RGCs and exhibited electrophysiological properties, including AMPA-mediated synaptic transmission. Additionally, we demonstrated that small molecule inhibitors of DLK/LZK and GCK-IV can block neuronal death in two pharmacological axon injury models. Combining developmental patterning with RGC-specific TFs thus provided valuable insight into strategies for cell replacement and neuroprotection.
Asian dust-deposition flux to the subarctic Pacific estimated using single quartz particles
Authors: Nagashima Kana , Kawakami Hajime , Sugie Koji , Fujiki Tetsuichi , Nishioka Jun , Iwamoto Yoko , Takemura Toshihiko , Miyakawa Takuma , Taketani Fumikazu , Aita Maki Noguchi 
Published: September 2023

AbstractIron availability limits marine ecosystem activities in large areas of the ocean. However, the sources and seasonal supply of iron, critically important for controlling surface ocean biogeochemistry and carbon cycling, are poorly understood. The western subarctic Pacific is a high-nutrient and low-chlorophyll region, and despite high concentrations of macronutrients, iron limits phytoplankton production in summer. Here, we determine the seasonal deposition flux of Asian dust using scanning electron microscope–cathodoluminescence analysis of single quartz particles derived from the western subarctic Pacific during 2003–2022 to trace provenance. We found a high (up to 6.9 mg m−2 day−1) deposition flux of Asian dust in May, June, and early July, with an annual average of 1.0 ± 0.2 mg m−2 day−1. The supply of dissolved-iron flux calculated from Asian dust was 0.9 ± 0.3 µg m−2 day−1 during the high productivity season (April–July), which is approximately half that from the deeper part of the ocean, calculated from vertical profiles of dissolved iron. Our study provides a reliable approach for estimating iron supply from dust to the surface ocean that may be critical for sustaining biological productivity under future ocean stratification, which suppresses nutrient supply from the subsurface ocean.
Exploring the link between coffee matrix microstructure and flow properties using combined X-ray microtomography and smoothed particle hydrodynamics simulations
Authors: Mo Chaojie , Johnston Richard , Navarini Luciano , Liverani Furio Suggi , Ellero Marco 
Published: September 2023

AbstractCoffee extraction involves many complex physical and transport processes extremely difficult to model. Among the many factors that will affect the final quality of coffee, the microstructure of the coffee matrix is one of the most critical ones. In this article, we use X-ray micro-computed (microCT) technique to capture the microscopic details of coffee matrices at particle-level and perform fluid dynamics simulation based on the smoothed particle hydrodynamics method (SPH) with the 3D reconstructured data. Information like flow permeability and tortuosity of the matrices can be therefore obtained from our simulation. We found that inertial effects can be quite significant at the normal pressure gradient conditions typical for espresso brewing, and can provide an explanation for the inconsistency of permeability measurements seen in the literature. Several types of coffee powder are further examined, revealing their distinct microscopic details and resulting flow features. By comparing the microCT images of pre- and post-extraction coffee matrices, it is found that a decreasing porosity profile (from the bottom-outlet to the top-inlet) always develops after extraction. This counterintuitive phenomenon can be explained using a pressure-dependent erosion model proposed in our prior work. Our results reveal not only some important hydrodynamic mechanisms of coffee extraction, but also show that microCT scan can provide useful microscopic details for coffee extraction modelling. MicroCT scan establishes the basis for a data-driven numerical framework to explore the link between coffee powder microstructure and extraction dynamics, which is the prerequisite to study the time evolution of both volatile and non-volatile organic compounds and then the flavour profile of coffee brews.
Identification of herpesvirus transcripts from genomic regions around the replication origins
Authors: Torma Gábor , Tombácz Dóra , Csabai Zsolt , Almsarrhad Islam A. A. , Nagy Gergely Ármin , Kakuk Balázs , Gulyás Gábor , Spires Lauren McKenzie , Gupta Ishaan , Fülöp Ádám , Dörmő Ákos , Prazsák István , Mizik Máté , Dani Virág Éva , Csányi Viktor , Harangozó Ákos , Zádori Zoltán , Toth Zsolt , Boldogkői Zsolt 
Published: September 2023

