bluuebunny/crossref_metadata_2025_split huggingface dataset:
Health outcomes in chronic kidney disease patients with cognitive impairment or dementia: a global collaborative analysis
Authors: Merlino Lino , Rainone Francesco , Chinnadurai Rajkumar , Hernandez Gema , Tollitt James , Battini Graziana G , Colombo Paolo M , Trivelli Marco , Stewart Stuart , Dunne Ross A , Kalra Philip A 
Published: December 2024

ABSTRACT

Background and hypothesis
Mild cognitive impairment and dementia (CI) are common in patients with CKD. We aim to clarify whether and how CKD and CI coexistence increases adverse health outcomes.

Methods
This retrospective observational cohort study was conducted on CKD patients (stages 3–5) from the TriNetX platform. CKD patients with and without pre-existing CI were included from 115 healthcare organizations, and their outcomes were compared. The two cohorts were propensity score matched (PSM) for age, sex, ethnicity, comorbidities, BMI, blood parameters, and medications. The proportional hazard assumption was tested with a 95% confidence interval. Kaplan–Meier analysis was used to calculate survival probability. Outcomes were included from 1 day after the CKD diagnosis until 10 years afterwards.

Results
We identified 533 772 CKD patients, and 8184 had co-existent CI. Two cohorts of 8170 PSM patients each were generated. The mean age was 60.5 ± 7.0 years and the eGFR was 52.1±19 mL/min. Mean follow-up was 23.2 months. CKD patients with CI had higher all-cause mortality (18.5% vs 12.6%), higher risk of cerebrovascular disease (11.3% vs 6.9%), transient cerebral ischemic attacks (2.7% vs 1.6%), hypotension (16.5%–12.5%), malnutrition (6.7% vs 4.0%), pneumonia (10.7% vs 7.9%), urinary infections (13.2% vs 9.3%), encephalopathy (9.9% vs 5.0%), mood disorders (13.6% vs 9.7%), psychosis (9.8% vs 4.6%), and epilepsy (4.3% vs 1.5%). Higher use of antidepressants (26.3% vs 16.3%), anticonvulsants (19.5% vs 15.1%), antipsychotics (18.6% vs 9.1%), anticholinesterase (5.6% vs 0.1%), and benzodiazepines (30.6% vs 26.6%) was noted in those with CI. All these findings were statistically significant.

Conclusion
Despite the limitations of a retrospective study, real-world data demonstrate that concomitant CI is a decisive risk factor for higher mortality and increased adverse outcomes in patients with CKD. These results highlight the need for routine comprehensive cognitive assessments in patients at any stage of CKD.
Algorithm for solving quantum linear systems of equations with coherent superposition and extended applications
Authors: Xia Qiqing , Zhu Qianru , Xie Huiqin , Yang Li 
Published: December 2024

Abstract
Many quantum algorithms for attacking symmetric cryptography involve the rank problem of quantum linear equations. In this paper, two quantum algorithms are proposed to solve quantum linear systems of equations with coherent superposition, and their specific quantum circuits are constructed. In contrast to previous related studies, our quantum algorithms are universal, computing both the rank and general solution by one measurement. The difference between them is whether the data register containing the quantum coefficient matrix can be disentangled from the other registers while keeping the data qubits unchanged. On this basis, the two quantum algorithms are applied as subroutines to parallel Simon’s algorithm (with multiple periods), Grover Meets Simon algorithm, and Alg-PolyQ2 algorithm. Subsequently, a quantum classifier within Grover Meets Simon algorithm and a detailed test oracle within Alg-PolyQ2 algorithms are constructed, including their respective quantum circuits. To the best of our knowledge, no such specific analysis has been previously performed. The success probability of these algorithms is rigorously analyzed to ensure that the probability of success on the proposed quantum algorithms will not be lower than that of the original algorithms. Finally, we discuss the lower bound of the number of controlled-NOT gates for solving quantum linear systems of equations with coherent superposition. Our analysis indicates that the proposed algorithms are suitable for conducting attacks against lightweight symmetric ciphers within the effective working time of an ion-trap quantum computer.
Genetic resonance: dissecting the heritability and genetic correlations of human hearing acuity
Authors: Duran Jerry A , Watkins W Scott , Neklason Deborah W , Jorde Lynn B 
Published: December 2024

