bluuebunny/crossref_metadata_2025_split huggingface dataset:
Psychosocial Experiences of Spanish-Speaking Parents of Children With Craniofacial Microsomia
Authors: Rahman Muhammad , Avila Sandra , Heike Carrie L. , Stock Nicola M. , Stueckle Laura , Schefer Amy , Johns Alexis L. 
Published: May 2024

Craniofacial microsomia (CFM) and microtia psychosocial research in the US is primarily with English-speaking participants. Given that 19% of the US is Latino, and there is a higher prevalence of CFM in Latino populations, this study aims to describe psychosocial experiences related to CFM among Spanish-speaking Latino caregivers to better inform health care. Narrative interviews (mean 73±17 min) were completed in Spanish with parents of children with CFM aged 3 to 17 (mean age 10.8±4.8 years). Transcripts were analyzed using quantitative linguistic analyses and reflexive thematic analysis. Participants (N=12) were mostly mothers (83%) who had immigrated to the US and had low socioeconomic status. Based upon analysis of grouped word counts, participants spent approximately half of their narratives discussing the first two years of their child’s life. Themes selected based on US Latino sociodemographics and cultural values included the Impact of Language, Healthcare Challenges, Supportive Healthcare Experiences, Caregiver Coping with CFM, Family Roles, and Addressing Social Implications of CFM. Results highlighted that the first years of care are of critical importance to parents and suggest this is an optimal time to focus on education and support services for families. Additional treatment suggestions include providing interpretation and informational materials in Spanish, addressing care barriers, supporting familial and child coping, accounting for the role of extended family, and helping address social concerns. Ongoing research with Latino families can further assist in guiding culturally sensitive CFM health care.
Prognostic Significance of Preoperative and Postoperative Evaluation of Combined Tumor Markers for Patients With Colon Cancer
Authors: Pan Hong-Feng , Zheng Zhi-Fang , Zhao Ze-Yi , Liu Zhun , Huang Sheng-Hui , Chi Pan 
Published: May 2024

Background:
The combined value of the tumor markers carcinoembryonic antigen (CEA) and carbohydrate antigen 19-9 (CA19-9) in patients with colon cancer (CC) is unclear. This study aimed to investigate the role of composite tumor markers in the prognosis of CC.

Methods:
Patients who underwent curative resection of colon adenocarcinoma were enrolled. The tumor marker status before and after the operation was used to divide the patients into groups according to the number of tumor markers with abnormal expression, and recurrence-free survival (RFS) and overall survival (OS) of different groups were compared. The impact of changes in composite tumor markers in the perioperative period on outcomes was further explored.

Results:
Ultimately, 531 patients were enrolled in the study. As the number of preoperative and postoperative elevated tumor markers increased, both RFS and OS rates became lower (both P<0.05). Further analysis revealed that the number of elevated tumor markers after resection can significantly affect the outcomes (both P<0.05). In patients with abnormal preoperative tumor markers, normalization of markers after surgery was a protective factor for prognosis (both P<0.05), and patients with postoperative elevated levels of both tumor markers had a 5.5-fold and 6-fold increase in the risk of recurrence and death. In addition, patients with elevated markers after surgery had a high risk of recurrence within 5 years after colectomy.

Conclusions:
Postoperative tumor markers had a better ability to differentiate postoperative outcomes in patients with CC than preoperative tumor markers. Patients whose tumor markers normalized after surgery had a better prognosis.
Micrometeorite collections: a review and their current status
Authors: van Ginneken Matthias , Wozniakiewicz Penelope J. , Brownlee Donald E. , Debaille Vinciane , Della Corte Vincenzo , Delauche Lucie , Duprat Jean , Engrand Cecile , Folco Luigi , Fries Marc , Gattacceca Jérôme , Genge Matthew J. , Goderis Steven , Gounelle Matthieu , Harvey Ralph P. , Jonker Guido , Krämer Ruggiu Lisa , Larsen Jon , Lever James H. , Noguchi Takaaki , Peterson Scott , Rochette Pierre , Rojas Julien , Rotundi Alessandra , Rudraswami N. G. , Suttle Martin D. , Taylor Susan , Van Maldeghem Flore , Zolensky Michael 
Published: May 2024

