bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automating literature screening and curation with applications to computational neuroscience
Authors: Ji Ziqing , Guo Siyan , Qiao Yujie , McDougal Robert A 
Published: May 2024

Abstract

Objective
ModelDB (https://modeldb.science) is a discovery platform for computational neuroscience, containing over 1850 published model codes with standardized metadata. These codes were mainly supplied from unsolicited model author submissions, but this approach is inherently limited. For example, we estimate we have captured only around one-third of NEURON models, the most common type of models in ModelDB. To more completely characterize the state of computational neuroscience modeling work, we aim to identify works containing results derived from computational neuroscience approaches and their standardized associated metadata (eg, cell types, research topics).

Materials and Methods
Known computational neuroscience work from ModelDB and identified neuroscience work queried from PubMed were included in our study. After pre-screening with SPECTER2 (a free document embedding method), GPT-3.5, and GPT-4 were used to identify likely computational neuroscience work and relevant metadata.

Results
SPECTER2, GPT-4, and GPT-3.5 demonstrated varied but high abilities in identification of computational neuroscience work. GPT-4 achieved 96.9% accuracy and GPT-3.5 improved from 54.2% to 85.5% through instruction-tuning and Chain of Thought. GPT-4 also showed high potential in identifying relevant metadata annotations.

Discussion
Accuracy in identification and extraction might further be improved by dealing with ambiguity of what are computational elements, including more information from papers (eg, Methods section), improving prompts, etc.

Conclusion
Natural language processing and large language model techniques can be added to ModelDB to facilitate further model discovery, and will contribute to a more standardized and comprehensive framework for establishing domain-specific resources.
The use of master protocols for efficient trial design to evaluate radiotherapy interventions: a systematic review
Authors: Gilbert Alexandra , Samuel Robert , Cagney Daniel , Sebag-Montefiore David , Brown Julia , Brown Sarah R 
Published: May 2024

Abstract
The aim of this review was to highlight why the use of master protocols trial design is particularly useful for radiotherapy intervention trials where complex setup pathways (including quality assurance, user training, and integrating multiple modalities of treatment) may hinder clinical advances.
We carried out a systematic review according to Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines, reviewing the findings using a landscape analysis. Results were summarized descriptively, reporting on trial characteristics highlighting the benefits, limitations, and challenges of developing and implementing radiotherapy master protocols, with three case studies selected to explore these issues in more detail.
Twelve studies were suitable for inclusion (4 platform trials, 3 umbrella trials, and 5 basket trials), evaluating a mix of solid tumor sites in both curative and palliative settings. The interventions were categorized into 1) novel agent and radiotherapy combinations; 2) radiotherapy dose personalization; and 3) device evaluation, with a case study provided for each intervention. Benefits of master protocol trials for radiotherapy intervention include protocol efficiency for implementation of novel radiotherapy techniques; accelerating the evaluation of novel agent drug and radiotherapy combinations; and more efficient translational research opportunities, leading to cost savings and research efficiency to improve patient outcomes.
Master protocols offer an innovative platform under which multiple clinical questions can be addressed within a single trial. Due to the complexity of radiotherapy trial setup, cost and research efficiency savings may be more apparent than in systemic treatment trials. Use of this research approach may be the change needed to push forward oncological innovation within radiation oncology.
Personal genital satisfaction is associated with differences in perception of male and female sexual anatomy and function
Authors: Choi Una E , Nicholson Ryan C , Grutman Aurora J , Cohen Andrew J 
Published: May 2024

Abstract

Background
Prior studies primarily of men correlated low personal genital satisfaction (PGS) with decreased sexual activity; however, the association between PGS and genital anatomy perceptions is unknown, and there is a paucity of studies examining women.

Aim
We assessed the relationship between genital satisfaction, survey respondent sexual activity, and perceptions of anatomy and function.

Methods
A 54-item REDCap survey was distributed to any-gendered volunteers ≥18 years of age through ResearchMatch from January to March 2023. Responses were split into (1) high PGS and (2) low PGS. Analysis was performed using chi-square tests on survey responses and a Mann Whitney U test on median satisfaction level.

