bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extracellular circular RNA profiles in plasma and urine of healthy, male college athletes
Authors: Hutchins Elizabeth , Reiman Rebecca , Winarta Joseph , Beecroft Taylor , Richholt Ryan , De Both Matt , Shahbander Khalouk , Carlson Elizabeth , Janss Alex , Siniard Ashley , Balak Chris , Bruhns Ryan , Whitsett Timothy G. , McCoy Roger , Anastasi Matthew , Allen April , Churas Brian , Huentelman Matthew , Van Keuren-Jensen Kendall 
Published: October 2021

AbstractCircular RNA (circRNA) are a recently discovered class of RNA characterized by a covalently-bonded back-splice junction. As circRNAs are inherently more stable than other RNA species, they may be detected extracellularly in peripheral biofluids and provide novel biomarkers. While circRNA have been identified previously in peripheral biofluids, there are few datasets for circRNA junctions from healthy controls. We collected 134 plasma and 114 urine samples from 54 healthy, male college athlete volunteers, and used RNASeq to determine circRNA content. The intersection of six bioinformatic tools identified 965 high-confidence, characteristic circRNA junctions in plasma and 72 in urine. Highly-expressed circRNA junctions were validated by qRT-PCR. Longitudinal samples were collected from a subset, demonstrating circRNA expression was stable over time. Lastly, the ratio of circular to linear transcripts was higher in plasma than urine. This study provides a valuable resource for characterization of circRNA in plasma and urine from healthy volunteers, one that can be developed and reassessed as researchers probe the circRNA contents of biofluids across physiological changes and disease states.
Characterization of hormone-producing cell types in the teleost pituitary gland using single-cell RNA-seq
Authors: Siddique Khadeeja , Ager-Wick Eirill , Fontaine Romain , Weltzien Finn-Arne , Henkel Christiaan V. 
Published: October 2021

AbstractThe pituitary is the vertebrate endocrine gland responsible for the production and secretion of several essential peptide hormones. These, in turn, control many aspects of an animal’s physiology and development, including growth, reproduction, homeostasis, metabolism, and stress responses. In teleost fish, each hormone is presumably produced by a specific cell type. However, key details on the regulation of, and communication between these cell types remain to be resolved. We have therefore used single-cell sequencing to generate gene expression profiles for 2592 and 3804 individual cells from the pituitaries of female and male adult medaka (Oryzias latipes), respectively. Based on expression profile clustering, we define 15 and 16 distinct cell types in the female and male pituitary, respectively, of which ten are involved in the production of a single peptide hormone. Collectively, our data provide a high-quality reference for studies on pituitary biology and the regulation of hormone production, both in fish and in vertebrates in general.
APExpose_DE, an air quality exposure dataset for Germany 2010–2019
Authors: Caseiro Alexandre , von Schneidemesser Erika 
Published: October 2021

AbstractExposure to poor air quality is considered a major influence on the occurrence of cardiovascular and respiratory diseases. Air pollution has also been linked to the severity of the effects of epidemics such as COVID-19 caused by the SARS-CoV-2 virus. Epidemiological studies require datasets of the long-term exposure to air pollution. We present the APExpose_DE dataset, a long-term (2010–2019) dataset providing ambient air pollution metrics at yearly time resolution for NO2, NO, O3, PM10 and PM2.5 at the NUTS-3 spatial resolution level for Germany (corresponding to the Landkreis or Kreisfreie Stadt in Germany, 402 in total).
Identifying critical higher-order interactions in complex networks
Authors: Aktas Mehmet Emin , Nguyen Thu , Jawaid Sidra , Riza Rakin , Akbas Esra 
Published: October 2021

