bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hypoxia Triggered by Expanding River Plume on the East China Sea Inner Shelf During Flood Years
Authors: Li Dewang , Chen Jianfang , Wang Bin , Jin Haiyan , Shou Lu , Lin Hua , Miao Yanyi , Sun Qianwen , Jiang Zhibing , Meng Qicheng , Zeng Jiangning , Zhou Feng , Cai Wei‐Jun 
Published: July 2024

AbstractThe frequency of riverine floods is predicted to increase in East Asia. However, the response of coastal hypoxia (<63 μmol L−1) to floods has not been well understood. In the summer of 2020, characterized by one of the most significant Changjiang water fluxes in three decades, we conducted a cruise during the flood period on the East China Sea inner shelf. Our observations revealed severe bottom hypoxia with a maximum spatial coverage of ∼11,600 km2 and a minimum dissolved oxygen concentration (DO) of 21 μmol L−1. In the surface layer, the relationships between salinity and nitrate, dissolved inorganic carbon (DIC) indicated significant organic matter production, validated by a high‐Chlorophyll‐a (Chl a) patch (>5 μg L−1). Furthermore, the significant relationship between apparent oxygen utilization and DIC of deep waters reveals that the organic matter decomposition primarily drove the hypoxia during the flood period. Episodic wind events also influenced bottom DO and DIC, by transporting surface waters to the deep. Multiple‐years data set shows that the average Changjiang nitrate flux during flood years is about 1.4 times that during non‐flood years. The flood waters mix with estuarine waters, forming the high‐nutrient plume waters, which expanded farther offshore during the flood period. While high turbidity remained confined to the inner estuary. Consequently, the high‐Chl a area significantly expanded, which significantly exacerbated the hypoxia.
Forward and Inverse Modeling of Ice Sheet Flow Using Physics‐Informed Neural Networks: Application to Helheim Glacier, Greenland
Authors: Cheng Gong , Morlighem Mathieu , Francis Sade 
Published: July 2024

AbstractPredicting the future contribution of the ice sheets to sea level rise over the next decades presents several challenges due to a poor understanding of critical boundary conditions, such as basal sliding. Traditional numerical models often rely on data assimilation methods to infer spatially variable friction coefficients by solving an inverse problem, given an empirical friction law. However, these approaches are not versatile, as they sometimes demand extensive code development efforts when integrating new physics into the model. Furthermore, this approach makes it difficult to handle sparse data effectively. To tackle these challenges, we use the Physics‐Informed Neural Networks (PINNs) to seamlessly integrate observational data and governing equations of ice flow into a unified loss function, facilitating the solution of both forward and inverse problems within the same framework. We illustrate the versatility of this approach by applying the framework to two‐dimensional problems on the Helheim Glacier in southeast Greenland. By systematically concealing one variable (e.g., ice speed, ice thickness, etc.), we demonstrate the ability of PINNs to accurately reconstruct hidden information. Furthermore, we extend this application to address a challenging mixed inversion problem. We show how PINNs are capable of inferring the basal friction coefficient while simultaneously filling gaps in the sparsely observed ice thickness. This unified framework offers a promising avenue to enhance the predictive capabilities of ice sheet models, reducing uncertainties, and advancing our understanding of poorly constrained physical processes.
Multi-polygenic score prediction of mathematics, reading, and language abilities independent of general cognitive ability
Authors: Procopio Francesca , Liao Wangjingyi , Rimfeld Kaili , Malanchini Margherita , von Stumm Sophie , Allegrini Andrea G. , Plomin Robert 
Published: July 2024

