bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of pedestrian paths in the trade area with water transport: Case study of Old Town Pekanbaru
Authors: Masrul W 
Published: April 2024

Abstract
Pekanbaru grew and developed starting from a pekan or market located on the banks of the Siak River. The development of Pekanbaru city is inseparable from the history that shaped it, where in the 16th century Pekanbaru was once the center of government of the kingdom of Siak Sri Indra Pura which then grew and developed with trade activities, and settlements to form a potential regional structure as a tourist destination, both shopping tourism, religious tourism, and tourism in the old residential area. Therefore, to accommodate and support the activities of the old city area of Pekanbaru, it is necessary to have adequate infrastructure such as pedestrian paths (Pedestrian Way). This study aims to evaluate the pedestrian path in the aspect of accessibility that connects the potential of the old city area of Pekanbaru such as the port area, trade area, and old residential area. The method used in this research is descriptive with a qualitative approach through mapping the potential conditions of each character area that is reinforced by using quantitative methods with descriptive and simulation research frameworks. The results of the analysis show that some corridors in the trade area show better integration, which means that it is possible that in the trade area, there is more movement of people because it is easily accessible from various directions (accessible) while in the port area shows moderate integration and in residential areas tends to be low.
A Study of the Effect of Addition of Nano SiO2 and Polyamide Fiber toward Swelling Potential Expansive Clay
Authors: Hirwo N T , Pratikso  , Karlinasari R 
Published: April 2024

Abstract
Expansive clay with great swelling potential requires improvement or stabilization of the soil. It can be successfully done by mechanical and chemical stabilization techniques. This study aims to determine the effect of adding Polyamide (PA) fibre as the material for mechanical stabilization and nano SiO2 as the material for chemical stabilization. The expansive clay used in this study deployed a sample of clay containing mineral montmorillonite with the USCS classification in the high plasticity (CH) category. The mixed materials used include PA fibre with variations of 0.5%, 0.75% and 1% by weight of dry soil and nano SiO2 with variations of 1%, 2% and 3% by dry soil weight. To prove the effectiveness of using nano SiO2, this study compares the treatment with the use of micro SiO2 materials under the same comparison variations. This result indicates that the expansive clay that has been stabilized using PA fibre and nano SiO2 is capable of preventing the swelling potential.
The concept of waqf-based communal space in supporting the independence of coastal communities (Case Study of Tugurejo Village, Semarang)
Authors: Rochani A , Puspitasari A Y , Yuliastuti N , Sudarwanto B 
Published: April 2024

Abstract
One aspect of Islamic culture that combines spatial, ritual, and social aspects is land waqf, or the generous granting of land and buildings on it for public use. Waqf forms an esoteric culture that connects the community to Islamic values through the establishment of places of worship and social existence. The fact that waqf has developed in various places raise the question of why waqf has been able to survive for so long, and what are the factors behind this. To answer this question, a study was conducted aimed at formulating the concept of waqf space to support the self-reliance of coastal communities. The research site is a coastal village in Tugurejo village, Semarang city. Through a comprehensive single case study approach, this study yielded the finding that waqf forms his seven spatial themes including: 1) Prayer space theme, 2) studying space theme, 3) Space sharing theme, 4) The business space theme, 5) Settlement infrastructure space theme, 6) Islamic shiar space theme, 7) Conservation space theme. These seven themes of his form a socio-economic concept in the form of a space of fraternity, and are the pillars that support the self-reliance of the community of Tugurejo village.
Multimodal protein representation learning and target-aware variational auto-encoders for protein-binding ligand generation
Authors: Khang Ngo Nhat , Son Hy Truong 
Published: April 2024

