bluuebunny/crossref_metadata_2025_split huggingface dataset:
Short treatment of peripheral blood cells product with Fas ligand using closed automated cell processing system significantly reduces immune cell reactivity of the graft in vitro and in vivo
Authors: Rodionov Galina , Rosenzwaig Michal , Tzadok Michal Schrift , Kvint Moran , Gevir Elazar , Zorde-Khvalevsky Elina , Peled Amnon , Yarkoni Shai , Ofer Amos 
Published: May 2022

AbstractMobilized peripheral blood cells (MPBCs) graft and peripheral blood cells apheresis are used for bone marrow transplantation and for treatment of graft versus host disease (GvHD). We demonstrate that a short treatment of MPBCs with Fas ligand (FasL, CD95L) for 2 h using a closed automated cell processing system selectively induces apoptosis of specific donor T cells, B cells and antigen presenting cells, but, critically, not CD34+ hematopoietic stem cells and progenitors, all of which may contribute to an increased likelihood of graft survival and functionality and reduced GvHD. Treated cells secreted lower levels of interferon-gamma as compared with control, untreated, cells. Moreover, FasL treatment of immune cells increased signals, which led to their phagocytosis by activated macrophages. FasL treated immune cells also reduced the ability of activated macrophages to secrete pro-inflammatory cytokines. Most importantly, FasL ex vivo treated MPBCs prior to transplantation in NOD-SCID NSG mice prevented GvHD and improved stem cell transplantation in vivo. In conclusion, MPBCs, as well as other blood cell products, treated with FasL by automated manufacturing (AM), may be used as potential treatments for conditions where the immune system is over-responding to both self and non-self-antigens.
Helicobacter pylori infection activates Wnt/β-catenin pathway to promote the occurrence of gastritis by upregulating ASCL1 and AQP5
Authors: Zuo Wei , Yang Hui , Li Nianshuang , Ouyang Yaobin , Xu Xinbo , Hong Junbo 
Published: May 2022

AbstractHelicobacter pylori (H. pylori)infection is a well-recognized contributing factor to gastritis, but the underlying mechanisms remain to be established. It is interesting to note that AQP5 was predicted to be highly expressed in intestinal metaplasia (IM) based onH. pyloriinfection-related microarray data, and the transcription factor ASCL1 was bioinformatically predicted to associate with AQP5. Therefore, the purpose of this study is to evaluate the mechanistic significance of ASCL1 and AQP5 inH. pyloriinfection of gastritis. Gastritis mouse models were established byH. pyloriinfection, followed by determination of AQP5 and ASCL1 in gastric mucosa. Besides, the effects of AQP5 onH. pylori-induced gastritis were explored using AQP5−/−mice. It was observed thatH. pyloriinfection elevated expression of AQP5 and ASCL1 in gastric mucosa and gastric epithelial cells (GECs).H. pyloriinduced AQP5 expression by regulating ASCL1 and activated WNT/β-catenin signaling pathway in GECs. It was also found that AQP5 knockdown suppressed inflammatory response and apoptosis inH. pylori-infected mice. Moreover,H. pyloriinfection-elevated ASCL1 and AQP5 expression promoted apoptosis and inflammation in GECs. Taken together, the key findings of the present study demonstrate thatH. pyloriinfection activated WNT/β-catenin signaling pathway by upregulating ASCL1/AQP5 to induce gastritis.
Systematic and quantitative view of the antiviral arsenal of prokaryotes
Authors: Tesson Florian , Hervé Alexandre , Mordret Ernest , Touchon Marie , d’Humières Camille , Cury Jean , Bernheim Aude 
Published: May 2022