Outcomes
Outcomes were genital anatomy perceptions, sexual activity, and respondents’ PGS.

Results
Of the 649 respondents who started the survey, 560 (86.3%) completed it. Median PGS was 7 of 10, forming subgroups of high (≥7 of 10) satisfaction (n = 317 of 560 [56.6%]) and low (&lt;7 of 10) satisfaction (n = 243 of 560 [43.4%]). The mean age was 45.8 ± 16.8 years, and demographics were notable for 72.1% women (n = 404 of 560), 83.2% White (n = 466 of 560), 47.9% married (n = 268 of 560), and 75.5% bachelor’s degree holders (n = 423 of 560). Comparing high- and low-PGS groups, more low-PGS respondents felt normal flaccid penis length to be &lt;2 inches (11.1% vs 5.1%; P = .008). High-PGS respondents more often responded that it is normal for women to have orgasms over half the time (20.8% vs 13.2%; P = .0002) or to identify as being sexually active (81.1% vs 71.6%; P = .008). Women were more likely than men to report larger normal testicle sizes as 60.1 to 90 mL (24.5% vs 10.3%; P &lt; .0001), whereas more men felt that normal testicle size was 7 to 15 mL (26.3% vs 11.4%; P &lt; .0001). Orgasm length perceptions also differed: more women felt female orgasm length was 2.6 to 5 seconds (36.6% vs 16.7%; P &lt; .0001), and more men believed female orgasms to be longer, at 7.6 to 10 seconds (29.5% vs 17.3%; P = .002), 10.1 to 12.5 seconds (11.5% vs 5.2%; P = .0008), and &gt;12.5 seconds (12.2% vs 5.7%; P = .009). Respondents’ views on their genitalia differed by gender, with women more likely to feel that their genitals are normal compared with men (89.4% vs 75.0%; P &lt; .0001).

Clinical Implications
PGS may be a useful screening tool given its association with sexual activity.

Strengths and Limitations
Our large-scale survey assesses public perceptions of genital anatomy and function. Limitations include a lack of gender nonbinary perceptions.

Conclusion
Gender and PGS interact with perceptions of male anatomy and female sexual activity, and the frequency of sexual activity was higher among high-PGS respondents; however, the direction of these interactions remains unclear and requires future causal analysis.
The density of virialized clusters as a probe of dark energy
Authors: Paraskevas Evangelos A , Perivolaropoulos Leandros 
Published: May 2024

ABSTRACT
We use the spherical collapse model to demonstrate that the observable average density of virialized clusters depends on the properties of dark energy along with the properties of gravity on cluster scales and can therefore be used as a probe of these properties. As an application of this approach, we derive the predicted virialized densities and radii of cluster mass structures for a wide range of values of the cosmological constant (including negative values) as a function of the turnaround redshift. For the value of ΩΛ,0 = −0.7 (with Ωm,0 = 0.3), we find an amplification of the density of virialized clusters which can be as large as 80 per cent compared to Planck18/lambda Cold Dark Matter (ΛCDM) for a turnaround redshift zmax ≳ 2. Such an amplification may lead to more efficient early galaxy formation in this class of models, in accordance with the recent findings of JWST, which may be partially pertinent to the Λ sign switching models (ΛsCDM), which have been suggested as potential solutions to the observed Hubble and S8 discrepancies.
Estimating major merger rates and spin parameters ab initio via the clustering of critical events
Authors: Cadiou Corentin , Pichon-Pharabod Eric , Pichon Christophe , Pogosyan Dmitri 
Published: May 2024