Abstract
Without knowledge of specific pockets, generating ligands based on the global structure of a protein target plays a crucial role in drug discovery as it helps reduce the search space for potential drug-like candidates in the pipeline. However, contemporary methods require optimizing tailored networks for each protein, which is arduous and costly. To address this issue, we introduce TargetVAE, a target-aware variational auto-encoder that generates ligands with desirable properties including high binding affinity and high synthesizability to arbitrary target proteins, guided by a multimodal deep neural network built based on geometric and sequence models, named Protein Multimodal Network (PMN), as the prior for the generative model. PMN unifies different representations of proteins (e.g. primary structure—sequence of amino acids, 3D tertiary structure, and residue-level graph) into a single representation. Our multimodal architecture learns from the entire protein structure and is able to capture their sequential, topological, and geometrical information by utilizing language modeling, graph neural networks, and geometric deep learning. We showcase the superiority of our approach by conducting extensive experiments and evaluations, including predicting protein-ligand binding affinity in the PBDBind v2020 dataset as well as the assessment of generative model quality, ligand generation for unseen targets, and docking score computation. Empirical results demonstrate the promising and competitive performance of our proposed approach. Our software package is publicly available at https://github.com/HySonLab/Ligand_Generation.
Atomic force microscopy simulations for CO-functionalized tips with deep learning
Authors: Carracedo-Cosme Jaime , Hapala Prokop , Pérez Rubén 
Published: April 2024

Abstract
Atomic force microscopy (AFM) operating in the frequency modulation mode with a metal tip functionalized with a CO molecule is able to image the internal structure of molecules with an unprecedented resolution. The interpretation of these images is often difficult, making the support of theoretical simulations important. Current simulation methods, particularly the most accurate ones, require expertise and resources to perform ab initio calculations for the necessary inputs (i.e charge density and electrostatic potential of the molecule). Here, we propose a computationally inexpensive and fast alternative to the physical simulation of these AFM images based on a conditional generative adversarial network (CGAN), that avoids all force calculations, and uses as the only input a 2D ball–and–stick depiction of the molecule. We discuss the performance of the model when trained with different subsets extracted from the previously published QUAM-AFM database. Our CGAN reproduces accurately the intramolecular contrast observed in the simulated images for quasi–planar molecules, but has limitations for molecules with a substantial internal corrugation, due to the strictly 2D character of the input.
Subtitled speech: the neural mechanisms of ticker-tape synaesthesia
Authors: Hauw Fabien , Béranger Benoît , Cohen Laurent 
Published: April 2024

Abstract
The acquisition of reading modifies areas of the brain associated with vision and with language, in addition to their connections. These changes enable reciprocal translation between orthography and the sounds and meaning of words. Individual variability in the pre-existing cerebral substrate contributes to the range of eventual reading abilities, extending to atypical developmental patterns, including dyslexia and reading-related synaesthesias. The present study is devoted to the little-studied but highly informative ticker-tape synaesthesia, in which speech perception triggers the vivid and irrepressible perception of words in their written form in the mind’s eye.
We scanned a group of 17 synaesthetes and 17 matched controls with functional MRI, while they listened to spoken sentences, words, numbers or pseudowords (Experiment 1), viewed images and written words (Experiment 2) or were at rest (Experiment 3).
First, we found direct correlates of the ticker-tape synaesthesia phenomenon: during speech perception, as ticker-tape synaesthesia was active, synaesthetes showed over-activation of left perisylvian regions supporting phonology and of the occipitotemporal visual word form area, where orthography is represented. Second, we provided support to the hypothesis that ticker-tape synaesthesia results from atypical relationships between spoken and written language processing: the ticker-tape synaesthesia-related regions overlap closely with cortices activated during reading, and the overlap of speech-related and reading-related areas is larger in synaesthetes than in controls. Furthermore, the regions over-activated in ticker-tape synaesthesia overlap with regions under-activated in dyslexia. Third, during the resting state (i.e. in the absence of current ticker-tape synaesthesia), synaesthetes showed increased functional connectivity between left prefrontal and bilateral occipital regions. This pattern might reflect a lowered threshold for conscious access to visual mental contents and might imply a non-specific predisposition to all synaesthesias with a visual content.
These data provide a rich and coherent account of ticker-tape synaesthesia as a non-detrimental developmental condition created by the interaction of reading acquisition with an atypical cerebral substrate.
Nursing home finances associated with real estate investment trust and private equity investments
Authors: Williams Dunc , Fernandez Rahul , Stevenson David , Unruh Mark , Braun Robert Tyler 
Published: April 2024

