bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unraveling hidden interactions in complex systems with deep learning
Authors: Ha Seungwoong , Jeong Hawoong 
Published: June 2021

AbstractRich phenomena from complex systems have long intrigued researchers, and yet modeling system micro-dynamics and inferring the forms of interaction remain challenging for conventional data-driven approaches, being generally established by scientists with human ingenuity. In this study, we propose AgentNet, a model-free data-driven framework consisting of deep neural networks to reveal and analyze the hidden interactions in complex systems from observed data alone. AgentNet utilizes a graph attention network with novel variable-wise attention to model the interaction between individual agents, and employs various encoders and decoders that can be selectively applied to any desired system. Our model successfully captured a wide variety of simulated complex systems, namely cellular automata (discrete), the Vicsek model (continuous), and active Ornstein–Uhlenbeck particles (non-Markovian) in which, notably, AgentNet’s visualized attention values coincided with the true variable-wise interaction strengths and exhibited collective behavior that was absent in the training data. A demonstration with empirical data from a flock of birds showed that AgentNet could identify hidden interaction ranges exhibited by real birds, which cannot be detected by conventional velocity correlation analysis. We expect our framework to open a novel path to investigating complex systems and to provide insight into general process-driven modeling.
Association between ankle brachial index and development of postoperative intensive care unit delirium in patients with peripheral arterial disease
Authors: Kang Jihee , An Ji Hyun , Jeon Hong Jin , Park Yang Jin 
Published: June 2021

AbstractPatients with vascular diseases are prone to developing postoperative delirium (POD). Ankle brachial index (ABI) is a non-invasive clinical indicator of lower-extremities peripheral arterial disease (PAD) and has been identified as an indicator of cognitive impairment. We investigated the association between ABI and POD. 683 PAD patients who underwent elective leg arterial bypass surgery between October 1998 and August 2019 were collected for retrospective analysis. Demographic information, comorbidities, preoperative ABI and the Rutherford classification within one month prior to surgery were obtained. POD was assessed using the Confusion assessment method -intensive care unit. Logistic regression and receiver operating characteristics (ROC) curve analysis were used to assess the association between ABI and POD. The mean value of ABI was significantly lower in patients with POD than it was those without POD. Older age, more medical comorbidities, longer length of surgery, decreased ABI, and higher Rutherford class were all significantly associated with POD. The area under ROC (0.74) revealed that ABI below 0.35 was associated with development of POD. Lower preoperative ABI was associated with POD in PAD patients who underwent arterial bypass surgery.
Paired analysis of tumor mutation burden for lung adenocarcinoma and associated idiopathic pulmonary fibrosis
Authors: Yoneshima Yasuto , Iwama Eiji , Matsumoto Shingo , Matsubara Taichi , Tagawa Testuzo , Ota Keiichi , Tanaka Kentaro , Takenoyama Mitsuhiro , Okamoto Tatsuro , Goto Koichi , Mori Masaki , Okamoto Isamu 
Published: June 2021

AbstractGenetic alterations underlying the development of lung cancer in individuals with idiopathic pulmonary fibrosis (IPF) have remained unclear. To explore whether genetic alterations in IPF tissue contribute to the development of IPF-associated lung cancer, we here evaluated tumor mutation burden (TMB) and somatic variants in 14 paired IPF and tumor samples from patients with IPF-associated lung adenocarcinoma. We also determined TMB for 22 samples of lung adenocarcinoma from patients without IPF. TMB for IPF-associated lung adenocarcinoma was significantly higher than that for matched IPF tissue (median of 2.94 vs. 1.26 mutations/Mb, P = 0.002). Three and 102 somatic variants were detected in IPF and matched lung adenocarcinoma samples, respectively, with only one pair of specimens sharing one somatic variant. TMB for IPF-associated lung adenocarcinoma was similar to that for lung adenocarcinoma samples with driver mutations (median of 2.94 vs. 2.51 mutations/Mb) and lower than that for lung adenocarcinoma samples without known driver mutations (median of 2.94 vs. 5.03 mutations/Mb, P = 0.130) from patients without IPF. Our findings suggest that not only the accumulation of somatic mutations but other factors such as inflammation and oxidative stress might contribute to the development and progression of lung cancer in patients with IPF.
Time–outcome relationship in acute large-vessel occlusion exists across all ages: subanalysis of RESCUE-Japan Registry 2
Authors: Todo Kenichi , Yoshimura Shinichi , Uchida Kazutaka , Yamagami Hiroshi , Sakai Nobuyuki , Kishima Haruhiko , Mochizuki Hideki , Ezura Masayuki , Okada Yasushi , Kitagawa Kazuo , Kimura Kazumi , Sasaki Makoto , Tanahashi Norio , Toyoda Kazunori , Furui Eisuke , Matsumaru Yuji , Minematsu Kazuo , Kitano Takaya , Okazaki Shuhei , Sasaki Tsutomu , Sakaguchi Manabu , Takagaki Masatoshi , Nishida Takeo , Nakamura Hajime , Morimoto Takeshi ,   RESCUE-Japan Registry 2 Investigators, Toyoda Kazunori , Takeuchi Masataka , Morimoto Masafumi , Onda Toshiyuki , Shibata Masunari , Yoshimura Shinichi , Sakai Nobuyuki , Ohta Takahiro , Imai Keisuke , Itabashi Ryo , Ezura Masayuki , Yamashita Taro , Fukawa Norihito , Kimura Naoto , Doijiri Ryosuke , Ohta Hajime , Enomoto Yukiko , Kanbayashi Chisaku , Yamaura Ikuya , Ishihara Hideyuki , Kamiya Yuki , Hayase Makoto , Nii Kouhei , Kobayashi Junya , Yasuda Hiroaki , Kondo Ryushi , Yamamoto Daisuke , Sakaguchi Manabu , Satomi Junichiro , Yagita Yoshiki , Handa Akira , Shindo Atsushi , Hiyama Nagayasu , Toma Naoki , Tsumoto Tomoyuki , Kimura Kazumi , Tsuruta Wataro , Matsumoto Keigo , Kiura Yoshihiro , Yamazaki Takaaki , Hatano Taketo , Matsumoto Yoshihisa , Kojima Takao , Ikeda Norio , Sakamoto Shigeyuki , Ohnishi Hiroyuki , Haraguchi Koichi , Uchiyama Naoyuki 
Published: June 2021

