bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 genomic surveillance in Rondônia, Brazilian Western Amazon
Authors: Botelho-Souza Luan Felipo , Nogueira-Lima Felipe Souza , Roca Tárcio Peixoto , Naveca Felipe Gomes , de Oliveria dos Santos Alcione , Maia Adriana Cristina Salvador , da Silva Cicileia Correia , de Melo Mendonça Aline Linhares Ferreira , Lugtenburg Celina Aparecida Bertoni , Azzi Camila Flávia Gomes , Fontes Juliana Loca Furtado , Cavalcante Suelen , de Cássia Pontello Rampazzo Rita , Santos Caio Henrique Nemeth , Di Sabatino Guimarães Alice Paula , Máximo Fernando Rodrigues , Villalobos-Salcedo Juan Miguel , Vieira Deusilene Souza 
Published: February 2021

AbstractSARS-CoV-2 has spread rapidly around the world, with Brazil currently considered an epicenter of the pandemic. The Northern region has the second highest incidence coefficient, as well as the third highest mortality rate in the country. This study aimed to investigate information about the evolutionary history of epidemic spread and genetic aspects of strains isolated on the Western Amazon, in the State of Rondônia, Brazil. It was possible to detect a total of 22 mutations. Some of these alterations may possibly be related to effects on transmissibility, the fidelity of RNA replication, the ability of cancer patients to respond to infection, beyond a mutation that emerged after the introduction of SARS-CoV-2 in Rondônia. At least two events of introduction were detected, corresponding to the B.1 and B.1.1 European lineages. An introduction was observed possibly through Argentina, where strains originated that circulated in the Minas Gerais and Ceará Brazilian states, prior to Rondônia (B.1.), as well as through the Minas Gerais state and the Federal District, which gave rise to strains that spread to Rondônia, from the capital to more rural parts of the state (B.1.1.). The findings show the need to monitor the genetic epidemiology of COVID-19, in order to surveil the virus’s evolution, dispersion and diversity.
Systematic competition between strain and electric field stimuli in tuning EELS of phosphorene
Authors: Yarmohammadi Mohsen , Hoi Bui Dinh , Phuong Le Thi Thu 
Published: February 2021

AbstractThe strongly anisotropic properties of phosphorene makes it an attractive material for applications in deciding the specific direction for different purposes. Here we have particularly reported the competition between strain and electric field stimuli in evaluating the band gap and electron energy loss spectrum (EELS) of single-layer black phosphorus using the tight-binding method and the Kubo conductivity. We construct possible configurations for this competition and evaluate the interband optical excitations considering the corresponding band gap variations. The band gap increases with the individual electric field, while it increases (decreases) with tensile (compressive) uniaxial in-plane strain. Contrary to the in-plane strains, the uniaxial out-of-plane strain shows a critical strain at which the system suffers from a phase transition. Furthermore, the presence of these stimuli simultaneously results in an extraordinary band gap engineering. Based on the EELS response in the electromagnetic spectrum, the armchair (zigzag) direction is classified into the infrared and visible (ultraviolet) region. We report that the electric field gives rise to the blue shift in the interband optical transitions along the armchair direction, while the compressive/tensile (tensile/compressive) in-plane/out-of-plane strain provides a red (blue) shift. Moreover, we observe an inverse behavior of EELS response to the individual and combined effects of electric field and strains compared to the band gap behavior except at critical out-of-plane strain for which the physical theory of interband excitation is simply violated. Our results provide a new perspective on the applicability of phosphorene in stimulated optical applications.
Effectiveness of e-Health cardiac rehabilitation program on quality of life associated with symptoms of anxiety and depression in moderate-risk patients
Authors: Bravo-Escobar Raquel , González-Represas Alicia , Gómez-González Adela María , Heredia-Torres Ángela 
Published: February 2021

