bluuebunny/crossref_metadata_2025_split huggingface dataset:
MuCoCP: a priori chemical knowledge-based multimodal contrastive learning pre-trained neural network for the prediction of cyclic peptide membrane penetration ability
Authors: Yu Yunxiang , Gu Mengyun , Guo Hai , Deng Yabo , Chen Danna , Wang Jianwei , Wang Caixia , Liu Xia , Yan Wenjin , Huang Jinqi 
Published: July 2024

Abstract

Motivation
There has been a burgeoning interest in cyclic peptide therapeutics due to their various outstanding advantages and strong potential for drug formation. However, it is undoubtedly costly and inefficient to use traditional wet lab methods to clarify their biological activities. Using artificial intelligence instead is a more energy-efficient and faster approach. MuCoCP aims to build a complete pre-trained model for extracting potential features of cyclic peptides, which can be fine-tuned to accurately predict cyclic peptide bioactivity on various downstream tasks. To maximize its effectiveness, we use a novel data augmentation method based on a priori chemical knowledge and multiple unsupervised training objective functions to greatly improve the information-grabbing ability of the model.

Results
To assay the efficacy of the model, we conducted validation on the membrane-permeability of cyclic peptides which achieved an accuracy of 0.87 and R-squared of 0.503 on CycPeptMPDB using semi-supervised training and obtained an accuracy of 0.84 and R-squared of 0.384 using a model with frozen parameters on an external dataset. This result has achieved state-of-the-art, which substantiates the stability and generalization capability of MuCoCP. It means that MuCoCP can fully explore the high-dimensional information of cyclic peptides and make accurate predictions on downstream bioactivity tasks, which will serve as a guide for the future de novo design of cyclic peptide drugs and promote the development of cyclic peptide drugs.

Availability and implementation
All code used in our proposed method can be found at https://github.com/lennonyu11234/MuCoCP.
BELHD: improving biomedical entity linking with homonym disambiguation
Authors: Garda Samuele , Leser Ulf 
Published: July 2024

Abstract

Motivation
Biomedical entity linking (BEL) is the task of grounding entity mentions to a given knowledge base (KB). Recently, neural name-based methods, system identifying the most appropriate name in the KB for a given mention using neural network (either via dense retrieval or autoregressive modeling), achieved remarkable results for the task, without requiring manual tuning or definition of domain/entity-specific rules. However, as name-based methods directly return KB names, they cannot cope with homonyms, i.e. different KB entities sharing the exact same name. This significantly affects their performance for KBs where homonyms account for a large amount of entity mentions (e.g. UMLS and NCBI Gene).

Results
We present BELHD (Biomedical Entity Linking with Homonym Disambiguation), a new name-based method that copes with this challenge. BELHD builds upon the BioSyn model with two crucial extensions. First, it performs pre-processing of the KB, during which it expands homonyms with a specifically constructed disambiguating string, thus enforcing unique linking decisions. Second, it introduces candidate sharing, a novel strategy that strengthens the overall training signal by including similar mentions from the same document as positive or negative examples, according to their corresponding KB identifier. Experiments with 10 corpora and 5 entity types show that BELHD improves upon current neural state-of-the-art approaches, achieving the best results in 6 out of 10 corpora with an average improvement of 4.55pp recall@1. Furthermore, the KB preprocessing is orthogonal to the prediction model and thus can also improve other neural methods, which we exemplify for GenBioEL, a generative name-based BEL approach.

Availability and implementation
The code to reproduce our experiments can be found at: https://github.com/sg-wbi/belhd.
Karyotype diversity and genome size in the Cyphomandra clade of Solanum L. (Solanaceae)
Authors: Mesquita Amanda T , Braz Guilherme T , Shimizu Gustavo H , Machado Raquel M , Romero-da Cruz Maria V , Forni-Martins Eliana R 
Published: July 2024

