bluuebunny/crossref_metadata_2025_split huggingface dataset:
Species-agnostic transfer learning for cross-species transcriptomics data integration without gene orthology
Authors: Park Youngjun , Muttray Nils P , Hauschild Anne-Christin 
Published: February 2024

Abstract
Novel hypotheses in biomedical research are often developed or validated in model organisms such as mice and zebrafish and thus play a crucial role. However, due to biological differences between species, translating these findings into human applications remains challenging. Moreover, commonly used orthologous gene information is often incomplete and entails a significant information loss during gene-id conversion. To address these issues, we present a novel methodology for species-agnostic transfer learning with heterogeneous domain adaptation. We extended the cross-domain structure-preserving projection toward out-of-sample prediction. Our approach not only allows knowledge integration and translation across various species without relying on gene orthology but also identifies similar GO among the most influential genes composing the latent space for integration. Subsequently, during the alignment of latent spaces, each composed of species-specific genes, it is possible to identify functional annotations of genes missing from public orthology databases. We evaluated our approach with four different single-cell sequencing datasets focusing on cell-type prediction and compared it against related machine-learning approaches. In summary, the developed model outperforms related methods working without prior knowledge when predicting unseen cell types based on other species’ data. The results demonstrate that our novel approach allows knowledge transfer beyond species barriers without the dependency on known gene orthology but utilizing the entire gene sets.
Deqformer: high-definition and scalable deep learning probe design method
Authors: Cai Yantong , Lv Jia , Li Rui , Huang Xiaowen , Wang Shi , Bao Zhenmin , Zeng Qifan 
Published: February 2024

Abstract
Target enrichment sequencing techniques are gaining widespread use in the field of genomics, prized for their economic efficiency and swift processing times. However, their success depends on the performance of probes and the evenness of sequencing depth among each probe. To accurately predict probe coverage depth, a model called Deqformer is proposed in this study. Deqformer utilizes the oligonucleotides sequence of each probe, drawing inspiration from Watson–Crick base pairing and incorporating two BERT encoders to capture the underlying information from the forward and reverse probe strands, respectively. The encoded data are combined with a feed-forward network to make precise predictions of sequencing depth. The performance of Deqformer is evaluated on four different datasets: SNP panel with 38 200 probes, lncRNA panel with 2000 probes, synthetic panel with 5899 probes and HD-Marker panel for Yesso scallop with 11 000 probes. The SNP and synthetic panels achieve impressive factor 3 of accuracy (F3acc) of 96.24% and 99.66% in 5-fold cross-validation. F3acc rates of over 87.33% and 72.56% are obtained when training on the SNP panel and evaluating performance on the lncRNA and HD-Marker datasets, respectively. Our analysis reveals that Deqformer effectively captures hybridization patterns, making it robust for accurate predictions in various scenarios. Deqformer leads to a novel perspective for probe design pipeline, aiming to enhance efficiency and effectiveness in probe design tasks.
PractiCPP: a deep learning approach tailored for extremely imbalanced datasets in cell-penetrating peptide prediction
Authors: Shi Kexin , Xiong Yuanpeng , Wang Yu , Deng Yifan , Wang Wenjia , Jing Bingyi , Gao Xin 
Published: February 2024

Abstract

Motivation
Effective drug delivery systems are paramount in enhancing pharmaceutical outcomes, particularly through the use of cell-penetrating peptides (CPPs). These peptides are gaining prominence due to their ability to penetrate eukaryotic cells efficiently without inflicting significant damage to the cellular membrane, thereby ensuring optimal drug delivery. However, the identification and characterization of CPPs remain a challenge due to the laborious and time-consuming nature of conventional methods, despite advances in proteomics. Current computational models, however, are predominantly tailored for balanced datasets, an approach that falls short in real-world applications characterized by a scarcity of known positive CPP instances.

Results
To navigate this shortfall, we introduce PractiCPP, a novel deep-learning framework tailored for CPP prediction in highly imbalanced data scenarios. Uniquely designed with the integration of hard negative sampling and a sophisticated feature extraction and prediction module, PractiCPP facilitates an intricate understanding and learning from imbalanced data. Our extensive computational validations highlight PractiCPP’s exceptional ability to outperform existing state-of-the-art methods, demonstrating remarkable accuracy, even in datasets with an extreme positive-to-negative ratio of 1:1000. Furthermore, through methodical embedding visualizations, we have established that models trained on balanced datasets are not conducive to practical, large-scale CPP identification, as they do not accurately reflect real-world complexities. In summary, PractiCPP potentially offers new perspectives in CPP prediction methodologies. Its design and validation, informed by real-world dataset constraints, suggest its utility as a valuable tool in supporting the acceleration of drug delivery advancements.