Micrometeorites are estimated to represent the main part of the present flux of extraterrestrial matter found on the Earth’s surface and provide valuable samples to probe the interplanetary medium. Here, we describe large and representative collections of micrometeorites currently available to the scientific community. These include Antarctic collections from surface ice and snow, as well as glacial sediments from the eroded top of nunataks—summits outcropping from the icesheet—and moraines. Collections extracted from deep-sea sediments (DSS) produced a large number of micrometeorites, in particular, iron-rich cosmic spherules that are rarer in other collections. Collections from the old and stable surface of the Atacama Desert show that finding large numbers of micrometeorites is not restricted to polar regions or DSS. The advent of rooftop collections marks an important step into involving citizen science in the study of micrometeorites, as well as providing potential sampling locations over all latitudes to explore the modern flux. We explore their strengths of the collections to address specific scientific questions and their potential weaknesses. The future of micrometeorite research will involve the finding of large fossil micrometeorite collections and benefit from recent advances in sampling cosmic dust directly from the air.
This article is part of the theme issue ‘Dust in the Solar System and beyond’.
Atypical presentation of varicella-zoster virus reactivation in a lung transplant patient: a case report
Authors: Hoff Ingrid , Rath Eivind , Pena-Karan Slobodanka , Sivy Nginamau Elisabeth , Holm Are Martin , Thune Turid , Mustafa Tehmina 
Published: May 2024

Background: Varicella zoster virus (VZV) is a human neurotropic virus which commonly causes infection during childhood. Later in life it may reactivate as herpes zoster. We report a rare manifestation of reactivation of VZV infection presenting as cutaneous vasculitis and varicella pneumonia in a lung transplant recipient.
Case presentation: A 65 year old man was lung transplanted bilaterally for emphysema. Nine months post-transplant he presented with dyspnea and a cutaneous vasculitis-like eruption. VZV reactivation was not suspected due to absence of the typical vesicular eruptions. The diagnosis was confirmed by VZV PCR from the swabs of the ulcer after skin punch biopsy of a lesion and from bronchoalveolar lavage (BAL). The histology of skin biopsy demonstrated epithelial and vascular damage but no typical epithelial virus associated changes. The patient responded to antiviral therapy with total remission of rash and VZV DNA was not detectable from repeated BAL after 29 days of therapy. However, the pulmonary radiological features and dyspnea persisted due to reasons possibly unrelated to the VZV infection.
Conclusion: Had it not been for the patient to mention the resemblance of the vasculitic rash with his primary VZV infection, the diagnosis would easily have been overlooked. In this case, the biopsy did not show typical histopathologic findings of VZV-vasculitis. What led the diagnosis was PCR from the wound swab taken after punch biopsy. This case serves as a reminder for atypical presentation of common conditions in immunosuppressed patients and that extensive diagnostic sampling may be warranted in this group.
Single–cell transcriptional and epigenetic mapping reveals cellular and molecular mechanisms driving non-ischemic cardiac fibrosis
Authors: Krstevski Crisdion , Farrugia Gabriella E. , Hsu Ian , Dona Malathi S. I. , Gaynor Taylah L. , Cohen Charles D. , Harper Rebecca L. , Harrison Thomas I. , Claridge Bethany , Drack Auriane , Lelliott Patrick , Kiriazis Helen , Brown Aascha , McMullen Julie R. , Donner Daniel G. , Lal Sean , Greening David W. , Pinto Alexander R. 
Published: May 2024