Abstract
Specific cognitive abilities (SCA) correlate genetically about 0.50, which underpins general cognitive ability (g), but it also means that there is considerable genetic specificity. If g is not controlled, then genomic prediction of specific cognitive abilities is not truly specific because they are all perfused with g. Here, we investigated the heritability of mathematics, reading, and language ability independent of g (SCA.g) using twins and DNA, and the extent to which multiple genome-wide polygenic scores (multi-PGS) can jointly predict these SCA.g as compared to SCA uncorrected for g. We created SCA and SCA.g composites from a battery of 14 cognitive tests administered at age 12 to 5,000 twin pairs in the Twins Early Development Study (TEDS). Univariate twin analyses yielded an average heritability estimate of 40% for SCA.g, compared to 53% for uncorrected SCA. Using genome-wide SNP genotypes, average SNP-based heritabilities were 26% for SCA.g and 35% for SCA. We then created multi-PGS from at least 50 PGS to predict each SCA and SCA.g using elastic net penalised regression models. Multi-PGS predicted 4.4% of the variance of SCA.g on average, compared to 11.1% for SCA uncorrected for g. The twin, SNP and PGS heritability estimates for SCA.g provide further evidence that the heritabilities of SCA are not merely a reflection of g. Although the relative reduction in heritability from SCA to SCA.g was greater for PGS heritability than for twin or SNP heritability, this decrease is likely due to the paucity of PGS for SCA. We hope that these results encourage researchers to conduct genome-wide association studies of SCA, and especially SCA.g, that can be used to predict PGS profiles of SCA strengths and weaknesses independent of g.
Virtual walking therapy in neuropathic spinal cord injury pain: a feasibility study
Authors: Landmann Gunther , Aerni Marina , Abächerli Roger , Ernst Mario , Ljutow André , Ottiger-Böttger Karina 
Published: July 2024

Abstract
Study design
A feasibility study.

Objectives
Chronic neuropathic pain is a prevalent comorbidity in patients with spinal cord injury (SCI), and current medical treatments remain unsatisfactory. New developments as virtual walking are emerging which has been established and further developed at our centre. This study aims to investigate the feasibility of our virtual walking setup in a small group of SCI patients.

Setting
The study was conducted at the Swiss Paraplegic Centre in Nottwil, Switzerland.

Methods
Four patients aged 22 to 60 years were observed during and after therapy. Three had complete paraplegia (levels Th4–Th8) with neuropathic at- and below-level pain, while one had incomplete paraplegia (Th10) with at-level pain. The primary outcome measured was satisfaction with acceptance of and adherence to virtual walking therapy, alongside suggestions for therapy improvements. Additionally, patients kept a pain diary and pain drawings to measure the extent of pain distribution and intensity before and after therapy. Therapy schedules included either two sessions per week for five weeks or five sessions per week for two weeks.

Results
There was a sound satisfaction and good acceptance amongst participants. Support, duration, and number of sessions were perceived well and acceptable. Pain as a secondary outcome did not change during or after therapy in all but one patient which improved in pain intensity, pain quality as well as pain distribution.

Conclusion
Results suggest that our virtual walking setting is a feasible tool that should be further studied in patients with SCI-related chronic neuropathic pain.
Neutrophil extracellular traps characterize caseating granulomas
Authors: Zlatar Leticija , Knopf Jasmin , Singh Jeeshan , Wang Han , Muñoz-Becerra Marco , Herrmann Irmgard , Chukwuanukwu Rebecca C. , Eckstein Markus , Eichhorn Philip , Rieker Ralf J. , Naschberger Elisabeth , Burkovski Andreas , Krenn Veit , Bilyy Rostyslav , Butova Tetiana , Liskina Iryna , Kalabukha Ihor , Khmel Oleg , Boettcher Michael , Schett Georg , Butov Dmytro , Tkachenko Anton , Herrmann Martin 
Published: July 2024

AbstractTuberculosis (TB) remains one of the top 10 causes of death worldwide and still poses a serious challenge to public health. Recent attention to neutrophils has uncovered unexplored areas demanding further investigation. Therefore, the aim of this study was to determine neutrophil activation and circulatory neutrophil extracellular trap (NET) formation in various types of TB. Sera from TB patients (n = 91) and healthy controls (NHD; n = 38) were analyzed for NE-DNA and MPO–DNA complexes, cell-free DNA (cfDNA), and protease activity (elastase). We show that these NET parameters were increased in TB sera. Importantly, NET formation and NE activity were elevated in TB patients with extensive tissue damage when compared to those with minor damage and in patients with relapse, compared to new cases. We discuss the importance of balancing NET formation to prevent tissue damage or even relapse and argue to analyze circulating NET parameters to monitor the risk of disease relapse. To investigate the tissues for NETs and to find the source of the circulating NET degradation products, we collected sections of granulomas in lung and lymph node biopsies. Samples from other diseases with granulomas, including sarcoidosis (SARC) and apical periodontitis (AP), served as controls. Whereas NET formation characterizes the caseating granulomas, both caseating and non-caseating granulomas harbor DNA with unusual conformation. As TB is associated with hypercoagulation and thromboembolism, we further imaged the pulmonary vessels of TB patients and detected vascular occlusions with neutrophil aggregates. This highlights the dual role of neutrophils in the pathology of TB.
Bardet-Biedl syndrome improved diagnosis criteria and management: Inter European Reference Networks consensus statement and recommendations
Authors: Dollfus Hélène , Lilien Marc R. , Maffei Pietro , Verloes Alain , Muller Jean , Bacci Giacomo M. , Cetiner Metin , van den Akker Erica L. T. , Grudzinska Pechhacker Monika , Testa Francesco , Lacombe Didier , Stokman Marijn F. , Simonelli Francesca , Gouronc Aurélie , Gavard Amélie , van Haelst Mieke M. , Koenig Jens , Rossignol Sylvie , Bergmann Carsten , Zacchia Miriam , Leroy Bart P. , Mosbah Héléna , Van Eerde Albertien M. , Mekahli Djalila , Servais Aude , Poitou Christine , Valverde Diana 
Published: July 2024

