bluuebunny/crossref_metadata_2025_split huggingface dataset:
Datacube segmentation via deep spectral clustering
Authors: Bombini Alessandro , García-Avello Bofías Fernando , Bracci Caterina , Ginolfi Michele , Ruberto Chiara 
Published: July 2024

Abstract
Extended vision techniques are ubiquitous in physics. However, the data cubes steaming from such analysis often pose a challenge in their interpretation, due to the intrinsic difficulty in discerning the relevant information from the spectra composing the data cube. Furthermore, the huge dimensionality of data cube spectra poses a complex task in its statistical interpretation; nevertheless, this complexity contains a massive amount of statistical information that can be exploited in an unsupervised manner to outline some essential properties of the case study at hand, e.g. it is possible to obtain an image segmentation via (deep) clustering of data-cube’s spectra, performed in a suitably defined low-dimensional embedding space. To tackle this topic, we explore the possibility of applying unsupervised clustering methods in encoded space, i.e. perform deep clustering on the spectral properties of datacube pixels. A statistical dimensional reduction is performed by an ad hoc trained (variational) AutoEncoder, in charge of mapping spectra into lower dimensional metric spaces, while the clustering process is performed by a (learnable) iterative K-means clustering algorithm. We apply this technique to two different use cases, of different physical origins: a set of macro mapping x-ray fluorescence (MA-XRF) synthetic data on pictorial artworks, and a dataset of simulated astrophysical observations.
Systematic review of climate change induced health impacts facing Malaysia: gaps in research
Authors: Pandya-Wood Raksha , Azhari Azliyana , Johar Hamimatunnisa , Johns-Putra Adeline , Muhamad Nurfashareena , Su Tin Tin 
Published: July 2024

Abstract
In Malaysia, climate change typically manifests as frequent and extreme weather events. The effects on human health of such meteorological and ecological imbalances are multiple and diverse. Urgent attention is needed to address the health-related threats facing Malaysia as a result of climate change. This systematic review (SR) of available evidence adopted Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines and identified and assessed a broad range of English language empirical, published research and excluded grey literature. Bias and quality of articles was assessed using Mixed Methods Assessment Tool. Using the search engines Scopus, PubMed, Ovid EMBASE, Web of Science, and EBSCO Host Medline, n = 374 results were yielded. Of these, after checking, n = 23 studies were examined. The studies can be grouped into three climatic themes
Exposure
,
Outcomes
and
Planning
. Our review confirms that urgent funding and investment is needed for larger-scale intervention studies on each of these themes. We observed a scarcity of high-quality empirical research, a preponderance of modelling studies to project and simulate scenarios, and a limited number of qualitative studies. Particular gaps in knowledge exist on climate change impacts on health in population groups in terms of demographic intersections to support these epidemiological data and simulation pathways. Furthermore, there was an absence of data on various topics concerning the effects of climate change on, for example, mental health, women, older people and/or the effects of displacement. The limitations of this work include accepting only English language publications and presenting only empirical studies. The study was not funded but was managed by the Monash Climate Change Communication Research node. This SR was registered on PROSPERO ID: CRD42023431868.
Accent Bias in Professional Evaluations: A Conceptual Replication Study in Brazil
Authors: Teló Cesar , Silveira Rosane , Marcelino Ana Flávia Boeing , O’Brien Mary G 
Published: July 2024