AbstractBacteria and archaea have developed multiple antiviral mechanisms, and genomic evidence indicates that several of these antiviral systems co-occur in the same strain. Here, we introduce DefenseFinder, a tool that automatically detects known antiviral systems in prokaryotic genomes. We use DefenseFinder to analyse 21000 fully sequenced prokaryotic genomes, and find that antiviral strategies vary drastically between phyla, species and strains. Variations in composition of antiviral systems correlate with genome size, viral threat, and lifestyle traits. DefenseFinder will facilitate large-scale genomic analysis of antiviral defense systems and the study of host-virus interactions in prokaryotes.
Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals
Authors: Brizzi Andrea , Whittaker Charles , Servo Luciana M. S. , Hawryluk Iwona , Prete Carlos A. , de Souza William M. , Aguiar Renato S. , Araujo Leonardo J. T. , Bastos Leonardo S. , Blenkinsop Alexandra , Buss Lewis F. , Candido Darlan , Castro Marcia C. , Costa Silvia F. , Croda Julio , de Souza Santos Andreza Aruska , Dye Christopher , Flaxman Seth , Fonseca Paula L. C. , Geddes Victor E. V. , Gutierrez Bernardo , Lemey Philippe , Levin Anna S. , Mellan Thomas , Bonfim Diego M. , Miscouridou Xenia , Mishra Swapnil , Monod Mélodie , Moreira Filipe R. R. , Nelson Bruce , Pereira Rafael H. M. , Ranzani Otavio , Schnekenberg Ricardo P. , Semenova Elizaveta , Sonabend Raphael , Souza Renan P. , Xi Xiaoyue , Sabino Ester C. , Faria Nuno R. , Bhatt Samir , Ratmann Oliver 
Published: May 2022

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Gamma variant of concern has spread rapidly across Brazil since late 2020, causing substantial infection and death waves. Here we used individual-level patient records after hospitalization with suspected or confirmed coronavirus disease 2019 (COVID-19) between 20 January 2020 and 26 July 2021 to document temporary, sweeping shocks in hospital fatality rates that followed the spread of Gamma across 14 state capitals, during which typically more than half of hospitalized patients aged 70 years and older died. We show that such extensive shocks in COVID-19 in-hospital fatality rates also existed before the detection of Gamma. Using a Bayesian fatality rate model, we found that the geographic and temporal fluctuations in Brazil’s COVID-19 in-hospital fatality rates were primarily associated with geographic inequities and shortages in healthcare capacity. We estimate that approximately half of the COVID-19 deaths in hospitals in the 14 cities could have been avoided without pre-pandemic geographic inequities and without pandemic healthcare pressure. Our results suggest that investments in healthcare resources, healthcare optimization and pandemic preparedness are critical to minimize population-wide mortality and morbidity caused by highly transmissible and deadly pathogens such as SARS-CoV-2, especially in low- and middle-income countries.
Arboviral disease record data - Dengue and Chikungunya, Brazil, 2013–2020
Authors: da Silva Neto Sebastião Rogério , Tabosa de Oliveira Thomás , Teixiera Igor Vitor , Medeiros Neto Leonides , Souza Sampaio Vanderson , Lynn Theo , Endo Patricia Takako 
Published: May 2022

AbstractOne of the main categories of Neglected Tropical Diseases (NTDs) are arboviruses, of which Dengue and Chikungunya are the most common. Arboviruses mainly affect tropical countries. Brazil has the largest absolute number of cases in Latin America. This work presents a unified data set with clinical, sociodemographic, and laboratorial data on confirmed patients of Dengue and Chikungunya, as well as patients ruled out of infection from these diseases. The data is based on case notification data submitted to the Brazilian Information System for Notifiable Diseases, from Portuguese Sistema de Informação de Agravo de Notificação (SINAN), from 2013 to 2020. The original data set comprised 13,421,230 records and 118 attributes. Following a pre-processing process, a final data set of 7,632,542 records and 56 attributes was generated. The data presented in this work will assist researchers in investigating antecedents of arbovirus emergence and transmission more generally, and Dengue and Chikungunya in particular. Furthermore, it can be used to train and test machine learning models for differential diagnosis and multi-class classification.
Decoding the protein–ligand interactions using parallel graph neural networks
Authors: Knutson Carter , Bontha Mridula , Bilbrey Jenna A. , Kumar Neeraj 
Published: May 2022