Abstract
The Cyphomandra clade, a distinct group within the Solanum L. genus, is characterized by remarkable traits, including large chromosomes and big genome sizes. We aimed to investigate whether these features are conserved within the Cyphomandra clade and how they differentiate this group from other Solanum species. We elaborated karyotypes based on CMA/DAPI banding and rDNA fluorescence in situ hybridization (FISH) and estimated the genome size from 12 species, eight belonging to Cyphomandra and four from related clades. All species showed metacentric or submetacentric chromosomes and symmetrical karyotypes, with 2n = 24, except S. mammosum L. (2n = 22). CMA/DAPI banding in combination with rDNA FISH revealed three distinct patterns of heterochromatin distribution (number and position of bands, all CMA+). Most species showed one pair of 35S and 5S rDNA on different chromosomes, except S. mammosum (one of the two pairs was observed in the same chromosome). Notable, the Cyphomandra clade species showed larger chromosomes and genome sizes than other species of Solanum, corroborating that these karyotype attributes are valuable to characterize the clade. The number of CMA/DAPI bands and rDNA sites does not justify the differences in the genome size. Therefore, the accumulation and dispersion of other repetitive sequences, like transposable elements, may be associated with the karyotype changes.
A trip of a bamboo lifetime: tracing the origin and evolution of Chusquea (Poaceae, Bambusoideae, Bambuseae) in Patagonia, southernmost South America
Authors: Guerreiro Carolina , Brignone Nicolás F , Clark Lynn G , Vega Andrea S 
Published: July 2024

Abstract
We performed a phylogenetic analysis with estimated clade ages and an ancestral-range estimation focused on the Patagonian species of Chusquea, i.e. the Chusquea culeou clade, to unravel their biogeographical history. Phylogenetic analyses were conducted with sequence data from four plastid markers, using maximum parsimony and Bayesian inference approaches. The complete sampling and addition of the Patagonian Chusquea species into a phylogenetic framework revealed the most likely origin and evolutionary history of the Chusquea culeou clade. The Patagonian Chusquea originated roughly 11.35 Mya, most likely from a common ancestor from the Atlantic Forest region, when this lineage underwent in situ diversification and its species evolved sympatrically. All the extant species have arisen in the last 8 Myr. Moreover, according to the present sampling, the most recent common ancestor of subtribe Chusqueinae originated in the Northern Andes, which is also the most common source area of the estimated dispersal events. Some other preliminary insights on the biogeographic history of the genus are included.
The ageing central nervous system in multiple sclerosis: the imaging perspective
Authors: Filippi Massimo , Preziosa Paolo , Barkhof Frederik , Ciccarelli Olga , Cossarizza Andrea , De Stefano Nicola , Gasperini Claudio , Geraldes Ruth , Granziera Cristina , Haider Lukas , Lassmann Hans , Margoni Monica , Pontillo Giuseppe , Ropele Stefan , Rovira Àlex , Sastre-Garriga Jaume , Yousry Tarek A , Rocca Maria A 
Published: July 2024

Abstract
The interaction between ageing and multiple sclerosis is complex and carries significant implications for patient care. Managing multiple sclerosis effectively requires an understanding of how ageing and multiple sclerosis impact brain structure and function. Ageing inherently induces brain changes, including reduced plasticity, diminished grey matter volume, and ischaemic lesion accumulation. When combined with multiple sclerosis pathology, these age-related alterations may worsen clinical disability. Ageing may also influence the response of multiple sclerosis patients to therapies and/or their side effects, highlighting the importance of adjusted treatment considerations. MRI is highly sensitive to age- and multiple sclerosis-related processes. Accordingly, MRI can provide insights into the relationship between ageing and multiple sclerosis, enabling a better understanding of their pathophysiological interplay and informing treatment selection. This review summarizes current knowledge on the immunopathological and MRI aspects of ageing in the CNS in the context of multiple sclerosis. Starting from immunosenescence, ageing-related pathological mechanisms and specific features like enlarged Virchow-Robin spaces, this review then explores clinical aspects, including late-onset multiple sclerosis, the influence of age on diagnostic criteria, and comorbidity effects on imaging features. The role of MRI in understanding neurodegeneration, iron dynamics and myelin changes influenced by ageing and how MRI can contribute to defining treatment effects in ageing multiple sclerosis patients, are also discussed.
Top-down and bottom-up oscillatory dynamics regulate implicit visuomotor sequence learning
Authors: Lum Jarrad A G , Barham Michael P , Hyde Christian , Hill Aron T , White David J , Hughes Matthew E , Clark Gillian M 
Published: July 2024