Abstract
In 2021, real estate investment trusts (REITs) and private equity (PE) held investments in 1915 (16%) and 1569 (13%) US nursing homes (NHs), respectively. We created a database of REIT and PE investments in NHs, merged it with Medicare Cost Report data (2011–2019), and used a difference-in-differences approach within an event-study framework to compare NH spending and financial performance before and after REIT or PE investment to NHs that did not receive REIT or PE investment. REIT investments were associated with higher total wages (3%), total nursing wages (3%; both logged, per resident day [PRD]), and current ratio (81%). PE investments were associated with lower net patient service revenue (7%), total expenses (7%), and total wages (8%; all logged, PRD). The impact of REIT and PE investments in NHs may vary in different market conditions, as may occur in the current environment of low, falling NH profits, potentially higher minimum staffing requirements, and rising interest rates. Therefore, it is important for stakeholders to understand the impact of these large, growing investments on the financial performance of NHs.
Mitochondrial abnormalities contribute to muscle weakness in a Dnajb6 deficient zebrafish model
Authors: McKaige Emily A , Lee Clara , Calcinotto Vanessa , Giri Saveen , Crawford Simon , McGrath Meagan J , Ramm Georg , Bryson-Richardson Robert J 
Published: April 2024

Abstract
Mutations in DNAJB6 are a well-established cause of limb girdle muscular dystrophy type D1 (LGMD D1). Patients with LGMD D1 develop progressive muscle weakness with histology showing fibre damage, autophagic vacuoles, and aggregates. Whilst there are many reports of LGMD D1 patients, the role of DNAJB6 in the muscle is still unclear. In this study, we developed a loss of function zebrafish model in order to investigate the role of Dnajb6. Using a double dnajb6a and dnajb6b mutant model, we show that loss of Dnajb6 leads to a late onset muscle weakness. Interestingly, we find that adult fish lacking Dnajb6 do not have autophagy or myofibril defects, however, they do show mitochondrial changes and damage. This study demonstrates that loss of Dnajb6 causes mitochondrial defects and suggests that this contributes to muscle weakness in LGMD D1. These findings expand our knowledge of the role of Dnajb6 in the muscle and provides a model to screen novel therapies for LGMD D1.
Chlamydiae in corals: shared functional potential despite broad taxonomic diversity
Authors: Maire Justin , Collingro Astrid , Horn Matthias , van Oppen Madeleine J H 
Published: April 2024

Abstract
Cnidarians, such as corals and sea anemones, associate with a wide range of bacteria that have essential functions, including nutrient cycling and the production of antimicrobial compounds. Within cnidarians, bacteria can colonize all microhabitats including the tissues. Among them are obligate intracellular bacteria of the phylum Chlamydiota (chlamydiae) whose impact on cnidarian hosts and holobionts, especially corals, remain unknown. Here, we conducted a meta-analysis of previously published 16S rRNA gene metabarcoding data from cnidarians (e.g. coral, jellyfish, and anemones), eight metagenome-assembled genomes (MAGs) of coral-associated chlamydiae, and one MAG of jellyfish-associated chlamydiae to decipher their diversity and functional potential. While the metabarcoding dataset showed an enormous diversity of cnidarian-associated chlamydiae, six out of nine MAGs were affiliated with the Simkaniaceae family. The other three MAGs were assigned to the Parasimkaniaceae, Rhabdochlamydiaceae, and Anoxychlamydiaceae, respectively. All MAGs lacked the genes necessary for an independent existence, lacking any nucleotide or vitamin and most amino acid biosynthesis pathways. Hallmark chlamydial genes, such as a type III secretion system, nucleotide transporters, and genes for host interaction, were encoded in all MAGs. Together these observations suggest an obligate intracellular lifestyle of coral-associated chlamydiae. No unique genes were found in coral-associated chlamydiae, suggesting a lack of host specificity. Additional studies are needed to understand how chlamydiae interact with their coral host, and other microbes in coral holobionts. This first study of the diversity and functional potential of coral-associated chlamydiae improves our understanding of both the coral microbiome and the chlamydial lifestyle and host range.
The Effect of Terrorism on Income Inequality
Authors: McGauvran Ronald J , Biglaiser Glen , Hunter Lance Y , Lee Hoon 
Published: April 2024