AbstractExploring new models of medical care requires evaluating the impact of new care strategies not only on physiological parameters but also on the quality of life of the patient. On the other hand the presence of anxiety together with depression requires further consideration when planning appropriate management strategies. The aim of this study was to examine the effectiveness of a home-based cardiac rehabilitation program incorporating an e-Health technology on health-related quality of life associated with symptoms of anxiety and depression in moderate-risk patients. A multicenter, randomized controlled clinical trial was designed to compare a traditional hospital based cardiac rehabilitation program (n = 38, 35 male) with a mixed home surveillance program where patients exercised at home with a remote electrocardiographic monitoring device (n = 33, 31 male). The Short Form-36 (SF-36) Health Survey and the Goldberg questionnaire were used to evaluate quality of life and the presence of symptoms of anxiety and depression respectively. The results of this study show that the type of cardiac rehabilitation program did not influence the improvement in quality of life (p = 0.854), but the presence of symptoms of anxiety and depression did (p = 0.001). Although both programs achieved a decrease in anxiety and depression symptoms and improved functional capacity (p ≤ 0.001), a significant interaction effect was found between the group with or without anxiety and depression symptoms and the type of program in the bodily pain dimension (p = 0.021). Trial registration: Retrospectively registered NCT02796404 (10/06/2016) in clinialtrials.gov.
A small-molecular inhibitor against Proteus mirabilis urease to treat catheter-associated urinary tract infections
Authors: Milo Scarlet , Heylen Rachel A. , Glancy John , Williams George T. , Patenall Bethany L. , Hathaway Hollie J. , Thet Naing T. , Allinson Sarah L. , Laabei Maisem , Jenkins A. Toby A. 
Published: February 2021

AbstractInfection and blockage of indwelling urinary catheters is significant owing to its high incidence rate and severe medical consequences. Bacterial enzymes are employed as targets for small molecular intervention in human bacterial infections. Urease is a metalloenzyme known to play a crucial role in the pathogenesis and virulence of catheter-associated Proteus mirabilis infection. Targeting urease as a therapeutic candidate facilitates the disarming of bacterial virulence without affecting bacterial fitness, thereby limiting the selective pressure placed on the invading population and lowering the rate at which it will acquire resistance. We describe the design, synthesis, and in vitro evaluation of the small molecular enzyme inhibitor 2-mercaptoacetamide (2-MA), which can prevent encrustation and blockage of urinary catheters in a physiologically representative in vitro model of the catheterized urinary tract. 2-MA is a structural analogue of urea, showing promising competitive activity against urease. In silico docking experiments demonstrated 2-MA’s competitive inhibition, whilst further quantum level modelling suggests two possible binding mechanisms.
Preservation of epoxyeicosatrienoic acid bioavailability prevents renal allograft dysfunction and cardiovascular alterations in kidney transplant recipients
Authors: Duflot Thomas , Laurent Charlotte , Soudey Anne , Fonrose Xavier , Hamzaoui Mouad , Iacob Michèle , Bertrand Dominique , Favre Julie , Etienne Isabelle , Roche Clothilde , Coquerel David , Le Besnerais Maëlle , Louhichi Safa , Tarlet Tracy , Li Dongyang , Brunel Valéry , Morisseau Christophe , Richard Vincent , Joannidès Robinson , Stanke-Labesque Françoise , Lamoureux Fabien , Guerrot Dominique , Bellien Jérémy 
Published: February 2021

AbstractThis study addressed the hypothesis that epoxyeicosatrienoic acids (EETs) synthesized by CYP450 and catabolized by soluble epoxide hydrolase (sEH) are involved in the maintenance of renal allograft function, either directly or through modulation of cardiovascular function. The impact of single nucleotide polymorphisms (SNPs) in the sEH gene EPHX2 and CYP450 on renal and vascular function, plasma levels of EETs and peripheral blood monuclear cell sEH activity was assessed in 79 kidney transplant recipients explored at least one year after transplantation. Additional experiments in a mouse model mimicking the ischemia–reperfusion (I/R) injury suffered by the transplanted kidney evaluated the cardiovascular and renal effects of the sEH inhibitor t-AUCB administered in drinking water (10 mg/l) during 28 days after surgery. There was a long-term protective effect of the sEH SNP rs6558004, which increased EET plasma levels, on renal allograft function and a deleterious effect of K55R, which increased sEH activity. Surprisingly, the loss-of-function CYP2C9*3 was associated with a better renal function without affecting EET levels. R287Q SNP, which decreased sEH activity, was protective against vascular dysfunction while CYP2C8*3 and 2C9*2 loss-of-function SNP, altered endothelial function by reducing flow-induced EET release. In I/R mice, sEH inhibition reduced kidney lesions, prevented cardiac fibrosis and dysfunction as well as preserved endothelial function. The preservation of EET bioavailability may prevent allograft dysfunction and improve cardiovascular disease in kidney transplant recipients. Inhibition of sEH appears thus as a novel therapeutic option but its impact on other epoxyfatty acids should be carefully evaluated.
Rainfall as a trigger of ecological cascade effects in an Australian groundwater ecosystem
Authors: Saccò Mattia , Blyth Alison J. , Humphreys William F. , Cooper Steven J. B. , White Nicole E. , Campbell Matthew , Mousavi-Derazmahalleh Mahsa , Hua Quan , Mazumder Debashish , Smith Colin , Griebler Christian , Grice Kliti 
Published: February 2021

