bluuebunny/crossref_metadata_2025_split huggingface dataset:
RCPedia: a global resource for studying and exploring retrocopies in diverse species
Authors: Conceição Helena B , Mercuri Rafael L V , de Castro Matheus P M , Ohara Daniel T , Guardia Gabriela D A , Galante Pedro A F 
Published: September 2024

Abstract

Motivation
Gene retrocopies arise from the reverse transcription and genomic insertion of processed mRNA transcripts. These elements have significantly contributed to genetic diversity and novelties throughout the evolution of many species. However, the study of retrocopies has been challenging, owing to the absence of comprehensive, complete, and user-friendly databases for diverse species.

Results
Here, we introduce an improved version of RCPedia, an integrative database meticulously designed for the study of retrocopies. RCPedia offers an extensive catalog of retrocopies identified across 44 species, which includes 13 primates, 4 rodents, 6 chiropterans, 12 other mammals, 4 birds, turtles, lizards, frogs, zebrafish, and Drosophila. The database offers the most complete compilation of retrocopies per species, accompanied by detailed genomic annotations, expression data, and links to other data portals. Furthermore, RCPedia features a streamlined representation of data and an efficient querying system, establishing it as an invaluable tool for researchers in the fields of genomics, evolutionary biology, and transposable elements (TEs). In summary, RCPedia aims to enhance the investigation of retrocopies and their pivotal roles in shaping the genomic landscapes of diverse species.

Availability and implementation
RCPedia is available at https://www.rcpediadb.org.
SAAMBE-MEM: a sequence-based method for predicting binding free energy change upon mutation in membrane protein–protein complexes
Authors: Rimal Prawin , Panday Shailesh Kumar , Xu Wang , Peng Yunhui , Alexov Emil 
Published: September 2024

Abstract

Motivation
Mutations in protein–protein interactions can affect the corresponding complexes, impacting function and potentially leading to disease. Given the abundance of membrane proteins, it is crucial to assess the impact of mutations on the binding affinity of these proteins. Although several methods exist to predict the binding free energy change due to mutations in protein–protein complexes, most require structural information of the protein complex and are primarily trained on the SKEMPI database, which is composed mainly of soluble proteins.

Results
A novel sequence-based method (SAAMBE-MEM) for predicting binding free energy changes (ΔΔG) in membrane protein–protein complexes due to mutations has been developed. This method utilized the MPAD database, which contains binding affinities for wild-type and mutant membrane protein complexes. A machine learning model was developed to predict ΔΔG by leveraging features such as amino acid indices and position-specific scoring matrices (PSSM). Through extensive dataset curation and feature extraction, SAAMBE-MEM was trained and validated using the XGBoost regression algorithm. The optimal feature set, including PSSM-related features, achieved a Pearson correlation coefficient of 0.64, outperforming existing methods trained on the SKEMPI database. Furthermore, it was demonstrated that SAAMBE-MEM performs much better when utilizing evolution-based features in contrast to physicochemical features.

Availability and implementation
The method is accessible via a web server and standalone code at http://compbio.clemson.edu/SAAMBE-MEM/. The cleaned MPAD database is available at the website.
Scywalker: scalable end-to-end data analysis workflow for long-read single-cell transcriptome sequencing
Authors: De Rijk Peter , Watzeels Tijs , Küçükali Fahri , Van Dongen Jasper , Faura Júlia , Willems Patrick , De Deyn Lara , Duchateau Lena , Grones Carolin , Eekhout Thomas , De Pooter Tim , Joris Geert , Rombauts Stephane , De Rybel Bert , Rademakers Rosa , Van Breusegem Frank , Strazisar Mojca , Sleegers Kristel , De Coster Wouter 
Published: September 2024

Abstract

Motivation
Existing nanopore single-cell data analysis tools showed severe limitations in handling current data sizes.

Results
We introduce scywalker, an innovative and scalable package developed to comprehensively analyze long-read sequencing data of full-length single-cell or single-nuclei cDNA. We developed novel scalable methods for cell barcode demultiplexing and single-cell isoform calling and quantification and incorporated these in an easily deployable package. Scywalker streamlines the entire analysis process, from sequenced fragments in FASTQ format to demultiplexed pseudobulk isoform counts, into a single command suitable for execution on either server or cluster. Scywalker includes data quality control, cell type identification, and an interactive report. Assessment of datasets from the human brain, Arabidopsis leaves, and previously benchmarked data from mixed cell lines demonstrate excellent correlation with short-read analyses at both the cell-barcoding and gene quantification levels. At the isoform level, we show that scywalker facilitates the direct identification of cell-type-specific expression of novel isoforms.

