bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unraveling the epigenetic code: human kidney DNA methylation and chromatin dynamics in renal disease development
Authors: Yan Yu , Liu Hongbo , Abedini Amin , Sheng Xin , Palmer Matthew , Li Hongzhe , Susztak Katalin 
Published: January 2024

AbstractEpigenetic changes may fill a critical gap in our understanding of kidney disease development, as they not only reflect metabolic changes but are also preserved and transmitted during cell division. We conducted a genome-wide cytosine methylation analysis of 399 human kidney samples, along with single-nuclear open chromatin analysis on over 60,000 cells from 14 subjects, including controls, and diabetes and hypertension attributed chronic kidney disease (CKD) patients. We identified and validated differentially methylated positions associated with disease states, and discovered that nearly 30% of these alterations were influenced by underlying genetic variations, including variants known to be associated with kidney disease in genome-wide association studies. We also identified regions showing both methylation and open chromatin changes. These changes in methylation and open chromatin significantly associated gene expression changes, most notably those playing role in metabolism and expressed in proximal tubules. Our study further demonstrated that methylation risk scores (MRS) can improve disease state annotation and prediction of kidney disease development. Collectively, our results suggest a causal relationship between epigenetic changes and kidney disease pathogenesis, thereby providing potential pathways for the development of novel risk stratification methods.
A hybridization of evolution strategies with iterated greedy algorithm for no-wait flow shop scheduling problems
Authors: Khurshid Bilal , Maqsood Shahid , Khurshid Yahya , Naeem Khawar , Khalid Qazi Salman 
Published: January 2024

AbstractThis study investigates the no-wait flow shop scheduling problem and proposes a hybrid (HES-IG) algorithm that utilizes makespan as the objective function. To address the complexity of this NP-hard problem, the HES-IG algorithm combines evolution strategies (ES) and iterated greedy (IG) algorithm, as hybridizing algorithms helps different algorithms mitigate their weaknesses and leverage their respective strengths. The ES algorithm begins with a random initial solution and uses an insertion mutation to optimize the solution. Reproduction is carried out using (1 + 5)-ES, generating five offspring from one parent randomly. The selection process employs (µ + λ)-ES, allowing excellent parent solutions to survive multiple generations until a better offspring surpasses them. The IG algorithm’s straightforward search mechanism aids in further improving the solution and avoiding local minima. The destruction operator randomly removes d-jobs, which are then inserted one by one using a construction operator. The local search operator employs a single insertion approach, while the acceptance–rejection criteria are based on a constant temperature. Parameters of both ES and IG algorithms are calibrated using the Multifactor analysis of variance technique. The performance of the HES-IG algorithm is calibrated with other algorithms using the Wilcoxon signed test. The HES-IG algorithm is tested on 21 Nos. Reeves and 30 Nos. Taillard benchmark problems. The HES-IG algorithm has found 15 lower bound values for Reeves benchmark problems. Similarly, the HES-IG algorithm has found 30 lower bound values for the Taillard benchmark problems. Computational results indicate that the HES-IG algorithm outperforms other available techniques in the literature for all problem sizes.
Identifying key players in dark web marketplaces through Bitcoin transaction networks
Authors: dos Reis Elohim Fonseca , Teytelboym Alexander , ElBahrawy Abeer , De Loizaga Ignacio , Baronchelli Andrea 
Published: January 2024

AbstractDark web marketplaces have been a significant outlet for illicit trade, serving millions of users worldwide for over a decade. However, not all users are the same. This paper aims to identify the key players in Bitcoin transaction networks linked to dark markets and assess their role by analysing a dataset of 40 million Bitcoin transactions involving the 31 major markets in the period 2011–2021. First, we propose an algorithm that categorizes users either as buyers or sellers, and show that a large fraction of the trading volume is concentrated in a small group of elite market participants. We find that the dominance of markets is reflected in trading properties of buyers and sellers. Then, we investigate both market star-graphs and user-to-user networks, and highlight the importance of a new class of users, namely ‘multihomers’, who operate on multiple marketplaces concurrently. Specifically, we show how the networks of multihomers and seller-to-seller interactions can shed light on the resilience of the dark market ecosystem against external shocks. Our findings suggest that understanding the behavior of key players in dark web marketplaces is critical to effectively disrupting illegal activities.
Integration-free induced pluripotent stem cells from three endangered Southeast Asian non-human primate species
Authors: Bao Qiuye , Tay Nicole Liling , Lim Christina Yingyan , Chua Delia Hwee Hoon , Kee Su Keyau , Choolani Mahesh , Loh Yuin-Han , Ng Soon Chye , Chai Chou 
Published: January 2024