Abstract
Evidence from Canada suggests that accent bias can be moderated by speakers’ demonstrated job-relevant performance and the prestige level of their occupation (Teló et al. 2022). In this study, we replicated Teló et al.’s (2022) work in Brazil. First language (L1) Brazilian Portuguese-speaking listeners rated audio recordings of L1 Brazilian Portuguese and L1 Spanish speakers along continua capturing one professional (competence), one experiential (treatment preference), and one linguistic (comprehensibility) dimension. Our findings challenge the notion of consistent bias, as listeners did not uniformly perceive L1 Brazilian Portuguese speakers as more competent and comprehensible than L1 Spanish speakers, and, in fact, generally preferred treatment provided by L1 Spanish speakers. Complex interactions provided a nuanced account of listeners’ evaluations, revealing, among other patterns, that demonstrated performance level and job prestige affected the evaluated dimensions differently depending on the speaker’s L1. This replication further expands the initial study by examining the role of four listener variables as predictors of speaker ratings. Greater listener familiarity with the context depicted in the script was associated with the assignment of higher ratings overall.
GAPS: a geometric attention-based network for peptide binding site identification by the transfer learning approach
Authors: Zhu Cheng , Zhang Chengyun , Shang Tianfeng , Zhang Chenhao , Zhai Silong , Cao Lujing , Xu Zhenyu , Su Zhihao , Song Ying , Su An , Li Chengxi , Duan Hongliang 
Published: July 2024

AbstractProtein–peptide interactions (PPepIs) are vital to understanding cellular functions, which can facilitate the design of novel drugs. As an essential component in forming a PPepI, protein–peptide binding sites are the basis for understanding the mechanisms involved in PPepIs. Therefore, accurately identifying protein–peptide binding sites becomes a critical task. The traditional experimental methods for researching these binding sites are labor-intensive and time-consuming, and some computational tools have been invented to supplement it. However, these computational tools have limitations in generality or accuracy due to the need for ligand information, complex feature construction, or their reliance on modeling based on amino acid residues. To deal with the drawbacks of these computational algorithms, we describe a geometric attention-based network for peptide binding site identification (GAPS) in this work. The proposed model utilizes geometric feature engineering to construct atom representations and incorporates multiple attention mechanisms to update relevant biological features. In addition, the transfer learning strategy is implemented for leveraging the protein–protein binding sites information to enhance the protein–peptide binding sites recognition capability, taking into account the common structure and biological bias between proteins and peptides. Consequently, GAPS demonstrates the state-of-the-art performance and excellent robustness in this task. Moreover, our model exhibits exceptional performance across several extended experiments including predicting the apo protein–peptide, protein–cyclic peptide and the AlphaFold-predicted protein–peptide binding sites. These results confirm that the GAPS model is a powerful, versatile, stable method suitable for diverse binding site predictions.
Gram matrix: an efficient representation of molecular conformation and learning objective for molecular pretraining
Authors: Xiang Wenkai , Zhong Feisheng , Ni Lin , Zheng Mingyue , Li Xutong , Shi Qian , Wang Dingyan 
Published: July 2024

Abstract
Accurate prediction of molecular properties is fundamental in drug discovery and development, providing crucial guidance for effective drug design. A critical factor in achieving accurate molecular property prediction lies in the appropriate representation of molecular structures. Presently, prevalent deep learning–based molecular representations rely on 2D structure information as the primary molecular representation, often overlooking essential three-dimensional (3D) conformational information due to the inherent limitations of 2D structures in conveying atomic spatial relationships. In this study, we propose employing the Gram matrix as a condensed representation of 3D molecular structures and for efficient pretraining objectives. Subsequently, we leverage this matrix to construct a novel molecular representation model, Pre-GTM, which inherently encapsulates 3D information. The model accurately predicts the 3D structure of a molecule by estimating the Gram matrix. Our findings demonstrate that Pre-GTM model outperforms the baseline Graphormer model and other pretrained models in the QM9 and MoleculeNet quantitative property prediction task. The integration of the Gram matrix as a condensed representation of 3D molecular structure, incorporated into the Pre-GTM model, opens up promising avenues for its potential application across various domains of molecular research, including drug design, materials science, and chemical engineering.
Atypical intrinsic neural timescale in the left angular gyrus in Alzheimer’s disease
Authors: Murai Shota A , Mano Tatsuo , Sanes Jerome N , Watanabe Takamitsu 
Published: July 2024