Abstract
Implicit visuomotor sequence learning is crucial for acquiring skills that result in automated behaviors. The oscillatory dynamics underpinning this learning process are not well understood. To address this gap, the current study employed electroencephalography with a medium-density array (64 electrodes) to investigate oscillatory activity associated with implicit visuomotor sequence learning in the Serial Reaction Time task. In the task, participants unknowingly learn a series of finger movements. Eighty-five healthy adults participated in the study. Analyses revealed that theta activity at the vertex and alpha/beta activity over the motor areas decreased over the course of learning. No associations between alpha/beta and theta power were observed. These findings are interpreted within a dual-process framework: midline theta activity is posited to regulate top-down attentional processes, whereas beta activity from motor areas underlies the bottom-up encoding of sensory information from movement. From this model, we suggest that during implicit visuomotor sequence learning, top-down processes become disengaged (indicated by a reduction in theta activity), and modality specific bottom-up processes encode the motor sequence (indicated by a reduction in alpha/beta activity).
Frontal pole–precuneus connectivity is associated with a discrepancy between self-rated and observer-rated depression severity in mood disorders: a resting-state functional magnetic resonance imaging study
Authors: Kawakami Shintaro , Okada Naohiro , Satomura Yoshihiro , Shoji Eimu , Mori Shunsuke , Kiyota Masahiro , Omileke Favour , Hamamoto Yu , Morita Susumu , Koshiyama Daisuke , Yamagishi Mika , Sakakibara Eisuke , Koike Shinsuke , Kasai Kiyoto 
Published: July 2024

Abstract
Discrepancies in self-rated and observer-rated depression severity may underlie the basis for biological heterogeneity in depressive disorders and be an important predictor of outcomes and indicators to optimize intervention strategies. However, the neural mechanisms underlying this discrepancy have been understudied. This study aimed to examine the brain networks that represent the neural basis of the discrepancy between self-rated and observer-rated depression severity using resting-state functional MRI. To examine the discrepancy between self-rated and observer-rated depression severity, self- and observer-ratings discrepancy (SOD) was defined, and the higher and lower SOD groups were selected from depressed patients as participants showing extreme deviation. Resting-state functional MRI analysis was performed to examine regions with significant differences in functional connectivity in the two groups. The results showed that, in the higher SOD group compared to the lower SOD group, there was increased functional connectivity between the frontal pole and precuneus, both of which are subregions of the default mode network that have been reported to be associated with ruminative and self-referential thinking. These results provide insight into the association of brain circuitry with discrepancies between self- and observer-rated depression severity and may lead to more treatment-oriented diagnostic reclassification in the future.
Disentangling transcriptomic heterogeneity within the human subgenual anterior cingulate cortex
Authors: Jenkins Aaron K , Shelton Micah A , Yin RuoFei , Gorczyca Michael T , Zong Wei , Glausier Jill R , Lewis David A , Tseng George C , Seney Marianne L , McClung Colleen A 
Published: July 2024

Abstract
The subgenual anterior cingulate cortex (sgACC) is a critical site for understanding the neural correlates of affect and emotion. While the activity of the sgACC is functionally homogenous, it is comprised of multiple Brodmann Areas (BAs) that possess different cytoarchitectures. In some sgACC BAs, Layer 5 is sublaminated into L5a and L5b which has implications for its projection targets. To understand how the transcriptional profile differs between the BAs, layers, and sublayers of human sgACC, we collected layer strips using laser capture microdissection followed by RNA sequencing. We found no significant differences in transcript expression in these specific cortical layers between BAs within the sgACC. In contrast, we identified striking differences between Layers 3 and 5a or 5b that were concordant across sgACC BAs. We found that sublayers 5a and 5b were transcriptionally similar. Pathway analyses of L3 and L5 revealed overlapping biological processes related to synaptic function. However, L3 was enriched for pathways related to cell-to-cell junction and dendritic spines whereas L5 was enriched for pathways related to brain development and presynaptic function, indicating potential functional differences across layers. Our study provides important insight into normative transcriptional features of the sgACC.
US Food and Drug Administration, Centers for Disease Control and Prevention, and National Institutes of Health Co-Sponsored Public Workshop Summary—Development Considerations of Antimicrobial Drugs for the Treatment of Gonorrhea
Authors: Hiruy Hiwot , Bala Shukal , Byrne James M , Roche Kerian Grande , Jang Seong H , Kim Peter , Nambiar Sumathi , Rubin Dan , Yasinskaya Yuliya , Bachmann Laura H , Bernstein Kyle , Botgros Radu , Cammarata Sue , Chaves Ricardo L , Deal Carolyn D , Drusano George L , Duffy Erin M , Eakin Ann E , Gelone Steve , Hiltke Thomas , Hook Edward W , Jerse Ann E , McNeil Candice J , Newman Lori , O’Brien Seamus , Perry Caroline , Reno Hilary E L , Romaguera Raul A , Sato Junko , Unemo Magnus , Wi Teodora E C , Workowski Kimberly , O’May Graeme A , Shukla Sunita J , Farley John J 
Published: July 2024