Availability and implementation
Scywalker is available on github.com/derijkp/scywalker under the GNU General Public License (GPL) and at https://zenodo.org/records/13359438/files/scywalker-0.108.0-Linux-x86_64.tar.gz.
Randomized clinical trial on accelerated preoperative hyperfractionated radiotherapy versus preoperative hyperfractionated radio-chemotherapy in locally advanced rectal cancer
Authors: Idasiak Adam , Ziółkowska Barbara , Rajczykowski Marcin , Galwas Katarzyna , Dębosz-Suwińska Iwona , Zeman Marcin , Mrochem-Kwarciak Jolanta , Suwiński Rafał 
Published: September 2024

Abstract

Objectives
The aim of this study was to compare pathological response rates after preoperative hyperfractionated radiotherapy with co-administration of chemotherapy based on 5FU (HART-CT) versus preoperative hyperfractionated radiotherapy (HART) in patients with resectable rectal cancer.

Methods
Patients with T2/N+ or T3/any N rectal cancer were randomized either to HART twice a day (28 fractions of 1.5 Gy) to total dose 42 Gy or to HART-CT. Tumour regression grade was postoperatively assessed according to the 4-point scale as recommended by the American Joint Committee on Cancer (AJCC). The secondary endpoints included overall survival (OS), disease-free survival (DFS), toxicity of preoperative treatment, locoregional, and distant failure rates. There were 187 patients eligible for analysis: 95 in HART and 92 in the HART-CT. Median follow-up was 5.6 years.

Results
The analysis demonstrated a significantly higher chance of achieving pathologic complete response in HART-CT arm: complete response was achieved in 4/95, 4% (HART) and 11/92, 12% (HART-CT) (P = .045). The differences in OS and DFS, while tending to favour HART-CT, were not significant: OS (P = .13, hazard ratio [HR] = 0.82, 95% CI, 0.63-1.06) and DFS (P = .32; HR = 0.88, 95% CI, 0.69-1.13). The locoregional failure and distant metastases rates did not statistically differ between the trial arms. The rate of late complications was similar (P = .51), grade 3+ being 8% versus 11% in the HART/HART-CT group, respectively.

Conclusions
The hyperfractionated preoperative radiotherapy with concurrent 5-Fu-based chemotherapy (HART-CT) improved pathological response rate compared to HART. This translated into favourable OS and DFS in HART-CT, but the differences did not reach the threshold for significance.

Advances in knowledge
A new hyperfractionated chemo-RT scheme is proposed. Histopathological major response (TRG 0-1) is associated with better clinical outcome.
Changes in electrophysiological aperiodic activity during cognitive control in Parkinson’s disease
Authors: Monchy Noémie , Modolo Julien , Houvenaghel Jean-François , Voytek Bradley , Duprez Joan 
Published: September 2024

Abstract
Cognitive symptoms in Parkinson’s disease are common and can significantly affect patients’ quality of life. Therefore, there is an urgent clinical need to identify a signature derived from behavioural and/or neuroimaging indicators that could predict which patients are at increased risk for early and rapid cognitive decline. Recently, converging evidence identified that aperiodic activity of the EEG reflects meaningful physiological information associated with age, development, cognitive and perceptual states or pathologies. In this study, we aimed to investigate aperiodic activity in Parkinson’s disease during cognitive control and characterize its possible association with behaviour. Here, we recorded high-density EEG in 30 healthy controls and 30 Parkinson’s disease patients during a Simon task. We analysed task-related behavioural data in the context of the activation–suppression model and extracted aperiodic parameters (offset, exponent) at both scalp and source levels. Our results showed lower behavioural performances in cognitive control as well as higher offsets in patients in the parieto-occipital areas, suggesting increased excitability in Parkinson’s disease. A small congruence effect on aperiodic parameters in pre- and post-central brain areas was also found, possibly associated with task execution. Significant differences in aperiodic parameters between the resting-state, pre- and post-stimulus phases were seen across the whole brain, which confirmed that the observed changes in aperiodic activity are linked to task execution. No correlation was found between aperiodic activity and behaviour or clinical features. Our findings provide evidence that EEG aperiodic activity in Parkinson’s disease is characterized by greater offsets, and that aperiodic parameters differ depending on arousal state. However, our results do not support the hypothesis that the behaviour-related differences observed in Parkinson’s disease are related to aperiodic changes. Overall, this study highlights the importance of considering aperiodic activity contributions in brain disorders and further investigating the relationship between aperiodic activity and behaviour.
Vaccine Development Should Be Polytheistic, Not Monotheistic
Authors: Plotkin Stanley A , Robinson James M , Fitchett Joseph R A , Gershburg Edward 
Published: September 2024