Abstract
Conflict research has recently found that increased inequality weakens institutional conditions, opening the door for terrorism. While this research often accounts for endogeneity, or the possibility of a reverse causal relationship, there has yet to be an empirical investigation of the impact of terrorism on income inequality. Using a sample of 139 countries between 1994 and 2018, we show that both domestic and transnational terrorism result in higher levels of income inequality. Our results are consistent for both pre- and post-tax and transfer inequality as well as multiple model specifications. Additionally, we explore multiple potential causal mechanisms that link terrorism and income inequality finding that the effect is, in part, due to terrorism’s negative effects on institutional stability, increased military expenditure, possibly to fund counterterrorism operations, and reduced foreign capital, especially for greenfield investment. Our analysis indicates a positive relationship between terrorism and inequality and the mechanisms that produce the effect, contributing to the terrorism and inequality literatures.
A Meta-Analysis of the Mortality and the Prevalence of Burn Complications in Western Populations
Authors: Foppiani Jose A , Weidman Allan , Hernandez Alvarez Angelica , Valentine Lauren , Bustos Valeria P , Galinaud Cécilia , Hrdina Radim , Hrdina Radim , Musil Zdenek , Lee Bernard T , Lin Samuel J 
Published: April 2024

Abstract
Management of burn injuries is complex, with highly variable outcomes occurring among different populations. This meta-analysis aims to assess the outcomes of burn therapy in North American and European adults, specifically mortality and complications, to guide further therapeutic advances. A systematic review of PubMed, Web of Science, and Cochrane was performed. Random-effect meta-analysis of proportions was conducted to assess the overall prevalence of the defined outcomes. In total, 54 studies were included, pooling 60 269 adult patients. A total of 53 896 patients were in North America (NA, 89.4%), and 6373 were in Europe (10.6%). Both populations experienced similar outcomes. The overall pooled prevalence of mortality was 13% (95% CI, 8%-19%) for moderate burns, 20% (95% CI, 12%-29%) for severe burns in the NA region, and 22% (95% CI, 16%-28%) for severe burns in Europe. Infectious complications were the most common across both regions. European studies showed an infection rate for patients with moderate and severe burns at 8% and 76%, respectively, while NA studies had rates of 35% and 54%. Acute kidney injury (39% vs 37%) and shock (29% vs 35%) were the next most common complications in European and NA studies, respectively. The length of stay was 27.52 days for patients with severe burns in Europe and 31.02 days for patients with severe burns in NA. Burn outcomes are similar between Western populations. While outcomes are reasonably good overall, infectious complications remain high. These findings encourage the development of further therapeutic strategies disclosing respective costs to enable cost/efficiency evaluations in burn management.
Development of a Wound Epithelialization Healing Model: Reducing the Impact of Contraction Healing on the Wound Surface
Authors: Chang Fei , Yan Lei , Zha Yuanyuan , Hong Xudong , Zhu Kaisi , Fei Yanghonghong , Si Tingting , Ding Yinjia , Chen Aifen , Zhang Xudong , Chen Zhengli , Li Huatao , Jin Jian 
Published: April 2024

