bluuebunny/crossref_metadata_2025_split huggingface dataset:
One organ to infect them all: the Cuscuta haustorium
Authors: Balios Vasili A , Fischer Karsten , Bawin Thomas , Krause Kirsten 
Published: December 2024

Abstract

Background
Research on the parasitic plant genus Cuscuta has flourished since the genomes of several of its species were published. Most of the research revolves around the iconic infection organ that secures the parasite’s sustenance: the haustorium. Interest in understanding the structure–function–regulation relationship of the haustorium is based as much on the wish to find ways to keep the parasite under control as on the opportunities it offers to shed light on various open questions in plant biology.

Scope
This review will briefly introduce parasitism among plants, using the genus Cuscuta as the main example, before presenting its haustorium alongside the terminology that is used to describe its architecture. Possible evolutionary origins of this parasitic organ are presented. The haustorium is then followed from its initiation to maturity with regard to the molecular landscape that accompanies the morphological changes and in light of the challenges it must overcome before gaining access to the vascular cells of its hosts. The fact that Cuscuta has an unusually broad host range stresses how efficient its infection strategy is. Therefore, particular consideration will be given in the final section to a comparison with the process of grafting, being the only other type of tissue connection that involves interspecific vascular continuity.

Conclusions
Studies on Cuscuta haustoriogenesis have revealed many molecular details that explain its success. They have also unearthed some mysteries that wait to be solved. With a better understanding of the complexity of the infection with its combination of universal as well as host-specific elements that allow Cuscuta to parasitize on a wide range of host plant species, we may be many steps closer to not only containing the parasite better but also exploiting its tricks where they can serve us in the quest of producing more and better food and fodder.
RIOT—Rapid Immunoglobulin Overview Tool—annotation of nucleotide and amino acid immunoglobulin sequences using an open germline database
Authors: Dudzic Paweł , Janusz Bartosz , Satława Tadeusz , Chomicz Dawid , Gawłowski Tomasz , Grabowski Rafał , Jóźwiak Przemek , Tarkowski Mateusz , Mycielski Maciej , Wróbel Sonia , Krawczyk Konrad 
Published: December 2024

Abstract
Antibodies are a cornerstone of the immune system, playing a pivotal role in identifying and neutralizing infections caused by bacteria, viruses, and other pathogens. Understanding their structure, and function, can provide insights into both the body’s natural defenses and the principles behind many therapeutic interventions, including vaccines and antibody-based drugs. The analysis and annotation of antibody sequences, including the identification of variable, diversity, joining, and constant genes, as well as the delineation of framework regions and complementarity-determining regions, is essential for understanding their structure and function. Currently analyzing large volumes of antibody sequences is routine in antibody discovery, requiring fast and accurate tools. While there are existing tools designed for the annotation and numbering of antibody sequences, they often have limitations such as being restricted to either nucleotide or amino acid sequences; slow execution times; or reliance on germline databases that are closed, frequently changed, or have sparse coverage for some species. Here, we present the Rapid Immunoglobulin Overview Tool (RIOT), a novel open-source solution for antibody numbering that addresses these shortcomings. RIOT handles nucleotide and amino acid sequence processing, comes integrated with an Open Germline Receptor Database, and is computationally efficient. We hope that the tool will facilitate rapid annotation of antibody sequencing outputs for the benefit of understanding antibody biology and discovering novel therapeutics.
epiTCR-KDA: knowledge distillation model on dihedral angles for TCR-peptide prediction
Authors: Pham My-Diem Nguyen , Su Chinh Tran-To , Nguyen Thanh-Nhan , Nguyen Hoai-Nghia , Nguyen Dinh Duy An , Giang Hoa , Nguyen Dinh-Thuc , Phan Minh-Duy , Nguyen Vy 
Published: December 2024

Abstract

Motivation
The prediction of the T-cell receptor (TCR) and antigen bindings is crucial for advancements in immunotherapy. However, most current TCR-peptide interaction predictors struggle to perform well on unseen data. This limitation may stem from the conventional use of TCR and/or peptide sequences as input, which may not adequately capture their structural characteristics. Therefore, incorporating the structural information of TCRs and peptides into the prediction model is necessary to improve its generalizability.