AbstractEarly reperfusion after endovascular thrombectomy is associated with an improved outcome in ischemic stroke patients; however, the time dependency in elderly patients remains unclear. We investigated the time–outcome relationships in different age subgroups. Of 2420 patients enrolled in the RESCUE-Japan Registry 2 study, a study based on a prospective registry of stroke patients with acute cerebral large-vessel occlusion at 46 centers, we analyzed the data of 1010 patients with successful reperfusion after endovascular therapy (mTICI of 2b or 3). In 3 age subgroups (< 70, 70 to < 80, and ≥ 80 years), the mRS scores at 90 days were analyzed according to 4 categories of onset-to-reperfusion time (< 180, 180 to < 240, 240 to < 300, and ≥ 300 min). In each age subgroup, the distributions of mRS scores were better with shorter onset-to-reperfusion times. The adjusted common odds ratios for better outcomes per 1-category delay in onset-to-reperfusion time were 0.66 (95% CI 0.55–0.80) in ages < 70 years, 0.66 (95% CI 0.56–0.79) in ages 70 to < 80 years, and 0.83 (95% CI 0.70–0.98) in ages ≥ 80 years. Early reperfusion was associated with better outcomes across all age subgroups. Achieving early successful reperfusion is important even in elderly patients.
Multivariable mortality risk prediction using machine learning for COVID-19 patients at admission (AICOVID)
Authors: Kar Sujoy , Chawla Rajesh , Haranath Sai Praveen , Ramasubban Suresh , Ramakrishnan Nagarajan , Vaishya Raju , Sibal Anupam , Reddy Sangita 
Published: June 2021

AbstractIn Coronavirus disease 2019 (COVID-19), early identification of patients with a high risk of mortality can significantly improve triage, bed allocation, timely management, and possibly, outcome. The study objective is to develop and validate individualized mortality risk scores based on the anonymized clinical and laboratory data at admission and determine the probability of Deaths at 7 and 28 days. Data of 1393 admitted patients (Expired—8.54%) was collected from six Apollo Hospital centers (from April to July 2020) using a standardized template and electronic medical records. 63 Clinical and Laboratory parameters were studied based on the patient’s initial clinical state at admission and laboratory parameters within the first 24 h. The Machine Learning (ML) modelling was performed using eXtreme Gradient Boosting (XGB) Algorithm. ‘Time to event’ using Cox Proportional Hazard Model was used and combined with XGB Algorithm. The prospective validation cohort was selected of 977 patients (Expired—8.3%) from six centers from July to October 2020. The Clinical API for the Algorithm is http://20.44.39.47/covid19v2/page1.php being used prospectively. Out of the 63 clinical and laboratory parameters, Age [adjusted hazard ratio (HR) 2.31; 95% CI 1.52–3.53], Male Gender (HR 1.72, 95% CI 1.06–2.85), Respiratory Distress (HR 1.79, 95% CI 1.32–2.53), Diabetes Mellitus (HR 1.21, 95% CI 0.83–1.77), Chronic Kidney Disease (HR 3.04, 95% CI 1.72–5.38), Coronary Artery Disease (HR 1.56, 95% CI − 0.91 to 2.69), respiratory rate > 24/min (HR 1.54, 95% CI 1.03–2.3), oxygen saturation below 90% (HR 2.84, 95% CI 1.87–4.3), Lymphocyte% in DLC (HR 1.99, 95% CI 1.23–2.32), INR (HR 1.71, 95% CI 1.31–2.13), LDH (HR 4.02, 95% CI 2.66–6.07) and Ferritin (HR 2.48, 95% CI 1.32–4.74) were found to be significant. The performance parameters of the current model is at AUC ROC Score of 0.8685 and Accuracy Score of 96.89. The validation cohort had the AUC of 0.782 and Accuracy of 0.93. The model for Mortality Risk Prediction provides insight into the COVID Clinical and Laboratory Parameters at admission. It is one of the early studies, reflecting on ‘time to event’ at the admission, accurately predicting patient outcomes.
Association between alterations in plasma metabolome profiles and laminitis in intensively finished Holstein bulls in a randomized controlled study
Authors: Bäßler Sonja Christiane , Kenéz Ákos , Scheu Theresa , Koch Christian , Meyer Ulrich , Dänicke Sven , Huber Korinna 
Published: June 2021