Abstract
Alzheimer’s disease is characterized by cognitive impairment and progressive brain atrophy. Recent human neuroimaging studies reported atypical anatomical and functional changes in some regions in the default mode network in patients with Alzheimer’s disease, but which brain area of the default mode network is the key region whose atrophy disturbs the entire network activity and consequently contributes to the symptoms of the disease remains unidentified. Here, in this case–control study, we aimed to identify crucial neural regions that mediated the phenotype of Alzheimer’s disease, and as such, we examined the intrinsic neural timescales—a functional metric to evaluate the capacity to integrate diverse neural information—and grey matter volume of the regions in the default mode network using resting-state functional MRI images and structural MRI data obtained from individuals with Alzheimer’s disease and cognitively typical people. After confirming the atypically short neural timescale of the entire default mode network in Alzheimer’s disease and its link with the symptoms of the disease, we found that the shortened neural timescale of the default mode network was associated with the aberrantly short neural timescale of the left angular gyrus. Moreover, we revealed that the shortened neural timescale of the angular gyrus was correlated with the atypically reduced grey matter volume of this parietal region. Furthermore, we identified an association between the neural structure, brain function and symptoms and proposed a model in which the reduced grey matter volume of the left angular gyrus shortened the intrinsic neural time of the region, which then destabilized the entire neural timescale of the default mode network and resultantly contributed to cognitive decline in Alzheimer’s disease. These findings highlight the key role of the left angular gyrus in the anatomical and functional aetiology of Alzheimer’s disease.
Challenges for Novel Antiretroviral Development in an Era of Widespread tenofovir-disoproxil/lamivudine (or emtricitabine)/dolutegravir availability (TLD) Availability
Authors: Fairhead Cassandra , Levi Jacob , Hill Andrew 
Published: July 2024

Abstract
More than 80% of people with human immunodeficiency virus (HIV) in low- and middle-income countries (LMICs) take first-line tenofovir-disoproxil/lamivudine (or emtricitabine)/dolutegravir (TLD). Due to hard-fought activism, TLD now costs &lt;$45 per person per year in more than 100 LMICs under Voluntary License. With final dolutegravir (DTG) patents expiring by 2029, generic TLD will soon be available globally. Here, we identify seven critical benchmarks that underpin TLDs' success which novel antiretroviral therapy (ART) should now meet, and an eighth benchmark for which novel ART should aim. These benchmarks are superior efficacy; high genetic barrier to resistance; safety in hepatitis B coinfection; favourable drug interaction profiles; HIV2 efficacy; safety in pregnancy, long-acting formulation availability and affordable pricing. We compare the generic TLD availability timeline with development timelines for two case-study novel ART combinations: islatravir/doravirine and cabotegravir/rilpivirine. We demonstrate that currently these regimens and trial programs will not meet key benchmarks required to compete with TLD.
Long-term atrial arrhythmia characterization and treatment efficacy evaluation using non-invasive echocardiography-based electromechanical cycle length mapping: a case series
Authors: Tourni Melina , Weber Rachel , Biviano Angelo , Konofagou Elisa 
Published: July 2024

Abstract

Background
Atrial fibrillation (AF) is a prevalent cardiac condition characterized by irregular heart rhythm. Conventional non-invasive diagnostic techniques, while useful, have limitations in providing comprehensive information for treatment planning. To address this gap, electromechanical cycle length mapping (ECLM), a non-invasive echocardiography-based technique, has emerged as a promising approach. Electromechanical cycle length mapping offers quantitative and spatially specific insights into atrial electromechanical activation rate mapping, thereby enhancing our understanding of arrhythmia disease progression in AF patients.

Case summary
In this case series, we present two patient cases demonstrating the potential utility of ECLM in monitoring and evaluating treatment responses in atrial arrhythmia. The 1st case involved a 61-year-old male with persistent AF who underwent multiple procedures, including direct current cardioversion (DCCV) and radiofrequency ablation. Over three different DCCV encounters, pre- and post-procedure ECLM scans were performed, and the results showed the localization and incomplete elimination of arrhythmic triggers post-DCCV, which were used as early indicators of AF recurrence. The 2nd case involved a 71-year-old male with paroxysmal AF who also underwent cardioversion and ablation procedures. Electromechanical cycle length mapping imaging demonstrated a progressive reduction and elimination of arrhythmia triggers after each encounter, resulting in long-term maintenance of sinus rhythm.