Availability and implementation
The source code of PractiCPP is available on Figshare at https://doi.org/10.6084/m9.figshare.25053878.v1.
Engineered Wnt7a ligands rescue blood–brain barrier and cognitive deficits in a COVID-19 mouse model
Authors: Trevino Troy N , Fogel Avital B , Otkiran Guliz , Niladhuri Seshadri B , Sanborn Mark A , Class Jacob , Almousawi Ali A , Vanhollebeke Benoit , Tai Leon M , Rehman Jalees , Richner Justin M , Lutz Sarah E 
Published: February 2024

Abstract
Respiratory infection with SARS-CoV-2 causes systemic vascular inflammation and cognitive impairment. We sought to identify the underlying mechanisms mediating cerebrovascular dysfunction and inflammation following mild respiratory SARS-CoV-2 infection.
To this end, we performed unbiased transcriptional analysis to identify brain endothelial cell signalling pathways dysregulated by mouse adapted SARS-CoV-2 MA10 in aged immunocompetent C57Bl/6 mice in vivo.
This analysis revealed significant suppression of Wnt/β-catenin signalling, a critical regulator of blood–brain barrier (BBB) integrity. We therefore hypothesized that enhancing cerebrovascular Wnt/β-catenin activity would offer protection against BBB permeability, neuroinflammation, and neurological signs in acute infection. Indeed, we found that delivery of cerebrovascular-targeted, engineered Wnt7a ligands protected BBB integrity, reduced T-cell infiltration of the brain, and reduced microglial activation in SARS-CoV-2 infection. Importantly, this strategy also mitigated SARS-CoV-2 induced deficits in the novel object recognition assay for learning and memory and the pole descent task for bradykinesia.
These observations suggest that enhancement of Wnt/β-catenin signalling or its downstream effectors could be potential interventional strategies for restoring cognitive health following viral infections.
PTCH1 mutation as a potential predictive biomarker for immune checkpoint inhibitors in gastrointestinal cancer
Authors: Deng Shuangya , Gu Haoran , Chen ZongYao , Liu Yaqin , Zhang Qin , Chen Dongsheng , Yi Shengen 
Published: February 2024

Abstract
Immune checkpoint inhibitors (ICIs) have become prominent therapies for gastrointestinal cancer (GC). However, it is urgent to screen patients who can benefit from ICIs. Protein patched homolog 1 (PTCH1) is a frequently altered gene in GC. We attempt to explore the association between PTCH1 mutation and immunotherapy efficacy. The Memorial Sloan Kettering Cancer Center (MSKCC) cohort (n = 236) with GC (esophageal, gastric and colorectal cancers) patients receiving ICIs was used for discovery and the Peking University Cancer Hospital (PUCH) GC cohort (n = 92) was used for validation. Overall survival (OS) and tumor mutational burden (TMB) of the PTCH1 mutant-type (PTCH1-MUT) and PTCH1 wild-type (PTCH1-WT) groups were compared. Furthermore, GC data were collected from The Cancer Genome Atlas to assess the potential mechanisms. In the MSKCC cohort, PTCH1-MUT group showed significantly better OS (P = 0.017) and higher TMB. Multivariate analysis showed that PTCH1 mutation was associated with better OS. In the PUCH cohort, PTCH1-MUT group showed significantly longer OS (P = 0.036) and progression-free survival, and higher durable clinical benefit and TMB. Immune cell infiltration analysis revealed that PTCH1-MUT group had significantly higher distributions of CD8 T cells, CD4 T cells, NK cells, mast cells and M1 cells. The PTCH1-MUT group showed significantly higher expression of most immune-related genes. Gene set enrichment analysis showed that the PTCH1-MUT group had enriched INF-γ response, INF-α response, glycolysis and reactive oxygen species pathway gene sets. PTCH1 mutation may represent a potential biomarker for predicting ICIs response in GC. Nevertheless, prospective cohort studies should be performed to further validate our results.
‘I know how to live from what the hill gives’: biocultural uses, tensions and partial reconstructions around the common goods of the Cerro Caracol urban park
Authors: Cid-Aguayo Beatriz E , Oliveros Verónica , Vargas Diego Oñate , Gajardo Anahi , Silva Graciela , Pinela Joaquín , Vejar Pablo 
Published: February 2024