Abstract
Vaccines based on messenger RNA technology have been tremendously successful, but their properties are not necessarily ideal for all pathogens. There is a risk that concentration on that technology alone for new vaccine development will ignore older technologies that have properties giving broader and more persistent protection.
Hydroxychloroquine as an add-on therapy for the induction therapy of MPO-AAV: a retrospective observational cohort study
Authors: Gong Yizi , Meng Ting , Lin Wei , Hu Xueling , Tang Rong , Xiong Qi , Ooi Joshua D , Eggenhuizen Peter J , Chen Jinbiao , Zhou Ya-Ou , Luo Hui , Xu Jia , Liu Ning , Xiao Ping , Xiao Xiangcheng , Zhong Yong 
Published: September 2024

ABSTRACT

Background
The remission rate of myeloperoxidase (MPO)-antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) patients who received standard induction therapy is far from satisfactory. Improving the remission rate of MPO-AAV patients is essential. Hydroxychloroquine (HCQ), one of the classic antimalarial drugs, has been widely used in various autoimmune rheumatic diseases. This retrospective observational cohort study is aimed to evaluate the efficacy and safety of HCQ during induction treatment for MPO-AAV.

Methods
The medical records of patients diagnosed with MPO-AAV at Xiangya Hospital, Central South University from January 2021 to September 2023 were collected. They were assigned to the HCQ group or control group according to whether they used HCQ. The patients included were screened by propensity score matching. To evaluate whether MPO-AAV patients benefited from HCQ, we compared the prognosis of the two groups. The adverse effects of HCQ during follow-up were recorded.

Results
The composition ratio of complete remission, response and treatment resistance between HCQ group and control group were different statistically (P = .021). There was no significant difference between the two groups in 1-year renal survival (P = .789). The HCQ group had better 1-year patient survival than the control group (P = .049). No serious adverse effects were documented in the HCQ group.

Conclusions
HCQ together with standard induction treatment may improve the remission rate of MPO-AAV patients, and HCQ had good safety in our study.
Circulating dimethylguanidino valeric acid, dietary factors, and risk of coronary heart disease
Authors: Heianza Yoriko , Wang Xuan , Kou Minghao , Tiwari Saumya , Watrous Jeramie D , Rexrode Kathryn M , Alotaibi Mona , Jain Mohit , Sun Qi , Manson JoAnn E , Qi Lu 
Published: September 2024

Abstract

Aims
Circulating dimethylguanidino valeric acid (DMGV) was identified as a novel metabolite related to cardiorespiratory fitness and cardiometabolic abnormalities. Circulating DMGV levels are subjective to dietary modulation; however, studies on its associations with intakes of coronary heart disease (CHD)–related foods/nutrients are limited. We investigated whether plasma DMGV was related to risk of incident CHD. We tested associations of DMGV with CHD-related dietary intakes measured by 7-day dietary records and estimated corresponding disease risk.