AbstractFour European Reference Networks (ERN-EYE, ERKNet, Endo-ERN, ERN-ITHACA) have teamed up to establish a consensus statement and recommendations for Bardet-Biedl syndrome (BBS). BBS is an autosomal recessive ciliopathy with at least 26 genes identified to date. The clinical manifestations are pleiotropic, can be observed in utero and will progress with age. Genetic testing has progressively improved in the last years prompting for a revision of the diagnostic criteria taking into account clinical Primary and Secondary features, as well as positive or negative molecular diagnosis. This consensus statement also emphasizes on initial diagnosis, monitoring and lifelong follow-up, and symptomatic care that can be provided to patients and family members according to the involved care professionals. For paediatricians, developmental anomalies can be at the forefront for diagnosis (such as polydactyly) but can require specific care, such as for associated neuro developmental disorders. For ophthalmology, the early onset retinal degeneration requires ad hoc functional and imaging technologies and specific care for severe visual impairment. For endocrinology, among other manifestations, early onset obesity and its complications has benefited from better evaluation of eating behaviour problems, improved lifestyle programs, and from novel pharmacological therapies. Kidney and urinary track involvements warrants lifespan attention, as chronic kidney failure can occur and early management might improve outcome. This consensus recommends revised diagnostic criteria for BBS that will ensure certainty of diagnosis, giving robust grounds for genetic counselling as well as in the perspective of future trials for innovative therapies.
Characterization and prevalence of ocular comorbidities and risk of legal blindness across the United States
Authors: Chu Jeffrey , Shaia Jacqueline K. , Sharma Neha , Russell Matthew W. , Rachitskaya Aleksandra V. , Talcott Katherine E. , Singh Rishi P. 
Published: July 2024

Abstract
Background/Objectives
Vision loss is a top disability in the United States (US). Patients commonly present with multiple ocular diseases, but the extent to which this places them at risk for vision loss, and if sex and race impacts this, is poorly understood. This exploratory analysis evaluated which ocular comorbidities and demographics are at highest risk for visual impairment.

Subjects/Methods
A retrospective cross-sectional study was conducted through the TriNetX Analytics Network, an aggregated network encompassing over 90 million insured and uninsured patients across 50 healthcare organizations from all regions in the US. Patients with diabetic retinopathy (DR), age-related macular degeneration (AMD), retinal vein occlusion (RVO), glaucoma, and uveitis were included in this study. Ocular diseases and visual impairment were determined through ICD-10 codes. Prevalence and odds ratios were calculated while stratifying by sex and racial demographics. Statistical analyses were completed using RStudio and Excel with 95% confidence intervals calculated.

Results
The comorbid conditions with the highest prevalence of visual impairment were uveitis and RVO (39.94%), uveitis and neovascular AMD (37.61%), and uveitis and glaucoma (33.23%). The comorbidity with the highest odds for visual impairment was uveitis and RVO (POR 4.86; 95% CI 4.49, 5.26). Compared to white males, Black and Hispanic males were disproportionately affected by visual impairment across ocular comorbidities.