AbstractAdvanced molecular and cellular technologies provide promising tools for wildlife and biodiversity conservation. Induced pluripotent stem cell (iPSC) technology offers an easily accessible and infinite source of pluripotent stem cells, and have been derived from many threatened wildlife species. This paper describes the first successful integration-free reprogramming of adult somatic cells to iPSCs, and their differentiation, from three endangered Southeast Asian primates: the Celebes Crested Macaque (Macaca nigra), the Lar Gibbon (Hylobates lar), and the Siamang (Symphalangus syndactylus). iPSCs were also generated from the Proboscis Monkey (Nasalis larvatus). Differences in mechanisms could elicit new discoveries regarding primate evolution and development. iPSCs from endangered species provides a safety net in conservation efforts and allows for sustainable sampling for research and conservation, all while providing a platform for the development of further in vitro models of disease.
Fish diversity and selection of taxa for conservation in the Salween and Irrawaddy Rivers, Southeast Asia
Authors: Zhou W. , Li X. 
Published: January 2024

AbstractSpecies diversity indices provide quantitative data for understanding the variations and trends in fish species diversity, as well as information on species richness and evenness. However, these diversity indices do not reflect differences in specific taxa, which can be of importance as key conservation targets, especially during the planning and construction of protected areas. In this study, simultaneously combining our improved traditional fish fauna analysis (TFFA) with the value of fish fauna presence (VFFP) methods, we studied fish diversity in the Salween and Irrawaddy basins. The results of the TFFA reflected the families (subfamilies) and genera that constitute the main body of fish diversity in the river basins. The results of the VFFP assessment showed which families (subfamilies) and genera were representative of certain characteristics in the basins. The VFFP scores of genera could be used as indicator indices and as priority taxa in the planning and construction of fish resource reserves. In this paper, we propose for the first time that the role and status of monotypic genera (genera comprising only a single species) in the conservation of fish diversity should not be ignored, and they should rather be a priority for protection.
NLP-based tools for localization of the epileptogenic zone in patients with drug-resistant focal epilepsy
Authors: Mora Sara , Turrisi Rosanna , Chiarella Lorenzo , Consales Alessandro , Tassi Laura , Mai Roberto , Nobili Lino , Barla Annalisa , Arnulfo Gabriele 
Published: January 2024

AbstractEpilepsy surgery is an option for people with focal onset drug-resistant (DR) seizures but a delayed or incorrect diagnosis of epileptogenic zone (EZ) location limits its efficacy. Seizure semiological manifestations and their chronological appearance contain valuable information on the putative EZ location but their interpretation relies on extensive experience. The aim of our work is to support the localization of EZ in DR patients automatically analyzing the semiological description of seizures contained in video-EEG reports. Our sample is composed of 536 descriptions of seizures extracted from Electronic Medical Records of 122 patients. We devised numerical representations of anamnestic records and seizures descriptions, exploiting Natural Language Processing (NLP) techniques, and used them to feed Machine Learning (ML) models. We performed three binary classification tasks: localizing the EZ in the right or left hemisphere, temporal or extra-temporal, and frontal or posterior regions. Our computational pipeline reached performances above 70% in all tasks. These results show that NLP-based numerical representation combined with ML-based classification models may help in localizing the origin of the seizures relying only on seizures-related semiological text data alone. Accurate early recognition of EZ could enable a more appropriate patient management and a faster access to epilepsy surgery to potential candidates.
Comparative evaluation of mechanical injury methods for establishing stable tracheal stenosis animal models
Authors: Lin Hongbin , Ainiwaer Mailudan , Jiang Zheng , Wang Zhenyan , Liu Jun , Chen Fei 
Published: January 2024