Results
We developed epiTCR-KDA (KDA stands for Knowledge Distillation model on Dihedral Angles), a new predictor of TCR-peptide binding that utilizes the dihedral angles between the residues of the peptide and the TCR as a structural descriptor. This structural information was integrated into a knowledge distillation model to enhance its generalizability. epiTCR-KDA demonstrated competitive prediction performance, with an area under the curve (AUC) of 1.00 for seen data and AUC of 0.91 for unseen data. On public datasets, epiTCR-KDA consistently outperformed other predictors, maintaining a median AUC of 0.93. Further analysis of epiTCR-KDA revealed that the cosine similarity of the dihedral angle vectors between the unseen testing data and training data is crucial for its stable performance. In conclusion, our epiTCR-KDA model represents a significant step forward in developing a highly effective pipeline for antigen-based immunotherapy.

Availability and implementation
epiTCR-KDA is available on GitHub (https://github.com/ddiem-ri-4D/epiTCR-KDA).
SurfR: Riding the wave of RNA-seq data with a comprehensive bioconductor package to identify surface protein-coding genes
Authors: Maurizio Aurora , Tascini Anna Sofia , Morelli Marco J 
Published: December 2024

Abstract

Motivation
Proteins at the cell surface connect signaling networks and largely determine a cell’s capacity to communicate and interact with its environment. In particular, variations in transcriptomic profiles are often observed between healthy and diseased cells, leading to distinct sets of cell-surface proteins. For these reasons, cell-surface proteins may act as biomarkers for the detection of cells of interest in tissues or body fluids, are often the target of pharmaceutical agents, and hold significant promise in the clinical practice for diagnosis, prognosis, treatment development, and evaluation of therapy response. Therefore, implementing robust methods to identify condition-specific cell-surface proteins is of pivotal importance to advance biomedical research.

Results
We developed SurfR, an R/Bioconductor package providing a streamlined end-to-end workflow for computationally identifying surface protein-coding genes from expression data. Our user-friendly, comprehensive workflow performs systematic expression data retrieval from public databases, differential gene expression across conditions, integration of datasets, enrichment analysis, identification of targetable proteins on a condition of interest, and data visualization

Availability and implementation
SurfR is released under GNU-GPL-v3.0 License. Source code, documentation, examples, and tutorials are available through Bioconductor (http://www.bioconductor.org/packages/SurfR). RMD notebooks with the use cases code described in the manuscript can be found on GitHub (https://github.com/auroramaurizio/SurfR_UseCases).
JARVIS3: an efficient encoder for genomic data
Authors: Sousa Maria J P , Pinho Armando J , Pratas Diogo 
Published: December 2024

Abstract

Motivation
Large-scale genomic projects grapple with the complex challenge of reducing medium- and long-term storage space and its associated energy consumption, monetary costs, and environmental footprint.

Results
We present JARVIS3, an advanced tool engineered for the efficient reference-free compression of genomic sequences. JARVIS3 introduces a pioneering approach, specifically through enhanced table memory models and probabilistic lookup-tables applied in repeat models. These optimizations are pivotal in substantially enhancing computational efficiency. JARVIS3 offers three distinct profiles: (i) rapid computation with moderate compression, (ii) a balanced trade-off between time and compression, and (iii) slower computation with significantly higher compression ratios. The implementation of JARVIS3 is rooted in the C programming language, building upon the success of its predecessor, JARVIS2. JARVIS3 shows substantial speed improvements relative to JARVIS2 while providing slightly better compression. Furthermore, we provide a versatile C/Bash implementation, facilitating the application in FASTA and FASTQ data, including the capability for parallel computation. In addition, JARVIS3 includes a mode for outputting bit information, as well as providing the Normalized Compression and bit rates, facilitating compression-based analysis. This establishes JARVIS3 as an open-source solution for genomic data compression and analysis.