AbstractProtein–ligand interactions (PLIs) are essential for biochemical functionality and their identification is crucial for estimating biophysical properties for rational therapeutic design. Currently, experimental characterization of these properties is the most accurate method, however, this is very time-consuming and labor-intensive. A number of computational methods have been developed in this context but most of the existing PLI prediction heavily depends on 2D protein sequence data. Here, we present a novel parallel graph neural network (GNN) to integrate knowledge representation and reasoning for PLI prediction to perform deep learning guided by expert knowledge and informed by 3D structural data. We develop two distinct GNN architectures:$$\hbox {GNN}_{\mathrm{F}}$$GNNFis the base implementation that employs distinct featurization to enhance domain-awareness, while$$\hbox {GNN}_{\mathrm{P}}$$GNNPis a novel implementation that can predict with no prior knowledge of the intermolecular interactions. The comprehensive evaluation demonstrated that GNN can successfully capture the binary interactions between ligand and protein’s 3D structure with 0.979 test accuracy for$$\hbox {GNN}_{\mathrm{F}}$$GNNFand 0.958 for$$\hbox {GNN}_{\mathrm{P}}$$GNNPfor predicting activity of a protein–ligand complex. These models are further adapted for regression tasks to predict experimental binding affinities and$$\hbox {pIC}_{\mathrm{50}}$$pIC50crucial for compound’s potency and efficacy. We achieve a Pearson correlation coefficient of 0.66 and 0.65 on experimental affinity and 0.50 and 0.51 on$$\hbox {pIC}_{\mathrm{50}}$$pIC50with$$\hbox {GNN}_{\mathrm{F}}$$GNNFand$$\hbox {GNN}_{\mathrm{P}}$$GNNP, respectively, outperforming similar 2D sequence based models. Our method can serve as an interpretable and explainable artificial intelligence (AI) tool for predicted activity, potency, and biophysical properties of lead candidates. To this end, we show the utility of$$\hbox {GNN}_{\mathrm{P}}$$GNNPon SARS-Cov-2 protein targets by screening a large compound library and comparing the prediction with the experimentally measured data.
Cost-utility analysis on robot-assisted and laparoscopic prostatectomy based on long-term functional outcomes
Authors: Lindenberg Melanie A. , Retèl Valesca P. , van der Poel Henk G. , Bandstra Ferdau , Wijburg Carl , van Harten Wim H. 
Published: May 2022

AbstractRobot-Assisted Radical Prostatectomy (RARP) is one of the standard treatment options for prostate cancer. However, controversy still exists on its added value. Based on a recent large-sample retrospective cluster study from the Netherlands showing significantly improved long-term urinary functioning after RARP compared to Laparoscopic RP (LRP), we evaluated the cost-effectiveness of RARP compared to LRP. A decision tree was constructed to measure the costs and effects from a Dutch societal perspective over a ~ 7 year time-horizon. The input was based on the aforementioned study, including patient-reported consumption of addition care and consumed care for ergonomic issues reported by surgeons. Intervention costs were calculated using a bottom-up costing analysis in 5 hospitals. Finally, a probabilistic-, one-way sensitivity- and scenario analyses were performed to show possible decision uncertainty. The intervention costs were €9964 for RARP and €7253 for LRP. Total trajectory costs were €12,078 for RARP and €10,049 for LRP. RARP showed higher QALYs compared to LRP (6.17 vs 6.11). The incremental cost-utility ratio (ICUR) was €34,206 per QALY gained, in favour of RARP. As a best-case scenario, when RARP is being centralized (> 150 cases/year), total trajectory costs decreased to €10,377 having a higher utilization, and a shorter procedure time and length of stay resulting in an ICUR of €3495 per QALY gained. RARP showed to be cost-effective compared to LRP based on data from a population-based, large scale study with 7 years of follow-up. This is a clear incentive to fully reimburse RARP, especially when hospitals provide RARP centralized.
The impact of metformin use on the outcomes of locally advanced breast cancer patients receiving neoadjuvant chemotherapy: an open-labelled randomized controlled trial
Authors: Barakat Hadeer Ehab , Hussein Raghda R. S. , Elberry Ahmed Abdullah , Zaki Mamdouh Ahmed , Ramadan Mamdouh Elsherbiny 
Published: May 2022