AbstractThe study aimed to assess the stability of various mechanical injury techniques in creating tracheal stenosis animal models using endoscopic assistance and investigate the viability of tracheal stoma in this process. Twenty-six healthy adult New Zealand white rabbits were randomly assigned to an experimental and control group. The experimental group underwent tracheal incision followed by steel brush scraping with endoscopic assistance, while the control group received nylon brush scraping. Within the control group, two subgroups were formed: Group A underwent scraping without tracheal stoma, and Group B underwent scraping followed by tracheal stoma. Additionally, a sham operation was performed on a separate group without subsequent scratching, resulting in no stenosis formation. Endoscopic observations were conducted at 7, 14, and 21 days post-scraping, followed by histological examinations of euthanized rabbits on the 21st day. Notably, all rabbits in the non-stoma group survived without complications, whereas Group B rabbits faced mortality post-operation. Histological assessments revealed inflammatory cell infiltration, fibroblast proliferation, and collagen fiber deposition in narrowed tracheal specimens. Steel brush scraping with endoscopic assistance proved more effective in inducing stable tracheal stenosis compared to nylon brush scraping. However, the survival challenges of rabbits with tracheal fistula require further investigation.
Action-outcome delays modulate the temporal expansion of intended outcomes
Authors: Donapati Rohan R. , Shukla Anuj , Bapi Raju S. 
Published: January 2024

AbstractThe phenomenon of intentional binding pertains to the perceived connection between a voluntary action and its anticipated result. When an individual intends an outcome, it appears to subjectively extend in time due to a pre-activation of the intended result, particularly evident at shorter action-outcome delays. However, there is a concern that the operationalisation of intention might have led to a mixed interpretation of the outcome expansion attributed to the pre-activation of intention, given the sensitivity of time perception and intentional binding to external cues that could accelerate the realisation of expectations. To investigate the expansion dynamics of an intended outcome, we employed a modified version of the temporal bisection task in two experiments. Experiment 1 considered the action-outcome delay as a within-subject factor, while experiment 2 treated it as a between-subject factor. The results revealed that the temporal expansion of an intended outcome was only evident under the longer action-outcome delay condition. We attribute this observation to working memory demands and attentional allocation due to temporal relevancy and not due to pre-activation. The discrepancy in effects across studies is explained by operationalising different components of the intentional binding effect, guided by the cue integration theory. Moreover, we discussed speculative ideas regarding the involvement of specific intentions based on the proximal intent distal intent (PIDI) theory and whether causality plays a role in temporal binding. Our study contributes to the understanding of how intention influences time perception and sheds light on how various methodological factors, cues, and delays can impact the dynamics of temporal expansion associated with an intended outcome.
Exploring the role of country-level gender equality in the link between relationship status and perceived social support across 49 countries
Authors: Łyś Agnieszka E. , Adamczyk Katarzyna 
Published: January 2024

AbstractPast studies have demonstrated that higher perceived social support among coupled individuals and greater gender equality foster a more supportive social context. Less is known about how the link between relationship status and perceived social support may vary across countries that differ in gender equality. Employing the data collected from the COVIDiSTRESS I (39 countries; N = 99,075) and COVIDiSTRESS II (23 countries; N = 8293) projects, we examined whether country-level gender equality moderates the link between relationship status and perceived social support. Multilevel regression analyses indicated that gender equality moderated the link between relationship status and perceived social support. Single people in countries with less gender equality reported less perceived social support than was reported by both coupled people and single people from countries with moderate and high levels of gender equality, however, the effect of the interaction between relationship status and gender equality on perceived social support was very low. The results suggest that gender equality fosters perceived social support, both for single people and for partnered people.
A new approach to characterize cardiac sodium storage by combining fluorescence photometry and magnetic resonance imaging in small animal research
Authors: Christa Martin , Dithmar Franziska , Weinaus Tobias , Kohlhaas Michael , Arias-Loza Anahi-Paula , Hofmann Michelle , Elabyad Ibrahim A. , Gutjahr Fabian T. , Maack Christoph , Bauer Wolfgang R. 
Published: January 2024

