bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cluster-efficient pangenome graph construction with nf-core/pangenome
Authors: Heumos Simon , Heuer Michael L , Hanssen Friederike , Heumos Lukas , Guarracino Andrea , Heringer Peter , Ehmele Philipp , Prins Pjotr , Garrison Erik , Nahnsen Sven 
Published: October 2024

Abstract

Motivation
Pangenome graphs offer a comprehensive way of capturing genomic variability across multiple genomes. However, current construction methods often introduce biases, excluding complex sequences or relying on references. The PanGenome Graph Builder (PGGB) addresses these issues. To date, though, there is no state-of-the-art pipeline allowing for easy deployment, efficient and dynamic use of available resources, and scalable usage at the same time.

Results
To overcome these limitations, we present nf-core/pangenome, a reference-unbiased approach implemented in Nextflow following nf-core’s best practices. Leveraging biocontainers ensures portability and seamless deployment in High-Performance Computing (HPC) environments. Unlike PGGB, nf-core/pangenome distributes alignments across cluster nodes, enabling scalability. Demonstrating its efficiency, we constructed pangenome graphs for 1000 human chromosome 19 haplotypes and 2146 Escherichia coli sequences, achieving a two to threefold speedup compared to PGGB without increasing greenhouse gas emissions.

Availability and implementation
nf-core/pangenome is released under the MIT open-source license, available on GitHub and Zenodo, with documentation accessible at https://nf-co.re/pangenome/docs/usage.
Cleavage-Stage Embryo Segmentation Using SAM-Based Dual Branch Pipeline: Development and Evaluation with the CleavageEmbryo Dataset
Authors: Zhang Chensheng , Shi Xintong , Yin Xinyue , Sun Jiayi , Zhao Jianhui , Zhang Yi 
Published: October 2024

Abstract

Motivation
Embryo selection is one of the critical factors in determining the success of pregnancy in in vitro fertilization (IVF) procedures. Using artificial intelligence to aid in embryo selection could effectively address the current time-consuming, expensive, subjectively influenced process of embryo assessment by trained embryologists. However, current deep learning-based methods often focus on blastocyst segmentation, grading, or predicting cell development via time-lapse videos, often overlooking morphokinetic parameters or lacking interpretability. Given the significance of both morphokinetic and morphological evaluation in predicting the implantation potential of cleavage-stage embryos, as emphasized by previous research, there is a necessity for an automated method to segment cleavage-stage embryos to improve this process.

Results
In this article, we introduce the SAM-based Dual Branch Segmentation Pipeline for automated segmentation of blastomeres in cleavage-stage embryos. Leveraging the powerful segmentation capability of SAM, the instance branch conducts instance segmentation of blastomeres, while the semantic branch performs semantic segmentation of fragments. Due to the lack of publicly available datasets, we construct the CleavageEmbryo dataset, the first dataset of human cleavage-stage embryos with pixel-level annotations containing fragment information. We train and test a series of state-of-the-art segmentation algorithms on CleavageEmbryo. Our experiments demonstrate that our method outperforms existing algorithms in terms of objective metrics (mAP 0.748 on blastomeres, Dice 0.694 on fragments) and visual quality, enabling more accurate segmentation of cleavage-stage embryos.

Availability and Implementation
The code and sample data in this study can be found at: Https://github.com/12austincc/Cleavage-StageEmbryoSegmentation.

Supplementary information
Supplementary data are available at Bioinformatics online.
THI1 Gene Evolutionary Trends: A Comprehensive Plant-Focused Assessment via Data Mining and Large-Scale Analysis
Authors: Dias Henrique Moura , de Toledo Naiara Almeida , Mural Ravi V , Schnable James C , Van Sluys Marie-Anne 
Published: October 2024