AbstractGroundwaters host vital resources playing a key role in the near future. Subterranean fauna and microbes are crucial in regulating organic cycles in environments characterized by low energy and scarce carbon availability. However, our knowledge about the functioning of groundwater ecosystems is limited, despite being increasingly exposed to anthropic impacts and climate change-related processes. In this work we apply novel biochemical and genetic techniques to investigate the ecological dynamics of an Australian calcrete under two contrasting rainfall periods (LR—low rainfall and HR—high rainfall). Our results indicate that the microbial gut community of copepods and amphipods experienced a shift in taxonomic diversity and predicted organic functional metabolic pathways during HR. The HR regime triggered a cascade effect driven by microbes (OM processors) and exploited by copepods and amphipods (primary and secondary consumers), which was finally transferred to the aquatic beetles (top predators). Our findings highlight that rainfall triggers ecological shifts towards more deterministic dynamics, revealing a complex web of interactions in seemingly simple environmental settings. Here we show how a combined isotopic-molecular approach can untangle the mechanisms shaping a calcrete community. This design will help manage and preserve one of the most vital but underrated ecosystems worldwide.
An equation of state for insect swarms
Authors: Sinhuber Michael , van der Vaart Kasper , Feng Yenchia , Reynolds Andrew M. , Ouellette Nicholas T. 
Published: February 2021

AbstractCollective behaviour in flocks, crowds, and swarms occurs throughout the biological world. Animal groups are generally assumed to be evolutionarily adapted to robustly achieve particular functions, so there is widespread interest in exploiting collective behaviour for bio-inspired engineering. However, this requires understanding the precise properties and function of groups, which remains a challenge. Here, we demonstrate that collective groups can be described in a thermodynamic framework. We define an appropriate set of state variables and extract an equation of state for laboratory midge swarms. We then drive swarms through “thermodynamic” cycles via external stimuli, and show that our equation of state holds throughout. Our findings demonstrate a new way of precisely quantifying the nature of collective groups and provide a cornerstone for potential future engineering design.
Down-regulation of habenular calcium-dependent secretion activator 2 induces despair-like behavior
Authors: Yoo Hyeijung , Yang Soo Hyun , Kim Jin Yong , Yang Esther , Park Hyung Sun , Lee Se Jeong , Rhyu Im Joo , Turecki Gustavo , Lee Hyun Woo , Kim Hyun 
Published: February 2021

AbstractCalcium-dependent secretion activator 2 (CAPS2) regulates the trafficking and exocytosis of neuropeptide-containing dense-core vesicles (DCVs). CAPS2 is prominently expressed in the medial habenula (MHb), which is related to depressive behavior; however, how MHb neurons cause depressive symptoms and the role of CAPS2 remains unclear. We hypothesized that dysfunction of MHb CAPS neurons might cause defects in neuropeptide secretion and the activity of monoaminergic centers, resulting in depressive-like behaviors. In this study, we examined (1) CAPS2 expression in the habenula of depression animal models and major depressive disorder patients and (2) the effects of down-regulation of MHb CAPS2 on the animal behaviors, synaptic transmission in the interpeduncular nucleus (IPN), and neuronal activity of monoamine centers. Habenular CAPS2 expression was decreased in the rat chronic restraint stress model, mouse learned helplessness model, and showed tendency to decrease in depression patients who died by suicide. Knockdown of CAPS2 in the mouse habenula evoked despair-like behavior and a reduction of the release of DCVs in the IPN. Neuronal activity of IPN and monoaminergic centers was also reduced. These results implicate MHb CAPS2 as playing a pivotal role in depressive behavior through the regulation of neuropeptide secretion of the MHb-IPN pathway and the activity of monoaminergic centers.
Neural correlates of mating system diversity: oxytocin and vasopressin receptor distributions in monogamous and non-monogamous Eulemur
Authors: Grebe Nicholas M. , Sharma Annika , Freeman Sara M. , Palumbo Michelle C. , Patisaul Heather B. , Bales Karen L. , Drea Christine M. 
Published: February 2021

