bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep mining reveals the diversity of endogenous viral elements in vertebrate genomes
Authors: Nino Barreat Jose Gabriel , Katzourakis Aris 
Published: October 2024

AbstractIntegration of viruses into host genomes can give rise to endogenous viral elements (EVEs), which provide insights into viral diversity, host range and evolution. A systematic search for EVEs is becoming computationally challenging given the available genomic data. We used a cloud-computing approach to perform a comprehensive search for EVEs in the kingdoms Shotokuvirae and Orthornavirae across vertebrates. We identified 2,040 EVEs in 295 vertebrate genomes and provide evidence for EVEs belonging to the families Chuviridae, Paramyxoviridae, Nairoviridae and Benyviridae. We also find an EVE from the Hepacivirus genus of flaviviruses with orthology across murine rodents. In addition, our analyses revealed that reptarenaviruses and filoviruses probably acquired their glycoprotein ectodomains three times independently from retroviral elements. Taken together, these findings encourage the addition of 4 virus families and the Hepacivirus genus to the growing virus fossil record of vertebrates, providing key insights into their natural history and evolution.
Biochemical and biological studies of irradiated and non-irradiated extracts of Solanum aculeastrum Dunal fruit
Authors: Amer Asmaa A. , Soliman Ahmed A. F. , Alshareef Walaa A. , Mandour Yasmine M. , Abdelrahman Mohamad T. 
Published: October 2024

AbstractThis study explores the impact of γ-irradiation on ethanolic extracts of Solanum aculeastrum Dunal. The anti-cancer and antimicrobial properties were investigated. The obtained results revealed that total phenol (TP) and total flavonoid (TF) of total ethanol extract (100%) (FTE) were higher than 70% ethanol extract (SE), and these contents increased after gamma radiation with 5 kGy. The results of minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of the Solanum aculeastrum extracts suggested that FTE and 5 kGy-irradiated FTE can be used to control and prevent skin infections caused by MRSA and endocarditis, urinary tract infections, and prostatitis caused by Enterococcus faecalis. The FTE sample irradiated at 5 kGy showed cytotoxicity for A431 and Hct-116 cell lines similar to the control sample and higher than the toxicity revealed by the samples irradiated at 10 kGy. In normal cells (Bj-1), the toxicity was decreased after irradiation (IC50 = 31 μg/ml) compared to the non-irradiated extract (IC50 = 26.1 μg/ml). Molecular docking suggested Sortase A to play a role in chlorogenic acid antibacterial activity towards Staphylococcus aureus. In conclusion, γ-irradiation can be used to enhance the phytoconstituents of Solanum aculeastrum fruit extracts and, consequently, its biological properties.
Molecular identification of hyaluronate lyase, not hyaluronidase, as an intrinsic hyaluronan-degrading enzyme in Clostridium perfringens strain ATCC 13124
Authors: Kumon Tomoya , Oiki Sayoko , Hashimoto Wataru 
Published: October 2024

AbstractClostridium perfringens, an opportunistic pathogen, produces mu-toxin hyaluronidases including endo-β-N-acetylglucosaminidases (Nags) as a virulence invasion factor. To clarify an intrinsic factor for degradation of host extracellular hyaluronan, we focused on hyaluronate lyase (HysA), distinct from endo-β-N-acetylglucosaminidases. C. perfringens strain ATCC 13124 was found to assimilate host-derived extracellular mucosubstances, hyaluronan and mucin, which induced expression of the hyaluronan-related genetic cluster, including hyaluronate lyase gene (hysA), but repressed endo-β-N-acetylglucosaminidase genes. This genetic cluster is conserved in some strains of C. perfringens. The recombinant strain ATCC 13124 hyaluronate lyase HysA showed an hyaluronan-degrading activity through β-elimination reaction. The hyaluronan-degrading enzyme in the culture supernatant of strain ATCC 13124 exhibited the lyase activity and was identical to the recombinant hyaluronate lyase on the native-PAGE gel, followed by activity straining. These results demonstrated that the intrinsic hyaluronan-degrading enzyme of C. perfringens strain ATCC 13124 is hyaluronate lyase HysA, but not hyaluronidases NagH, NagJ, and NagK.
Thioflavin-T: application as a neuronal body and nucleolar stain and the blue light photo enhancement effect
Authors: Min Jin-Hong , Sarlus Heela , Oasa Sho , Harris Robert A. 
Published: October 2024