Abstract
Molecular evolution analysis typically involves identifying selection pressure and reconstructing evolutionary trends. This process usually requires access to specific data related to a target gene or gene family within a particular group of organisms. While recent advancements in high-throughput sequencing techniques have resulted in the rapid accumulation of extensive genomics and transcriptomics data and the creation of new databases in public repositories, extracting valuable insights from such vast data sets remains a significant challenge for researchers. Here, we elucidated the evolutionary history of THI1, a gene responsible for encoding thiamine thiazole synthase. The thiazole ring is a precursor for vitamin B1 and a crucial cofactor in primary metabolic pathways. A thorough search of complete genomes available within public repositories reveals 702 THI1 homologs of Archaea and Eukarya. Throughout its diversification, the plant lineage has preserved the THI1 gene by incorporating the N-terminus and targeting the chloroplasts. Likewise, evolutionary pressures and lifestyle appear to be associated with retention of TPP riboswitch sites and consequent dual posttranscriptional regulation of the de novo biosynthesis pathway in basal groups. Multicopy retention of THI1 is not a typical plant pattern, even after successive genome duplications. Examining cis-regulatory sites in plants uncovers two shared motifs across all plant lineages. A data mining of 484 transcriptome data sets supports the THI1 homolog expression under a light/dark cycle response and a tissue-specific pattern. Finally, the work presented brings a new look at public repositories as an opportunity to explore evolutionary trends to THI1.
Parallel Spectral Tuning of a Cone Visual Pigment Provides Evidence for Ancient Deep-Sea Adaptations in Cetaceans
Authors: Chi Hai , Sun Linxia , Li Na , Zhan Yue , Guo Jinqu , Lei Lei , Irwin David M , Yang Guang , Xu Shixia , Liu Yang 
Published: October 2024

Abstract
Dichromatic color vision is mediated by two cone visual pigments in many eutherian mammals. After reentry into the sea, early cetaceans lost their violet-sensitive visual pigment (short wavelength-sensitive 1) independently in the baleen and toothed whale ancestors and thus obtained only monochromatic cone vision. Subsequently, losses of the middle/long wavelength-sensitive (M/LWS) pigment have also been reported in multiple whale lineages, leading to rhodopsin (RH1)-mediated rod monochromatic vision. To further elucidate the phenotypic evolution of whale visual pigments, we assessed the spectral tuning of both M/LWS and RH1 from representative cetacean taxa. Interestingly, although the coding sequences for M/LWS are intact in both the pygmy right whale and the Baird's beaked whale, no spectral sensitivity was detected in vitro. Pseudogenization of other cone vision-related genes is observed in the pygmy right whale, suggesting a loss of cone-mediated vision. After ancestral sequence reconstructions, ancient M/LWS pigments from cetacean ancestors were resurrected and functionally measured. Spectral tuning of M/LWS from the baleen whale ancestor shows that it is green sensitive, with a 40-nm shift in sensitivity to a shorter wavelength. For the ancestor of sperm whales, although no spectral sensitivity could be recorded for its M/LWS pigment, a substantial sensitivity shift (20 to 30 nm) to a shorter wavelength may have also occurred before its functional inactivation. The parallel phenotypic evolution of M/LWS to shorter wavelength sensitivity might be visual adaptations in whales allowing more frequent deep-sea activities, although additional ecological differentiations may have led to their subsequent losses.
The prescriptive nature of market timing and predictive portfolios
Authors: Kyriazi Foteini 
Published: October 2024

Abstract
Accepted by: Konstantinos Nikolopoulos
We explore the ability of market timing, model-based forecasts that include incremental information over and above momentum, to create long-short portfolios that consistently provide superior returns to traditional benchmarks, and frame our analysis in the idea of “prediction-led prescription” for forward-looking decision making. Our methodology consists of linear and non-linear forecasts with model selection, that predict the direction of future returns and apply then into the construction of portfolios. Our results strongly recommend that predictive-based portfolio allocation can produce excess returns and higher Sharpe ratios, above and beyond the individual return series that are utilized to create the forecasts and traditional portfolio benchmarks. The use of “predictive methods in portfolio construction reinforces the idea of prediction-led prescription” as portfolios are prescriptions for investment management and have an exclusively forward-looking nature.
Biological and experimental factors that define the effectiveness of microbial inoculation on plant traits: a meta-analysis
Authors: Azarbad Hamed , Junker Robert R 
Published: October 2024