ABSTRACTCardiac fibrosis is a major cause of cardiac dysfunction. Recently, single-cell genomic approaches have revealed in unprecedented resolution the orchestrated cellular responses driving cardiac fibrosis. Yet, the fibrosis-causing phenotypes that emerge in the heart following non-ischemic cardiac stress, and the transcriptional circuits that govern cell identity and drive fibrosis, are not well understood. Applying a paired multiomic approach, we reveal key transcriptional circuits, in mouse and human hearts, which are associated with fibrosis development following non-ischemic cardiac insults, independent of disease model, species or biological sex. Strikingly, we find the key regulatory events driving fibrosis are reversible at the single-cell transcriptional and epigenomic level, further pointing to key factors regulating fibrosis development and resolution. The transcriptional regulators identified in this study represent promising targets to ameliorate the development of fibrosis in the context of chronic stressors such as aging and hypertension.
The replicative helicase CMG is required for the divergence of cell fates during asymmetric cell divisionin vivo
Authors: Memar Nadin , Sherrard Ryan , Sethi Aditya , Fernandez Carla Lloret , Schmidt Henning , Lambie Eric , Poole Richard , Schnabel Ralf , Conradt Barbara 
Published: May 2024

AbstractThe mechanisms that enable differential gene expression in daughter cells produced by asymmetric cell divisions are not well understood. We discovered that the eukaryotic replicative helicase CMG (Cdc45-MCM-GINS) is required for this process inC. elegans. DuringC. elegansdevelopment, some dividing cells give rise to a daughter that survives and a daughter that dies. We found that PSF-2 GINS2, a component ofC. elegansCMG, is necessary for the transcriptional burst of the pro-apoptotic geneegl-1BH3-only, which occurs in the daughter that dies immediately following mother cell division. We present evidence that this requirement is independent of the function of CMG in DNA unwinding. We propose that the recently described histone chaperone activity of CMG causes epigenetic changes at theegl-1locus during replication in mother cells, and that these changes are required for the increase inegl-1transcription in the daughter that dies. We also find that PSF-2 is required for the divergence of other cell fates duringC. elegansdevelopment, suggesting that this function is not restricted to the regulation ofegl-1expression. Our work uncovers a new and unexpected role of CMG in cell fate and a novel intrinsic mechanism for gene expression plasticity in the context of asymmetric cell division.
Fast adaptive super-resolution lattice light-sheet microscopy for rapid, long-term, near-isotropic subcellular imaging
Authors: Qiao Chang , Li Ziwei , Wang Zongfa , Lin Yuhuan , Liu Chong , Zhang Siwei , Liu Yong , Feng Yun , Wang Xinyu , Dong Xue , Guo Jiabao , Jiang Tao , Wang Qinghua , Dai Qionghai , Li Dong 
Published: May 2024

AbstractLattice light-sheet microscopy (LLSM) provides a crucial observation window into intra- and inter-cellular physiology of living specimens with high speed and low phototoxicity, however, at the diffraction-limited resolution or anisotropic super-resolution with structured illumination. Here we present the meta-learning-empowered reflective lattice light-sheet virtual structured illumination microscopy (Meta-rLLS-VSIM), which instantly upgrades LLSM to a near-isotropic super resolution of ∼120-nm laterally and ∼160-nm axially, more than twofold improvement in each dimension, without any modification of the optical system or sacrifice of other imaging metrics. Moreover, to alleviate the tremendous demands on training data and time necessitated by existing deep-learning (DL) methods, we devised an adaptive online training approach by synergizing the front-end imaging system and back-end meta-learning framework, which reduced the total time for data acquisition and model training down to tens of seconds. With this method, a new model can be well-trained with tenfold less data and three orders of magnitude less time than current standard supervised learning. We demonstrate the versatile functionalities of Meta-rLLS-VSIM by imaging a variety of bioprocesses with ultrahigh spatiotemporal resolution for long duration of hundreds of multi-color volumes, characterizing the dynamic regulation of contractile ring filaments during mitosis and the growth of pollen tubes, and delineating the nanoscale distributions, dispersion, and interaction pattern of multiple organelles in embryos and eukaryotic cells.
Ligandability at the membrane interface of GPx4 revealed through a reverse micelle fragment screening platform
Authors: Labrecque Courtney L. , Fuglestad Brian 
Published: May 2024

