bluuebunny/crossref_metadata_2025_split huggingface dataset:
Can the Wild Perennial, Rhizomatous Rice Species Oryza longistaminata be a Candidate for De Novo Domestication?
Authors: Tong Shuai , Ashikari Motoyuki , Nagai Keisuke , Pedersen Ole 
Published: March 2023

AbstractAs climate change intensifies, the development of resilient rice that can tolerate abiotic stresses is urgently needed. In nature, many wild plants have evolved a variety of mechanisms to protect themselves from environmental stresses. Wild relatives of rice may have abundant and virtually untapped genetic diversity and are an essential source of germplasm for the improvement of abiotic stress tolerance in cultivated rice. Unfortunately, the barriers of traditional breeding approaches, such as backcrossing and transgenesis, make it challenging and complex to transfer the underlying resilience traits between plants. However, de novo domestication via genome editing is a quick approach to produce rice with high yields from orphans or wild relatives. African wild rice, Oryza longistaminata, which is part of the AA-genome Oryza species has two types of propagation strategies viz. vegetative propagation via rhizome and seed propagation. It also shows tolerance to multiple types of abiotic stress, and therefore O. longistaminata is considered a key candidate of wild rice for heat, drought, and salinity tolerance, and it is also resistant to lodging. Importantly, O. longistaminata is perennial and propagates also via rhizomes both of which are traits that are highly valuable for the sustainable production of rice. Therefore, O. longistaminata may be a good candidate for de novo domestication through genome editing to obtain rice that is more climate resilient than modern elite cultivars of O. sativa.
Retrograde Intrarenal Surgery for Partial Staghorn Calculus in Thoracic Kidney: Case Report
Authors: Venkatachalapathy Vigneswara Srinivasan Sockkalingam , Palathullil Datson George , Sam Dempsey Mohan , Abraham George Palathullil 
Published: March 2023

Abstract
Background
Thoracic kidney (TK) presenting with symptomatic urolithiasis is a rare case scenario. Retrograde intrarenal surgery (RIRS) for calculus in TK is not reported in the literature. We report a case of partial staghorn calculus in TK managed by RIRS.

Case presentation
A young adult male presented with back pain and was found to have right TK and bilateral partial staghorn calculus. He also had right cryptorchidism with intraabdominally located testis. He underwent staged bilateral RIRS and laparoscopic right orchiectomy. Follow-up ultrasound imaging showed complete stone clearance in both kidneys.

Conclusions
RIRS is safe and effective treatment option, in the management of urolithiasis in TK. The anatomical abnormalities in TK did not play any hindrance role in the ureteral access, renal maneuverability of the flexible ureterorenoscope and subsequent drainage of the stone dust after RIRS.
Evaluation of macroscopic fundamental diagram characteristics for a quantified penetration rate of autonomous vehicles
Authors: Bilal Muhammad Tabish , Giglio Davide 
Published: March 2023

Abstract
Background
The availability of private vehicles with autonomous features is widespread nowadays. Various car manufacturers are providing attributes like collision warning, city automatic emergency braking, adaptive cruise control, pedestrian detection, lane-keeping assistance and lane departure warning, rear cross-traffic and blind-spot warning in their high-end models.

Purpose
Such features can automatically manage the macroscopic fundamental traffic parameters such as speed, headway, etc adaptively. Consequently leading to a heterogeneous traffic stream with diverse car-following behaviour comprising completely manual/traditional (TVs) and autonomous vehicles (AVs). This questions the applicability of classic traffic flow theory relationships on such heterogeneous traffic streams.

Methodology
This paper focuses on developing the macroscopic fundamental diagram for such heterogeneous traffic streams based on the quantified penetration rate (QPR) for autonomous vehicles. The penetration rate is devised by taking into account user demographics, land usage and road network properties. QPR is used as an input for heterogeneous urban traffic stream scenarios to calculate the aggregated urban traffic network dynamics of flow and density for the same network. Travel time versus flow characteristics is evaluated based on calibrated hyperbolic urban link travel time function for both interrupted and uninterrupted flows following the aggregated speed and density output from MFDs for heterogeneous traffic streams. Also, two scenarios are generated for comparison to explain the improvement in the network characteristics together with a sensitivity analysis.