Abstract
Thioflavin-T (THT) is a common and indispensable tool for the study of amyloid pathologies and protein aggregation, both in vitro and for histological samples. In this study we expand the use of THT beyond its canonical usage for staining amyloid plaques and demonstrate its novel use as an easy and rapid stain comparable to fluorescent Nissl staining, allowing for clear discernment of neuronal cell bodies and also nucleoli in fixed tissue and live cells. We believe that this is of value for any lab that studies central nervous system (CNS) tissues. Furthermore, we show that THT could potentially be used as a an alternative to the use of fluorescent reporters or other more costly RNA binding compounds in the study of nucleolar dynamics owing to its ability to clearly stain nucleoli in live cells. We also discovered the previously unreported effect of blue light exposure on the photo enhancement of THT excited by a 488 nm laser in stained tissue sample and how to avoid complications arising from this effect. Finally, we provide a simple protocol that can be easily adjusted either for using THT as a neuronal cell body and nucleoli stain, compatible with antibody based staining methods tested up to 4 fluorophores, or alternatively by using an additional washing step the protocol may be used for amyloid plaque detection in fixed brain tissue.
Heterochronous mitogenomes shed light on the Holocene history of the Scandinavian brown bear
Authors: Feinauer Isabelle Sofie , Lord Edana , von Seth Johanna , Xenikoudakis Georgios , Ersmark Erik , Dalén Love , Meleg Ioana-Nicoleta 
Published: October 2024

AbstractFollowing glacial retreat after the last ice age, brown bears (Ursus arctos) recolonised Scandinavia. Previous research based on mitochondrial markers suggests that bears recolonised from both the north and the south, with a contact zone in central Scandinavia. More recently, the Scandinavian brown bear was subjected to a strong population decline with only ca. 130 remaining individuals, due to intense human persecution approximately 100 years ago. Here, we analyse 41 ancient, historical, and modern mitochondrial genomes, to examine the number of female lineages involved in the postglacial recolonisation event and temporal changes in the Scandinavian brown bears’ mitochondrial genetic diversity. Our results support the bi-directional recolonisation hypothesis, indicating multiple mitochondrial lineages from clade 1a possibly followed a southern route, while only a single lineage from clade 3a appears to have followed a northern route. Furthermore, we found that the recent bottleneck had a strong impact on the southern subpopulation, resulting in only one remaining haplotype in the contemporary brown bears. For the northern subpopulation, the impact was moderate, and most haplotypes were retained throughout the bottleneck. By exploring the postglacial recolonisation and recent population pressures, our study enhances understanding of how these factors have influenced the genetic diversity of Scandinavian brown bears.
Anisotropy of radiation-induced defects in Yb-implanted β-Ga2O3
Authors: Ratajczak Renata , Sarwar Mahwish , Kalita Damian , Jozwik Przemysław , Mieszczynski Cyprian , Matulewicz Joanna , Wilczopolska Magdalena , Wozniak Wojciech , Kentsch Ulrich , Heller René , Guziewicz Elzbieta 
Published: October 2024

AbstractRE-doped β-Ga2O3 seems attractive for future high-power LEDs operating in high irradiation environments. In this work, we pay special attention to the issue of radiation-induced defect anisotropy in β-Ga2O3, which is crucial for device manufacturing. Using the RBS/c technique, we have carefully studied the structural changes caused by implantation and post-implantation annealing in two of the most commonly used crystallographic orientations of β-Ga2O3, namely the (-201) and (010). The analysis was supported by advanced computer simulations using the McChasy code. Our studies reveal a strong dependence of the structural damage induced by Yb-ion implantation on the crystal orientation, with a significantly higher level of extended defects observed in the (-201) direction than for the (010). In contrast, the concentration and behavior of simple defects seem similar for both oriented crystals, although their evolution suggests the co-existence of two different types of defects in the implanted zone with their different sensitivity to both, radiation and annealing. It has also been found that Yb ions mostly occupy the interstitial positions in β-Ga2O3 crystals that remain unchanged after annealing. The location is independent of the crystal orientations. We believe that these studies noticeably extend the knowledge of the radiation-induced defect structure, because they dispel doubts about the differences in the damage level depending on crystal orientation, and are important for further practical applications.
The spatial overlap between left atrial epicardial adipose tissue and fibrosis is not associated to clinical stage of atrial fibrillation
Authors: Skoda Iulia , Henningsson Markus , Karlsson Lars O. , Carlhäll Carl-Johan 
Published: October 2024