AbstractWhile they account for a large portion of drug targets, membrane proteins (MPs) present a unique challenge for drug discovery. Peripheral membrane proteins (PMPs), a class of proteins that bind reversibly to membranes, are also difficult targets, particularly those that function only while bound to membranes. The protein-membrane interface in PMPs is often where functional interactions and catalysis occur, making it a logical target for inhibition. However, interfaces are underexplored spaces in inhibitor design and there is a need for enhanced methods for small-molecule ligand discovery. In an effort to better initiate drug discovery efforts for PMPs, this study presents a screening methodology using membrane-mimicking reverse micelles (mmRM) and NMR-based fragment screening to assess ligandability in the protein-membrane interface. The proof-of-principle target, glutathione peroxidase 4 (GPx4), is a lipid hydroperoxidase which is essential for the oxidative protection of membranes and thereby the prevention of ferroptosis. GPx4 inhibition is promising for therapy-resistant cancer therapy, but current inhibitors are generally covalent ligands with limited clinical utility. Presented here is the discovery of non-covalent small-molecule ligands for membrane-bound GPx4 revealed through the mmRM fragment screening methodology. The fragments were tested against GPx4 in bulk aqueous conditions and displayed little to no binding to the protein without embedment into the membrane. The 9 hits had varying affinities and partitioning coefficients and revealed properties of fragments that bind within the protein-membrane interface. Additionally, a secondary screen confirmed the potential to progress the fragments by enhancing the affinity from > 200 µM to ∼15 µM with the addition of certain hydrophobic groups. This study presents an advancement of screening capabilities for membrane associated proteins, reveals ligandability within the GPx4 protein-membrane interface, and may serve as a starting point for developing non-covalent inhibitors of GPx4.
Impedance-based assay for pan-cancer early and rapid detection of cell-free DNA
Authors: Dube Tejal , Prasad Puja , Swami Pragya , Singh Ankita , Verma Meenakshi , Tanwar Parul , Chowdhury Shantanu , Gupta Shalini 
Published: May 2024

AbstractAberrant DNA methylation is a hallmark of cancer, and plasma cell-free DNA (cfDNA) containing these abnormal methylation patterns has emerged as a promising non-invasive biomarker for pan-cancer detection. However, intrinsic challenges remain that continue to limit its broad clinical application. Here we show a simple and rapid impedance biosensor called Asima™ Rev that can detect cancer cfDNA in under 5 min without the need for any molecular labelling, electrode modification, signal amplification, or target enrichment steps. Using 216 clinical samples (50 healthy) from 15 different cancer types (all stages) we show an overall sensitivity and specificity of 96.4% and 94.0%, respectively. Differences in methylation content between cancerous and healthy cfDNA lead to distinct solvation behaviour and electro-physicochemical property that remain consistent across cancer types regardless of the distribution patterns of methyl cytosine. Our test exploits this inherent difference.
Xylem perforation plate phenotypes affect water use and drought adaptation in maize (Zea maysL.)
Authors: Strock Christopher F. , DePew Cody L. , Sidhu Jagdeep S. , Xu Tianyu , Lynch Jonathan P. 
Published: May 2024

SummaryRationale: Xylem morphology in annual monocots is important for water use strategies in many agronomically important species.Methods:We assess how xylem perforation plates affect water use strategies in maize (Zea maysL.) throughin silicomodeling, empirical studies under water deficit in controlled environments, and in the field.Key Result: Significant genotypic variation for the prominence and frequency of perforation plates was observed in maize germplasm. Perforation plate phenotypes had high heritability, were associated with several QTL, and were pleiotropic across leaves, aerial nodal roots, and subterranean nodal roots. Perforation plate phenotypes did not affect vulnerability to cavitation, but modeling predicted that they should affect axial water transport, which was supported byin situmeasurements of root segments. Metaxylem vessel length was correlated with the rate of root elongation, root depth, and deep-water utilization in mesocosms. Under drought stress in the field, variation in xylem vessel length was associated with leaf roll, leaf temperature, transpiration, photosynthesis, and grain yield.Main Conclusion:Phenotypic variation for xylem perforation plate phenotypes in maize directly affects axial water conductance and is part of a pleiotropic syndrome with greater root elongation and deeper rooting that improves adaptation to water deficit stress.
Towards high throughput in-field detection and quantification of wheat foliar diseases with deep learning
Authors: Zenkl Radek , McDonald Bruce A. , Walter Achim , Anderegg Jonas 
Published: May 2024