Results
Compared to the base scenario there could be 25-35% of AVs on the road networks based on the analysis in coming fifteen years. This increment in usage impacts the capacity of road networks positively by increasing it up to 59%.

Conclusions
Results obtained after the application of the suggested model approach to the real network can be used to define a realistic method for multi-vehicle equilibrium assignment models for heterogeneous traffic streams including autonomous vehicles instead of approximating the penetration rates.
A correction procedure for the working hours variable in the IAB employee history
Authors: vom Berge Philipp , Umkehrer Matthias , Wanger Susanne 
Published: March 2023

AbstractAdministrative labour market data for Germany do not contain detailed information on working hours. This poses a serious challenge for many empirical research questions. Between 2010 and 2014, however, it is possible to merge a supplementary data source containing information on working hours reported by employers for each job to the German Social Accident Insurances. One complicating factor is that employers were allowed to report actual working hours, contractual working hours or a full-time worker reference value, and it is not obvious from the data which re-porting scheme was actually used. In this report, we describe this supplementary data source and propose a correction procedure that maps all data entries so that they uniformly reflect contractual working time. After this correction, the distribution of contractual weekly working hours in the combined administrative labour market data closely resembles the distribution from the German Structural Earnings Survey.
nPoRe: n-polymer realigner for improved pileup-based variant calling
Authors: Dunn Tim , Blaauw David , Das Reetuparna , Narayanasamy Satish 
Published: March 2023

AbstractDespite recent improvements in nanopore basecalling accuracy, germline variant calling of small insertions and deletions (INDELs) remains poor. Although precision and recall for single nucleotide polymorphisms (SNPs) now exceeds 99.5%, INDEL recall remains below 80% for standard R9.4.1 flow cells. We show that read phasing and realignment can recover a significant portion of false negative INDELs. In particular, we extend Needleman-Wunsch affine gap alignment by introducing new gap penalties for more accurately aligning repeated n-polymer sequences such as homopolymers ($$n=1$$

n
=
1

) and tandem repeats ($$2 \le n \le 6$$

2
≤
n
≤
6

). At the same precision, haplotype phasing improves INDEL recall from 63.76 to $$70.66\%$$

70.66
%

and nPoRe realignment improves it further to $$73.04\%$$

73.04
%

.
Seven bacterial response-related genes are biomarkers for colon cancer
Authors: Xiong Zuming , Li Wenxin , Luo Xiangrong , Lin Yirong , Huang Wei , Zhang Sen 
Published: March 2023

Abstract
Background
Colon cancer (CC) is a common tumor that causes significant harm to human health. Bacteria play a vital role in cancer biology, particularly the biology of CC. Genes related to bacterial response were seldom used to construct prognosis models. We constructed a bacterial response-related risk model based on three Molecular Signatures Database gene sets to explore new markers for predicting CC prognosis.

Methods
The Cancer Genome Atlas (TCGA) colon adenocarcinoma samples were used as the training set, and Gene Expression Omnibus (GEO) databases were used as the test set. Differentially expressed bacterial response-related genes were identified for prognostic gene selection. Univariate Cox regression analysis, least absolute shrinkage and selection operator-penalized Cox regression analysis, and multivariate Cox regression analysis were performed to construct a prognostic risk model. The individual diagnostic effects of genes in the prognostic model were also evaluated. Moreover, differentially expressed long noncoding RNAs (lncRNAs) were identified. Finally, the expression of these genes was validated using quantitative polymerase chain reaction (qPCR) in cell lines and tissues.

Results
A prognostic signature was constructed based on seven bacterial response genes: LGALS4, RORC, DDIT3, NSUN5, RBCK1, RGL2, and SERPINE1. Patients were assigned a risk score based on the prognostic model, and patients in the TCGA cohort with a high risk score had a poorer prognosis than those with a low risk score; a similar finding was observed in the GEO cohort. These seven prognostic model genes were also independent diagnostic factors. Finally, qPCR validated the differential expression of the seven model genes and two coexpressed lncRNAs (C6orf223 and SLC12A9-AS1) in 27 pairs of CC and normal tissues. Differential expression of LGALS4 and NSUN5 was also verified in cell lines (FHC, COLO320DM, SW480).