Abstract
Bacterial and fungal microbiomes associated with plants can significantly affect the host’s phenotype. Inoculating plants with one or multiple bacterial and fungal species can affect specific plant traits, which is exploited in attempts to increase plant performance and stress tolerance by microbiome engineering. Currently, we lack a comprehensive synthesis on the generality of these effects related to different biological (e.g. plant models, plant traits, and microbial taxa) and experimental factors. In a meta-analysis, we showed that the plant trait under consideration and the microbial taxa used to inoculate plants significantly influenced the strength of the effect size. In a methodological context, experiments under sterilized conditions and short-term periods resulted in larger positive effects on plant traits than those of unsterilized and long-term experiments. We recommend that future studies should not only consider (short-term) laboratory experiments with sterilized plants and single inoculants but also and more often (long-term) field or greenhouse experiments with naturally occurring microbial communities associated with the plants and inoculated consortia including both bacteria and fungi.
Enhancing learning to solve multicomponent fractional viscoelastic equations with U-net Fourier neural operators
Authors: Tian Wenbin , Liu Yang , Zhang Yibo 
Published: October 2024

Abstract
The research of viscoelastic media is currently a hot topic in the interpretation and processing of seismic data. To accurately simulate the propagation of seismic waves in viscoelastic media, the fractional viscoelastic equation has emerged as an indispensable method. However, solving this equation numerically has proven to be challenging due to the complexity introduced by its fractional Laplacian operators. Recently, deep learning, especially Fourier neural operators (FNO), has shown excellent performance in learning to fast solve partial differential equations. Traditional FNO methods may face crosstalk problems and this make it difficult to achieve satisfactory accuracy when solving the multicomponent fractional order viscoelastic equation. To solve this problem, we introduce a novel approach based on U-net Fourier neural operator (U-FNO). As an enhanced learning method to the traditional FNO-based method, the U-FNO-based method integrates a U-Fourier layer following the standard Fourier layer as a form of regularization, thereby achieving superior prediction accuracy for multicomponent equations. Specifically, both the Fourier layers and U-Fourier layers in U-FNO are trained with the solutions of the equation from previous time steps as inputs. This training process enables the U-FNO to efficiently produce more accurate solutions for subsequent wavefield. Numerical simulations reveal that the U-FNO-based method efficiently learns to solve the fractional viscoelastic wave equation independent of fractional Laplacian operators. Additionally, U-FNO-based method offers superior prediction accuracy in comparison with the traditional FNO-based method.
Breast cancer screening in women with SCD: a single-center exploratory study
Authors: Elmileik Eiman , Farooqui Marwah , Zhang Xu , Hussain Faiz , Haqqani Rayyan , Sung Kaitlin , Saraf Santosh L 
Published: October 2024

Abstract

Objectives
SCD is one of the most common inherited blood disorders and is associated with reduced life expectancy. As a result of prophylactic and disease-modifying medications, morbidity and mortality have improved, and research focusing on cancer screening has become more relevant. This study therefore aimed to identify patterns regarding breast cancer screening and breast composition in women with SCD.

Methods
This was a single-center retrospective study. Medical records of 156 individuals with SCD between 2018 and 2022 were analyzed.

Results
Of 156 individuals, 56% had screening mammography within the past 2 years. In comparison, the latest Centers for Disease Control and Prevention report showed that 70.8% of non-Hispanic Black women aged 40 and over had undergone screening mammography within the past 2 years. The difference was not statistically significant. Fifty-four percent of those screened had dense breasts. There was an inverse relationship between body mass index (BMI) and breast density.

Conclusion
The results suggest that there was no statistically significant difference in breast cancer screening rates between women with SCD and those without SCD. Our study found that there was an inverse relationship between BMI and breast density in women with SCD, which was consistent with well-established data about breast density and BMI in the general female population. Prospective studies with larger cohorts are recommended to enhance statistical power, fostering a comprehensive understanding of cancer and cancer risk in individuals with SCD.
Dapagliflozin for rheumatic musculoskeletal disease in patients with chronic kidney disease
Authors: Hanaoka Hironari , Kikuchi Jun , Hiramoto Kazuoto , Akiyama Mitsuhiro , Saito Shutaro , Kondo Yasushi , Azegami Tatsuhiko , Kaneko Yuko 
Published: October 2024

ABSTRACT

Objectives
To elucidate the effectiveness of dapagliflozin, a sodium–glucose cotransporter 2 inhibitor, on renal function in patients with rheumatic musculoskeletal diseases complicated by chronic kidney disease (CKD).

Methods
We conducted a retrospective analysis of patients with rheumatic musculoskeletal disease and chronic kidney disease who were treated with dapagliflozin for more than a year. The good response was defined as an improvement in the estimated glomerular filtration rate slope per year after dapagliflozin treatment compared to that before treatment. Additionally, we investigated the response rate and its predictive factors.