Availability and implementation
JARVIS3 is freely available at https://github.com/cobilab/jarvis3.
DiffPaSS—high-performance differentiable pairing of protein sequences using soft scores
Authors: Lupo Umberto , Sgarbossa Damiano , Milighetti Martina , Bitbol Anne-Florence 
Published: December 2024

Abstract

Motivation
Identifying interacting partners from two sets of protein sequences has important applications in computational biology. Interacting partners share similarities across species due to their common evolutionary history, and feature correlations in amino acid usage due to the need to maintain complementary interaction interfaces. Thus, the problem of finding interacting pairs can be formulated as searching for a pairing of sequences that maximizes a sequence similarity or a coevolution score. Several methods have been developed to address this problem, applying different approximate optimization methods to different scores.

Results
We introduce Differentiable Pairing using Soft Scores (DiffPaSS), a differentiable framework for flexible, fast, and hyperparameter-free optimization for pairing interacting biological sequences, which can be applied to a wide variety of scores. We apply it to a benchmark prokaryotic dataset, using mutual information and neighbor graph alignment scores. DiffPaSS outperforms existing algorithms for optimizing the same scores. We demonstrate the usefulness of our paired alignments for the prediction of protein complex structure. DiffPaSS does not require sequences to be aligned, and we also apply it to nonaligned sequences from T-cell receptors.

Availability and implementation
A PyTorch implementation and installable Python package are available at https://github.com/Bitbol-Lab/DiffPaSS.
Roe deer uterine fluid metabolome reveals elevated glycolysis, fatty acid breakdown, and spermidine synthesis upon reactivation from diapause
Authors: Elsafadi Sara , Hankele Anna-Katharina , Giesbertz Pieter , Ulbrich Susanne E 
Published: December 2024

Abstract
The blastocyst of the European roe deer (Capreolus capreolus) undergoes a period of decelerated growth and limited metabolism. During this period known as embryonic diapause, it floats freely in the uterus encircled by the histotroph. Prior to implantation, reactivation is marked by rapid embryonic growth and conceptus elongation. We hypothesized that the uterine fluid, which is known to undergo changes in its composition to support early embryonic development, contributes to controlling embryonic growth during diapause and elongation. We therefore characterized the pre-implantation uterine fluid metabolome during diapause and at elongation by mass spectrometry and particularly assessed nonpolar lipids, polar metabolites, acylcarnitines, and polyamines. Our results show that triglycerides and diglycerides levels decreased at elongation, likely serving as a source for membrane synthesis rather than for energy production. A functional analysis identified glycolysis as a key pathway during elongation, which may compensate for the energy requirements during this phase. We also observed an increase of sphingomyelin; prostaglandin precursors; and the amino acids asparagine, glutamine, and methionine upon elongation. The sphingolipid and glycerophospholipid metabolism pathways were implicated during elongation. Particularly, spermidine, and to some extent spermine but not putrescine-levels significantly increased in the uterine fluid during elongation, indicating their significance for reactivation and/or proliferation at embryo elongation. We conclude that the roe deer uterine fluid sustained dynamic compositional changes necessary to support the energy- and resource-intensive conceptus elongation. However, it remains to be determined whether these changes are the cause or a consequence of embryo elongation. Studying the metabolic changes and molecular interactions in the roe deer during diapause and elongation not only reveals insights into aspects of its reproductive strategy, but also deepens our knowledge of embryo metabolic demands and developmental velocities across species.
Directed evolution of peroxidase DNAzymes by a function-based approach
Authors: Bhuyan Soubhagya K , He Weisi , Cui Jingyu , Tanner Julian A 
Published: December 2024