ABSTRACT
We build a model to predict from first principles the properties of major mergers. We predict these from the coalescence of peaks and saddle points in the vicinity of a given larger peak, as one increases the smoothing scale in the initial linear density field as a proxy for cosmic time. To refine our results, we also ensure, using a suite of ∼400 power-law Gaussian random fields smoothed at ∼30 different scales, that the relevant peaks and saddles are topologically connected: they should belong to a persistent pair before coalescence. Our model allows us to (a) compute the probability distribution function of the satellite-merger separation in Lagrangian space: they peak at three times the smoothing scale; (b) predict the distribution of the number of mergers as a function of peak rarity: haloes typically undergo two major mergers (&gt;1:10) per decade of mass growth; (c) recover that the typical spin brought by mergers: it is of the order of a few tens of per cent.
EXO1 and DNA2-mediated ssDNA gap expansion is essential for ATR activation and to maintain viability in BRCA1-deficient cells
Authors: García-Rodríguez Néstor , Domínguez-García Iria , Domínguez-Pérez María del Carmen , Huertas Pablo 
Published: May 2024

Abstract
DNA replication faces challenges from DNA lesions originated from endogenous or exogenous sources of stress, leading to the accumulation of single-stranded DNA (ssDNA) that triggers the activation of the ATR checkpoint response. To complete genome replication in the presence of damaged DNA, cells employ DNA damage tolerance mechanisms that operate not only at stalled replication forks but also at ssDNA gaps originated by repriming of DNA synthesis downstream of lesions. Here, we demonstrate that human cells accumulate post-replicative ssDNA gaps following replicative stress induction. These gaps, initiated by PrimPol repriming and expanded by the long-range resection factors EXO1 and DNA2, constitute the principal origin of the ssDNA signal responsible for ATR activation upon replication stress, in contrast to stalled forks. Strikingly, the loss of EXO1 or DNA2 results in synthetic lethality when combined with BRCA1 deficiency, but not BRCA2. This phenomenon aligns with the observation that BRCA1 alone contributes to the expansion of ssDNA gaps. Remarkably, BRCA1-deficient cells become addicted to the overexpression of EXO1, DNA2 or BLM. This dependence on long-range resection unveils a new vulnerability of BRCA1-mutant tumors, shedding light on potential therapeutic targets for these cancers.
Genome-wide analysis of mRNA decay in Arabidopsis shoot and root reveals the importance of co-translational mRNA decay in the general mRNA turnover
Authors: Carpentier Marie-Christine , Receveur Anne-Elodie , Boubegtitene Alexandre , Cadoudal Adrien , Bousquet-Antonelli Cécile , Merret Rémy 
Published: May 2024

Abstract
Until recently, the general 5′-3′ mRNA decay was placed in the cytosol after the mRNA was released from ribosomes. However, the discovery of an additional 5′ to 3′ pathway, the Co-Translational mRNA Decay (CTRD), changed this paradigm. Up to date, defining the real contribution of CTRD in the general mRNA turnover has been hardly possible as the enzyme involved in this pathway is also involved in cytosolic decay. Here we overcame this obstacle and created an Arabidopsis line specifically impaired for CTRD called XRN4ΔCTRD. Through a genome-wide analysis of mRNA decay rate in shoot and root, we tested the importance of CTRD in mRNA turnover. First, we observed that mRNAs tend to be more stable in root than in shoot. Next, using XRN4ΔCTRD line, we demonstrated that CTRD is a major determinant in mRNA turnover. In shoot, the absence of CTRD leads to the stabilization of thousands of transcripts while in root its absence is highly compensated resulting in faster decay rates. We demonstrated that this faster decay rate is partially due to the XRN4-dependent cytosolic decay. Finally, we correlated this organ-specific effect with XRN4ΔCTRD line phenotypes revealing a crucial role of CTRD in mRNA homeostasis and proper organ development.
Cerebral clues: serum neurofilament light chain (sNfL) as a novel biomarker for immune check point inhibitor (ICI) mediated seronegative encephalitis
Authors: Zahid Anza , Tummala Sudhakar 
Published: May 2024