AbstractThere is an unmet need for developing drugs for the treatment of gonorrhea due to rapidly evolving resistance of Neisseria gonorrhoeae against antimicrobial drugs used for empiric therapy, an increase in globally reported multidrug-resistant cases, and the limited available therapeutic options. Furthermore, few drugs are under development. Development of antimicrobials is hampered by challenges in clinical trial design, limitations of available diagnostics, changes in and varying standards of care, lack of robust animal models, and clinically relevant pharmacodynamic targets. On 23 April 2021, the US Food and Drug Administration, Centers for Disease Control and Prevention, and National Institute of Allergy and Infectious Diseases of the National Institutes of Health co-sponsored a workshop with stakeholders from academia, industry, and regulatory agencies to discuss the challenges and strategies, including potential collaborations and incentives, to facilitate the development of drugs for the treatment of gonorrhea. This article provides a summary of that workshop.
A generic multi-level framework for building term-weighting schemes in text classification
Authors: Tang Zhong 
Published: July 2024

Abstract
Term weighting is essential for text classification tasks, and thus various supervised term-weighting (STW) methods have been designed and presented in recent years, such as TF (term frequency)-IG (information gain), TF-MI (mutual information), TF-RF (relevance frequency), and TF-IDF (inverse document frequency)-ICSDF (inverse class space density frequency). Unlike other schemes, TF-IDF-ICSDF considers not only the local factor (i.e. TF) and the category factor (i.e. ICSDF) but also the global factor (i.e. IDF) in the weighting process. Hence, a natural question is whether IDF is really useful for improving the classification performance of STW schemes. To explore this issue, a generic multi-level framework composed of term-level, text-level, and category-level is first established, which corresponds to local factor, global factor, and category factor, respectively. Based on the generic multi-level framework, a new two-level STW method, TF-ICSDF, can be generated by removing the IDF from the TF-IDF-ICSDF scheme. Conversely, we also integrated the IDF with other two-level STW schemes (e.g. TF-IG, TF-MI, TF-RF) to obtain several three-level STW schemes. We verified the general classification performance of our proposed STW schemes on three open benchmark datasets. The results manifest that performance can usually be boosted if IDF is incorporated into the STW schemes, indicating that weighting terms utilizing the IDF factor could provide better text representation. Therefore, the generic multi-level framework and STW schemes we proposed are effective.
Transverse aortic constriction multi-omics analysis uncovers pathophysiological cardiac molecular mechanisms
Authors: Gjerga Enio , Dewenter Matthias , Britto-Borges Thiago , Grosso Johannes , Stein Frank , Eschenbach Jessica , Rettel Mandy , Backs Johannes , Dieterich Christoph 
Published: July 2024