Abstract
This study presents a frequency-specific, pedigree-based assessment of hearing acuity heritability. We analysed 34 Utah Centre d'Etude du Polymorphisme Humain (CEPH) pedigrees comprising 464 individuals, using whole-genome sequencing (WGS) and audiometric evaluations. Our analysis reveals a general decline in narrow-sense heritability as frequency increases. When calculated using the Sequential Oligogenic Linkage Analysis Routines (SOLAR) software package, narrow-sense heritability estimates drop from 51% at 250 Hz to 30% at 8000 Hz. Genetic correlations (Rho(G)), the degree to which genetic variation in one trait correlates with another, are higher for hearing acuity at similar frequencies. For example, Rho(G) between 250 and 500 Hz is 0.80, and Rho(G) between 6000 and 8000 Hz is 0.91. In contrast, frequencies distant from each other exhibit decreased Rho(G) with a genetic correlation of only 0.21 for hearing acuity at frequencies 250 and 8000 Hz. This assessment of the genetics underlying hearing acuity in a family-based design provides new details of genetic factors influencing hearing acuity in a frequency-specific approach.
Robust sex determination in the Caenorhabditis nigoni germ line
Authors: Harbin Jonathan P , Shen Yongquan , Lin Shin-Yi , Kemper Kevin , Haag Eric S , Schwarz Erich M , Ellis Ronald E 
Published: December 2024

Abstract
Sexual characteristics and reproductive systems are dynamic traits in many taxa, but the developmental modifications that allow change and innovation are largely unknown. A leading model for this process is the evolution of self-fertile hermaphrodites from male/female ancestors. However, these studies require direct analysis of sex determination in male/female species, as well as in the hermaphroditic species that are related to them. In Caenorhabditis nematodes, this has only become possible recently, with the discovery of new species. Here, we use gene editing to characterize major sex determination genes in Caenorhabditis nigoni, a sister to the widely studied hermaphroditic species Caenorhabditis briggsae. These 2 species are close enough to mate and form partially fertile hybrids. First, we find that tra-1 functions as the master regulator of sex in C. nigoni, in both the soma and the germ line. Surprisingly, these mutants make only sperm, in contrast to tra-1 mutants in related hermaphroditic species. Moreover, the XX mutants display a unique defect in somatic gonad development that is not seen elsewhere in the genus. Second, the fem-3 gene acts upstream of tra-1 in C. nigoni, and the mutants are females, unlike in the sister species C. briggsae, where they develop as hermaphrodites. This result points to a divergence in the role of fem-3 in the germ line of these species. Third, tra-2 encodes a transmembrane receptor that acts upstream of fem-3 in C. nigoni. Outside of the germ line, tra-2 mutations in all species cause a similar pattern of partial masculinization. However, heterozygosity for tra-2 does not alter germ cell fates in C. nigoni, as it can in sensitized backgrounds of 2 hermaphroditic species of Caenorhabditis. Finally, the epistatic relationships point to a simple, linear germline pathway in which tra-2 regulates fem-3 which regulates tra-1, unlike the more complex relationships seen in hermaphrodite germ cell development. Taking these results together, the regulation of sex determination is more robust and streamlined in the male/female species C. nigoni than in related species that make self-fertile hermaphrodites, a conclusion supported by studies of interspecies hybrids using sex determination mutations. Thus, we infer that the origin of self-fertility not only required mutations that activated the spermatogenesis program in XX germ lines, but prior to these there must have been mutations that decanalized the sex determination process, allowing for subsequent changes to germ cell fates.
Assessing the Feasibility and Efficacy of Virtual Reality Navigational Training for Older Adults
Authors: Xu Tong Bill , Mostafavi Armin , Boot Walter R , Czaja Sara , Kalantari Saleh 
Published: December 2024

Abstract

Background and Objectives
This study evaluates the feasibility of virtual reality (VR) wayfinding training with aging adults and assesses the impact of the training on wayfinding performance.

Research Design and Methods
49 participants were recruited using a convenience sample approach. Wayfinding tasks were conducted by 3 participant groups: active VR training, passive video training, and no training, assigned randomly. The training featured 5 tasks in a digital version of a real building. Post-training assessments used 10 tasks in this same building, half of the tasks familiar from the training and half new. The study was double-blinded, with each intervention lasting 10 min. The primary outcomes include the Distance Traveled and Duration for each wayfinding task, with a fixed 10-min limit.

Results
Participants in the VR group reported moderate usability and a high sense of Self Location in the environment with respect to the training intervention. No significant differences were found in performance for the first group of similar wayfinding tasks; however, in the subsequent set of new tasks the VR group significantly outperformed the Control group. This suggests a possible spatial learning effect across multiple exposures (VR training followed by similar task). No adverse effects were reported during or post intervention.