Abstract
Immune checkpoint inhibitor (ICI) mediated encephalitides are increasingly being recognized in the literature, but atypical cases may be missed or misdiagnosed. Recent efforts are directed to identify biomarkers to help elucidate early diagnosis and treatment. Herein, we describe two cases of antibody negative ICI-mediated encephalitis with elevated serum Neurofilament light chain (sNfL) levels. Practical Implication: Baseline and longitudinal measurements of serum neurofilament light chains can help determine treatment strategies and prognosis in patients with suspected immune checkpoint inhibitor encephalitis.
Depletion of squalene epoxidase in synergy with glutathione peroxidase 4 inhibitor RSL3 overcomes oxidative stress resistance in lung squamous cell carcinoma
Authors: Li Guo , Chen Lu , Bai Hua , Zhang Li , Wang Jie , Li Weimin 
Published: May 2024

Abstract

Background
Lung squamous cell carcinoma (LUSC) lacks effective targeted therapies and has a poor prognosis. Disruption of squalene epoxidase (SQLE) has been implicated in metabolic disorders and cancer. However, the role of SQLE as a monooxygenase involved in oxidative stress remains unclear.

Methods
We analyzed the expression and prognosis of lung adenocarcinoma (LUAD) and LUSC samples from GEO and TCGA databases. The proliferative activity of the tumors after intervention of SQLE was verified by cell and animal experiments. JC-1 assay, flow cytometry, and Western blot were used to show changes in apoptosis after intervention of SQLE. Flow cytometry and fluorescence assay of ROS levels were used to indicate oxidative stress status.

Results
We investigated the unique role of SQLE expression in the diagnosis and prognosis prediction of LUSC. Knockdown of SQLE or treatment with the SQLE inhibitor terbinafine can suppress the proliferation of LUSC cells by inducing apoptosis and reactive oxygen species accumulation. However, depletion of SQLE also results in the impairment of lipid peroxidation and ferroptosis resistance such as upregulation of glutathione peroxidase 4. Therefore, prevention of SQLE in synergy with glutathione peroxidase 4 inhibitor RSL3 effectively mitigates the proliferation and growth of LUSC.

Conclusion
Our study indicates that the low expression of SQLE employs adaptive survival through regulating the balance of apoptosis and ferroptosis resistance. In future, the combinational therapy of targeting SQLE and ferroptosis could be a promising approach in treating LUSC.
Substantial unrealised global biodiversity of continental microcrustaceans
Authors: Macêdo Rafael L , Toutain Mathieu , Reid Janet , Soto Ismael , Haubrock Phillip J , Cuthbert Ross N , Rocha Odete 
Published: May 2024

Abstract
Freshwater ecosystems provide essential services for human well-being, with their conservation success reliant on the precise quantification of biodiversity. Diplostraca (= Cladocera) and Copepoda are diverse groups of microcrustaceans in aquatic ecosystems, important for a multitude of these services. We examined biodiversity trends of these groups, utilizing a comprehensive dataset, approximately 2341 studies, spanning from the early 19th Century to the present day, aiming at predicting the total number of microcrustacean species that will have been described by 2100. Descriptions increased until the 1900s, surged, and then declined after 1975. The predictive models indicate that by the year 2100, an additional 16–68% of cladoceran species and 37–126% of copepod species are likely to be identified, representing a significant portion of currently unrealised biodiversity. Eighteen prolific authors contributed to a quarter of these descriptions, with the rest spread among numerous authorities. Based on our extrapolation, the total number of microcrustacean species could potentially exceed 6114 by 2050 and 9046 by 2100, notwithstanding extinctions. These findings, which point to a significant amount of unrealised biodiversity, underscore the need to refine biodiversity estimates beyond conventional expert opinion. Such accuracy is crucial for addressing the underappreciated scale of the current biodiversity crisis.
UVC (254 nm) and Far UVC (222 nm) Irradiation Affects In Vitro Growth of Colletotrichum sp. Isolates and Their Infection of Detached Strawberry Leaves
Authors: Smith Barbara J. , Sampson Blair J. , Copes Warren E. , Takeda Fumiomi , Janisiewicz Wojciech J. , Stafne Eric T. , Sakhanokho Hamidou F. , Carroll Jennifer B. 
Published: May 2024