Results
In this analysis, 43 patients were included. The average estimated glomerular filtration rate slope demonstrated a significant improvement after dapagliflozin treatment compared to that before the treatment (0.04 vs −0.55 ml/min/1.73 m2/year, P = .001). A good response rate was 69.8% and was associated with low average levels of C-reactive protein, a high frequency of angiotensin II receptor blocker (ARB) use, and a low frequency of tacrolimus use compared to nonresponse (0.08 ± 0.18 vs 0.25 ± 0.29 mg/dl, P = .03; 80.0 vs 38.4%, P = .01; 10.0 vs 76.9%, P &lt; .01).

Conclusions
Dapagliflozin is effective for rheumatic musculoskeletal disease patients with CKD for preventing deterioration of renal function. Antihypertensive treatment with ARB and inflammation control without tacrolimus was associated with a high likelihood of favourable response to dapagliflozin.
Nose-to-brain delivery of stem cells in stroke: the role of extracellular vesicles
Authors: Borlongan Cesar V , Lee Jea-Young , D’Egidio Francesco , de Kalbermatten Matthieu , Garitaonandia Ibon , Guzman Raphael 
Published: October 2024

Abstract
Stem cell transplantation offers a promising therapy that can be administered days, weeks, or months after a stroke. We recognize 2 major mitigating factors that remain unresolved in cell therapy for stroke, notably: (1) well-defined donor stem cells and (2) mechanism of action. To this end, we advance the use of ProtheraCytes, a population of non-adherent CD34+ cells derived from human peripheral blood and umbilical cord blood, which have been processed under good manufacturing practice, with testing completed in a phase 2 clinical trial in post-acute myocardial infarction (NCT02669810). We also reveal a novel mechanism whereby ProtheraCytes secrete growth factors and extracellular vesicles (EVs) that are associated with angiogenesis and vasculogenesis. Our recent data revealed that intranasal transplantation of ProtheraCytes at 3 days after experimentally induced stroke in adult rats reduced stroke-induced behavioral deficits and histological damage up to 28 days post-stroke. Moreover, we detected upregulation of human CD63+ EVs in the ischemic brains of stroke animals that were transplanted with ProtheraCytes, which correlated with increased levels of DCX-labeled neurogenesis and VEGFR1-associated angiogenesis and vasculogenesis, as well as reduced Iba1-marked inflammation. Altogether, these findings overcome key laboratory-to-clinic translational hurdles, namely the identification of well-characterized, clinical grade ProtheraCytes and the elucidation of a potential CD63+ EV-mediated regenerative mechanism of action. We envision that additional translational studies will guide the development of clinical trials for intranasal ProtheraCytes allografts in stroke patients, with CD63 serving as a critical biomarker.
Urticarial vasculitis
Authors: Ergun Tülin 
Published: October 2024

Purpose of review
Urticarial vasculitis is a rare condition manifesting with a variety of clinical presentations ranging from skin limited lesions to life-threatening systemic illnesses. This review aims to highlight the recent findings on the etiology, diagnostic modalities, and therapeutic strategies and course of urticarial vasculitis.

Recent findings
In addition to well established triggers, urticarial vasculitis (UV) cases associated with severe acute respiratory syndrome coronavirus 2 (SARS-Cov2) disease and COVID-19 vaccines, vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic (VEXAS) syndrome, and adenosine deaminase (ADA) deficiency have been reported. A clinical-dermoscopic model for differentiating urticarial vasculitis has been developed with purpuric patches and globules favoring UV diagnosis and thus diminishing the need for histopathology. The efficacy of treatment modalities has been reviewed, and antihistamines, systemic corticosteroids, omalizumab, cyclophosphamide, tocilizumab, anti-interleukin (IL)-1 agents, and rituximab were shown to have the highest success rates. Regarding the durability of remission, rituximab, dapsone, and MMF were related to long-lasting treatment free responses. The course of hypocomplementemic urticarial vasculitis was investigated in an epidemiological study, revealing 5- and 10-year survival rates of 92% and 83%, respectively. Chronic obstructive pulmonary disease, septicemia, and end-stage renal disease were identified as causes of mortality.