Discussion and Implications
This study provides preliminary evidence that VR training can help to improve wayfinding performance in older adults with no reported adverse effects.
Effective governance of marine recreational fisheries in Europe is needed to maximize the societal benefits of its fisheries
Authors: Grati Fabio , Hyder Kieran , Mugerza Estanis , Arlinghaus Robert , Baudrier Jerome , Bell Brigid , Bolognini Luca , De Groote Annica I , Diogo Hugo , Haase Kevin , Pita Pablo , Potts Warren , Radford Zachary , Regimbart Amelie , Scanu Martina , Skov Christian , Ustups Didzis , Verleye Thomas , Vølstad Jon Helge , Weltersbach Marc Simon , Strehlow Harry V 
Published: December 2024

Abstract
Marine recreational fishing (MRF) is a socially and economically relevant fishing activity in Europe, but its impacts on ecosystems and the economy remain poorly understood, and management is limited. This paper evaluates the current European fisheries governance, particularly the Common Fisheries Policy, in addressing MRF issues. Our evaluation highlights the lack of explicit recognition of MRF in European Union legislation, where recreational fisheries are not or insufficiently managed within a commercial fisheries-oriented policy framework. We recommend policy reform that explicitly recognizes recreational fisheries as a distinct fisheries sector with its own interests, values and objectives, and dynamics that differ from those typical in commercial fisheries. On the operational level, we recommend involving key organizations representing MRF interests in advisory groups dealing with marine fisheries, nature conservation, and marine spatial use, and encourage sustainable fishing practices among all types of fisheries. To achieve this, there is a need for better and more comprehensive data collection, stakeholder engagement, and outreach to support effective MRF governance and management. By addressing these issues, Europe can maximize the benefits of MRF, while ensuring the sustainability of fisheries.
A logical framework for data-driven reasoning
Authors: Baldi Paolo , Corsi Esther Anna , Hosni Hykel 
Published: December 2024

Abstract
We introduce and investigate a family of consequence relations with the goal of capturing certain important patterns of data-driven inference. The inspiring idea for our framework is the fact that data may reject, possibly to some degree, and possibly by mistake, any given scientific hypothesis. There is no general agreement in science about how to do this, which motivates putting forward a logical formulation of the problem. We do so by investigating distinct definitions of ‘rejection degrees’ each yielding a consequence relation. Our investigation leads to novel variations on the theme of rational consequence relations, prominent among non-monotonic logics.
Synchronous bilateral breast cancer with heterogeneous hormone receptor status: a case report
Authors: Luitel Prajjwol , Karki Badal , Paudel Sujan , Shrestha Asim , Pariyar Suraj , Hirachan Suzita 
Published: December 2024

Abstract
The expression of estrogen, progesterone, and HER2 receptors in breast cancer cells helps guide treatment and predict outcomes. When the status of these receptors is heterogeneous, it makes treatment planning more complex. We present the case of a 72-year-old woman with bilateral breast cancer with heterogenous receptor status and subsequent challenges in management.
Machine learning-based prognostic subgrouping of glioblastoma: A multicenter study
Authors: Akbari Hamed , Bakas Spyridon , Sako Chiharu , Fathi Kazerooni Anahita , Villanueva-Meyer Javier , Garcia Jose A , Mamourian Elizabeth , Liu Fang , Cao Quy , Shinohara Russell T , Baid Ujjwal , Getka Alexander , Pati Sarthak , Singh Ashish , Calabrese Evan , Chang Susan , Rudie Jeffrey , Sotiras Aristeidis , LaMontagne Pamela , Marcus Daniel S , Milchenko Mikhail , Nazeri Arash , Balana Carmen , Capellades Jaume , Puig Josep , Badve Chaitra , Barnholtz-Sloan Jill S , Sloan Andrew E , Vadmal Vachan , Waite Kristin , Ak Murat , Colen Rivka R , Park Yae Won , Ahn Sung Soo , Chang Jong Hee , Choi Yoon Seong , Lee Seung-Koo , Alexander Gregory S , Ali Ayesha S , Dicker Adam P , Flanders Adam E , Liem Spencer , Lombardo Joseph , Shi Wenyin , Shukla Gaurav , Griffith Brent , Poisson Laila M , Rogers Lisa R , Kotrotsou Aikaterini , Booth Thomas C , Jain Rajan , Lee Matthew , Mahajan Abhishek , Chakravarti Arnab , Palmer Joshua D , DiCostanzo Dominic , Fathallah-Shaykh Hassan , Cepeda Santiago , Santonocito Orazio Santo , Di Stefano Anna Luisa , Wiestler Benedikt , Melhem Elias R , Woodworth Graeme F , Tiwari Pallavi , Valdes Pablo , Matsumoto Yuji , Otani Yoshihiro , Imoto Ryoji , Aboian Mariam , Koizumi Shinichiro , Kurozumi Kazuhiko , Kawakatsu Toru , Alexander Kimberley , Satgunaseelan Laveniya , Rulseh Aaron M , Bagley Stephen J , Bilello Michel , Binder Zev A , Brem Steven , Desai Arati S , Lustig Robert A , Maloney Eileen , Prior Timothy , Amankulor Nduka , Nasrallah MacLean P , O’Rourke Donald M , Mohan Suyash , Davatzikos Christos ,   ReSPOND consortium, Davatzikos Christos 
Published: December 2024