AbstractLong-read sequencing (LRS) techniques enable the identification of full-length RNA molecules in a single run eliminating the need for additional assembly steps. LRS research has exposed unanticipated transcriptomic complexity in various organisms, including viruses. Herpesviruses are known to produce a range of transcripts, either close to or overlapping replication origins (Oris) and neighboring genes related to transcription or replication, which possess confirmed or potential regulatory roles. In our research, we employed both new and previously published LRS and short-read sequencing datasets to uncover additional Ori-proximal transcripts in nine herpesviruses from all three subfamilies (alpha, beta and gamma). We discovered novel long non-coding RNAs, as well as splice and length isoforms of mRNAs. Moreover, our analysis uncovered an intricate network of transcriptional overlaps within the examined genomic regions. We demonstrated that herpesviruses display distinct patterns of transcriptional overlaps in the vicinity of or at the Oris. Our findings suggest the existence of a ‘super regulatory center’ in the genome of alphaherpesviruses that governs the initiation of both DNA replication and global transcription through multilayered interactions among the molecular machineries.
Holocene extreme hydroclimate events in the Asian monsoon region were more frequent during cooler intervals
Authors: Zhang Enlou , Meng Xianqiang , Ning Dongliang , Shulmeister James , Sun Weiwei , Zhang Wenfang , Ni Zhenyu 
Published: September 2023

AbstractThe areas affected by the East and South Asian monsoons contain almost half the world’s population. Understanding natural variability in these monsoons under warmer climates is critical for managing future changes. Here we present a high-resolution record of Holocene drought events derived from lake level changes in the South Asian monsoon region. By combining the published storm events in the East Asian monsoon region, we demonstrate that extreme hydroclimate events frequently occurred within a ca. 500-year cycle during the cool early-late Holocene, exhibiting a fierce Asian monsoon. In contrast, there were fewer extreme hydroclimate events during the warm mid-Holocene period. We propose that tropical temperatures and air-sea interaction in the Indo-Pacific Oceans are responsible for the occurrences of centennial-scale extreme events. Our findings suggest that tropical influences can module climate responses in monsoon regions, and the Asian monsoon may be more peaceful than hitherto expected under future global warming scenarios.
Benchmarking satellite-derived shoreline mapping algorithms
Authors: Vos K. , Splinter K. D. , Palomar-Vázquez J. , Pardo-Pascual J. E. , Almonacid-Caballer J. , Cabezas-Rabadán C. , Kras E. C. , Luijendijk A. P. , Calkoen F. , Almeida L. P. , Pais D. , Klein A. H. F. , Mao Y. , Harris D. , Castelle B. , Buscombe D. , Vitousek S. 
Published: September 2023

AbstractSatellite remote sensing is becoming a widely used monitoring technique in coastal sciences. Yet, no benchmarking studies exist that compare the performance of popular satellite-derived shoreline mapping algorithms against standardized sets of inputs and validation data. Here we present a new benchmarking framework to evaluate the accuracy of shoreline change observations extracted from publicly available satellite imagery (Landsat and Sentinel-2). Accuracy and precision of five established shoreline mapping algorithms are evaluated at four sandy beaches with varying geologic and oceanographic conditions. Comparisons against long-term in situ beach surveys reveal that all algorithms provide horizontal accuracy on the order of 10 m at microtidal sites. However, accuracy deteriorates as the tidal range increases, to more than 20 m for a high-energy macrotidal beach (Truc Vert, France) with complex foreshore morphology. The goal of this open-source, collaborative benchmarking framework is to identify areas of improvement for present algorithms, while providing a stepping stone for testing future developments, and ensuring reproducibility of methods across various research groups and applications.
Penser, représenter, la problématique de la féminité et du maternel dans l’anorexie mentale
Authors: Corcos Maurice , Letranchant Aurélie , Nicolas Isabelle , Shadili Gérard 
Published: September 2023

L’épidémiologie des Troubles des conduites alimentaires (TCA) permet d’envisager que la problématique dans ces affections soit liée en grande partie à la problématique plus générale de la féminité et à celle de la constitution de l’identité de genre psychique et corporelle à l’adolescence. Nous allons particulièrement aborder ici la problématique des affects, de l’attachement insécure, le rôle des conflits émotionnels, de la psychopathologie parentale, la dynamique familiale dans cette population de patient(e)s.
Notre regard psychopathologique se focalisera également sur les aspects transgénérationnels de l’identification avec la quête imaginaire d’une identité, d’une filiation du corps à corps, et sur le rôle particulier de l’éprouvé corporel dans la construction de la conscience de sa féminité et du maternel. Nous en conclurons que cette prison, que le sujet entretient jusqu’à en être -avec son corps-le co-geôlier, n’est pas qu’une simple prison mentale.
Séduction éthique et éthique du bien-dire au vu des parentalités contemporaines
Authors: Chetrit-Vatine Viviane 
Published: September 2023