Discussion
The findings from this case series highlight the potential of ECLM as a non-invasive imaging tool for long-term monitoring and evaluating immediate and long-term treatment responses in AF patients. The integration of ECLM with standard echocardiograms holds promise in guiding clinical decisions and improving patient outcomes in managing atrial fibrillation.
Goldfish phenomics reveals commonalities and a lack of universality in the domestication process for ornamentation
Authors: Le Verger Kévin , Küng Laurelle C , Fabre Anne-Claire , Schmelzle Thomas , Wegmann Alexandra , Sánchez-Villagra Marcelo R 
Published: July 2024

Abstract
Domestication process effects are manifold, affecting genotype and phenotype, and assumed to be universal in animals by part of the scientific community. While mammals and birds have been thoroughly investigated, from taming to intensive selective breeding, fish domestication remains comparatively unstudied. The most widely bred and traded ornamental fish species worldwide, the goldfish, underwent the effect of long-term artificial selection on differing skeletal and soft tissue modules through ornamental domestication. Here, we provide a global morphological analysis in this emblematic ornamental domesticated fish. We demonstrate that goldfish exhibit unique morphological innovations in whole-body, cranial, and sensory (Weberian ossicles and brain) anatomy compared to their evolutionary clade, highlighting a remarkable morphological disparity within a single species comparable to that of a macroevolutionary radiation. In goldfish, as in the case of dogs and pigeons in their respective evolutionary contexts, the most ornamented varieties are extremes in the occupied morphological space, emphasizing the power of artificial selection for nonadaptive traits. Using 21st century tools on a dataset comprising the 16 main goldfish breeds, 23 wild close relatives, and 39 cypriniform species, we show that Charles Darwin’s expressed wonder at the goldfish is justified. There is a commonality of overall pattern in the morphological differentiation of domesticated forms selected for ornamental purposes, but the singularity of goldfish occupation and extension within (phylo)morphospaces, speaks against a universality in the domestication process.
Non-ribosomal peptide synthase profiles remain structurally similar despite minimally shared features across fungus-farming termite microbiomes
Authors: Murphy Robert , Strube Mikael Lenz , Schmidt Suzanne , Silué Kolotchèlèma Simon , Koné N’golo Abdoulaye , Rosendahl Søren , Poulsen Michael 
Published: July 2024

Abstract
Fungus-farming termites (Macrotermitinae) engage in an obligate mutualism with members of the fungal genus Termitomyces, which they maintain as a monoculture on specialized comb structures. Both these comb structures and the guts of the termites host diverse bacterial communities that are believed to assist in sustaining monoculture farming through antagonist suppression. Among candidate bacteria-derived compounds serving this function are non-ribosomal peptides (NRPs), which are a highly bioactive class of specialized metabolites, frequently produced by symbionts within eukaryotic hosts. However, our understanding of specialized metabolites in termite-associated microbiomes is limited. Here we use amplicon sequencing to characterize both bacterial composition and NRP potential. We show that bacterial and NRP diversity are correlated and that the former varies more than the latter across termite host and gut and comb samples. Compositions of the two are governed by host species and sample type, with topological similarity indicating a diverse set of biosynthetic potential that is consistent with the long evolutionary history of the Macrotermitinae. The structure of both bacterial and NRP compositional networks varied similarly between guts and combs across the Macrotermitinae albeit with auxiliary termite genus-specific patterns. We observed minimal termite species-specific cores, with essentially no Macrotermitinae-wide core and an abundance of putatively novel biosynthetic gene clusters, suggesting that there is likely no single solution to antagonist suppression via specialized NRP metabolites. Our findings contribute to an improved understanding of the distribution of NRP potential in the farming termite symbiosis and will help guide targeted exploration of specialized metabolite production.
Following hip fracture, hospital organizational factors associated with prescription of anti-osteoporosis medication on discharge, to address imminent refracture risk: a record-linkage study
Authors: Patel Rita , Judge Andrew , Johansen Antony , Javaid Muhammad K , Griffin Xavier L , Chesser Tim , Griffin Jill , Marques Elsa M R ,   REDUCE Study Group, Gregson Celia L , Johansen Antony , Chesser Tim , Javaid Muhammad K , Griffin Xavier L , Griffin Jill , Marques Elsa M R , Ben-Shlomo Yoav , Drew Sarah , Judge Andrew , Patel Rita , Whale Katie , Ben-Shlomo Yoav , Gregson Celia L 
Published: July 2024