AbstractDiffusion on networks is an important concept in network science observed in many situations such as information spreading and rumor controlling in social networks, disease contagion between individuals, and cascading failures in power grids. The critical interactions in networks play critical roles in diffusion and primarily affect network structure and functions. While interactions can occur between two nodes as pairwise interactions, i.e., edges, they can also occur between three or more nodes, which are described as higher-order interactions. This report presents a novel method to identify critical higher-order interactions in complex networks. We propose two new Laplacians to generalize standard graph centrality measures for higher-order interactions. We then compare the performances of the generalized centrality measures using the size of giant component and the Susceptible-Infected-Recovered (SIR) simulation model to show the effectiveness of using higher-order interactions. We further compare them with the first-order interactions (i.e., edges). Experimental results suggest that higher-order interactions play more critical roles than edges based on both the size of giant component and SIR, and the proposed methods are promising in identifying critical higher-order interactions.
Blood transfusions increase the risk for venous thromboembolism events following total joint arthroplasty
Authors: Shohat Noam , Ludwick Leanne , Goh Graham S. , Sherman Matthew , Paladino Joseph , Parvizi Javad 
Published: October 2021

AbstractThe association between blood transfusions and thromboembolic events (VTE) following total joint arthroplasty (TJA) remains debatable. Using contemporary institutional data, this study aimed to determine whether blood transfusions increase the risk of VTE following primary and revision TJA. This was a single institution, retrospective cohort study. The clinical records of all patients (n = 34,824) undergoing primary and revision TJA between 2009 and 2020 were reviewed. Demographic variables, co-morbidities, type of chemoprophylaxis and intraoperative factors such as use of tranexamic acid were collected. Clinical notes, hospital orders, and discharge summaries were reviewed to determine if a patient received a blood transfusion. Comprehensive queries utilizing keywords for VTE were conducted in clinical notes, physician dictations, and patient-provider phone-call logs. Propensity score matching as well as adjusted mixed models were performed. After adjusting for various confounders, results from regression analysis showed a significant association between allogenic blood transfusions and risk for developing VTE following primary and revision TJA (OR 4.11, 95% CI 2.53–6.69 and OR 2.15, 95% CI 1.12–4.13, respectively). While this strong association remained significant for PE in both primary (p < 0.001) and revision (p < 0.001) matched cohorts, it was no longer statistically significant for DVT (p = 0.802 and p = 0.65, respectively). These findings suggest that the risk of VTE is increased by approximately three-folds when blood transfusions are prescribed. This association was mainly due to higher symptomatic PE events which makes it even more worrisome. Surgeons should be aware of this association, revisit criteria for blood transfusions and use all means available in the perioperative period to optimize the patients and avoid transfusion.
Artifact-free holographic light shaping through moving acousto-optic holograms
Authors: Treptow Dorian , Bola Raúl , Martín-Badosa Estela , Montes-Usategui Mario 
Published: October 2021

AbstractHolographic light modulation is the most efficient method to shape laser light into well-defined patterns and is therefore the means of choice for many intensity demanding applications. During the last two decades, spatial light modulators based on liquid crystals prevailed among several technologies and became the standard tool to shape light holographically. But in the near future, this status might be challenged by acousto-optic deflectors. These devices are well known for their excelling modulation rates and high optical power resilience. But only few scattered precedents exist that demonstrate their holographic capabilities, despite the many interesting properties that they provide. We implemented a holographic acousto-optic light modulation (HALM) system, that is based on displaying holograms on acousto-optic deflectors. We found that this system can eliminate the ubiquitous coherent artifacts that arise in holography through the inherent motion of acousto-optic holograms. That distinguishes our approach from any other holographic modulation technique and allows to reconstruct intensity patterns of the highest fidelity. A mathematical description of this effect is presented and experimentally confirmed by reconstructing images holographically with unprecedented quality. Our results suggest that HALM promotes acousto-optic deflectors from highly specialized devices to full-fledged spatial light modulators, that can compete in a multitude of applications with LC-SLMs. Especially applications that require large optical output powers, high modulation speeds or accurate gray-scale intensity patterns will profit from this technology. We foresee that HALM may play a major role in future laser projectors and displays, structured illumination microscopy, laser material processing and optical trapping.
Soil organic matter is essential for colony growth in subterranean termites
Authors: Mullins Aaron , Chouvenc Thomas , Su Nan-Yao 
Published: October 2021