Les parentalités contemporaines (couple de parents homosexuels ou lesbiennes, enfants conçus à partir d’insémination d’ovocyte ou de sperme, avec l’aide éventuelle de mères porteuses, enfants élevés par des mères célibataires, etc.) sont réputées aujourd’hui ne pas entraîner plus de pathologies chez les enfants nés et élevés dans ces conditions que chez les enfants conçus et élevés dans les constellations parentales « classiques ». L’exposé d’une courte vignette clinique datant de plus de 30 ans nous conduira à reconsidérer les éléments nécessaires à un bon développement psychique et éthique des enfants en général et de ceux nés des parentalités contemporaines en particulier.
Je traiterai ainsi et de la question de l’origine première de la capacité éthique chez tout sujet humain, et de celle de l’éthique de responsabilité comme de l’éthique du bien-dire de la part des parents, avec en son centre le respect de la différence des générations, c’est-à-dire l’asymétrie parents/enfant, le respect de la différence des sexes et le respect de la capacité de représentation de l’enfant.
Interpersonal Influences on the Choice to Treat Nausea during Pregnancy with Medication or Cannabis
Authors: Mercer Amanda H. , MacDuffie Katherine E. , Weiss Elliott M. , Johnson Allegra , Dager Stephen R. , Kleinhans Natalia 
Published: September 2023

Objective This study aimed to better understand the interpersonal influences on a pregnant individual's decision of how to treat nausea and vomiting during pregnancy using a qualitative approach.
Study Design A semistructured interview guide was developed to assess pregnancy symptoms, decision-making regarding treating nausea, and interpersonal influences on treatment decisions. Interviews were conducted with 17 individuals enrolled in a neuroimaging and behavioral study of prenatal exposure to cannabis who used medication and/or cannabis to treat symptoms associated with pregnancy.
Results Interviews revealed four groups of stakeholders who influenced participant decision-making: medical providers, partners, family, and friends. Influence was categorized as either positive, negative, neutral, or absent (if not discussed or participant chose not to disclose). Those in the medication group reported only positive or neutral feedback from friends, family, partners, and providers. In contrast, the cannabis group participants reported positive feedback from friends, mixed feedback from family and partners, and negative feedback from providers, which was often felt to be stigmatizing. Many in the cannabis group also reported varying feedback from different medical providers. While the cannabis group frequently reported eliciting feedback from friends, family, and partners, the medication group often did not.
Conclusion Medication group participants reported entirely positive feedback from providers and often did not mention any feedback at all from partners, family, and friends. Cannabis group participants reported much more varied feedback, both positive and negative, from a variety of interpersonal contacts and sometimes decided to conceal their treatment choice after receiving or fearing negative feedback. We recommend further research into the health outcomes of pregnant patients who chose not to discuss their treatment decisions with providers, family, partners, or friends. We also suggest further study of possible reasons behind a lack of disclosure, including fear of stigma and/or legal consequences.
Key Points
Comparison of Anti-SARS-CoV-2-Specific Antibody Signatures in Maternal and Infant Blood after COVID-19 Infection versus COVID-19 Vaccination during Pregnancy
Authors: Sabharwal Vishakha , Taglauer Elizabeth , Demos Riley , Snyder-Cappione Jennifer , Shaik-Dasthagirisaheb Yazdani B. , Parker-Kelleher Samantha , Hunnewell Jessica , Boateng Jeffery , Clarke Katherine , Yuen Rachel , Barnett Elizabeth D. , Wachman Elisha M. , Yarrington Christina D. 
Published: September 2023