AbstractContemporary theory that emphasizes the roles of oxytocin and vasopressin in mammalian sociality has been shaped by seminal vole research that revealed interspecific variation in neuroendocrine circuitry by mating system. However, substantial challenges exist in interpreting and translating these rodent findings to other mammalian groups, including humans, making research on nonhuman primates crucial. Both monogamous and non-monogamous species exist withinEulemur, a genus of strepsirrhine primate, offering a rare opportunity to broaden a comparative perspective on oxytocin and vasopressin neurocircuitry with increased evolutionary relevance to humans. We performed oxytocin and arginine vasopressin 1a receptor autoradiography on 12Eulemurbrains from seven closely related species to (1) characterize receptor distributions across the genus, and (2) examine differences between monogamous and non-monogamous species in regions part of putative “pair-bonding circuits”. We find some binding patterns acrossEulemurreminiscent of olfactory-guided rodents, but others congruent with more visually oriented anthropoids, consistent with lemurs occupying an ‘intermediary’ evolutionary niche between haplorhine primates and other mammalian groups. We find little evidence of a “pair-bonding circuit” inEulemurakin to those proposed in previous rodent or primate research. Mapping neuropeptide receptors in these nontraditional species questions existing assumptions and informs proposed evolutionary explanations about the biological bases of monogamy.
Robotic pancreaticoduodenectomy provides better histopathological outcomes as compared to its open counterpart: a meta-analysis
Authors: Da Dong Xiang , Felsenreich Daniel Moritz , Gogna Shekhar , Rojas Aram , Zhang Ethan , Dong Michael , Azim Asad , Gachabayov Mahir 
Published: February 2021

AbstractThe aim of this meta-analysis was to evaluate whether robotic pancreaticoduodenectomy (PD) may provide better clinical and pathologic outcomes compared to its open counterpart. The Pubmed, EMBASE, and Cochrane Library were systematically searched. Overall postoperative morbidity and resection margin involvement rate were the primary endpoints. Secondary endpoints included operating time, estimated blood loss (EBL), incisional surgical site infection (SSI) rate, length of hospital stay (LOS), and number of lymph nodes harvested. Twenty-four studies totaling 12,579 patients (2,175 robotic PD and 10,404 open PD were included. Overall postoperative mortality did not significantly differ [OR (95%CI) = 0.86 (0.74, 1.01); p = 0.06]. Resection margin involvement rate was significantly lower in robotic PD [15.6% vs. 19.9%; OR (95%CI) = 0.64 (0.41, 1.00); p = 0.05; NNT = 23]. Operating time was significantly longer in robotic PD [MD (95%CI) = 75.17 (48.05, 102.28); p < 0.00001]. EBL was significantly decreased in robotic PD [MD (95%CI) = − 191.35 (− 238.12, − 144.59); p < 0.00001]. Number of lymph nodes harvested was significantly higher in robotic PD [MD (95%CI) = 2.88 (1.12, 4.65); p = 0.001]. This meta-analysis found that robotic PD provides better histopathological outcomes as compared to open PD at the cost of longer operating time. Furthermore, robotic PD did not have any detrimental impact on clinical outcomes, with lower wound infection rates.
Efficacy of MEK inhibition in a recurrent malignant peripheral nerve sheath tumor
Authors: Nagabushan Sumanth , Lau Loretta M. S. , Barahona Paulette , Wong Marie , Sherstyuk Alexandra , Marshall Glenn M. , Tyrrell Vanessa , Wegner Eva A. , Ekert Paul G. , Cowley Mark J. , Mayoh Chelsea , Trahair Toby N. , Crowe Philip , Anazodo Antoinette , Ziegler David S. 
Published: February 2021