AbstractIntrinsic dinitrogen (N2) fixation by diazotrophic bacteria in termite hindguts has been considered an important pathway for nitrogen acquisition in termites. However, studies that supported this claim focused on measuring instant N2 fixation rates and failed to address their relationship with termite colony growth and reproduction over time. We here argue that not all wood-feeding termites rely on symbiotic diazotrophic bacteria for colony growth. The present study looks at dietary nitrogen acquisition in a subterranean termite (Rhinotermitidae, Coptotermes). Young termite colonies reared with wood and nitrogen-rich organic soil developed faster, compared to those reared on wood and inorganic sand. More critically, further colony development was arrested if access to organic soil was removed. In addition, no difference of relative nitrogenase expression rates was found when comparing the hindguts of termites reared between the two conditions. We therefore propose that subterranean termite (Rhinotermitidae) colony growth is no longer restricted to metabolically expensive intrinsic N2 fixation, as the relationship between diazotrophic bacteria and subterranean termites may primarily be trophic rather than symbiotic. Such reliance of Rhinotermitidae on soil microbial decomposition activity for optimal colony growth may also have had a critical mechanistic role in the initial emergence of Termitidae.
Therapeutic effects of acylated ghrelin-specific receptor GHS-R1a antagonist in islet transplantation
Authors: Chinen Kiyoshi , Sakata Naoaki , Yoshimatsu Gumpei , Nakamura Masafumi , Kodama Shohta 
Published: October 2021

AbstractIslet transplantation is a type of cellular replacement therapy for severe diabetes that is limited by compromising effect on engrafted islets. Trials aiming to improve the function of transplanted islets have also been challenging. This study attempted to elucidate whether regulation of growth hormone secretagogue receptor-1a (GHS-R1a), one of the ghrelin receptors, improve the therapeutic effects of islet transplantation using [D-Lys3]-GHRP-6 (DLS), a specific GHS-R1a antagonist. The therapeutic effects of DLS were assessed in terms of the expression/production of endocrine genes/proteins, insulin-releasing function under glucose stimulation of mouse islets, and outcomes of syngeneic murine islet transplantation with systemic DLS administration. DLS treatment promoted insulin production and suppressed somatostatin production, suggesting that cancelation of the binding between ghrelin and GHS-R1a on β or δ cells improved insulin expression. DLS also promoted the glucose-dependent insulin-releasing function of β cells. However, the therapeutic effect of DLS in islet transplantation was fractional. In conclusion, the GHS-R1a antagonist showed preferable effects in improving the therapeutic outcomes of islet transplantation, including the promotion of insulin-releasing function.
Listeria monocytogenes sensitivity to antimicrobial treatments depends on cell origin
Authors: Montanari Chiara , Tabanelli Giulia , Barbieri Federica , Mora Diego , Duncan Robin , Gardini Fausto , Arioli Stefania 
Published: October 2021

AbstractIn this study we investigated how cell origin could affect the efficacy of an antimicrobial treatment (mild heating combined with terpenoids) in Listeria monocytogenes Scott A, considering cells from: 1. single colony, 2. glycerol stock, 3. cold adapted culture, and 4. fresh culture in stationary phase. After treatment, culturability on BHI medium and viability assessed by flow cytometry were evaluated. Our results showed that the cell origin significantly impacted viability and culturability of L. monocytogenes towards antimicrobial treatment. The mild heat treatment combined or not with terpenoids mainly affected culturability rather than viability, although the culturability of cells from single colony was less impacted. Therefore, to mimic the worst scenario, these latter were selected to contaminate Gorgonzola rind and roast beef slices and we evaluated the ability of L. monocytogenes cells to recover their culturability (on ALOA agar medium) and to growth on the food matrix stored at 4 °C for 7 days. Our results suggest that only Gorgonzola rind allowed a partial recovery of the culturability of cells previously heated in presence or not of terpens. In conclusion, we found a connection between the cell history and sensitivity toward an antimicrobial treatment, underlying the importance to standardize the experimental procedures (starting from the cells to be used in the assay) in the assessment of cell sensitivity to a specific treatment. Finally, our study clearly indicated that VBNC cells can resuscitate under favorable conditions on a food matrix, becoming a threat for consumer’s health.
Virtual 2D mapping of the viral proteome reveals host-specific modality distribution of molecular weight and isoelectric point
Authors: Mohanta Tapan Kumar , Mishra Awdhesh Kumar , Mohanta Yugal Kishore , Al-Harrasi Ahmed 
Published: October 2021