Abstract
In the south-central Chilean city of Concepción, an irregular urban settlement named ‘Agüita de la Perdiz’ (Partridge Creek) built on the slopes of Cerro Caracol (Snail Hill) has become an emblematic neighbourhood, located within an urban biodiversity hotspot. The richness and biodiversity of the landscape have been used in different ways by the inhabitants of Concepción, but in the case of the Agüita de la Perdiz residents, it is also part of their way of life, representing an unusual people–nature relationship in urban spaces. We analyze the relationship between the community and the hill, with its forest, fauna, waters and recreational areas; the successive territorial dispossessions and the various conflicts involved in the operation of the Metropolitan Park, created to protect the hill; and the efforts led by community members to recompose their relationship with the hill. The case problematizes urban bioculture, from a political ecology of commons perspective, and co-management approaches for conservation.
EEG biomarkers of behavioral inhibition in patients with depression who committed violent offenses: a Go/NoGo ERP study
Authors: Xian Zhuohang , Liu Hao , Gu Yan , Hu Zeqing , Li Gangqin 
Published: February 2024

Abstract
Understanding the neurobiological correlates of behavioral inhibition in patients with depression who committed violent offenses could contribute to the prediction and prevention of violence. The present study recruited 29 depressed patients with violent offenses (VD group), 27 depressed patients without violent behavior (NVD group), and 28 healthy controls (HC group) to complete a visual Go/NoGo task, during which their responses and electroencephalography were simultaneously recorded using an event-related potentiometer. The results showed that the VD group made more commission errors and responded more slowly relative to the NVD and HC groups. The P3 amplitude of the VD group was reduced in the frontal and central brain regions compared to the HC group and increased in the parietal regions compared to the NVD group. In comparison to Go stimuli, NoGo stimuli induced longer P3 latencies in frontal regions in both the VD and NVD groups; however, this difference was not statistically significant in the HC group. These results provide electrophysical evidence of behavioral inhibition deficits in patients with depression, especially in those with violent behaviors. The reduced P3 amplitude in the frontal-central regions, increased P3 amplitude in the parietal regions, and increased NoGo P3 latency may be potential electrophysiological features that can predict violent behavior in patients with depression.
The influence of self-esteem on interpersonal and competence evaluations: electrophysiological evidence from an ERP study
Authors: Li Mei , Zhong Bowei , Li Jin , Li Jialu , Zhang Xukai , Luo Xi , Li Hong 
Published: February 2024

Abstract
Using event-related potentials, this study examined how self-esteem affects neural responses to competence (interpersonal) feedback when the need for relatedness (competence) is thwarted or met. Participants with low and high self-esteem acted as advisors who selected one of two options for a putative advisee. Subsequently, they passively observed the advisee, accepted, or rejected their advice (i.e. interpersonal feedback) and received correct or incorrect outcomes (i.e. competence feedback). When interpersonal feedback was followed by competence feedback, high self-esteem participants showed a smaller P3 following incorrect than correct outcomes, irrespective of whether the advice had been accepted or rejected. However, low self-esteem participants showed this P3 effect only when the advice was rejected, and the P3 difference disappeared when the advice was accepted. When competence feedback was followed by interpersonal feedback, both low self-esteem and high self-esteem individuals showed a larger P2 for rejection than for acceptance and a larger late potential component for incorrect than correct outcomes. These findings suggest that when interpersonal feedback is followed by competence feedback, low self-esteem and high self-esteem individuals have a desire for self-positivity. When competence feedback is followed by interpersonal feedback, they may have motives for self-change. Our findings shed light on the motivational mechanisms for self-esteem and feedback.
New Manual Quantitative Polymerase Chain Reaction Assay Validated on Tongue Swabs Collected and Processed in Uganda Shows Sensitivity That Rivals Sputum-based Molecular Tuberculosis Diagnostics
Authors: Steadman Amy , Andama Alfred , Ball Alexey , Mukwatamundu Job , Khimani Khushboo , Mochizuki Tessa , Asege Lucy , Bukirwa Alice , Kato John Baptist , Katumba David , Kisakye Esther , Mangeni Wilson , Mwebe Sandra , Nakaye Martha , Nassuna Irene , Nyawere Justine , Nakaweesa Annet , Cook Catherine , Phillips Patrick , Nalugwa Talemwa , Bachman Christine M , Semitala Fred Collins , Weigl Bernhard H , Connelly John , Worodria William , Cattamanchi Adithya 
Published: February 2024

Abstract

Background
Sputum-based testing is a barrier to increasing access to molecular diagnostics for tuberculosis (TB). Many people with TB are unable to produce sputum, and sputum processing increases assay complexity and cost. Tongue swabs are emerging as an alternative to sputum, but performance limits are uncertain.