Abstract
Peroxidase DNAzymes are single-stranded, stable G-quadruplexes structures that exhibit catalytic activity with cofactor hemin. This class of DNAzymes offers several advantages over traditional protein and RNA catalysts, including thermal stability, resistance to hydrolysis, and easy of synthesis in the laboratory. However, their use in medicine, biology, and chemistry is limited due to their low catalytic rates. Selecting and evolving for higher catalytic rates has been challenging due to limitations in selection methodology which generally use affinity as the selection pressure instead of kinetics. We previously evolved a new peroxidase DNAzyme (mSBDZ-X-3) through a directed evolution method, which was subsequently used for proximity labelling in a proteomic experiment in cell culture. Herein, we present a detailed protocol for this function-based laboratory evolution method to evolve peroxidase DNAzymes for future laboratory implementation. This approach is based on capturing self-biotinylated DNA, which is catalyzed by intrinsic peroxidase activity to select for DNAzyme molecules. The selection method uses fluorescence-based real-time monitoring of the DNA pools, allowing for the enrichment of catalytic activity and capture of catalytic DNA across evolutionary selection rounds.
The evolved mSBDZ-X-3 DNAzyme attributes parallel G-quadruplex structure and demonstrates better catalytic properties than DNAzyme variants evolved previously. The influence of critical reaction parameters is outlined. This protocol enables discovery of improved peroxidase DNAzyme/RNAzyme variants from natural or chemical-modified nucleotide libraries. The approach could be applicable for the selection of catalytic activities in a variety of directed molecular evolution contexts.
Addition of contrast-enhanced mammography enhancement patterns and morphology for differentiating benign from malignant papillary breast lesions
Authors: Xu Weimin , Chen Lingjian , Zeng Weixiong , Xu Zeyuan , Ma Mengwei , Chen Weiguo , Liao Xin , Wen Chanjuan , Wang Sina 
Published: December 2024

Abstract

Objectives
To investigate the capability of morphological and enhancement pattern analysis in contrast-enhanced mammography (CEM) to differentiate between benign and malignant papillary breast lesions.

Methods
This study involved 63 patients diagnosed with papillary breast lesions between January 2018 and December 2022. CEM was performed at two time intervals: between 2-3 min (T1, early phase) and 4-5 min (T2, later phase) after the injection of the contrast agent. For each patient, Breast Imaging Reporting and Data System (BI-RADS) lesion features were recorded. Kinetic enhancement patterns were evaluated for both phases based on these changes, followed by the measurement of diagnostic performance.

Results
Among the 63 female patients, a total of 86 lesions were identified, including 18 malignant ones, three intraductal papillomas without atypical proliferation, and 42 benign papillary lesions. The areas under receiver operating characteristic curves for CEM with kinetic enhancement and for CEM alone were 0.856 and 0.800, respectively. Assessing the diagnostic value, specificity, and accuracy of morphological categorization combined with kinetic enhancement showed higher values compared to those of the CEM morphological categorization alone (71.1% vs 60.0% and 79.4% vs 71.4%, respectively). However, the sensitivity and negative predictive value of the CEM with kinetic enhancement were similar to those of CEM alone (100% for all).

Conclusion
For BI-RADS 3-5 papillary breast lesions, incorporating CEM kinetic enhancement to morphological patterns improved the confidence level in diagnosis.

Advances in knowledge
This article provides valuable references for distinguishing benign and malignant breast papillary lesions.
Postoperative complications after breast cancer surgery and effect on recurrence and survival: population-based cohort study
Authors: Adwall Linda , Fredriksson Irma , Hultin Hella , Mani Maria , Norlén Olov 
Published: December 2024

Abstract

Background
There is conflicting evidence regarding whether postoperative complications after breast cancer surgery are associated with worse oncological outcome. This study aimed to assess the risk of systemic breast cancer recurrence after surgical site infection and also the impact of surgical site infection on locoregional recurrence, breast cancer-specific survival and overall survival.

Methods
This nationwide cohort study included patients who underwent surgery for primary breast cancer in Sweden between January 2008 and September 2019. The study cohort was identified in the Breast Cancer Database Sweden 3.0, a database linking the National Breast Cancer Quality Register to national population-based healthcare registers held by the National Board of Health and Welfare and Statistics Sweden. The primary exposure was surgical site infection within 90 days from surgery, and the primary outcome was systemic recurrence of breast cancer. Secondary outcomes included locoregional recurrence, overall survival and breast cancer-specific survival. Multivariable Cox regression analysis was performed to assess the association between exposure, predictors and outcomes.