Conventional ultraviolet C at 254 nm (UVC) and Far UVC at 222 nm (Far UVC) were evaluated as alternatives to fungicides for disease control. Conidia of 13 isolates of strawberry anthracnose pathogens (five Colletotrichum species in two complexes: C. acutatum and C. gloeosporioides) were uniformly dispersed onto agar and irradiated with UVC and Far UVC doses ranging from 52 to 1,248 J·m−2. After 48 h of incubation, a UVC dose of 1,248 J·m−2 and Far UVC doses from 234 to 935 J·m−2 reduced Colletotrichum colony counts to <10 colonies/Petri dish. Cultures exposed to UVC light followed by 4 h of darkness had lower colony counts than cultures incubated under continuous light. This dark incubation period was not required for Far UVC to obtain optimal lethality, indicating Far UVC irradiation can be applied during the day or night and achieve similar fungal lethality. Inoculation of detached leaves of three anthracnose-susceptible strawberry cultivars with conidial suspensions of Colletotrichum spp. revealed that UV irradiation can affect development of anthracnose symptoms. Leaves receiving UVC doses of 312 and 624 J·m−2 or a Far UVC dose of 467 J·m−2 reduced anthracnose infection with little or no plant injury. A UVC dose of 1,248 J·m−2 and Far UVC doses ≥ 467 J·m−2 inflicted varying degrees of plant injury. Disease control intended to reduce the number of fungicidal applications could be developed with moderate doses of UVC and Far UVC irradiation while slowing the evolution of pesticide-resistant strains. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2024.
Host and Shelter Plants for the Beet Leafhopper, Which Vectors Curly Top Viruses and Phytoplasmas in Southern Idaho
Authors: Strausbaugh Carl A. , Wenninger Erik J. , Jackson Laurie K. , Vincill Eric 
Published: May 2024

Weeds and crop plants not only serve as reproductive hosts and transitory or shelter plants for the beet leafhopper (BLH; Circulifer tenellus) but also as sources of plant pathogens that can then be vectored by the BLH. Thus, the plants that the BLHs are feeding on and infecting are of interest and may be changing over time. Therefore, BLH samples from a recent survey were investigated through DNA barcoding via the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit ( rbcL) and maturase K ( matK) chloroplast gene regions to determine what the BLHs had been feeding on prior to capture on yellow sticky cards in southern Idaho during 2020 and 2021. In June of both years, the first generation of BLHs predominately fed on Pinus spp. (59 to 76% of samples), which were likely in mountainous areas, and dispersed approximately 48 to 80 km to crop and sagebrush steppe locations. During July to September, the BLHs predominantly fed on Salsola spp. (Russian thistle; 61 to 66% of samples) and Bassia scoparia (kochia; 15% of samples). In both years, the BLHs that fed on pine had the highest percentage (55 and 75%, respectively) of samples with beet curly top virus based on primers that can detect both the Worland and Colorado strains. In both years, BLHs that had fed on Russian thistle and alfalfa had the highest percentage of samples with Spinach curly top Arizona virus. These data will be utilized in the development of future curly top management plans. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2024.
Whole-Genome Sequence Resources for Pseudomonas amygdali pv. sesami and Xanthomonas arboricola Isolated from Sesame (Sesamum indicum) in North Carolina in 2022
Authors: D'Amico-Willman Katherine M. , Montalban Kimberly M. , Joglekar Prasanna , Duin Izabela Moura , Ritchie David F. , Fagen Jennie , Huerta Alejandra I. 
Published: May 2024

Sesame ( Sesamum indicum) is a specialty crop with increasing interest as an alternative, rotational crop for U.S. agricultural systems. This crop is susceptible to several pathogens, including Pseudomonas and Xanthomonas species. Two bacterial isolates were recently cultured from sesame in North Carolina symptomatic of bacterial spot and identified as Pseudomonas amygdali pv. sesami (Pas) and Xanthomonas sp. These isolates were used for hybrid whole-genome sequencing and assembly using Illumina and PacBio to develop robust genomic resources for these disease-causing strains. The results provide the most complete Pas genome available and placed the Xanthomonas sp. isolate into the X. arboricola species designation. Improved genomic resources for pathogens of sesame are needed to accurately detect, characterize, and employ timely management of the disease. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .