bluuebunny/crossref_metadata_2025_split huggingface dataset:
Melting of subducted sediments reconciles geophysical images of subduction zones
Authors: Förster M. W. , Selway K. 
Published: February 2021

AbstractSediments play a key role in subduction. They help control the chemistry of arc volcanoes and the location of seismic hazards. Here, we present a new model describing the fate of subducted sediments that explains magnetotelluric models of subduction zones, which commonly show an enigmatic conductive anomaly at the trenchward side of volcanic arcs. In many subduction zones, sediments will melt trenchward of the source region for arc melts. High-pressure experiments show that these sediment melts will react with the overlying mantle wedge to produce electrically conductive phlogopite pyroxenites. Modelling of the Cascadia and Kyushu subduction zones shows that the products of sediment melting closely reproduce the magnetotelluric observations. Melting of subducted sediments can also explain K-rich volcanic rocks that are produced when the phlogopite pyroxenites melt during slab roll-back events. This process may also help constrain models for subduction zone seismicity. Since melts and phlogopite both have low frictional strength, damaging thrust earthquakes are unlikely to occur in the vicinity of the melting sediments, while increased fluid pressures may promote the occurrence of small magnitude earthquakes and episodic tremor and slip.
Cerebrospinal fluid (CSF) augments metabolism and virulence expression factors in Acinetobacter baumannii
Authors: Martinez Jasmine , Razo-Gutierrez Chelsea , Le Casin , Courville Robert , Pimentel Camila , Liu Christine , Fung Sammie E. , Tuttobene Marisel R. , Phan Kimberly , Vila Alejandro J. , Shahrestani Parvin , Jimenez Veronica , Tolmasky Marcelo E. , Becka Scott A. , Papp-Wallace Krisztina M. , Bonomo Robert A. , Soler-Bistue Alfonso , Sieira Rodrigo , Ramirez Maria Soledad 
Published: February 2021

AbstractIn a recent report by the Centers for Disease Control and Prevention (CDC), multidrug resistant (MDR) Acinetobacter baumannii is a pathogen described as an “urgent threat.” Infection with this bacterium manifests as different diseases such as community and nosocomial pneumonia, bloodstream infections, endocarditis, infections of the urinary tract, wound infections, burn infections, skin and soft tissue infections, and meningitis. In particular, nosocomial meningitis, an unwelcome complication of neurosurgery caused by extensively-drug resistant (XDR) A. baumannii, is extremely challenging to manage. Therefore, understanding how A. baumannii adapts to different host environments, such as cerebrospinal fluid (CSF) that may trigger changes in expression of virulence factors that are associated with the successful establishment and progress of this infection is necessary. The present in-vitro work describes, the genetic changes that occur during A. baumannii infiltration into CSF and displays A. baumannii’s expansive versatility to persist in a nutrient limited environment while enhancing several virulence factors to survive and persist. While a hypervirulent A. baumannii strain did not show changes in its transcriptome when incubated in the presence of CSF, a low-virulence isolate showed significant differences in gene expression and phenotypic traits. Exposure to 4% CSF caused increased expression of virulence factors such as fimbriae, pilins, and iron chelators, and other virulence determinants that was confirmed in various model systems. Furthermore, although CSF's presence did not enhance bacterial growth, an increase of expression of genes encoding transcription, translation, and the ATP synthesis machinery was observed. This work also explores A. baumannii’s response to an essential component, human serum albumin (HSA), within CSF to trigger the differential expression of genes associated with its pathoadaptibility in this environment.
Recreation of the periodic table with an unsupervised machine learning algorithm
Authors: Kusaba Minoru , Liu Chang , Koyama Yukinori , Terakura Kiyoyuki , Yoshida Ryo 
Published: February 2021