AbstractCardiac myocyte sodium (Na+) homoeostasis is pivotal in cardiac diseases and heart failure. Intracellular Na+ ([Na+]i) is an important regulator of excitation–contraction coupling and mitochondrial energetics. In addition, extracellular Na+ ([Na+]e) and its water-free storage trigger collagen cross-linking, myocardial stiffening and impaired cardiac function. Therefore, understanding the allocation of tissue Na+ to intra- and extracellular compartments is crucial in comprehending the pathophysiological processes in cardiac diseases. We extrapolated [Na+]e using a three-compartment model, with tissue Na+ concentration (TSC) measured by in vivo 23Na-MRI, extracellular volume (ECV) data calculated from T1 maps, and [Na+]i measured by in vitro fluorescence microscopy using Na+ binding benzofuran isophthalate (SBFI). To investigate dynamic changes in Na+ compartments, we induced pressure overload (TAC) or myocardial infarction (MI) via LAD ligation in mice. Compared to SHAM mice, TSC was similar after TAC but increased after MI. Both TAC and MI showed significantly higher [Na+]i compared to SHAM (around 130% compared to SHAM). Calculated [Na+]e increased after MI, but not after TAC. Increased TSC after TAC was primarily driven by increased [Na+]i, but the increase after MI by elevations in both [Na+]i and [Na+]e.
Ecological modeling, biogeography, and phenotypic analyses setting the tiger cats’ hyperdimensional niches reveal a new species
Authors: de Oliveira Tadeu G. , Fox-Rosales Lester A. , Ramírez-Fernández José D. , Cepeda-Duque Juan C. , Zug Rebecca , Sanchez-Lalinde Catalina , Oliveira Marcelo J. R. , Marinho Paulo H. D. , Bonilla-Sánchez Alejandra , Marques Mara C. , Cassaro Katia , Moreno Ricardo , Rumiz Damián , Peters Felipe B. , Ortega Josué , Cavalcanti Gitana , Mooring Michael S. , Blankenship Steven R. , Brenes-Mora Esteban , Dias Douglas , Mazim Fábio D. , Eizirik Eduardo , Diehl Jaime L. , Marques Rosane V. , Ribeiro Ana Carolina C. , Cruz Reginaldo A. , Pasa Emanuelle , Meira Lyse P. C. , Pereira Alex , Ferreira Guilherme B. , de Pinho Fernando F. , Sena Liana M. M. , de Morais Vinícius R. , Ribeiro Luiz Micheli , Moura Vitor E. C. , Favarini Marina O. , Leal Karla P. G. , Wagner Paulo G. C. , dos Santos Maurício C. , Sanderson James , Araújo Elienê P. , Rodrigues Flávio H. G. 
Published: January 2024

AbstractRecently, the tiger-cat species complex was split into Leopardus tigrinus and Leopardus guttulus, along with other proposed schemes. We performed a detailed analysis integrating ecological modeling, biogeography, and phenotype of the four originally recognized subspecies—tigrinus, oncilla, pardinoides, guttulus—and presented a new multidimensional niche depiction of the species. Species distribution models used > 1400 records from museums and photographs, all checked for species accuracy. Morphological data were obtained from institutional/personal archives. Spotting patterns were established by integrating museum and photographic/camera-trap records. Principal component analysis showed three clearly distinct groups, with the Central American specimens (oncilla) clustering entirely within those of the Andes, namely the pardinoides group of the cloud forests of the southern Central-American and Andean mountain chains (clouded tiger-cat); the tigrinus group of the savannas of the Guiana Shield and central/northeastern Brazil (savanna tiger-cat); and the guttulus group in the lowland forests of the Atlantic Forest domain (Atlantic Forest tiger-cat). This scheme is supported by recent genetic analyses. All species displayed different spotting patterns, with some significant differences in body measurements/proportions. The new distribution presented alarming reductions from the historic range of − 50.4% to − 68.2%. This multidimensional approach revealed a new species of the elusive and threatened tiger-cat complex.
Reshaping the peripersonal space in virtual reality
Authors: Petrizzo Irene , Mikellidou Kyriaki , Avraam Savvas , Avraamides Marios , Arrighi Roberto 
Published: January 2024