1AbstractReliable, quantitative information on the presence and severity of crop diseases is critical for site-specific crop management and resistance breeding. Successful analysis of leaves under naturally variable lighting, presenting multiple disorders, and across phenological stages is a critical step towards high-throughput disease assessments directly in the field.Here, we present a dataset comprising 422 high resolution images of flattened leaves captured under variable outdoor lighting with polygon annotations of leaves, leaf necrosis and insect damage as well as point annotations of Septoria tritici blotch (STB) fruiting bodies (pycnidia) and rust pustules. Based on this dataset, we demonstrate the capability of deep learning for keypoint detection of pycnidia (F1 = 0.76) and rust pustules (F1 = 0.77) combined with semantic segmentation of leaves (IoU= 0.96), leaf necrosis (IoU= 0.77) and insect damage(IoU= 0.69) to reliably detect and quantify the presence of STB, leaf rusts, and insect damage under natural outdoor conditions. An analysis of intra- and inter-annotator agreement on selected images demonstrated that the proposed method achieved a performance close to that of annotators in the majority of the scenarios.We validated the generalization capabilities of the proposed method by testing it on images of unstructured canopies acquired directly in the field and with-out manual interaction with single leaves. The corresponding imaging procedure can be adapted to support automated data acquisition. Model predictions were in good agreement with visual assessments of in-focus regions in these images, despite the presence of new challenges such as variable orientation of leaves and more complex lighting. This underscores the principle feasibility of diagnosing and quantifying the severity of foliar diseases under field conditions using the proposed imaging setup and image processing methods. By demonstrating the ability to diagnose and quantify the severity of multiple diseases in highly natural complex scenarios, we lay out the groundwork for a significantly more efficient, non-invasive in-field analysis of foliar diseases that can support resistance breeding and the implementation of core principles of precision agriculture.
Legionella uses host Rab GTPases and BAP31 to create a unique ER niche
Authors: Chadha Attinder , Yanai Yu , Oide Hiromu , Wakana Yuichi , Inoue Hiroki , Saha Saradindu , Tagaya Mitsuo , Arasaki Kohei , Mukherjee Shaeri 
Published: May 2024

ABSTRACTUpon entry into host cells, the facultative intracellular bacteriumLegionella pneumophila(L.p.) uses its type IV secretion system, Dot/Icm, to secrete ~330 bacterial effector proteins into the host cell. Some of these effectors hijack endoplasmic reticulum (ER)-derived vesicles to form theLegionella-containing vacuole (LCV). Despite extensive investigation over decades, the fundamental question persists: Is the LCV membrane distinct from or contiguous with the host ER network? Here, we employ advanced photobleaching techniques, revealing a temporal acquisition of both smooth and rough ER (sER and rER) markers on the LCV. In the early stages of infection, the sER intimately associates with the LCV. Remarkably, as the infection progresses, the LCV evolves into a distinct niche comprising an rER membrane that is independent of the host ER network. We discover that theL.p.effector LidA binds to and recruits two host proteins of the Rab superfamily, Rab10, and Rab4, that play significant roles in acquiring sER and rER membranes, respectively. Additionally, we identify the pivotal role of a host ER-resident protein, BAP31, in orchestrating the transition from sER to rER. While previously recognized for shuttling between sER and rER, we demonstrate BAP31’s role as a Rab effector, mediating communication between these ER sub-compartments. Furthermore, using genomic deletion strains, we uncover a novelL.p.effector, Lpg1152, essential for recruiting BAP31 to the LCV and facilitating its transition from sER to rER. Depletion of BAP31 or infection with an isogenicL.p.strain lacking Lpg1152 results in a growth defect. Collectively, our findings illuminate the intricate interplay between molecular players from both host and pathogen, elucidating howL.p.orchestrates the transformation of its residing vacuole membrane from a host-associated sER to a distinct rER membrane that is not contiguous with the host ER network.