Methods
From June 2022 to July 2023, we enrolled 397 consecutive adults with cough &gt;2 weeks at 2 health centers in Kampala, Uganda. We collected demographic and clinical information, sputum for TB testing (Xpert MTB/RIF Ultra and 2 liquid cultures), and tongue swabs for same-day quantitative polymerase chain reaction (qPCR) testing. We evaluated tongue swab qPCR diagnostic accuracy versus sputum TB test results, quantified TB targets per swab, assessed the impact of serial swabbing, and compared 2 swab types (Copan FLOQSWAB and Steripack spun polyester).

Results
Among 397 participants, 43.1% were female, median age was 33 years, 23.5% were diagnosed with human immunodeficiency virus, and 32.0% had confirmed TB. Sputum Xpert Ultra and tongue swab qPCR results were concordant for 98.2% (95% confidence interval [CI]: 96.2–99.1) of participants. Tongue swab qPCR sensitivity was 92.6% (95% CI: 86.5 to 96.0) and specificity was 99.1% (95% CI: 96.9 to 99.8) versus microbiological reference standard. A single tongue swab recovered a 7-log range of TB copies, with a decreasing recovery trend among 4 serial swabs. Swab types performed equivalently.

Conclusions
Tongue swabs are a promising alternative to sputum for molecular diagnosis of TB, with sensitivity approaching sputum-based molecular tests. Our results provide valuable insights for developing successful tongue swab–based TB diagnostics.
An unusual complication after transcatheter aortic valve implantation: a case report
Authors: Abril Molina Alba , Fernández Quero Mónica , López Haldón José E , Villa Gil Ortega Manuel , Díaz Fernández José F 
Published: February 2024

Abstract

Background
Ventricular septal defect (VSD) is an unusual complication of transcatheter aortic valve implantation (TAVI). The risk factors are not well understood but may include oversizing, calcification amount and location, left-ventricular chamber morphology, and valve-in-valve (ViV) procedures. Percutaneous treatment is challenging but is usually the preferred option.

Case summary
An 80-year-old woman with two previous surgical aortic valve replacements was admitted to our Cardiology Department for decompensated heart failure. New bioprosthesis degeneration (19 mm Mitroflow™, Sorin Group, Canada) was observed with severe intraprosthetic aortic regurgitation. After evaluation, the heart team chose to perform ViV TAVI. Because of the high risk of coronary obstruction, chimney stenting of both coronary arteries was performed. A 23 mm self-expandable Navitor™ valve (Abbott, IL, USA) was implanted, but the Mitroflow™ valve had to be cracked to minimize the persistent high gradient. During valve fracture, the non-compliant balloon broke and a small iatrogenic VSD appeared. However, the patient remained stable, so conservative management was selected. During follow-up, she developed severe haemolytic anaemia and heart failure; therefore, percutaneous closure of the iatrogenic VSD was performed twice, which was a difficult challenge.

Discussion
A viable alternative to redo surgery is ViV TAVI. Risks include higher rates of prosthesis–patient mismatch and coronary obstruction. Occasionally, bioprosthetic valve fracture is required, particularly in small bioprostheses, to achieve low gradients. Anecdotally, fracture has led to annular rupture and VSD. Most VSDs are small and without clinical or haemodynamic repercussions; however, in symptomatic cases, percutaneous closure is a viable alternative to surgery.
Four-dimensional analysis of aortic root motion in normal population using retrospective multiphase computed tomography
Authors: Yuan Xun , Kan Xiaoxin , Li Jianpeng , Yan Yang , Mirsadraee Saeed , Mittal Tarun , Shah Andrew , Saunders Debbie , Xu Xiao Yun , Nienaber Christoph A 
Published: February 2024

Abstract

Aims
Aortic root motion is suspected to contribute to proximal aortic dissection. While motion of the aorta in four dimensions can be traced with real-time imaging, displacement and rotation in quantitative terms remain unknown. The hypothesis was to show feasibility of quantification of three-dimensional aortic root motion from dynamic CT imaging.