Abstract
Animal experiments are important in trauma-related studies because they simulate in vivo effects. Rodents are a good choice for preparing trauma models; however, contractile healing in rodents results in a healing pattern that differs considerably from that in humans. Therefore, this study developed a new rodent model that avoids contractile healing of the skin around the wound using an anticontraction ring, and the skin in the wound’s center remains intact and acts as a source for epithelialized diffusion healing. Cell proliferation, migration, revascularization, and collagen secretion did not differ between the novel and conventional full-skin defect trauma models. However, the healing rate at various stages significantly differed between the 2 groups owing to differences in the healing patterns. And without effective treatment, the experimental group cannot heal. The stabilities of the novel and conventional methods were good regardless of operator or batch. In summary, this new animal trauma model provides a stable experimental environment similar to that in humans, which may promote trauma-related research.
Dissecting the causal polymorphism of the Lr67res multipathogen resistance gene
Authors: Milne Ricky J , Dibley Katherine E , Bose Jayakumar , Riaz Adnan , Zhang Jianping , Schnippenkoetter Wendelin , Ashton Anthony R , Ryan Peter R , Tyerman Stephen D , Lagudah Evans S 
Published: April 2024

Abstract
Partial resistance to multiple biotrophic fungal pathogens in wheat (Triticum aestivum L.) is conferred by a variant of the Lr67 gene, which encodes a hexose–proton symporter. Two mutations (G144R and V387L) differentiate the resistant and susceptible protein variants (Lr67res and Lr67sus). Lr67res lacks sugar transport capability and was associated with anion transporter-like properties when expressed in Xenopus laevis oocytes. Here, we extended this functional characterization to include yeast and in planta studies. The Lr67res allele, but not Lr67sus, induced sensitivity to ions in yeast (including NaCl, LiCl, and KI), which is consistent with our previous observations that Lr67res expression in oocytes induces novel ion fluxes. We demonstrate that another naturally occurring single amino acid variant in wheat, containing only the Lr67G144R mutation, confers rust resistance. Transgenic barley plants expressing the orthologous HvSTP13 gene carrying the G144R and V387L mutations were also more resistant to Puccinia hordei infection. NaCl treatment of pot-grown adult wheat plants with the Lr67res allele induced leaf tip necrosis and partial leaf rust resistance. An Lr67res-like function can be introduced into orthologous plant hexose transporters via single amino acid mutation, highlighting the strong possibility of generating disease resistance in other crops, especially with gene editing.
Fourteen years of cellular deconvolution: methodology, applications, technical evaluation and outstanding challenges
Authors: Nguyen Hung , Nguyen Ha , Tran Duc , Draghici Sorin , Nguyen Tin 
Published: April 2024

Abstract
Single-cell RNA sequencing (scRNA-Seq) is a recent technology that allows for the measurement of the expression of all genes in each individual cell contained in a sample. Information at the single-cell level has been shown to be extremely useful in many areas. However, performing single-cell experiments is expensive. Although cellular deconvolution cannot provide the same comprehensive information as single-cell experiments, it can extract cell-type information from bulk RNA data, and therefore it allows researchers to conduct studies at cell-type resolution from existing bulk datasets. For these reasons, a great effort has been made to develop such methods for cellular deconvolution. The large number of methods available, the requirement of coding skills, inadequate documentation, and lack of performance assessment all make it extremely difficult for life scientists to choose a suitable method for their experiment. This paper aims to fill this gap by providing a comprehensive review of 53 deconvolution methods regarding their methodology, applications, performance, and outstanding challenges. More importantly, the article presents a benchmarking of all these 53 methods using 283 cell types from 30 tissues of 63 individuals. We also provide an R package named DeconBenchmark that allows readers to execute and benchmark the reviewed methods (https://github.com/tinnlab/DeconBenchmark).
Discrimination as a Public Wrong
Authors: Goldiner Adi 
Published: April 2024

Abstract
The enforcement mechanisms of anti-discrimination law manifest a puzzle: while the dominant view is that discrimination is a wrongdoing against individuals, which suggests that discriminatees should have the power to vindicate their rights, legal provisions sometimes authorise public officials to file claims against alleged discriminators, regardless of discriminatees’ preferences. Seeking to make sense of this puzzle, this article draws on theories of state enforcement under criminal law to explore the justification of public enforcement under anti-discrimination law and reflect on the nature of discrimination more broadly. It claims that an instrumental justification of public enforcement of anti-discrimination law is left wanting. Instead, it argues that public enforcement in this domain is warranted because discrimination is not only a private wrong against individuals, but is also a public wrong, namely a wrong against the community as a whole.