AbstractIn 1869, the first draft of the periodic table was published by Russian chemist Dmitri Mendeleev. In terms of data science, his achievement can be viewed as a successful example of feature embedding based on human cognition: chemical properties of all known elements at that time were compressed onto the two-dimensional grid system for a tabular display. In this study, we seek to answer the question of whether machine learning can reproduce or recreate the periodic table by using observed physicochemical properties of the elements. To achieve this goal, we developed a periodic table generator (PTG). The PTG is an unsupervised machine learning algorithm based on the generative topographic mapping, which can automate the translation of high-dimensional data into a tabular form with varying layouts on-demand. The PTG autonomously produced various arrangements of chemical symbols, which organized a two-dimensional array such as Mendeleev’s periodic table or three-dimensional spiral table according to the underlying periodicity in the given data. We further showed what the PTG learned from the element data and how the element features, such as melting point and electronegativity, are compressed to the lower-dimensional latent spaces.
Reconstitution and optimisation of the biosynthesis of bacterial sugar pseudaminic acid (Pse5Ac7Ac) enables preparative enzymatic synthesis of CMP-Pse5Ac7Ac
Authors: Chidwick Harriet S. , Flack Emily K. P. , Keenan Tessa , Walton Julia , Thomas Gavin H. , Fascione Martin A. 
Published: February 2021

AbstractPseudaminic acids present on the surface of pathogenic bacteria, including gut pathogens Campylobacter jejuni and Helicobacter pylori, are postulated to play influential roles in the etiology of associated infectious diseases through modulating flagella assembly and recognition of bacteria by the human immune system. Yet they are underexplored compared to other areas of glycoscience, in particular enzymes responsible for the glycosyltransfer of these sugars in bacteria are still to be unambiguously characterised. This can be largely attributed to a lack of access to nucleotide-activated pseudaminic acid glycosyl donors, such as CMP-Pse5Ac7Ac. Herein we reconstitute the biosynthesis of Pse5Ac7Ac in vitro using enzymes from C. jejuni (PseBCHGI) in the process optimising coupled turnover with PseBC using deuterium wash in experiments, and establishing a method for co-factor regeneration in PseH tunover. Furthermore we establish conditions for purification of a soluble CMP-Pse5Ac7Ac synthetase enzyme PseF from Aeromonas caviae and utilise it in combination with the C. jejuni enzymes to achieve practical preparative synthesis of CMP-Pse5Ac7Ac in vitro, facilitating future biological studies.
Prevalence of total hepatitis A antibody among 5 to 7 years old children and their mothers in Cambodia
Authors: Nagashima Shintaro , Ko Ko , Yamamoto Chikako , Bunthen E. , Ouoba Serge , Chuon Channarena , Ohisa Masayuki , Sugiyama Aya , Akita Tomoyuki , Hossain Md. Shafiqul , Ork Vichit , Mao Bunsoth , Tanaka Junko 
Published: February 2021

AbstractThis study determined the prevalence of total hepatitis A antibody (anti-HAV) among 5–7 years old children and their mothers in the whole Cambodia, using a nationwide study, and examined the differences between the two cohorts. A total of 4535 dried blood spot-driven (DBS) samples (2021 mothers and their 2514 children of 5–7 years old) and the concomitant 922 whole blood samples (subset of the whole participants) were collected using a multistage random sampling strategy throughout Cambodia in 2017. Total anti-HAV was detected using the chemiluminescence enzyme immunoassay method. Compared to gold standard whole blood samples, the sensitivity and specificity of DBS mediated anti-HAV detection were 94.8% and 98%, respectively. Total anti-HAV prevalence among mothers was 91.2% (95%CI: 90.0–92.5%), and that of their children was 31.5% (95%CI: 29.7–33.3%). In our study, the low prevalence of total anti-HAV among children indicates the country’s improvement of safe water and food supply, hygiene and sanitation. If the hygiene and sanitation are consistently improved in Cambodia, the prevalence might be no longer increased when the children become adults.
Improved sensitivity of microperimetric outcomes for clinical studies in age-related macular degeneration
Authors: Barkana Yaniv , Pondorfer Susanne G. , Schmitz-Valckenberg Steffen , Russ Hermann , Finger Robert P. 
Published: February 2021