AbstractLeft atrial (LA) epicardial adipose tissue (EAT) and wall fibrosis are both proven to contribute to the pathogenesis and progression of atrial fibrillation (AF). The theory of LA wall fibrosis induction by local EAT infiltration, paracrine secretions, and activation of the inflammatory process is strongly advocated, but the imaging evidence for anatomical proximity of the two tissue types and its association to AF stage is lacking. Accordingly, the aim of the study was to analyse the spatial overlap between LA EAT and adjacent wall fibrosis using 3D Dixon water-fat separated late gadolinium enhancement (LGE-Dixon) MRI and correlate the findings with the clinical AF stage. Forty-two AF patients (18 paroxysmal, 10 persistent, and 14 permanent) and nine non-AF patients were scanned. The permanent AF patients had greater LA volume and EAT than the paroxysmal group. The LA fibrosis area showed the same trend. The LA EAT-fibrosis overlap area was small and there was no significant difference between the three AF stages. There was no significant relationship between LA EAT- fibrosis overlap area and AF type. The findings shed light on the complex interplay between LA fibrosis and EAT during the progression from paroxysmal to permanent AF.
Plaid masking explained with input-dependent dendritic nonlinearities
Authors: Bertalmío Marcelo , Durán Vizcaíno Alexia , Malo Jesús , Wichmann Felix A. 
Published: October 2024

AbstractA serious obstacle for understanding early spatial vision comes from the failure of the so-called standard model (SM) to predict the perception of plaid masking. But the SM originated from a major oversimplification of single neuron computations, ignoring fundamental properties of dendrites. Here we show that a spatial vision model including computations mimicking the input-dependent nature of dendritic nonlinearities, i.e. including nonlinear neural summation, has the potential to explain plaid masking data.
Functional bias of contractile control in mouse resistance arteries
Authors: Haghbin Nadia , Richter David M. , Kharche Sanjay , Kim Michelle S. M. , Welsh Donald G. 
Published: October 2024

AbstractConstrictor agonists set arterial tone through two coupling processes, one tied to (electromechanical), the other independent (pharmacomechanical) of, membrane potential (VM). This dual arrangement raises an intriguing question: is the contribution of each mechanism (1) fixed and proportionate, or (2) variable and functionally biased. Examination began in mouse mesenteric arteries with a vasomotor assessment to a classic Gq/11 (phenylephrine) or Gq/11/G12/13 (U46619) agonist, in the absence and presence of nifedipine, to separate among the two coupling mechanisms. Each constrictor elicited a concentration response curve that was attenuated and rightward shifted by nifedipine, findings consistent with functional bias. Electromechanical coupling preceded pharmacomechanical, the latter’s importance rising with agonist concentration. In this regard, ensuing contractile and phosphorylation (CPI-17 & MYPT1 (T-855 & T-697)) measures revealed phenylephrine-induced pharmacomechanical coupling was tied to protein kinase C (PKC) activity, while that enabled by U46619 to PKC and Rho-kinase. A complete switch to pharmacomechanical coupling arose when agonist superfusion was replaced by pipet application to a small portion of artery. This switch was predicted, a priori, by a computer model of electromechanical control and supported by additional measures of VM and cytosolic Ca2+. We conclude that the coupling mechanisms driving agonist-induced constriction are variable and functionally biased, their relative importance set in accordance with agonist concentration and manner of application. These findings have important implications to hemodynamic control in health and disease, including hypertension and arterial vasospasm.
Phylogenetic analysis of selected species of Asteraceae on the basis of RPS 11 Gene
Authors: Zahra Syeda Anber , Iqbal Javed , Abbasi Banzeer Ahsan , Kanwal Sobia , Alwahibi Mona S. , Elshikh Mohamed S. , Rizwan Muhammad , Iqbal Rashid , Mahmood Tariq 
Published: October 2024