Summary
With the aid of dermoscopy, a noninvasive tool, differentiation from chronic spontaneous urticaria can be made, and the need for histopathological examination can be diminished. Although clear definitions and consensus criteria for performing disease severity are lacking, careful screening is needed to tailor the treatment on an individual basis. Emerging infections like SARS-CoV 2, vaccines, and autoinflammatory disorders like VEXAS syndrome and ADA deficiency are new associations. The optimal use of well established agents like systemic corticosteroids and immunomodulators are mainstay treatment modalities, whereas IL-1 inhibitors, omalizumab, rituximab and Janus Kinase inhibitors may represent viable alternatives in selected cases.
Polymyalgia rheumatica and giant cell arteritis: diagnosis and management
Authors: Sun Margaret Man-Ger , Pope Janet E. 
Published: October 2024

Purpose of review
There have been advances in the diagnosis and treatment of giant cell arteritis (GCA) and polymyalgia rheumatica (PMR).

Recent findings
Themes in PMR and GCA include classification criteria, ultrasound imaging of temporal and axillary arteries replacing biopsies for diagnosis of GCA, faster diagnosis and treatment with rapid access clinics for suspected GCA, and expanding treatment options with the goal of rapid suppression of inflammation and sparing steroids.

Summary
Treatment is aimed at suppressing inflammation quickly in both GCA and PMR. Randomized trials have demonstrated success in reducing glucocorticoids when adding advanced therapies such as interleukin 6 (IL6) inhibitors. Other treatments including Janus kinase (JAK) inhibitors (especially a phase 3 trial of upadacitinib at 15 mg daily and secukinumab (an IL17 inhibitor) are being tested. Some uncontrolled GCA protocols are limiting glucocorticoids to initial IV pulse therapy only or rapid tapering of oral glucocorticoids with upfront treatment with tocilizumab. There is uncertainty of who should have an advanced therapy and how long to use it for and what order to consider advanced therapies when treatment fails. In PMR, studies are performed when patients cannot taper glucocorticoids effectively, whereas in GCA, advanced therapies are started with disease onset or with recurrent GCA.
Cost-effectiveness Improves for Operative vs Nonoperative Treatment of Adult Symptomatic Lumbar Scoliosis at Eight-Year Follow-up
Authors: Carreon Leah Y. , Glassman Steven D. , Smith Justin S. , Kelly Michael P. , Yanik Elizabeth L. , Baldus Christine R. , Lurie Jon D. , Edwards Charles , Lenke Lawrence G. , Buchowski Jacob M. , Crawford Charles H. , Koski Tyler , Lafage Virginie , Gupta Munish , Kim Han Jo , Ames Christopher P. , Bess Shay , Schwab Frank J. , Shaffrey Christopher I. , Bridwell Keith H. 
Published: October 2024

Study Design.
Secondary data analysis of the NIH sponsored study on Adult Symptomatic Lumbar Scoliosis (ASLS).

Objectives.
The purpose of this study is to perform a cost-effectiveness analysis comparing operative versus non-operative care for ASLS eight years after enrollment.

Summary of Background Data.
A prior cost-effectiveness analysis of the current cohort comparing operative to non-operative care at five years after enrollment showed and ICER of $44,033 in the As-Treated analysis and a ICER of $27,480 in the Intent-to-treat analysis.

Methods.
Data was collected every three months for the first two years, then every six months for the remainder of the study. Data included use of non-operative modalities, medications and employment status. Costs for index and revision surgeries and non-operative modalities were determined using Medicare Allowable rates. Medication costs were determined using the RedBook and indirect costs were calculated based on reported employment status and income. Quality Adjusted Life Years (QALY) was determined using the SF6D.

Results.
There were 101 cases in the Operative (Op) and 103 in the Non-operative (Non-Op) group with complete eight year data. Thirty-eight patients (37%) in the Non-Op group had surgery from 3 to 72 months after enrollment. An As-Treated analysis including only cases who never had surgery (N=65) or cases with complete eight-year post-operative data (N=101) showed that operative treatment was favored with an ICER of $20,569 per QALY gained which is within Willingness-to-Pay (WTP) thresholds. An Intent-to-Treat analysis demonstrated greater QALY gains and lower cost in the Op group (ICER = $-13,911). However, Intent-to-Treat analysis is influenced by Non-Op patients who crossed over to operative treatment at variable times during follow-up.

Conclusion.
Operative treatment was more cost-effective than non-operative treatment for ASLS at eight-year follow-up. The ICER continued to improve as compared to the five-year values ($20,569 vs. $44,033).