Abstract
Patients who sustain a hip fracture are known to be at imminent refracture risk. Their complex multidisciplinary rehabilitation needs to include falls prevention and anti-osteoporosis medication (AOM) to prevent such fractures. This study aimed to determine which hospital-level organizational factors predict prescription of post-hip fracture AOM and refracture risk. A cohort of 178 757 patients aged ≥60 yr who sustained a hip fracture in England and Wales (2016-2019) was examined and followed for 1 yr. Patient-level hospital admission datasets from 172 hospitals, the National Hip Fracture Database, and mortality data were linked to 71 metrics extracted from 18 hospital-level organizational reports. Multilevel models determined organizational factors, independent of patient case-mix, associated with (1) AOM prescription and (2) refracture (by ICD10 coding). Patients were mean (SD) 82.7 (8.6) yr old, 71% female, with 18% admitted from care homes. Overall, 101 735 (57%) were prescribed AOM during admission, while 50 354 (28%) died during 1-yr follow-up, 12 240 (7%) refractured. Twelve organizational factors were associated with AOM prescription, for example, orthogeriatrician-led care compared to traditional care models (odds ratio [OR] 4.65 [95% CI, 2.25–9.59]); AOM was 9% (95% CI, 6%–13%) more likely to be prescribed in hospitals providing routine bone health assessment to all patients. Refracture occurred at median 126 d (IQR 59–234). Eight organizational factors were associated with refracture risk; hospitals providing orthogeriatrician assessment to all patients within 72 h of admission had an 18% (95% CI, 2%–31%) lower refracture risk, weekend physiotherapy provision had an 8% (95% CI, 3%–14%) lower risk, and where occupational therapists attended clinical governance meetings, a 7% (95% CI, 2%–12%) lower risk. Delays initiating post-discharge community rehabilitation were associated with a 15% (95% CI, 3%–29%) greater refracture risk. These novel, national findings highlight the importance of orthogeriatrician, physiotherapist, and occupational therapist involvement in secondary fracture prevention post hip fracture; notably, fracture risk reductions were seen within 12 mo of hip fracture.
Osteoclast-derived coupling factors: origins and state-of-play Louis V Avioli lecture, ASBMR 2023
Authors: Sims Natalie A 
Published: July 2024

Abstract
Coupling, the mechanism that controls the sequence of events in bone remodeling, is a fundamental theory for understanding the way the skeleton changes throughout life. This review is an adapted version of the Louis V Avioli lecture, delivered at the Annual Scientific Meeting of the American Society of Bone and Mineral Research in 2023. It outlines the history of the coupling concept, details how coupling is thought to occur within trabecular and cortical bone, and describes its multiple contexts and the many mechanisms suggested to couple bone-forming osteoblasts to the prior action of osteoclasts on the same bone surface. These mechanisms include signals produced at each stage of the remodeling sequence (resorption, reversal, and formation), such as factors released by osteoclasts through their resorptive action and through protein synthesis, molecules deposited in the cement line during the reversal phase, and potential signals from osteocytes within the local bone environment. The review highlights two examples of coupling factors (Cardiotrophin 1 and EphrinB2:EphB4) to illustrate the limited data available, the need to integrate the many functions of these factors within the basic multicellular unit (BMU), and the multiple origins of these factors, including the other cell types present during the remodeling sequence (such as osteocytes, macrophages, endothelial cells, and T-cells).