Methods and results
This nested case–control study on the incidence of CHD included 1520 women (760 incident cases of fatal CHD and nonfatal myocardial infarction and 760 controls) from the Nurses’ Health Study. Separately, plasma DMGV and CHD-related dietary intakes and cardiometabolic abnormalities were assessed in the Women’s Lifestyle Validation Study (WLVS; n = 724). Higher plasma DMGV was related to a greater risk of CHD [relative risk (RR) per 1 SD, 1.26 (95% CI 1.13, 1.40); P-for-linearity = 0.006]. Greater intakes of sodium, energy-dense foods, and processed/red meat were related to higher DMGV levels; every 1 SD intake of sodium was associated with β 0.13 (SE 0.05; P = 0.007) for DMGV Z-scores, which corresponded to a RR of 1.031 (1.016, 1.046) for CHD. High DMGV (the top quartile, Q4) showed a significant RR of 1.60 (1.17, 2.18) after adjusting for diet and lifestyle factors; the RR further adjusting for obesity and hypertension was 1.29 (0.93, 1.79) as compared with the lowest quartile. In both cohorts, greater adiposity and adverse cardiometabolic factor status were significantly related to higher DMGV levels.

Conclusion
Higher levels of plasma DMGV, a metabolite reflecting unfavourable CHD-related dietary intakes, were associated with an increased risk of CHD. The unfavourable association was attenuated by cardiometabolic risk factor status. Our study underscores the potential importance of plasma DMGV as an early biomarker associated with diet and the long-term risk of CHD among women.
Structural characteristics of the epidermis in marine and freshwater finless porpoises adapted to distinct osmotic environments
Authors: Zhou Haojie , Zhang Changqun , Tang Bin , Zhang Haobo , Zheng Jinsong , Wang Kexiong , He Dekui , Hao Yujiang 
Published: September 2024

Abstract
The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis, Pilleri & Gihr, 1972; YFP) is an exclusively freshwater cetacean species inhabiting the Yangtze River and its connecting large lakes. As the primary line of defense in maintaining physiological equilibrium, the epidermis of the porpoise is expected to have undergone structural adaptations due to the shift from the marine to the freshwater environment. This study compared the microstructural and ultrastructural features of the epidermis of YFP and its marine counterpart, the East Asian finless porpoise (Neophocaena asiaeorientalis sunameri, Pilleri & Gihr, 1975; EAFP). Microscopic structural observations and statistical analyses of the epidermal thickness demonstrated no significant differences in the cell structure or distribution between the two porpoise species. However, the epidermis of the YFP contained more abundant stratum basale cells. The outermost lipid stratum corneum exhibited a thinner cell layer with wider neutral lipid droplets to resist the passive entry of water molecules in the hypotonic environment. In contrast, for the EAFP, a more uniformly arranged stratum basale in the epidermis led to denser keratin fibers and robust desmosomes within each epidermal layer at the ultrastructural level. This tight arrangement of cells can reduce transepidermal water loss (TEWL) in an environment with higher osmotic pressure. In conclusion, the 2 finless porpoise species appear to employ different epidermal mechanisms to adapt to their distinct osmotic environments. The YFP appears to possess a “lipid waterproofing” epidermal structure, while the EAFP possesses a “thick and compact water-retaining” epidermal structure to cope with potential water loss.
Difference in cardiac response after transcatheter aortic valve implantation according to flow and gradient pattern
Authors: Yokoyama Hiroaki , Yamanaka Futoshi , Shishido Koki , Moriyama Noriaki , Ochiai Tomoki , Miyashita Hirokazu , Sugiyama Yoichi , Yashima Fumiaki , Ohno Yohei , Nishina Hidetaka , Izumo Masaki , Asami Masahiko , Naganuma Toru , Mizutani Kazuki , Yamawaki Masahiro , Tada Norio , Shirai Shinichi , Noguchi Masahiko , Ueno Hiroshi , Takagi Kensuke , Watanabe Yusuke , Yamamoto Masanori , Saito Shigeru , Hayashida Kentaro 
Published: September 2024

Abstract

Aims
In patients undergoing transcatheter aortic valve implantation (TAVI) for severe aortic stenosis (AS), data on the differences in subsequent cardiac structure and function among stratified groups with flow gradient patterns through the aortic valve are insufficient.