Abstract

Background
Glioblastoma (GBM) is the most aggressive adult primary brain cancer, characterized by significant heterogeneity, posing challenges for patient management, treatment planning, and clinical trial stratification.

Methods
We developed a highly reproducible, personalized prognostication, and clinical subgrouping system using machine learning (ML) on routine clinical data, magnetic resonance imaging (MRI), and molecular measures from 2838 demographically diverse patients across 22 institutions and 3 continents. Patients were stratified into favorable, intermediate, and poor prognostic subgroups (I, II, and III) using Kaplan–Meier analysis (Cox proportional model and hazard ratios [HR]).

Results
The ML model stratified patients into distinct prognostic subgroups with HRs between subgroups I–II and I–III of 1.62 (95% CI: 1.43–1.84, P &lt; .001) and 3.48 (95% CI: 2.94–4.11, P &lt; .001), respectively. Analysis of imaging features revealed several tumor properties contributing unique prognostic value, supporting the feasibility of a generalizable prognostic classification system in a diverse cohort.

Conclusions
Our ML model demonstrates extensive reproducibility and online accessibility, utilizing routine imaging data rather than complex imaging protocols. This platform offers a unique approach to personalized patient management and clinical trial stratification in GBM.
The circadian clock orchestrates spermatogonial differentiation and fertilization by regulating retinoic acid (RA) signaling in vertebrates
Authors: Liu Taole , He Wei , Zhong Zhaomin , Lu Chenchen , Wu Lianxin , Wang Ziming , Smith William Kojo , Shi Quan , Long Qiaoming , Wang Han 
Published: December 2024

Abstract
The circadian clock generates and maintains ∼24-hour oscillations in almost all organs. The testis, however, remains mysterious without a clear understanding of its circadian functions. Our time-series transcriptome analysis reveals more than 1,000 rhythmically expressed genes in the zebrafish and mouse testes, respectively. Canonical circadian clock genes are rhythmically expressed in Sertoli cells and regulate retinoic acid (RA) production, which is also evidenced by their co-expression with RA synthesis genes in single Sertoli cells. Genetic and pharmacological manipulations and temporal desynchronization revealed that the circadian clock-regulated RA signaling synchronizes spermatogonial differentiation via zbtb16a and promotes fertilization via izumo1 in zebrafish. Our findings indicate that the testicular circadian clock contributes to reproduction in a cell-specific manner through RA signaling, highlighting circadian roles in male fertility.
Sustainable management of riverine N2O emission baselines
Authors: Wang Shuo , Zhi Wei , Li Shengjie , Lyu Tao , Ji Guodong 
Published: December 2024

ABSTRACT
The riverine N2O fluxes are assumed to linearly increase with nitrate loading. However, this linear relationship with a uniform EF5r is poorly constrained, which impedes the N2O estimation and mitigation. Our meta-analysis discovered a universal N2O emission baseline (EF5r = k/[NO3−], k = 0.02) for natural rivers. Anthropogenic impacts caused an overall increase in baselines and the emergence of hotspots, which constitute two typical patterns of anthropogenic sources. The k values of agricultural and urban rivers increased to 0.09 and 0.05, respectively, with 11% and 14% of points becoming N2O hotspots. Priority control of organic and NH4+ pollution could eliminate hotspots and reduce emissions by 51.6% and 63.7%, respectively. Further restoration of baseline emissions on nitrate removal is a long-term challenge considering population growth and declining unit benefits (ΔN-N2O/N-NO3−). The discovery of EF lines emphasized the importance of targeting hotspots and managing baseline emissions sustainably to balance social and environmental benefits.
Impact of Vitamin A Deficiency on Iron Metabolism and Anemia: A Historical Perspective and Research Advances
Authors: Mejia Luis A , Erdman Jr John W 
Published: December 2024