AbstractA proteome-wide study of the virus kingdom based on 1.713 million protein sequences from 19,128 virus proteomes was conducted to construct an overall proteome map of the virus kingdom. Viral proteomes encode an average of 386.214 amino acids per protein with the variation in the number of protein-coding sequences being host-specific. The proteomes of viruses of fungi hosts (882.464) encoded the greatest number of amino acids, while the viral proteome of bacterial host (210.912) encoded the smallest number of amino acids. Viral proteomes were found to have a host-specific amino acid composition. Leu (8.556%) was the most abundant and Trp (1.274%) the least abundant amino acid in the collective proteome of viruses. Viruses were found to exhibit a host-dependent molecular weight and isoelectric point of encoded proteins. The isoelectric point (pI) of viral proteins was found in the acidic range, having an average pI of 6.89. However, the pI of viral proteins of algal (pI 7.08) and vertebrate (pI 7.09) hosts was in the basic range. The virtual 2D map of the viral proteome from different hosts exhibited host-dependent modalities. The virus proteome from algal hosts and archaea exhibited a bimodal distribution of molecular weight and pI, while the virus proteome of bacterial host exhibited a trimodal distribution, and the virus proteome of fungal, human, land plants, invertebrate, protozoa, and vertebrate hosts exhibited a unimodal distribution.
2 μm passively mode-locked thulium-doped fiber lasers with Ta2AlC-deposited tapered and side-polished fibers
Authors: Ahmad H. , Azri M. F. M. , Ramli R. , Samion M. Z. , Yusoff N. , Lim K. S. 
Published: October 2021

AbstractIn this work, mode-locked thulium-doped fiber lasers operating in the 2 µm wavelength region were demonstrated using tantalum aluminum carbide (Ta2AlC)-based saturable absorbers (SAs) utilizing the evanescent wave interaction. The Ta2AlC MAX Phase was prepared by dissolving the Ta2AlC powder in isopropyl alcohol and then deposited onto three different evanescent field-based devices, which were the tapered fiber, side-polished fiber, and arc-shaped fiber. Flame-brushing and wheel-polishing techniques were used to fabricate the tapered and arc-shaped fibers, respectively, while the side-polished fiber was purchased commercially. All three SA devices generated stable mode-locked pulses at center wavelengths of 1937, 1931, and 1929 nm for the tapered, side-polished, and arc-shaped fibers. The frequency of the mode-locked pulses was 10.73 MHz for the tapered fiber, 9.58 MHz for the side-polished fiber, and 10.16 MHz for the arc-shaped fiber. The measured pulse widths were 1.678, 1.734, and 1.817 ps for each of the three SA devices. The long-term stability of the mode-locked lasers was tested for each configuration over a 2-h duration. The lasers also showed little to no fluctuations in the center wavelengths and the peak optical intensities, demonstrating a reliable, ultrafast laser system.
Digital medicine and the curse of dimensionality
Authors: Berisha Visar , Krantsevich Chelsea , Hahn P. Richard , Hahn Shira , Dasarathy Gautam , Turaga Pavan , Liss Julie 
Published: October 2021

AbstractDigital health data are multimodal and high-dimensional. A patient’s health state can be characterized by a multitude of signals including medical imaging, clinical variables, genome sequencing, conversations between clinicians and patients, and continuous signals from wearables, among others. This high volume, personalized data stream aggregated over patients’ lives has spurred interest in developing new artificial intelligence (AI) models for higher-precision diagnosis, prognosis, and tracking. While the promise of these algorithms is undeniable, their dissemination and adoption have been slow, owing partially to unpredictable AI model performance once deployed in the real world. We posit that one of the rate-limiting factors in developing algorithms that generalize to real-world scenarios is the very attribute that makes the data exciting—their high-dimensional nature. This paper considers how the large number of features in vast digital health data can challenge the development of robust AI models—a phenomenon known as “the curse of dimensionality” in statistical learning theory. We provide an overview of the curse of dimensionality in the context of digital health, demonstrate how it can negatively impact out-of-sample performance, and highlight important considerations for researchers and algorithm designers.
Clinical impact and quality of randomized controlled trials involving interventions evaluating artificial intelligence prediction tools: a systematic review
Authors: Zhou Qian , Chen Zhi-hang , Cao Yi-heng , Peng Sui 
Published: October 2021