Methods and results
In this large multicenter study, 4523 patients undergoing TAVI for severe AS between 2013 and 2019 were divided into three groups according to the following criteria: (i) high-gradient AS (HG-AS) [mean pressure gradient (MPG) ≥ 40 mmHg], (ii) classical low-flow low-gradient AS (cLFLG-AS) [MPG &lt; 40 mmHg, left ventricular (LV) ejection fraction (LVEF) &lt;50%], and (iii) paradoxical low-flow low-gradient AS (pLFLG-AS) [MPG &lt; 40 mmHg, LVEF ≥ 50% but stroke volume index (SVi) &lt;35 mL/m2]. Echocardiography was performed at baseline, post-procedure, and 1 year post-TAVI. 3697, 507, and 319 patients had HG-AS, cLFLG-AS, and pLFLG-AS, respectively. After adjusting for clinical factors, cLFLG-AS and pLFLG-AS had an ∼1.5-fold higher 2-year all-cause mortality compared with HG-AS. During 1 year following TAVI, compared with HG-AS, cLFLG-AS showed greater reduction of LV systolic diameter (LVDs) and LV diastolic diameter (LVDd) and greater increase of LVEF (P &lt; 0.001 for all), and changes in LV mass index (LVMi) and SVi were comparable (P = 0.915 and P = 0.821, respectively). However, pLFLG-AS demonstrated less reduction of LVDs and LVDd (P = 0.039 and P = 0.001, respectively), less improvement of LVEF and LVMi (P = 0.045 and P &lt; 0.001, respectively), and comparable change in SVi (P = 0.364).

Conclusion
During 1 year post-TAVI, compared with HG-AS, cLFLG-AS achieves smaller LV diameters, greater increase in LVEF, and comparable regression of LVMi, whereas pLFLG-AS does not.
ST-segment elevation myocardial infarction with refractory cardiogenic shock due to coronary spasm: a case report
Authors: Renziehausen Stephan , Stöbe Stephan , Spies Christian , Metze Michael 
Published: September 2024

Abstract

Background
Acute coronary syndrome (ACS) is primarily due to obstructive coronary artery disease (CAD). Nevertheless, in 1–14% of cases, ACS is present without evidence of obstructive CAD. Coronary artery spasm is an uncommon cause of ACS. Diagnostic work-up includes acute invasive coronary angiography and afterwards provocation testing. The optimal patient management is for patients presenting with cardiogenic shock due to ACS caused by coronary artery spasm is unclear.

Case summary
A 67-year-old Caucasian, who underwent elective revision of hip arthroplasty, presented with ST elevations with circulatory collapse, leading to resuscitation due to anaesthesia induction. Extracorporeal membrane oxygenation (ECMO) implantation led to restoration of spontaneous circulation. Coronary angiography revealed coronary vasospasm, which was successfully treated with nitrates i.c. Later, despite of implanted ECMO, recurring haemodynamic deterioration required continuous administration of nitrates i.v., which finally resulted in the stabilization of circulatory system. Extracorporeal membrane oxygenation removal was possible 48 h after implantation and another 12 h later we extubated the patient. Furthermore, we administered calcium antagonists and an intra-cardiac defibrillator was implanted. Finally, the patient was discharged 12 days after admission with no physical or neurological restrictions after resuscitation.

Discussion
This unique case highlights that rare causes of severe ACS with cardiogenic shock need to be considered. Administration of vasodilators, which are not part of the standard care in cardiogenic shock, represents the adequate treatment of a patient with spasm of coronary arteries. Furthermore, the recurrence of acute coronary events must be prevented by drug and device therapy in these patients.
The Liberty of Whitby Strand: The Origins and Significance of a Jurisdictional Immunity
Authors: Pickles Thomas 
Published: September 2024

Abstract
The medieval abbey at Whitby, North Yorkshire, controlled a jurisdictional immunity from royal administration, which was territorial and was known as the Liberty of Whitby Strand. Since Frederick William Maitland, historians have analysed such jurisdictional immunities as an index of royal authority and power. However, the surviving documentation for jurisdictional immunities means that it is often difficult to establish precisely when they were created or what franchises they included. Whitby Abbey claimed that the Liberty of Whitby Strand originated in a grant of King William I and this was accepted by the Victoria County History at the beginning of the twentieth century. Since then, the Liberty has been almost completely ignored. This article revisits the evidence, suggesting that it is possible to pinpoint its origins with rare precision. It argues that the Whitby monks forged a series of charters to persuade King Richard I and King John to transform a narrower portfolio of franchises into the wider territorial Liberty. This article further considers the politics surrounding its creation under Richard and John, and its implications for our understanding of royal authority and power.