Conclusions
We created a seven-gene bacterial response‐related gene signature that can accurately predict the outcomes of patients with CC. This model can provide valuable insights for personalized treatment.
FDC-SP as a diagnostic and prognostic biomarker and modulates immune infiltrates in renal cell carcinoma
Authors: Chang Fan , Zhang Jiang-Hui , Wu Wen-Song , Tang Shuai , lv Zheng , Chen Fang-Min 
Published: March 2023

Abstract
Background
Renal cell carcinoma (RCC), one of the top 10 causes of cancer death, is responsible for more than 90% of all cases of primary renal cancer worldwide. Follicular dendritic cell-secreted protein (FDC-SP) specifically binds to activated B cells and regulates the generation of antibodies. It is also thought to promote cancer cell invasion and migration, which could help with tumor metastases. This study aimed to assess the efficacy of FDC-SP in the diagnosis and prognosis of RCC and to investigate the relationship between immune infiltration in RCC and these outcomes.

Results
RCC tissues had significantly higher levels of FDC-SP protein and mRNA than normal tissues. The high level of FDC-SP expression was linked to the T stage, histological grade, pathological stage, N stage, M stage, and OS event. Functional enrichment analysis identified the major pathways that were enriched as immune response regulation, complement, and coagulation. Immunological checkpoints and immune cell infiltration were observed to substantially correlate with the levels of FDC-SP expression. FDC-SP expression levels showed the ability to precisely distinguish high-grade or high-stage renal cancer (area under the curve (AUC) = 0.830, 0.722), and RCC patients with higher FDC-SP expression levels had worse prognoses. The AUC values for one-, two-, and five-year survival rates were all greater than 0.600. Moreover, the FDC-SP expression is an independent predictive biomarker of OS in RCC patients.

Conclusion
FDC-SP may be a prospective therapeutic target in RCC as well as a possible diagnostic and prognostic biomarker associated with immune infiltration.
LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution
Authors: Ascolani Gianluca , Angaroni Fabrizio , Maspero Davide , Craighero Francesco , Bhavesh Narra Lakshmi Sai , Piazza Rocco , Damiani Chiara , Ramazzotti Daniele , Antoniotti Marco , Graudenzi Alex 
Published: March 2023

Abstract
Background
Longitudinal single-cell sequencing experiments of patient-derived models are increasingly employed to investigate cancer evolution. In this context, robust computational methods are needed to properly exploit the mutational profiles of single cells generated via variant calling, in order to reconstruct the evolutionary history of a tumor and characterize the impact of therapeutic strategies, such as the administration of drugs. To this end, we have recently developed the LACE framework for the Longitudinal Analysis of Cancer Evolution.

Results
The LACE 2.0 release aimed at inferring longitudinal clonal trees enhances the original framework with new key functionalities: an improved data management for preprocessing of standard variant calling data, a reworked inference engine, and direct connection to public databases.

Conclusions
All of this is accessible through a new and interactive Shiny R graphical interface offering the possibility to apply filters helpful in discriminating relevant or potential driver mutations, set up inferential parameters, and visualize the results. The software is available at: .
PWN: enhanced random walk on a warped network for disease target prioritization
Authors: Han Seokjin , Hong Jinhee , Yun So Jeong , Koo Hee Jung , Kim Tae Yong 
Published: March 2023

Abstract
Background
Extracting meaningful information from unbiased high-throughput data has been a challenge in diverse areas. Specifically, in the early stages of drug discovery, a considerable amount of data was generated to understand disease biology when identifying disease targets. Several random walk-based approaches have been applied to solve this problem, but they still have limitations. Therefore, we suggest a new method that enhances the effectiveness of high-throughput data analysis with random walks.

Results
We developed a new random walk-based algorithm named prioritization with a warped network (PWN), which employs a warped network to achieve enhanced performance. Network warping is based on both internal and external features: graph curvature and prior knowledge.