Abstract
Time-course multi-omics data of a murine model of progressive heart failure (HF) induced by transverse aortic constriction (TAC) provide insights into the molecular mechanisms that are causatively involved in contractile failure and structural cardiac remodelling. We employ Illumina-based transcriptomics, Nanopore sequencing and mass spectrometry-based proteomics on samples from the left ventricle (LV) and right ventricle (RV, RNA only) of the heart at 1, 7, 21 and 56 days following TAC and Sham surgery. Here, we present Transverse Aortic COnstriction Multi-omics Analysis (TACOMA), as an interactive web application that integrates and visualizes transcriptomics and proteomics data collected in a TAC time-course experiment. TACOMA enables users to visualize the expression profile of known and novel genes and protein products thereof. Importantly, we capture alternative splicing events by assessing differential transcript and exon usage as well. Co-expression-based clustering algorithms and functional enrichment analysis revealed overrepresented annotations of biological processes and molecular functions at the protein and gene levels. To enhance data integration, TACOMA synchronizes transcriptomics and proteomics profiles, enabling cross-omics comparisons. With TACOMA (https://shiny.dieterichlab.org/app/tacoma), we offer a rich web-based resource to uncover molecular events and biological processes implicated in contractile failure and cardiac hypertrophy. For example, we highlight: (i) changes in metabolic genes and proteins in the time course of hypertrophic growth and contractile impairment; (ii) identification of RNA splicing changes in the expression of Tpm2 isoforms between RV and LV; and (iii) novel transcripts and genes likely contributing to the pathogenesis of HF. We plan to extend these data with additional environmental and genetic models of HF to decipher common and distinct molecular changes in heart diseases of different aetiologies.
Database URL: https://shiny.dieterichlab.org/app/tacoma
Chronic Poor Sleep is Associated with Increased Disease Activity in Patients with Ulcerative Colitis: Prospective Observational Study in Japan
Authors: Oyama Hideaki , Moroi Rintaro , Sakuma Atsushi , Shimoyama Yusuke , Nagai Hiroshi , Naito Takeo , Shiga Hisashi , Kakuta Yoichi , Kinouchi Yoshitaka , Masamune Atsushi 
Published: July 2024

Abstract

Background and Aim
Although sleep disorders are associated with the pathogenesis of inflammatory bowel disease, the causal relationship is unclear. Therefore, in this study we aimed to clarify the causal relationship between them.

Methods
We administered the Pittsburgh Sleep Questionnaire to participants during regular visits to evaluate their sleep condition, and prospectively observed the participants. Participants were divided into poor sleep and non-poor sleep groups according to their first and second questionnaire scores. We compared inflammatory bowel disease relapse rates between the two groups.

Results
The study population included 139 patients with inflammatory bowel disease, including 60 with chronic poor sleep. Disease relapse rate was significantly higher in the poor sleep group than in the non-poor sleep group [28.3% vs 8.9%; p = 0.0033]. Ulcerative colitis relapse rate was significantly higher in the poor sleep group than in the non-poor sleep group [34.5% vs 10.3%, p = 0.031]. Multivariate analysis identified chronic poor sleep as a clinical factor that affected inflammatory bowel disease relapse (odds ratio [OR] = 6.69, 95% confidence interval [CI]: 2.23–20.0, p = 0.0007] and ulcerative colitis relapse [OR = 8.89, 95% CI: 1.57–50.2, p = 0.014]. The Kaplan − Meier curve showed significantly lower cumulative treatment retention rates in the poor sleep group than in the non-poor sleep group [all patients, p = 0.0061; ulcerative colitis, p = 0.025].

Conclusions
Concomitant chronic poor sleep may have a negative influence on the disease activity in patients with inflammatory bowel disease, particularly in those with ulcerative colitis.
Surgical correction of total anomalous pulmonary venous connection to persistent left-sided superior vena cava: a case report
Authors: Tej Uday , Mishra Anand Kumar , Mittal Apeksha , Saini Kulbhushan , George Arun 
Published: July 2024

Abstract

Background
Total anomalous pulmonary venous connection (TAPVC) to left superior vena cava (LSVC) is an extremely rare congenital heart disease, and its surgical management is very challenging.

Case summary
We report one such case of a 5-year-old south Asian male with double outlet right ventricle and unbalanced atrioventricular canal defect, where all the pulmonary veins were found opening into LSVC, which was then opening into the left side of the common atrium. Intraoperatively, the LSVC was transected just below the left internal jugular vein and left subclavian vein junction and left-sided bidirectional Glenn shunt done using 8 mm Dacron tube graft. Pulmonary veins were left draining through the LSVC into the common atrium. Right-sided Glenn shunt was completed as usual. Currently, the patient is year and half post-surgery and is doing well; school going on par with the peer group maintaining a room air saturation of 87%.

Discussion
Here, we report a successful surgical correction of TAPVC to LSVC in a child with univentricular physiology, however due to the paucity of data and rarity of such cases, optimal surgical management is yet to be defined.