AbstractThe evidence of the impact of traditional statistical (TS) and artificial intelligence (AI) tool interventions in clinical practice was limited. This study aimed to investigate the clinical impact and quality of randomized controlled trials (RCTs) involving interventions evaluating TS, machine learning (ML), and deep learning (DL) prediction tools. A systematic review on PubMed was conducted to identify RCTs involving TS/ML/DL tool interventions in the past decade. A total of 65 RCTs from 26,082 records were included. A majority of them had model development studies and generally good performance was achieved. The function of TS and ML tools in the RCTs mainly included assistive treatment decisions, assistive diagnosis, and risk stratification, but DL trials were only conducted for assistive diagnosis. Nearly two-fifths of the trial interventions showed no clinical benefit compared to standard care. Though DL and ML interventions achieved higher rates of positive results than TS in the RCTs, in trials with low risk of bias (17/65) the advantage of DL to TS was reduced while the advantage of ML to TS disappeared. The current applications of DL were not yet fully spread performed in medicine. It is predictable that DL will integrate more complex clinical problems than ML and TS tools in the future. Therefore, rigorous studies are required before the clinical application of these tools.
Climate-assisted persistence of tropical fish vagrants in temperate marine ecosystems
Authors: Gajdzik Laura , DeCarlo Thomas M. , Koziol Adam , Mousavi-Derazmahalleh Mahsa , Coghlan Megan , Power Matthew W. , Bunce Michael , Fairclough David V. , Travers Michael J. , Moore Glenn I. , DiBattista Joseph D. 
Published: October 2021

AbstractRising temperatures and extreme climate events are propelling tropical species into temperate marine ecosystems, but not all species can persist. Here, we used the heatwave-driven expatriation of tropical Black Rabbitfish (Siganus fuscescens) to the temperate environments of Western Australia to assess the ecological and evolutionary mechanisms that may entail their persistence. Population genomic assays for this rabbitfish indicated little genetic differentiation between tropical residents and vagrants to temperate environments due to high migration rates, which were likely enhanced by the marine heatwave. DNA metabarcoding revealed a diverse diet for this species based on phytoplankton and algae, as well as an ability to feed on regional resources, including kelp. Irrespective of future climate scenarios, these macroalgae-consuming vagrants may self-recruit in temperate environments and further expand their geographic range by the year 2100. This expansion may compromise the health of the kelp forests that form Australia’s Great Southern Reef. Overall, our study demonstrates that projected favourable climate conditions, continued large-scale genetic connectivity between populations, and diet versatility are key for tropical range-shifting fish to establish in temperate ecosystems.
Dynamically expressed single ELAV/Hu orthologue elavl2 of bees is required for learning and memory
Authors: Ustaoglu Pinar , Gill Jatinder Kaur , Doubovetzky Nicolas , Haussmann Irmgard U. , Dix Thomas C. , Arnold Roland , Devaud Jean-Marc , Soller Matthias 
Published: October 2021

AbstractChanges in gene expression are a hallmark of learning and memory consolidation. Little is known about how alternative mRNA processing, particularly abundant in neuron-specific genes, contributes to these processes. Prototype RNA binding proteins of the neuronally expressed ELAV/Hu family are candidates for roles in learning and memory, but their capacity to cross-regulate and take over each other’s functions complicate substantiation of such links. Honey beesApis melliferahave only oneelav/Hufamily geneelavl2, that has functionally diversified by increasing alternative splicing including an evolutionary conserved microexon. RNAi knockdown demonstrates that ELAVL2 is required for learning and memory in bees. ELAVL2 is dynamically expressed with altered alternative splicing and subcellular localization in mushroom bodies, but not in other brain regions. Expression and alternative splicing ofelavl2change during memory consolidation illustrating an alternative mRNA processing program as part of a local gene expression response underlying memory consolidation.