Results
Of 82 102 patients included in the study, 15.7% experienced a surgical site infection within 90 days of surgery. Surgical site infection was not significantly associated with systemic recurrence, locoregional recurrence or breast cancer-specific survival after adjustment for confounding variables. Surgical site infection was significantly associated with worse overall survival, but the significant association disappeared in a sensitivity analysis excluding all patients with any kind of malignancy before breast cancer diagnosis.

Conclusion
Surgical site infection after breast cancer surgery does not significantly increase the risk of systemic recurrence. All possible actions should nevertheless be taken to reduce complication rates.
Focusing on the fellas: Stacey Abrams’ social media campaign addresses misogynoir in U.S. politics
Authors: Grant Rachel , Lyons Nikki L 
Published: December 2024

Abstract
After narrowly losing the Georgia (US) gubernatorial election in 2018, Stacey Abrams adopted a novel approach to secure the Black male vote, staging a series of events known as “Stacey and the Fellas.” This study delves into the discourse surrounding those events and their impact on misogynoir directed at Abrams. We employ a misogynoir framework to investigate the U.S. media narratives that Black women, particularly in politics, must redefine. Finding discourse on racialization, the masculinity of Blackness, and prominent misogynoir, our research sheds light on the communication surrounding Black female candidates on Twitter and their efforts to court Black male voters. These insights hold implications for future campaign strategies and discourse-centered approaches to political engagement.
The right kind of growth for everyone: policy challenges during the digital and green transformations
Authors: Coyle Diane 
Published: December 2024

Abstract
The UK, like other Organisation for Economic Co-operation and Development (OECD) economies, has experienced a dismal decade and a half since the financial crisis. The reason lies in the dual technological transition, energy and digital, which is prompting structural shifts in the economy that require a co-ordinated policy response. This implies the need for more co-ordinated policies and more active intervention in the structure of the economy than has been the case in recent decades. It requires a broader measure of economic progress than short-term Gross Domestic Product (GDP) growth and above all a long-term perspective.
Outcomes of patients with infective endocarditis–associated acute kidney injury: a retrospective cohort study
Authors: Ai SanXi , Feng Xiang , Sun Kai , Chen Gang , Liu XinPei , Miao Qi , Qin Yan , Li XueMei 
Published: December 2024

ABSTRACT

Background
The outcomes of patients with infective endocarditis (IE)-associated acute kidney injury (AKI) are poorly understood.

Methods
This retrospective cohort study was conducted in a tertiary hospital in China to analyze the short- and long-term outcomes among patients with IE-associated AKI. The risk factors for 90-day mortality, long-term outcomes and kidney non-recovery were analyzed via multivariable logistic regression, the Cox regression, and the Fine–Gray competing risk model, respectively.

Results
Among 294 patients with IE-associated AKI, 14.3% died within 90 days, and the risk factors for 90-day mortality were similar to those identified in the general IE population. Among the 230 AKI survivors in whom 90-day kidney recovery could be assessed, 17.4% did not recover kidney function at 90 days. Kidney non-recovery at 90 days was associated with an increased risk of the long-term composite outcome of mortality, end-stage renal disease or sustained doubling of serum creatinine [hazard ratio (HR) 3.00, 95% confidence interval (CI) 1.19–7.59]. Five variables were related to kidney non-recovery: low baseline estimated glomerular filtration rate (eGFR) (HR 2.52, 95% CI 1.73–3.65), stage of AKI (HR 3.03, 95% CI 2.07–4.42 for stage 3), shock (HR 5.56, 95% CI 3.02–10.22), glomerulonephritis-related AKI (HR 3.04, 95% CI 1.93–4.77) and drug-related AKI (HR 2.77, 95% CI 1.86–4.13).

Conclusion
Patients with IE-associated AKI had a high 90-day mortality, and a substantial proportion of survivors did not recover kidney function at 90 days. Kidney non-recovery at 90 days was associated with adverse long-term outcomes. Low baseline eGFR, severe AKI, shock, drug-related AKI and glomerulonephritis-related AKI were risk factors for kidney non-recovery.