AbstractPeripersonal space (PPS) is defined as the space that lies within reach. Previous research revealed that PPS can be dynamically reshaped with the use of tools extending the arm’s reach. Here we investigated whether PPS reshaping depends on the kind of selected tool and/or the motor routine associated with its use. Participants carried out a visuo-tactile detection task in an immersive VR environment that allowed to measure the PPS size before and after a short period of tools use. In Experiment 1, participants had to pull or push objects towards or away from themselves using a shovel. In Experiment 2, they were required to either hammer or shoot an avatar placed in the Extrapersonal space. We found, for the first time in a VR environment, that a period of pull training was effective in enlarging the PPS, a result that replicates and expands previous findings carried out in real life conditions. However, no significant change in PPS size was achieved for training with other tools and motor routines. Our results suggest that the reshaping of PPS is a complex phenomenon in which the kind of interaction between the agent, the targets and the exploited motor routines all play a critical role.
The clarithromycin-binding proteins NIPSNAP1 and 2 regulate cytokine production through mitochondrial quality control
Authors: Yamamoto Soh , Ogasawara Noriko , Mitsuhashi Yukari , Takano Kenichi , Yokota Shin-ichi 
Published: January 2024

AbstractThe mechanism underlying the anti-inflammatory effect of macrolide antibiotics, such as clarithromycin (CAM), remains to be clarified. The CAM-binding proteins 4-nitrophenylphosphatase domain and non-neuronal synaptosomal associated protein 25 (SNAP25)-like protein homolog (NIPSNAP) 1 and 2 are involved in the immune response and mitochondrial homeostasis. However, the axis between CAM-NIPSNAP-mitochondria and Toll-like receptor (TLR) and their molecular mechanisms remain unknown. In this study, we sought to elucidate the relationship between mitochondrial homeostasis mediated by NIPSNAP1 and 2 and the immunomodulatory effect of CAM. NIPSNAP1 or 2 knockdown (KD) by RNA interference impaired TLR4-mediated interleukin-8 (IL-8) production. Similar impairment was observed upon treatment with mitochondrial function inhibitors. However, IL-8 secretion was not impaired in NIPSNAP1 and 2 individual knockout (KO) and double KO (DKO) cells. Moreover, the oxygen consumption rate (OCR) in mitochondria measured using a flex analyzer was significantly reduced in NIPSNAP1 or 2 KD cells, but not in DKO cells. CAM also dose-dependently reduced the OCR. These results indicate that CAM suppresses the IL-8 production via the mitochondrial quality control regulated by temporary functional inhibition of NIPSNAP1 and 2. Our findings provide new insight into the mechanisms underlying cytokine production, including the TLR-mitochondria axis, and the immunomodulatory effects of macrolides.
Exploring the genetic factors behind the discrepancy in resistance to bovine tuberculosis between African zebu cattle and European taurine cattle
Authors: Lee SangJung , Clémentine Charton , Kim Heebal 
Published: January 2024

AbstractCaused by the pathogenic agent Mycobacterium bovis, bovine tuberculosis (bTB) is a major concern in cattle breeding due to both its zoonotic potential and economic impact. Greater resistance to this disease has been reported in certain African zebu breeds compared to European taurine breeds. However the genetic basis for the lower susceptibility to bTB infection observed in zebu cattle remains poorly explored. This study was conducted on whole genome sequencing data of three bTB infection-resistant African zebu breeds and two bTB infection-susceptible taurine breeds to decipher the genetic background. A set of four selection signature statistics based on linkage disequilibrium, site frequency spectrum, and population differentiation were used on SNPs whereas between population variance based VST and t-test were used on CNVs. As a complement, genes from previous literature reported as candidate genes for bTB resistance were also inspected to identify genetic variations. Interestingly, the resulting nine candidate genes had deleterious missense variants (SHC3, IFNGR1, TLR2, TLR6, IL1A, LRRK2, EP300 and IRAK4) or a CNV difference (CD48) segregating between the groups. The genes found in the study play a role in immune pathways activated during Mycobacterium infection, contributing to the proliferation of immune cells and the granuloma formation, ultimately modulating the outcome of the infectious event. In particular, a deleterious variant in the LRRK2 gene, whose deficiency has been linked to improved prognosis upon tuberculosis infection, was found in the bTB infection-resistant zebu breeds. Therefore, these genes constitute credible candidates in explaining the discrepancy in Mycobacterium bovis infection susceptibility among different breed.