AbstractTo investigate sensitive outcome measures based exclusively on abnormal points in microperimetry testing of eyes with intermediate age-related macular degeneration (iAMD). 25 eyes of 25 subjects with iAMD had undergone 2 successive tests of mesopic microperimetry with the Macular Integrity Assessment Microperimeter (MAIA), using a custom grid of 33 points spanning the central 14 degrees of the macula. Each point was defined as abnormal if its threshold sensitivity was lower than 1.65 standard deviations (SD) (5%) or 2 SD (2.5%) than the expected threshold in healthy eyes according to the MAIA internal database. Among the 25 eyes there were 11.8 ± 9 and 8.4 ± 8.2 abnormal points at < 5% and < 2.5%, with mean deviation of thresholds from normal − 4.9 ± 1.2 dB and − 5.8 ± 1.5 dB, respectively. These deviations were greater, and their SD smaller, compared with the complete microperimetry grid, − 2.3 ± 2.0 dB. The 95% limits of agreement for average threshold between the 2 successive tests were smaller when only abnormal points were included. Analyzing only abnormal grid points yields an outcome parameter with a greater deviation from normal, a more homogenous dataset, and better test–retest variability, compared with analysis of all grid points. This parameter may thus be more sensitive to change, while moderately limiting the number of potential recruits. The proposed outcome measures should be further investigated as potential endpoints in clinical trials in iAMD.
Autophagy-enhancing drugs limit mucosal HIV-1 acquisition and suppress viral replication ex vivo
Authors: Cloherty Alexandra P. M. , van Teijlingen Nienke H. , Eisden Tracy-Jane T. H. D. , van Hamme John L. , Rader Anusca G. , Geijtenbeek Teunis B. H. , Schreurs Renée R. C. E. , Ribeiro Carla M. S. 
Published: February 2021

AbstractCurrent direct-acting antiviral therapies are highly effective in suppressing HIV-1 replication. However, mucosal inflammation undermines prophylactic treatment efficacy, and HIV-1 persists in long-lived tissue-derived dendritic cells (DCs) and CD4+ T cells of treated patients. Host-directed strategies are an emerging therapeutic approach to improve therapy outcomes in infectious diseases. Autophagy functions as an innate antiviral mechanism by degrading viruses in specialized vesicles. Here, we investigated the impact of pharmaceutically enhancing autophagy on HIV-1 acquisition and viral replication. To this end, we developed a human tissue infection model permitting concurrent analysis of HIV-1 cellular targets ex vivo. Prophylactic treatment with autophagy-enhancing drugs carbamazepine and everolimus promoted HIV-1 restriction in skin-derived CD11c+ DCs and CD4+ T cells. Everolimus also decreased HIV-1 susceptibility to lab-adapted and transmitted/founder HIV-1 strains, and in vaginal Langerhans cells. Notably, we observed cell-specific effects of therapeutic treatment. Therapeutic rapamycin treatment suppressed HIV-1 replication in tissue-derived CD11c+ DCs, while all selected drugs limited viral replication in CD4+ T cells. Strikingly, both prophylactic and therapeutic treatment with everolimus or rapamycin reduced intestinal HIV-1 productive infection. Our findings highlight host autophagy pathways as an emerging target for HIV-1 therapies, and underscore the relevancy of repurposing clinically-approved autophagy drugs to suppress mucosal HIV-1 replication.
Quantitative modeling of multigenerational effects of chronic ionizing radiation using targeted and nontargeted effects
Authors: Shuryak Igor , Brenner David J. 
Published: February 2021

AbstractStress response signals can propagate between cells damaged by targeted effects (TE) of ionizing radiation (e.g. energy depositions and ionizations in the nucleus) and undamaged “bystander” cells, sometimes over long distances. Their consequences, called non-targeted effects (NTE), can substantially contribute to radiation-induced damage (e.g. cell death, genomic instability, carcinogenesis), particularly at low doses/dose rates (e.g. space exploration, some occupational and accidental exposures). In addition to controlled laboratory experiments, analysis of observational data on wild animal and plant populations from areas contaminated by radionuclides can enhance our understanding of radiation responses because such data span wide ranges of dose rates applied over many generations. Here we used a mechanistically-motivated mathematical model of TE and NTE to analyze published embryonic mortality data for plants (Arabidopsis thaliana) and rodents (Clethrionomys glareolus) from the Chernobyl nuclear power plant accident region. Although these species differed strongly in intrinsic radiosensitivities and post-accident radiation exposure magnitudes, model-based analysis suggested that NTE rather than TE dominated the responses of both organisms to protracted low-dose-rate irradiation. TE were predicted to become dominant only above the highest dose rates in the data. These results support the concept of NTE involvement in radiation-induced health risks from chronic radiation exposures.
Diffusion histology imaging differentiates distinct pediatric brain tumor histology
Authors: Ye Zezhong , Srinivasa Komal , Meyer Ashely , Sun Peng , Lin Joshua , Viox Jeffrey D. , Song Chunyu , Wu Anthony T. , Song Sheng-Kwei , Dahiya Sonika , Rubin Joshua B. 
Published: February 2021