Objective The Advisory Committee on Immunization Practices and The American College of Obstetricians and Gynecologists recommend coronavirus disease 2019 (COVID-19) vaccine for pregnant persons to prevent severe illness and death. The objective was to examine levels of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) IgG, IgM, and IgA against spike protein receptor binding domain (RBD) and nucleocapsid protein (NCP) in maternal and infant/cord blood at delivery after COVID 19 vaccination compared with SARS-CoV-2 infection at in mother–infant dyads at specified time points.
Study Design Mothers with SARS-CoV-2 infection (n = 31) or COVID-19 vaccination (n = 25) during pregnancy were enrolled between July 2020 and November 2021. Samples were collected at delivery and IgG, IgM, and IgA to RBD of spike and NCPs compared in the infected and vaccinated groups. Timing of infection/vaccination prior to delivery and correlation with antibody levels was performed.
Results The majority of participants received vaccination within 90 days of delivery and over half received the Pfizer BioNTech vaccine. There were no significant correlations between antibody levels and timing of infection or vaccination. Infant IgG levels to the RBD domain of spike protein were higher in the vaccinated group (n = 25) as compared with the infants born to mothers with infection (n = 31). Vaccination against COVID-19 during pregnancy was associated with detectable maternal and infant anti-RBD IgG levels at delivery irrespective of the timing of vaccination.
Conclusion Timing of vaccination had no correlation to the antibody levels suggesting that the timing of maternal vaccination in the cohort did not matter. There was no IgM detected in infants from vaccinated mothers. Infants from vaccinated mothers had robust IgG titers to RBD, which have a lasting protective effect in infants.
Key Points
Identification and Characterization of Chemical Constituents from Ammopiptanthus nanus Stem and Their Metabolites in Rats by UHPLC-Q-TOF-MS/MS
Authors: Chen Guanru , Sun Yanpei , Yushan Dilnur , Shaerbayi Nuerjiamali , Zhang Hongjuan , He Hongliang , Jin Yang , Chen Lina 
Published: September 2023

Abstract
Ammopiptanthus nanus as a Kirgiz medicine is widely used for the treatment of frostbite and chronic rheumatoid arthritis. However, due to a lack of systematic research on the
chemical components of A. nanus and their metabolites, the bioactive components in it remain unclear. Herein, a reliable strategy based on UHPLC-Q-TOF-MS/MS was established to
comprehensively analyze the chemical components and their metabolites in vivo. In total, 59 compounds were identified from A. nanus stem extract, among which 14 isoflavones, 10
isoprenylated isoflavones, 4 polyhydroxy flavonoids, 9 alkaloids and 1 polyol were characterized for the first time. After oral administration of A. nanus stem extract, 30 prototype
constituents and 28 metabolites (12 phase I and 16 phase II metabolites) were speculated on and identified in rat serum, urine and feces. Furthermore, the metabolic pathways of the chemical
components were systematically analyzed and proposed. In conclusion, the chemical components from A. nanus stem and their metabolites in vivo were first studied, which may
provide useful chemical information for further study on the effective material basis and pharmacological mechanism of A. nanus.
The Impact of Spontaneous versus Indicated Preterm Birth on Neonatal Outcomes among Extremely Premature Neonates
Authors: Townsel Courtney , Hesson Ashley M. , Greco Patricia , Kazzi Nayla G. , Treadwell Marjorie C. 
Published: September 2023

Objective This study aimed to investigate whether neonatal morbidity differs in spontaneous compared with indicated preterm births in extremely premature neonates.
Study Design This is a retrospective cohort study including births ≤28 weeks at a single institution from 2011 to 2020. Births were categorized as either medically indicated or spontaneous preterm deliveries. The primary outcome was inhospital mortality and serious morbidity in survivors. t-tests, Fisher's exact tests, chi-square tests, and logistic regression models were utilized as appropriate. p < 0.05 was significant.
Results Two hundred and twenty-seven births were included, with two-thirds representing spontaneous births (65.6%, 149/227) and one-third categorized as medically indicated births (34.4%, 78/227). Inhospital mortality was more common in the spontaneous preterm birth group (p = 0.04), while inhospital morbidity did not significantly vary between the medically indicated and spontaneous birth groups (p = 0.32). There was no difference in inhospital morbidity or mortality by maternal race. In multivariate models of inhospital morbidity and mortality, gestational age was the only significant predictor of adverse outcomes.
Conclusion Despite inhospital mortality being more common in spontaneous preterm births, inhospital mortality and significant morbidity are best accounted for by gestational age alone.
Key Points