Abstract
Vitamin A deficiency (VAD) and iron deficiency anemia coexist around the world, particularly in children and women of reproductive age in low- and middle-income countries. Within this scenario, there is a known interaction between vitamin A and iron, and it has been postulated that lack of vitamin A impairs iron metabolism, leading to vitamin A deficiency anemia (VADA). Current animal, epidemiological, and clinical studies support this notion. The objective of this study was to review the current literature on proposed metabolic mechanisms regarding how VAD modulates iron metabolism leading to anemia. To attain this objective, a literature search was conducted of research publications in the related field, without date restriction, using PubMed, Scopus, Google Scholar, and the University of Illinois’s reference system. The data support the essentiality of vitamin A for normal erythropoiesis. It indicates that, in VAD, iron mobilization is impaired, and that this mineral accumulates in the liver and spleen, making it less available for erythropoiesis. A triggering factor for the development of VADA seems to be inflammation and systemic infection, which release cytokines that upregulate the production of hepcidin by the liver. VAD may also increase hepcidin directly without the involvement of inflammation or infection. The elevated hepcidin, in turn, lowers circulating iron and sequesters iron in storage depots, downregulating erythropoietin, leading to inefficient erythropoiesis, decreased hemoglobin (Hb) production, and (subsequently) anemia. VAD may also impact the expression of iron regulatory protein 2 (IRP2), and thus affect intracellular iron metabolism gene expression. VADA is not due to iron deficiency, but to a redistribution of iron in the body. Understanding the mechanism of VADA will assist in designing more effective strategies for combating anemia worldwide.
Arabidopsis WALL-ASSOCIATED KINASES are not required for oligogalacturonide-induced signaling and immunity
Authors: Herold Laura , Ordon Jana , Hua Chenlei , Kohorn Bruce D , Nürnberger Thorsten , DeFalco Thomas A , Zipfel Cyril 
Published: December 2024

Abstract
Carbohydrate-based cell wall signaling impacts plant growth, development, and stress responses; however, how cell wall signals are perceived and transduced remains poorly understood. Several cell wall breakdown products have been described as typical damage-associated molecular patterns that activate plant immunity, including pectin-derived oligogalacturonides (OGs). Receptor kinases of the WALL-ASSOCIATED KINASE (WAK) family bind pectin and OGs and were previously proposed as OG receptors. However, unambiguous genetic evidence for the role of WAKs in OG responses is lacking. Here, we investigated the role of Arabidopsis (Arabidopsis thaliana) WAKs in OG perception using a clustered regularly interspaced short palindromic repeats mutant in which all 5 WAK genes were deleted. Using a combination of immune assays for early and late pattern-triggered immunity, we show that WAKs are dispensable for OG-induced signaling and immunity, indicating that they are not bona fide OG receptors.
Phosphorylation of the transcription factor OsNAC29 by OsMAPK3 activates diterpenoid genes to promote rice immunity
Authors: Lu Ling , Fang Jianbo , Xia Na , Zhang Jing , Diao Zhijuan , Wang Xun , Liu Yan , Tang Dingzhong , Li Shengping 
Published: December 2024

Abstract
Well-conserved mitogen-activated protein kinase (MAPK) cascades are essential for orchestrating of a wide range of cellular processes in plants, including defense responses against pathogen attack. NAC transcription factors (TFs) play important roles in plant immunity, but their targets and how they are regulated remain largely unknown. Here, we identified the TF OsNAC29 as a key component of a MAPK signaling pathway involved in rice (Oryza sativa) disease resistance. OsNAC29 binds directly to CACGTG motifs in the promoters of OsTPS28 and OsCYP71Z2, which are crucial for the biosynthesis of the phytoalexin 5,10-diketo-casbene and consequently rice blast resistance. OsNAC29 positively regulates rice blast resistance by promoting the expression of of OsTPS28 and OsCYP71Z2, and the function of OsNAC29 is genetically dependent on OsCYP71Z2 and OsTPS28. Furthermore, OsNAC29 interacts with OsRACK1A and OsMAPK3/6 to form an immune complex; OsMAPK3 phosphorylates OsNAC29 at Thr304 to prevent its proteasome-mediated degradation and promote its function against rice blast fungus. Phosphorylation of OsNAC29 at Thr304 is induced upon Magnaporthe oryzae infection and chitin treatment. Our data demonstrate the positive role of the OsMAPK3–OsNAC29–OsTPS28/OsCYP71Z2 module in rice blast resistance, providing insights into the molecular regulatory network and fine-tuning of NAC TFs in rice immunity.