Conclusions
We showed that these compositive features synergistically increased the resulting performance when applied to random walk algorithms, which led to PWN consistently achieving the best performance among several other known methods. Furthermore, we performed subsequent experiments to analyze the characteristics of PWN.
Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS
Authors: Vieira Ivo Henrique Provensi , Botelho Eduardo Buganemi , de Souza Gomes Thales Junior , Kist Roger , Caceres Rafael Andrade , Zanchi Fernando Berton 
Published: March 2023

Abstract
Background
The molecular dynamics is an approach to obtain kinetic and thermodynamic characteristics of biomolecular structures. The molecular dynamics simulation softwares are very useful, however, most of them are used in command line form and continue with the same common implementation difficulties that plague researchers who are not computer specialists.

Results
Here, we have developed the VisualDynamics—a WEB tool developed to automate biological simulations performed in Gromacs using a graphical interface to make molecular dynamics simulation user-friendly task. In this new application the researcher can submit a simulation of the protein in the free form or complexed with a ligand. Can also download the graphics analysis and log files at the end of the simulation.

Conclusions
VisualDynamics is a tool that will accelerate implementations and learning in the area of molecular dynamics simulation. Freely available at https://visualdynamics.fiocruz.br/login, is supported by all major web browsers. VisualDynamics was developed with Flask, which is a Python-based free and open-source framework for web development. The code is freely available for download at GitHub https://github.com/LABIOQUIM/visualdynamics.
Full-length transcriptome profiling for fruit development in Diospyros oleifera using nanopore sequencing
Authors: Xu Yang , Liu Cui-yu , Cheng Wen-qiang , Wu Kai-yun , Gong Bang-chu 
Published: March 2023

Abstract
Objectives
Diospyros oleifera, one of the most economically important Diospyros species, is an ideal model for studying the fruit development of persimmon. While, the lack of whole-transcriptome has hindered the complex transcriptional regulation mechanisms of sugar and tannin during fruit development.

Data description
We applied Oxford Nanopore Technologies to six developmental stage of fruit from D. oleifera for use in transcriptome sequencing. As a result of full-length transcriptome sequencing, 55.87 Gb of clean data were generated. After mapping onto the reference genome of D. oleifera, 51,588 full-length collapsing transcripts, including 2,727 new gene loci and 43,223 transcripts, were obtained. Comprehensively annotated, 38,086 of new transcripts were functional annotation, and 972 lncRNAs, 7,159 AS events were predicted. Here, we released the transcriptome database of D. oleifera at different stage of fruit development,which will provide a fundamention of to investigatethe transcript structure, variants and evolution of persimmon.
Highly accurate long reads are crucial for realizing the potential of biodiversity genomics
Authors: Hotaling Scott , Wilcox Edward R. , Heckenhauer Jacqueline , Stewart Russell J. , Frandsen Paul B. 
Published: March 2023

Abstract
Background
Generating the most contiguous, accurate genome assemblies given available sequencing technologies is a long-standing challenge in genome science. With the rise of long-read sequencing, assembly challenges have shifted from merely increasing contiguity to correctly assembling complex, repetitive regions of interest, ideally in a phased manner. At present, researchers largely choose between two types of long read data: longer, but less accurate sequences, or highly accurate, but shorter reads (i.e., >Q20 or 99% accurate). To better understand how these types of long-read data as well as scale of data (i.e., mean length and sequencing depth) influence genome assembly outcomes, we compared genome assemblies for a caddisfly, Hesperophylax magnus, generated with longer, but less accurate, Oxford Nanopore (ONT) R9.4.1 and highly accurate PacBio HiFi (HiFi) data. Next, we expanded this comparison to consider the influence of highly accurate long-read sequence data on genome assemblies across 6750 plant and animal genomes. For this broader comparison, we used HiFi data as a surrogate for highly accurate long-reads broadly as we could identify when they were used from GenBank metadata.

Results
HiFi reads outperformed ONT reads in all assembly metrics tested for the caddisfly data set and allowed for accurate assembly of the repetitive ~ 20 Kb H-fibroin gene. Across plants and animals, genome assemblies that incorporated HiFi reads were also more contiguous. For plants, the average HiFi assembly was 501% more contiguous (mean contig N50 = 20.5 Mb) than those generated with any other long-read data (mean contig N50 = 4.1 Mb). For animals, HiFi assemblies were 226% more contiguous (mean contig N50 = 20.9 Mb) versus other long-read assemblies (mean contig N50 = 9.3 Mb). In plants, we also found limited evidence that HiFi may offer a unique solution for overcoming genomic complexity that scales with assembly size.