Conclusion
This study quantified the prevalence and odds of visual impairment for unilateral and comorbid ocular disease, with the addition of uveitis causing the greatest increase. Black and Hispanic males were disproportionately affected by visual impairment across comorbid conditions.
A stress-induced source of phonon bursts and quasiparticle poisoning
Authors: Anthony-Petersen Robin , Biekert Andreas , Bunker Raymond , Chang Clarence L. , Chang Yen-Yung , Chaplinsky Luke , Fascione Eleanor , Fink Caleb W. , Garcia-Sciveres Maurice , Germond Richard , Guo Wei , Hertel Scott A. , Hong Ziqing , Kurinsky Noah , Li Xinran , Lin Junsong , Lisovenko Marharyta , Mahapatra Rupak , Mayer Adam , McKinsey Daniel N. , Mehrotra Siddhant , Mirabolfathi Nader , Neblosky Brian , Page William A. , Patel Pratyush K. , Penning Bjoern , Pinckney H. Douglas , Platt Mark , Pyle Matt , Reed Maggie , Romani Roger K. , Santana Queiroz Hadley , Sadoulet Bernard , Serfass Bruno , Smith Ryan , Sorensen Peter , Suerfu Burkhant , Suzuki Aritoki , Underwood Ryan , Velan Vetri , Wang Gensheng , Wang Yue , Watkins Samuel L. , Williams Michael R. , Yefremenko Volodymyr , Zhang Jianjie 
Published: July 2024

AbstractThe performance of superconducting qubits is degraded by a poorly characterized set of energy sources breaking the Cooper pairs responsible for superconductivity, creating a condition often called “quasiparticle poisoning”. Both superconducting qubits and low threshold dark matter calorimeters have observed excess bursts of quasiparticles or phonons that decrease in rate with time. Here, we show that a silicon crystal glued to its holder exhibits a rate of low-energy phonon events that is more than two orders of magnitude larger than in a functionally identical crystal suspended from its holder in a low-stress state. The excess phonon event rate in the glued crystal decreases with time since cooldown, consistent with a source of phonon bursts which contributes to quasiparticle poisoning in quantum circuits and the low-energy events observed in cryogenic calorimeters. We argue that relaxation of thermally induced stress between the glue and crystal is the source of these events.
All-visible-light-driven salicylidene schiff-base-functionalized artificial molecular motors
Authors: van Vliet Sven , Sheng Jinyu , Stindt Charlotte N. , Feringa Ben L. 
Published: July 2024

AbstractLight-driven rotary molecular motors are among the most promising classes of responsive molecular machines and take advantage of their intrinsic chirality which governs unidirectional rotation. As a consequence of their dynamic function, they receive considerable interest in the areas of supramolecular chemistry, asymmetric catalysis and responsive materials. Among the emerging classes of responsive photochromic molecules, multistate first-generation molecular motors driven by benign visible light remain unexplored, which limits the exploitation of the full potential of these mechanical light-powered systems. Herein, we describe a series of all-visible-light-driven first-generation molecular motors based on the salicylidene Schiff base functionality. Remarkable redshifts up to 100 nm in absorption are achieved compared to conventional first-generation motor structures. Taking advantage of all-visible-light-driven multistate motor scaffolds, adaptive behaviour is found as well, and potential application in multistate photoluminescence is demonstrated. These functional visible-light-responsive motors will likely stimulate the design and synthesis of more sophisticated nanomachinery with a myriad of future applications in powering dynamic systems.
A chimeric vaccine derived from Australian genotype IV Japanese encephalitis virus protects mice from lethal challenge
Authors: Harrison Jessica J. , Nguyen Wilson , Morgan Mahali S. , Tang Bing , Habarugira Gervais , de Malmanche Henry , Freney Morgan E. , Modhiran Naphak , Watterson Daniel , Cox Abigail L. , Yan Kexin , Yuen Nicholas K. Y. , Bowman Dylan H. , Kirkland Peter D. , Bielefeldt-Ohmann Helle , Suhrbier Andreas , Hall Roy A. , Rawle Daniel J. , Hobson-Peters Jody 
Published: July 2024