AbstractThe Asteraceae family is a prominent group of flowering plants found across the globe, with the exception of Antarctica. The Asteraceae family is a largest flowering family pivotal group in plant evolution and diversification. Despite its importance, the genetic diversity within this family remains understudied. We focused on the rps-11 gene, a chloroplast marker previously utilized in phylogenetic studies, to investigate its potential in resolving Asteraceae relationships. The focus was on examining genetic diversity within sixteen specifically chosen species from the Asteraceae family. This assessment was based on an analysis of a chloroplast gene responsible for encoding the ribosomal protein of the smaller subunit 11 (rps 11). Nearly 417 bp of rps 11 gene was amplified, sequenced, computationally translated into amino acid sequence and the data was used for phylogenetic analysis as well as for rps 11 protein structure predictions. Based on nucleotide and amino acid sequences phylograms were drawn with the help of Molecular Evolutionary Genetic Analysis (MEGA 6), which exhibited clear genetic relationship among species under investigation. The observed genetic distance was 0.02 for Maximum likelihood tree based on nucleotide sequences whereas it was 0.05 for phylogram based on amino acid sequences. These values revealed that amino acid-based tree has demonstrated greater diversity among selected species in comparison to nucleotides-based tree. On the basis of pair wise distance calculations, genetic divergence values were found within the range of 0.015–0.309. Moreover, 3D protein modeling for rps 11 protein of sixteen selected species was also carried out by iterative threading assembly refinement (I-Tasser) software. The models exhibiting the highest C-score were picked with satisfactory plot statistics (> 90%) and structurally validated by PROCHECK. Furthermore, Ramachandran plots displayed that the rps 11 protein structures of Tagetes minuta, Xanthium strumarium, Lactuca sativa and Chrysanthemum indicum have best feature models with > 90% of residues in the allowed region and ≤ 2% in the disallowed region. The research is not enough to stand alone to validate the viability of the rps11 gene as a prospective contender for phylogenetic analysis. İn future we will focus on the maximum genetic diversity theory for phylogenetic analysis of this family.
Adaptive control of magnetic levitation system based on fuzzy inversion
Authors: Jastrzębski Marcin , Kabziński Jacek 
Published: October 2024

AbstractA novel adaptive tracking controller for magnetic levitation systems (MLS) is developed. The controller is based on a special adaptive control scheme incorporating fuzzy model of electromagnetic acceleration enabling fast and accurate fuzzy inversion. The controller ensures accurate tracking of any smooth desired position signal, despite unknown MLS parameters. The closed-loop system stability, in the sense of uniform ultimate boundedness (UUB) of error trajectories, is proved using Lyapunov approach. The closed-loop system performance is investigated during numerical experiments. Finally the proposed controller is verified by successful implementation on a DSP board controlling a typical magnetic levitation ball system. Performed tests and experiments demonstrate that the proposed control technique is robust against discretization and unknown MLS model parameters, provides high tracking accuracy, is easily implementable, and simple to tune.
Ecological implications of row width and cultivar selection on rice (Oryza sativa) and barnyardgrass (Echinochloa crus-galli)
Authors: Reed Noah H. , Butts Thomas R. , Norsworthy Jason K. , Hardke Jarrod T. , Barber L. Tom , Bond Jason A. , Bowman Hunter D. , Bateman Nick R. , Poncet Aurelie M. , Kouame Koffi B. J. 
Published: October 2024

AbstractRice (Oryza sativa L.) producers in the Mid-south are experiencing difficulties with herbicide-resistant weeds such as barnyardgrass [Echinochloa crus-galli (L.) P. Beauv.]. As a result, methods that can alter E. crus-galli ecology are needed. This research evaluated the ecological implications of rice cultivar and row widths on crop and E. crus-galli growth. Overall, for E. crus-galli, as the row width increased, greater density, panicle counts, and seed production occurred. Echinochloa crus-galli density was 120% greater in a 38-cm row width than the 13-cm row width at the preflood rice stage. Reduced early-season rice canopy coverage in the wider row widths allowed for increased E. crus-galli densities. At the preharvest stage, E. crus-galli panicle counts were similar for the 13- and 19-cm rows. Row width did not affect rice yield, indicating wider row widths could be feasible agronomically, but additional weed management efforts would be needed because greater ecological advantages were obtained in narrower rows. Less E. crus-galli seed production occurred in competition with hybrid cultivars compared to inbred cultivars. Overall, the standard row width (19-cm) and hybrid cultivars would provide the greatest ecological advantage over E. crus-galli.
Nonlinear changes in urban heat island intensity, urban breeze intensity, and urban air pollutant concentration with roof albedo
Authors: Park Kyeongjoo , Baik Jong-Jin 
Published: October 2024