AbstractHigh-grade pediatric brain tumors exhibit the highest cancer mortality rates in children. While conventional MRI has been widely adopted for examining pediatric high-grade brain tumors clinically, accurate neuroimaging detection and differentiation of tumor histopathology for improved diagnosis, surgical planning, and treatment evaluation, remains an unmet need in their clinical management. We employed a novel Diffusion Histology Imaging (DHI) approach employing diffusion basis spectrum imaging (DBSI) derived metrics as the input classifiers for deep neural network analysis. DHI aims to detect, differentiate, and quantify heterogeneous areas in pediatric high-grade brain tumors, which include normal white matter (WM), densely cellular tumor, less densely cellular tumor, infiltrating edge, necrosis, and hemorrhage. Distinct diffusion metric combination would thus indicate the unique distributions of each distinct tumor histology features. DHI, by incorporating DBSI metrics and the deep neural network algorithm, classified pediatric tumor histology with an overall accuracy of 85.8%. Receiver operating analysis (ROC) analysis suggested DHI’s great capability in distinguishing individual tumor histology with AUC values (95% CI) of 0.984 (0.982–0.986), 0.960 (0.956–0.963), 0.991 (0.990–0.993), 0.950 (0.944–0.956), 0.977 (0.973–0.981) and 0.976 (0.972–0.979) for normal WM, densely cellular tumor, less densely cellular tumor, infiltrating edge, necrosis and hemorrhage, respectively. Our results suggest that DBSI-DNN, or DHI, accurately characterized and classified multiple tumor histologic features in pediatric high-grade brain tumors. If these results could be further validated in patients, the novel DHI might emerge as a favorable alternative to the current neuroimaging techniques to better guide biopsy and resection as well as monitor therapeutic response in patients with high-grade brain tumors.
A state-space model to derive motorboat noise effects on fish movement from acoustic tracking data
Authors: Barcelo-Serra Margarida , Cabanellas Sebastià , Palmer Miquel , Bolgan Marta , Alós Josep 
Published: February 2021

AbstractMotorboat noise is recognized as a major source of marine pollution, however little is known about its ecological consequences on coastal systems. We developed a State Space Model (SSM) that incorporates an explicit dependency on motorboat noise to derive its effects on the movement of resident fish that transition between two behavioural states (swimming vs. hidden). To explore the performance of our model, we carried out an experiment where free-living Serranus scriba were tracked with acoustic tags, while motorboat noise was simultaneously recorded. We fitted the generated tracking and noise data into our SSM and explored if the noise generated by motorboats passing at close range affected the movement pattern and the probability of transition between the two states using a Bayesian approach. Our results suggest high among individual variability in movement patterns and transition between states, as well as in fish response to the presence of passing motorboats. These findings suggest that the effects of motorboat noise on fish movement are complex and require the precise monitoring of large numbers of individuals. Our SSM provides a methodology to address such complexity and can be used for future investigations to study the effects of noise pollution on marine fish.
Tobacco use and age are associated with different morphologic features of anterior communicating artery aneurysms
Authors: Zhang Jian , Lai Pui Man Rosalind , Can Anil , Mukundan Srinivasan , Castro Victor M. , Dligach Dmitriy , Finan Sean , Gainer Vivian S. , Shadick Nancy A. , Savova Guergana , Murphy Shawn N. , Cai Tianxi , Weiss Scott T. , Du Rose 
Published: February 2021