AbstractThe prognosis of recurrent malignant peripheral nerve sheath tumors (MPNST) is dismal, with surgical resection being the only definitive salvage therapy. Treatment with chemoradiation approaches has not significantly improved patient outcomes. Similarly, trials of therapies targeting MPNST genomic drivers have thus far been unsuccessful. Improved understanding of the molecular pathogenesis of MPNST indicates frequent activation of the mitogen-activated protein kinase (MAPK) cell signaling pathway. MEK inhibitors have shown activity in preclinical studies; however, their clinical efficacy has not been reported to date. We describe here a case of sustained complete response to MEK inhibition in an adolescent patient with a recurrent metastatic MPNST with multiple alterations in the MAPK pathway, guided by a precision oncology approach.
Predicting adverse outcomes due to diabetes complications with machine learning using administrative health data
Authors: Ravaut Mathieu , Sadeghi Hamed , Leung Kin Kwan , Volkovs Maksims , Kornas Kathy , Harish Vinyas , Watson Tristan , Lewis Gary F. , Weisman Alanna , Poutanen Tomi , Rosella Laura 
Published: February 2021

AbstractAcross jurisdictions, government and health insurance providers hold a large amount of data from patient interactions with the healthcare system. We aimed to develop a machine learning-based model for predicting adverse outcomes due to diabetes complications using administrative health data from the single-payer health system in Ontario, Canada. A Gradient Boosting Decision Tree model was trained on data from 1,029,366 patients, validated on 272,864 patients, and tested on 265,406 patients. Discrimination was assessed using the AUC statistic and calibration was assessed visually using calibration plots overall and across population subgroups. Our model predicting three-year risk of adverse outcomes due to diabetes complications (hyper/hypoglycemia, tissue infection, retinopathy, cardiovascular events, amputation) included 700 features from multiple diverse data sources and had strong discrimination (average test AUC = 77.7, range 77.7–77.9). Through the design and validation of a high-performance model to predict diabetes complications adverse outcomes at the population level, we demonstrate the potential of machine learning and administrative health data to inform health planning and healthcare resource allocation for diabetes management.
Histone variant H2A.B-H2B dimers are spontaneously exchanged with canonical H2A-H2B in the nucleosome
Authors: Hirano Rina , Arimura Yasuhiro , Kujirai Tomoya , Shibata Mikihiro , Okuda Aya , Morishima Ken , Inoue Rintaro , Sugiyama Masaaki , Kurumizaka Hitoshi 
Published: February 2021

AbstractH2A.B is an evolutionarily distant histone H2A variant that accumulates on DNA repair sites, DNA replication sites, and actively transcribing regions in genomes. In cells, H2A.B exchanges rapidly in chromatin, but the mechanism has remained enigmatic. In the present study, we found that the H2A.B-H2B dimer incorporated within the nucleosome exchanges with the canonical H2A-H2B dimer without assistance from additional factors, such as histone chaperones and nucleosome remodelers. High-speed atomic force microscopy revealed that the H2A.B nucleosome, but not the canonical H2A nucleosome, transiently forms an intermediate “open conformation”, in which two H2A.B-H2B dimers may be detached from the H3-H4 tetramer and bind to the DNA regions near the entry/exit sites. Mutational analyses revealed that the H2A.B C-terminal region is responsible for the adoption of the open conformation and the H2A.B-H2B exchange in the nucleosome. These findings provide mechanistic insights into the histone exchange of the H2A.B nucleosome.
pH-dependent and dynamic interactions of cystatin C with heparan sulfate
Authors: Zhang Xiaoxiao , Liu Xinyue , Su Guowei , Li Miaomiao , Liu Jian , Wang Chunyu , Xu Ding 
Published: February 2021

AbstractCystatin C (Cst-3) is a potent inhibitor of cysteine proteases with diverse biological functions. As a secreted protein, the potential interaction between Cst-3 and extracellular matrix components has not been well studied. Here we investigated the interaction between Cst-3 and heparan sulfate (HS), a major component of extracellular matrix. We discovered that Cst-3 is a HS-binding protein only at acidic pH. By NMR and site-directed mutagenesis, we identified two HS binding regions in Cst-3: the highly dynamic N-terminal segment and a flexible region located between residue 70-94. The composition of the HS-binding site by two highly dynamic halves is unique in known HS-binding proteins. We further discovered that HS-binding severely impairs the inhibitory activity of Cst-3 towards papain, suggesting the interaction could actively regulate Cst-3 activity. Using murine bone tissues, we showed that Cst-3 interacts with bone matrix HS at low pH, again highlighting the physiological relevance of our discovery.