AbstractRecently, several clinical trials have attempted to find evidence that supports the anticancer use of metformin in breast cancer (BC) patients. The current study evaluates the anticancer activity of metformin in addition to neoadjuvant chemotherapy (NACT) in locally advanced BC patients. Additionally, we assess the safety and tolerability of this combination and its effect on the quality of life (QoL) of BC patients. Eighty non-diabetic female patients with proven locally advanced BC were randomized into two arms. The first arm received anthracycline/taxane-based NACT plus metformin. The second arm received anthracycline/taxane-based NACT only. Overall response rate (ORR), clinical complete response (cCr), pathological complete response (pCR), and breast conservative rate (BCR) were evaluated between both groups, and correlated with serum metformin concentration. ORR, cCr, pCR, and BCR increased non-significantly in the metformin group compared to the control group; 80.6% vs 68.4%, 27.8% vs 10.5%, 22.2% vs 10.5%, and 19.4% vs 13.2%, respectively. A trend towards cCR and pCR was associated with higher serum metformin concentrations. Metformin decreased the incidence of peripheral neuropathy, bone pain, and arthralgia, although worsened the gastrointestinal adverse events. Metformin combination with NACT has no effect on the QoL of BC patients. Metformin combination with NACT is safe, tolerable, and improves non-significantly the clinical and pathological tumor response of BC patients.
Temporal patterns in the soundscape of a Norwegian gateway to the Arctic
Authors: Aniceto A. S. , Ferguson E. L. , Pedersen G. , Tarroux A. , Primicerio R. 
Published: May 2022

AbstractAs an Arctic gateway, the Norwegian Sea sustains a rich diversity of seasonal and resident species of soniferous animals, vulnerable to the effects of climate change and anthropogenic activities. We show the occurrence of seasonal patterns of acoustic signals in a small canyon off Northern Norway, and investigate cetacean vocal behavior, human-made noise, and climatic contributions to underwater sound between January and May 2018. Mostly median sound levels ranged between 68.3 and 96.31 dB re 1 μPa2 across 1/3 octave bands (13 Hz–16 kHz), with peaks in February and March. Frequencies under 2 kHz were dominated by sounds from baleen whales with highest rates of occurrence during winter and early spring. During late-spring non-biological sounds were predominant at higher frequencies that were linked mainly to ship traffic. Seismic pulses were also recorded during spring. We observed a significant effect of wind speed and ship sailing time on received sound levels across multiple distance ranges. Our results provide a new assessment of high-latitude continental soundscapes in the East Atlantic Ocean, useful for management strategies in areas where anthropogenic pressure is increasing. Based on the current status of the local soundscape, we propose considerations for acoustic monitoring to be included in future management plans.
Curvature dependence of BAR protein membrane association and dissociation kinetics
Authors: Jin Rui , Cao Rui , Baumgart Tobias 
Published: May 2022

AbstractBAR (Bin/Amphiphysin/Rvs) domain containing proteins function as lipid bilayer benders and curvature sensors, and they contribute to membrane shaping involved in cell signaling and metabolism. The mechanism for their membrane shape sensing has been investigated by both equilibrium binding and kinetic studies. In prior research, stopped-flow spectroscopy has been used to deduce a positive dependence on membrane curvature for the binding rate constant, kon, of a BAR protein called endophilin. However, the impact of bulk diffusion of endophilin, on the kinetic binding parameters has not been thoroughly considered. Employing similar methods, and using lipid vesicles of multiple sizes, we obtained a linear dependence of kon on vesicle curvature. However, we found that the observed relation can be explained without considering the local curvature sensing ability of endophilin in the membrane association process. In contrast, the diffusion-independent unbinding rate constant (koff) obtained from stopped-flow measurements shows a negative dependence on membrane curvature, which is controlled/mediated by endophilin-membrane interactions. This latter dependency, in addition to protein–protein interactions on the membrane, explains the selective binding of BAR proteins to highly curved membranes in equilibrium binding experiments.
Maximizing citizen scientists’ contribution to automated species recognition
Authors: Koch Wouter , Hogeweg Laurens , Nilsen Erlend B. , Finstad Anders G. 
Published: May 2022

AbstractTechnological advances and data availability have enabled artificial intelligence-driven tools that can increasingly successfully assist in identifying species from images. Especially within citizen science, an emerging source of information filling the knowledge gaps needed to solve the biodiversity crisis, such tools can allow participants to recognize and report more poorly known species. This can be an important tool in addressing the substantial taxonomic bias in biodiversity data, where broadly recognized, charismatic species are highly over-represented. Meanwhile, the recognition models are trained using the same biased data, so it is important to consider what additional images are needed to improve recognition models. In this study, we investigated how the amount of training data influenced the performance of species recognition models for various taxa. We utilized a large citizen science dataset collected in Norway, where images are added independently from identification. We demonstrate that while adding images of currently under-represented taxa will generally improve recognition models more, there are important deviations from this general pattern. Thus, a more focused prioritization of data collection beyond the basic paradigm that “more is better” is likely to significantly improve species recognition models and advance the representativeness of biodiversity data.
Research on permeable pores in collapse column fillings with different gradation structures
Authors: Song Shuang , Zhang Tianjun , Pan Hongyu , Pang Mingkun , Zhang Xiufeng , Zhang Lei , Bao Ruoyu 
Published: May 2022