AbstractWe present a cohort of patients with anterior communicating artery (ACoA) aneurysms to investigate morphological characteristics and clinical factors associated with rupture of the aneurysms. 505 patients with ACoA aneurysms were identified at the Brigham and Women’s Hospital and Massachusetts General Hospital between 1990 and 2016, with available CT angiography (CTA). Three-dimensional (3D) reconstructions were performed to evaluate aneurysmal morphologic features, including location, projection, irregularity, the presence of daughter dome, height, height/width ratio, and relationships between surrounding vessels. Patient risk factors assessed included patient age, sex, tobacco use, alcohol use, and family history of aneurysms and aneurysmal subarachnoid hemorrhage. Logistic regression was used to build a predictive ACoA score for rupture. Morphologic features associated with ruptured ACoA aneurysms were the presence of a daughter dome (OR 21.4, 95% CI 10.6–43.1), smaller neck diameter (OR 0.55, 95% CI 0.42–0.71), larger aspect ratio (OR 3.57, 95% CI 2.05–6.24), larger flow angle (OR 1.03, 95% CI 1.02–1.05), and smaller ipsilateral A2-ACoA angle (OR 0.98, 95% CI 0.97–1.00). Tobacco use was predominantly associated with morphological factors intrinsic to the aneurysm that were associated with rupture while younger age was also associated with morphologic features extrinsic to the aneurysm that were associated with rupture. The ACoA score had good predictive capacity for rupture with AUC = 0.92 using the 0.632 bootstrap cross-validation for correction of overfitting bias. Ruptured ACoA aneurysms were associated with morphological features that are simple to assess using a simple scoring system. Tobacco use and younger age were predominantly associated with intrinsic and extrinsic morphological features characteristic of rupture, respectively.
Oxygen extraction ratio to identify patients at increased risk of intradialytic hypotension
Authors: Rotondi Silverio , Tartaglione Lida , De Martini Natalia , Bagordo Domenico , Caissutti Sara , Pasquali Marzia , Muci Maria Luisa , Mazzaferro Sandro 
Published: February 2021

AbstractIntradialytic hypotension (IDH) is a hemodynamic phenomenon recently associated with decreased blood oxygen saturation (SO2). The ratio between peripheral oxygen saturation (SpO2) and central venous SO2 (ScvO2) or Oxygen Extraction Ratio (OER), which represents a roughly estimate of the amount of oxygen claimed by peripheral tissues, might be used to estimate haemodialysis (HD) related hypoxic stress. Aim of this pilot study was to evaluate the relationship between OER increments during dialysis sessions (ΔOER) and episodes of IDH. We enrolled chronic HD patients with permanent central venous catheter (CVC) and no fistula, in whom ScvO2 measurement is at hand. OER ([(SpO2 − ScvO2)/SpO2] × 100) was measured in three consecutive HD sessions (HD OER sessions) before HD, after 15′, 30′ and 60′ min and at the end of HD. Then, a one-year follow-up was planned to record the number of IDH episodes. In the 28 enrolled patients (age 74 ± 2.6 years), during 12 ± 1.2 months of follow up, incidence of IDH was 3.6%. We divided patients into two groups, above or below the median value of ΔOER at the end of HD, which was 36%. In these groups, the average incidence of IDH was 7% and 2% respectively (p < 0.01), while OER values before HD were not different. Notably, in the high ΔOER group the OER increment was evident since after 15′ and was significantly higher than in the low ∆OER group (∆OER-15′ = 19 ± 3.0% vs. 9.0 ± 3.0%; p < 0.05). By comparison, blood volume changes overlapped in the two groups (average change − 9 ± 0.8%). Values of ∆OER > 19% after only 15′ of HD treatment or > 36% at the end of the session characterize patients with higher rates of hypotension. Intradialytic ∆OER, a parameter of tissue hypoxic stress, identifies more fragile patients at greater risk of IDH.
Cardiac glycosides target barrier inflammation of the vasculature, meninges and choroid plexus
Authors: Jansson Deidre , Dieriks Victor Birger , Rustenhoven Justin , Smyth Leon C. D. , Scotter Emma , Aalderink Miranda , Feng Sheryl , Johnson Rebecca , Schweder Patrick , Mee Edward , Heppner Peter , Turner Clinton , Curtis Maurice , Faull Richard , Dragunow Mike 
Published: February 2021

AbstractNeuroinflammation is a key component of virtually all neurodegenerative diseases, preceding neuronal loss and associating directly with cognitive impairment. Neuroinflammatory signals can originate and be amplified at barrier tissues such as brain vasculature, surrounding meninges and the choroid plexus. We designed a high content screening system to target inflammation in human brain-derived cells of the blood–brain barrier (pericytes and endothelial cells) to identify inflammatory modifiers. Screening an FDA-approved drug library we identify digoxin and lanatoside C, members of the cardiac glycoside family, as inflammatory-modulating drugs that work in blood–brain barrier cells. An ex vivo assay of leptomeningeal and choroid plexus explants confirm that these drugs maintain their function in 3D cultures of brain border tissues. These results suggest that cardiac glycosides may be useful in targeting inflammation at border regions of the brain and offer new options for drug discovery approaches for neuroinflammatory driven degeneration.