AbstractThis study systematically examines how the urban heat island (UHI) and urban breeze circulation (UBC) respond to an increase in roof albedo (αr) and its influence on urban air pollutant dispersion. For this, idealized ensemble simulations are performed using the Weather Research and Forecasting (WRF) model. The increase in αr from 0.20 to 0.65 decreases the UHI intensity, UBC intensity, and urban planetary boundary layer (PBL) height in the daytime (from 1200 to 1700 LST) by 47%, 36%, and 6%, respectively. As both UBC intensity and urban PBL height decrease, the daytime urban near-surface passive tracer concentration increases by 115%. The daytime UHI intensity, UBC intensity, and urban tracer concentration nonlinearly change with αr: For 0.10 ≤ αr < 0.80, the rates of changes in the UHI intensity, UBC intensity, and urban tracer concentration with αr overall increase as αr increases. For αr ≥ 0.80, the daytime roof surface temperature is notably lower than the daytime urban near-surface air temperature, the UHI intensity, UBC intensity, and urban tracer concentration very slightly changing with αr. This study provides insights into the associations between changes in roof surface temperature and roof surface energy fluxes with αr and those in UHI intensity.
Multifaceted effects of variable biotic interactions on population stability in complex interaction webs
Authors: Hashimoto Koya , Hayasaka Daisuke , Eguchi Yuji , Seko Yugo , Cai Ji , Suzuki Kenta , Goka Koichi , Kadoya Taku 
Published: October 2024

AbstractRecent studies have revealed that biotic interactions in ecological communities vary over time, possibly mediating community responses to anthropogenic disturbances. This study investigated the heterogeneity of such variability within a real community and its impact on population stability in the face of pesticide application, particularly focusing on density-dependence of the interaction effect. Using outdoor mesocosms with a freshwater community, we found considerable heterogeneity in density-dependent interaction variability among links in the same community. This variability mediated the stability of recipient populations, with negative density-dependent interaction variability stabilizing whereas positive density-dependence and density-independent interaction variability destabilizing populations. Unexpectedly, the mean interaction strength, which is typically considered crucial for stability, had no significant effect, suggesting that how organisms interact on average is insufficient to predict the ecological impacts of pesticides. Our findings emphasize the multifaceted role of interaction variability in predicting the ecological consequences of anthropogenic disturbances such as pesticide application.
A click-based electrocorticographic brain-computer interface enables long-term high-performance switch scan spelling
Authors: Candrea Daniel N. , Shah Samyak , Luo Shiyu , Angrick Miguel , Rabbani Qinwan , Coogan Christopher , Milsap Griffin W. , Nathan Kevin C. , Wester Brock A. , Anderson William S. , Rosenblatt Kathryn R. , Uchil Alpa , Clawson Lora , Maragakis Nicholas J. , Vansteensel Mariska J. , Tenore Francesco V. , Ramsey Nicolas F. , Fifer Matthew S. , Crone Nathan E. 
Published: October 2024

Abstract
Background
Brain-computer interfaces (BCIs) can restore communication for movement- and/or speech-impaired individuals by enabling neural control of computer typing applications. Single command click detectors provide a basic yet highly functional capability.

Methods
We sought to test the performance and long-term stability of click decoding using a chronically implanted high density electrocorticographic (ECoG) BCI with coverage of the sensorimotor cortex in a human clinical trial participant (ClinicalTrials.gov, NCT03567213) with amyotrophic lateral sclerosis. We trained the participant’s click detector using a small amount of training data (<44 min across 4 days) collected up to 21 days prior to BCI use, and then tested it over a period of 90 days without any retraining or updating.

Results
Using a click detector to navigate a switch scanning speller interface, the study participant can maintain a median spelling rate of 10.2 characters per min. Though a transient reduction in signal power modulation can interrupt usage of a fixed model, a new click detector can achieve comparable performance despite being trained with even less data (<15 min, within 1 day).

Conclusions
These results demonstrate that a click detector can be trained with a small ECoG dataset while retaining robust performance for extended periods, providing functional text-based communication to BCI users.
Stability of [10–12]cycloparaphenylene complexes with pristine fullerenes C76,78,84 and endohedral metallofullerenes M3N@C78,80
Authors: Freiberger Markus , Stasyuk Olga A. , Pérez-Ojeda M. Eugenia , Echegoyen Luis A. , Solà Miquel , Drewello Thomas 
Published: October 2024

The stability and charge distributions of noncovalent complexes of [10–12]CPP with the pristine fullerenes C76/78/84 and the endohedral metallofullerenes Sc3N@D3h-C78, Sc3N@D5h-C80 and M3N@Ih-C80 (M = Sc, Y, Lu, Gd) are studied in the gas phase.