Methods and results
Dynamic CT images of 40 patients for coronary assessment were acquired using a dynamic protocol. Scans were ECG-triggered and segmented in 10 time-stepped phases (0–90%) per cardiac cycle. With identification of the sinotubular junction (STJ), a patient-specific co-ordinate system was created with the z-axis (out-of-plane) parallel to longitudinal direction. The left and right coronary ostia were traced at each time-step to quantify downward motion in reference to the STJ plane, motion within the STJ plane (in-plane), and the degree of rotation. Enrolled individuals had an age of 65 ± 12, and 14 were male (35%). The out-of-plane motion was recorded with the largest displacement of 10.26 ± 2.20 and 8.67 ± 1.69 mm referenced by left and right coronary ostia, respectively. The mean downward movement of aortic root was 9.13 ± 1.86 mm. The largest in-plane motion was recorded at 9.17 ± 2.33 mm and 6.51 ± 1.75 mm referenced by left and right coronary ostia, respectively. The largest STJ in-plane motion was 7.37 ± 1.96 mm, and rotation of the aortic root was 11.8 ± 4.60°.

Conclusion
In vivo spatial and temporal displacement of the aortic root can be identified and quantified from multiphase ECG-gated contrast-enhanced CT images. Knowledge of normal 4D motion of the aortic root may help understand its biomechanical impact in patients with aortopathy and pre- and post-surgical or transcatheter aortic valve replacement.
Cardiovascular disease in transgender people: a systematic review and meta-analysis
Authors: van Zijverden Lieve Mees , Wiepjes Chantal Maria , van Diemen Jeske Joanna Katarina , Thijs Abel , den Heijer Martin 
Published: February 2024

Abstract

Objective
Hormone therapy in transgender people might be associated with an increased risk of cardiovascular disease (CVD). We aimed to investigate whether the risk of CVD is increased in transgender people compared with people of the same birth sex.

Design and methods
PubMed, Cochrane, Embase, and Google Scholar were searched until July 2022. Studies evaluating cardiovascular events in transgender women or men were included. Primary outcomes were stroke, myocardial infarction (MI), and venous thromboembolism (VTE). The risk for transgender women versus cisgender men and for transgender men versus cisgender women was analysed through random-effects meta-analysis.

Results
Twenty-two studies involving 19 893 transgender women, 14 840 transgender men, 371 547 cisgender men, and 434 700 cisgender women were included. The meta-analysis included 10 studies (79% of transgender women and 76% of transgender men). In transgender women, incidence of stroke was 1.8%, which is 1.3 (95% confidence interval [CI], 1.0-1.8) times higher than in cisgender men. Incidence of MI was 1.2%, with a pooled relative risk of 1.0 (95% CI, 0.8-1.2). Venous thromboembolism incidence was 1.6%, which is 2.2 (95% CI, 1.1-4.5) times higher. Stroke occurred in 0.8% of transgender men, which is 1.3 (95% CI, 1.0-1.6) times higher compared with cisgender women. Incidence of MI was 0.6%, with a pooled relative risk of 1.7 (95% CI, 0.8-3.6). For VTE, this was 0.7%, being 1.4 (95% CI, 1.0-2.0) times higher.

Conclusions
Transgender people have a 40% higher risk of CVD compared with cisgender people of the same birth sex. This emphasizes the importance of cardiovascular risk management. Future studies should assess the potential influence of socio-economic and lifestyle factors.
Ideologies and practices of the use of L1 in L2 vocabulary tasks
Authors: Altalhab Sultan , Said Fatma F S 
Published: February 2024

Abstract
This qualitative study sets out to understand the beliefs, functions, and practices of using L1 among EFL learners while they learned new L2 vocabulary. Forty-two Saudi male university students were randomly assigned to 21 pairs and asked to complete three reading comprehension tasks. All pair interactions were audio-recorded. Afterward, interviews were conducted with 21 students. The results suggest that the use of L1 in L2 vocabulary tasks assists students in understanding the meaning of new words. They also revealed the complex sociocultural nature of peer-to-peer collaborative interaction and the role L1 plays in L2 vocabulary learning. The interviews revealed that some participants thought that L1 should not be used in the L2 class, a belief that contradicted their actions. The paper calls for Saudi L2 educational contexts to embrace translanguaging as a beneficial practice that enhances student L2 acquisition and reduces the emotional stress of using L1 in the classroom.