AbstractParticle loss is an important cause of water inrush catastrophes in collapsed columns. In order to study the relationship between the lost particles of different graded rock samples and the pore structure of the subsidence column filling, experiments were designed and the changes of the seepage parameters of graded rock samples during the particle migration process under different permeable water pressures P and axial loads F were determined. The results show that: (1) There will be obvious collapse, silting and particle loss behaviors in the sample during different loading processes, and the rock samples with gradation values of n = 0.3 and n = 0.5 are dominant; (2) The relationship between porosity φ and bearing pressure The exponential function can be used to fit the loads F well, and the porosity decreases with the increase of the bearing load. The water surging characteristics before and after 1.2 MPa are mainly in the turbulent water gushing stage, accompanied by instantaneous slurry. Possibility of splashing and indenter sliding; (3) After infiltration, the condition of the remaining skeleton rock samples in the cylinder generally shows a trend of first decreasing rapidly, then increasing slowly, and then decreasing; (4) The gradation value n of the sample and the bottom There is a good correlation between the damaged area and the mean value S of the maximum area of the top water inrush channel. The maximum area increase of the damaged area and the maximum area increase of the water inrush channel show an opposite trend. The permeable pores of the graded samples can be divided into There are three situations of digging and collapse, water inrush gap and scouring hole, and the pore seepage process can be divided into 4 stages of inoculation of water seepage, rapid adjustment, rapid scour and steady flow.
Spatial–temporal variability and health impact of particulate matter during a 2019–2020 biomass burning event in Southeast Asia
Authors: Othman Murnira , Latif Mohd Talib , Hamid Haris Hafizal Abd , Uning Royston , Khumsaeng Thipsukon , Phairuang Worradorn , Daud Zawawi , Idris Juferi , Sofwan Nurzawani Md , Lung Shih-Chun Candice 
Published: May 2022

AbstractTo understand the characteristics of particulate matter (PM) in the Southeast Asia region, the spatial–temporal concentrations of PM10, PM2.5 and PM1 in Malaysia (Putrajaya, Bukit Fraser and Kota Samarahan) and Thailand (Chiang Mai) were determined using the AS-LUNG V.2 Outdoor sensor. The period of measurement was over a year from 2019 to 2020. The highest concentrations of all sizes of PM in Putrajaya, Bukit Fraser and Kota Samarahan were observed in September 2019 while the highest PM10, PM2.5 and PM1 concentrations in Chiang Mai were observed between March and early April 2020 with 24 h average concentrations during haze days in ranges 83.7–216 µg m−3, 78.3–209 µg m−3 and 57.2–140 µg m−3, respectively. The average PM2.5/PM10 ratio during haze days was 0.93 ± 0.05, which was higher than the average for normal days (0.89 ± 0.13) for all sites, indicating higher PM2.5 concentrations during haze days compared to normal days. An analysis of particle deposition in the human respiratory tract showed a higher total deposition fraction value during haze days than on non-haze days. The result from this study indicated that Malaysia and Thailand are highly affected by biomass burning activity during the dry seasons and the Southwest monsoon.
Darcy resistance flow of Sutterby nanofluid with microorganisms with applications of nano-biofuel cells
Authors: Aldabesh Abdulmajeed , Haredy A. , Al-Khaled Kamel , Khan Sami Ullah , Tlili Iskander 
Published: May 2022

AbstractThe objective of current research is to endorse the thermal aspect of Sutterby nanofluid containing the microorganisms due the stretched cylinder. The features of nonlinear thermal radiation, Darcy resistance and activation energy are also incorporated to inspect the thermal prospective. The problem is further extended with implementation of modified Fourier and Fick’s theories. The results are presented for the stretched cylinder and also for stationary plate. The numerical formulation for the problem is presented by following the shooting technique. The comparative numerical is performed to verify the computed simulations. The results convey that the presence of Darcy resistance parameter enhanced the velocity more effectively for stretched cylinder. A reduction in velocity due to Sutterby fluid parameter and buoyancy ratio parameter has been observed. Moreover, the temperature profile enhanced with larger sponginess parameter more effectively for stretching cylinder.