Conclusions
Highly accurate long-reads generated with HiFi or analogous technologies represent a key tool for maximizing genome assembly quality for a wide swath of plants and animals. This finding is particularly important when resources only allow for one type of sequencing data to be generated. Ultimately, to realize the promise of biodiversity genomics, we call for greater uptake of highly accurate long-reads in future studies.
Associations of genome-wide and regional autozygosity with 96 complex traits in old order Amish
Authors: Lynch Megan T. , Maloney Kristin A. , Xu Huichun , Perry James A. , Center Regeneron Genetics , Shuldiner Alan R. , Mitchell Braxton D. 
Published: March 2023

AbstractBackground: Autozygosity, the proportion of the genome that is homozygous by descent, has been associated with variation in multiple health-related traits impacting evolutionary fitness. Autozygosity (FROH) is typically measured from runs of homozygosity (ROHs) that arise when identical-by-descent (IBD) haplotypes are inherited from each parent. Population isolates with a small set of common founders have elevated autozygosity relative to outbred populations. Methods: In this study, we examined whether degree of autozygosity was associated with variation in 96 cardiometabolic traits among 7221 Old Order Amish individuals residing in Lancaster County, PA. We estimated the average length of an ROH segment to be 6350 KB, with each individual having on average 17.2 segments 1.5 KB or larger. Measurements of genome-wide and regional FROH were used as the primary predictors of trait variation in association analysis. Results: In genome-wide FROH analysis, we did not identify any associations that withstood Bonferroni-correction (p = 0.0005). However, on regional FROH analysis, we identified associations exceeding genome-wide thresholds for two traits: serum bilirubin levels, which were significantly associated with a region on chromosome 2 localized to a region surrounding UGT1A10 (p = 1 × 10− 43), and HbA1c levels, which were significantly associated with a region on chromosome 8 localized near CHRNB3 (p = 8 × 10− 10). Conclusions: These analyses highlight the potential value of autozygosity mapping in founder populations.
No association of a Vascular endothelial growth factor A (VEGFA) gene polymorphism with pre-eclampsia among pregnant women in Uganda
Authors: Nabweyambo Sheila , Kanyerezi Stephen , Petterson John H.-O. , Katabazi Fred Ashaba , Ssekagiri Alfred , Mwesigwa Savannah , Mboowa Gerald , Nakazzi Faith , Keesiga Annette , Adroma Moses , Bwanga Freddie , McGovern Naomi , Sande Obondo James , Nakimuli Annettee 
Published: March 2023

Abstract
Background
Vascular endothelial growth factor A (VEGFA) is a major angiogenic factor that plays an important role in the formation of blood vessels during embryonic development. VEGFA has been implicated in the pathophysiology of pre-eclampsia (PE), since pre-eclamptic women present with reduced levels of free circulating VEGFA. The 3’ untranslated region (3’-UTR) of the VEGFA gene consists of elements that regulate the transcription and hence expression of the VEGFA protein in circulation. Hence it is suggested that variations thereof could underlie the reduced VEGFA levels observed in pre-eclamptic women. The purpose of this study was to investigate presence of the + 936C/T polymorphism, a common single nucleotide polymorphism (SNP) in the 3’-UTR of the VEGFA gene, and determine its association with PE among pregnant women in Uganda.

Results
There was no significant difference observed in the allele and genotype frequencies of the + 936C/T 3’ UTR-VEGFA polymorphism between pre-eclamptic and normotensive pregnant women (P > 0.05). Additionally, there was no significant difference in the median plasma levels of free VEGFA among women with the wild type, CT and TT genotypes of the + 936C/T VEGFA polymorphism (median = 0.84 pg/mL (IQR = 0.39–1.41) Vs 1.05 (0.61–1.18) Vs 1.05 (1.05–1.05) respectively, p-value = 0.7161).

Conclusions
These study findings indicate that the + 936C/T 3’ UTR-VEGFA polymorphism had no significant association with increased susceptibility to PE among women in Uganda. Further studies with a larger sample size are recommended.