AbstractIn 2022, a genotype IV (GIV) strain of Japanese encephalitis virus (JEV) caused an unprecedented and widespread outbreak of disease in pigs and humans in Australia. As no veterinary vaccines against JEV are approved in Australia and all current approved human and veterinary vaccines are derived from genotype (G) III JEV strains, we used the recently described insect-specific Binjari virus (BinJV) chimeric flavivirus vaccine technology to produce a JEV GIV vaccine candidate. Herein we describe the production of a chimeric virus displaying the structural prM and E proteins of a JEV GIV isolate obtained from a stillborn piglet (JEVNSW/22) in the genomic backbone of BinJV (BinJ/JEVNSW/22-prME). BinJ/JEVNSW/22-prME was shown to be antigenically indistinguishable from the JEVNSW/22 parental virus by KD analysis and a panel of JEV-reactive monoclonal antibodies in ELISA. BinJ/JEVNSW/22-prME replicated efficiently in C6/36 cells, reaching titres of >107 infectious units/mL - an important attribute for vaccine manufacture. As expected, BinJ/JEVNSW/22-prME failed to replicate in a variety of vertebrate cells lines. When used to immunise mice, the vaccine induced a potent virus neutralising response against JEVNSW/22 and to GII and GIII JEV strains. The BinJ/JEVNSW/22-prME vaccine provided complete protection against lethal challenge with JEVNSW/22, whilst also providing partial protection against viraemia and disease for the related Murray Valley encephalitis virus. Our results demonstrate that BinJ/JEVNSW/22-prME is a promising vaccine candidate against JEV.
FANCD2–FANCI surveys DNA and recognizes double- to single-stranded junctions
Authors: Alcón Pablo , Kaczmarczyk Artur P. , Ray Korak Kumar , Liolios Themistoklis , Guilbaud Guillaume , Sijacki Tamara , Shen Yichao , McLaughlin Stephen H. , Sale Julian E. , Knipscheer Puck , Rueda David S. , Passmore Lori A. 
Published: July 2024

Abstract
DNA crosslinks block DNA replication and are repaired by the Fanconi anaemia pathway. The FANCD2–FANCI (D2–I) protein complex is central to this process as it initiates repair by coordinating DNA incisions around the lesion1. However, D2–I is also known to have a more general role in DNA repair and in protecting stalled replication forks from unscheduled degradation2–4. At present, it is unclear how DNA crosslinks are recognized and how D2–I functions in replication fork protection. Here, using single-molecule imaging, we show that D2–I is a sliding clamp that binds to and diffuses on double-stranded DNA. Notably, sliding D2–I stalls on encountering single-stranded–double-stranded (ss–ds) DNA junctions, structures that are generated when replication forks stall at DNA lesions5. Using cryogenic electron microscopy, we determined structures of D2–I on DNA that show that stalled D2–I makes specific interactions with the ss–dsDNA junction that are distinct from those made by sliding D2–I. Thus, D2–I surveys dsDNA and, when it reaches an ssDNA gap, it specifically clamps onto ss–dsDNA junctions. Because ss–dsDNA junctions are found at stalled replication forks, D2–I can identify sites of DNA damage. Therefore, our data provide a unified molecular mechanism that reconciles the roles of D2–I in the recognition and protection of stalled replication forks in several DNA repair pathways.
Cranioencephalic functional lymphoid units in glioblastoma
Authors: Dobersalske Celia , Rauschenbach Laurèl , Hua Yichao , Berliner Christoph , Steinbach Anita , Grüneboom Anika , Kokkaliaris Konstantinos D. , Heiland Dieter H. , Berger Pia , Langer Sarah , Tan Chin L. , Stenzel Martin , Landolsi Somaya , Weber Flora , Darkwah Oppong Marvin , Werner Rudolf A. , Gull Hanah , Schröder Thomas , Linsenmann Thomas , Buck Andreas K. , Gunzer Matthias , Stuschke Martin , Keyvani Kathy , Forsting Michael , Glas Martin , Kipnis Jonathan , Steindler Dennis A. , Reinhardt Hans Christian , Green Edward W. , Platten Michael , Tasdogan Alpaslan , Herrmann Ken , Rambow Florian , Cima Igor , Sure Ulrich , Scheffler Björn 
Published: July 2024

AbstractThe ecosystem of brain tumors is considered immunosuppressed, but our current knowledge may be incomplete. Here we analyzed clinical cell and tissue specimens derived from patients presenting with glioblastoma or nonmalignant intracranial disease to report that the cranial bone (CB) marrow, in juxtaposition to treatment-naive glioblastoma tumors, harbors active lymphoid populations at the time of initial diagnosis. Clinical and anatomical imaging, single-cell molecular and immune cell profiling and quantification of tumor reactivity identified CD8+ T cell clonotypes in the CB that were also found in the tumor. These were characterized by acute and durable antitumor response rooted in the entire T cell developmental spectrum. In contrast to distal bone marrow, the CB niche proximal to the tumor showed increased frequencies of tumor-reactive CD8+ effector types expressing the lymphoid egress marker S1PR1. In line with this, cranial enhancement of CXCR4 radiolabel may serve as a surrogate marker indicating focal association with improved progression-free survival. The data of this study advocate preservation and further exploitation of these cranioencephalic units for the clinical care of glioblastoma.