AbstractMetabolic consequences of an energy and protein rich diet can compromise metabolic health of cattle by promoting a pro-inflammatory phenotype. Laminitis is a common clinical sign, but affected metabolic pathways, underlying pathophysiology and causative relationships of a systemic pro-inflammatory phenotype are unclear. Therefore, the aim of this study was to elucidate changes in metabolome profiles of 20 months old Holstein bulls fed a high energy and protein diet and to identify novel metabolites and affected pathways, associated with diet-related laminitis. In a randomized controlled feeding trial using bulls fed a high energy and protein diet (HEP; metabolizable energy [ME] intake 169.0 ± 1.4 MJ/day; crude protein [CP] intake 2.3 ± 0.02 kg/day; calculated means ± SEM; n = 15) versus a low energy and protein diet (LEP; ME intake 92.9 ± 1.3 MJ/day; CP intake 1.0 ± 0.01 kg/day; n = 15), wide ranging effects of HEP diet on metabolism were demonstrated with a targeted metabolomics approach using the AbsoluteIDQ p180 kit (Biocrates Life Sciences). Multivariate statistics revealed that lower concentrations of phosphatidylcholines and sphingomyelins and higher concentrations of lyso-phosphatidylcholines, branched chain amino acids and aromatic amino acids were associated with an inflammatory state of diet-related laminitis in Holstein bulls fed a HEP diet. The latter two metabolites share similarities with changes in metabolism of obese humans, indicating a conserved pathophysiological role. The observed alterations in the metabolome provide further explanation on the underlying metabolic consequences of excessive dietary nutrient intake.
Comparative untargeted metabolome analysis of ruminal fluid and feces of Nelore steers (Bos indicus)
Authors: Malheiros Jessica Moraes , Correia Banny Silva Barbosa , Ceribeli Caroline , Cardoso Daniel Rodrigues , Colnago Luiz Alberto , Junior Stanislau Bogusz , Reecy James Mark , Mourão Gerson Barreto , Coutinho Luiz Lehmann , Palhares Julio Cesar Pascale , Berndt Alexandre , de Almeida Regitano Luciana Correia 
Published: June 2021

AbstractWe conducted a study to identify the fecal metabolite profile and its proximity to the ruminal metabolism of Nelore steers based on an untargeted metabolomic approach. Twenty-six Nelore were feedlot with same diet during 105 d. Feces and rumen fluid were collected before and at slaughter, respectively. The metabolomics analysis indicated 49 common polar metabolites in the rumen and feces. Acetate, propionate, and butyrate were the most abundant polar metabolites in both bio-samples. The rumen presented significantly higher concentrations of the polar compounds when compared to feces (P < 0.05); even though, fecal metabolites presented an accentuated representability of the ruminal fluid metabolites. All fatty acids present in the ruminal fluid were also observed in the feces, except for C20:2n6 and C20:4n6. The identified metabolites offer information on the main metabolic pathways (higher impact factor and P < 0.05), as synthesis and degradation of ketone bodies; the alanine, aspartate and glutamate metabolisms, the glycine, serine; and threonine metabolism and the pyruvate metabolism. The findings reported herein on the close relationship between the ruminal fluid and feces metabolic profiles may offer new metabolic information, in addition to facilitating the sampling for metabolism investigation in animal production and health routines.
A step towards sustainable glass fiber reinforced concrete utilizing silica fume and waste coconut shell aggregate
Authors: Zaid Osama , Ahmad Jawad , Siddique Muhammad Shahid , Aslam Fahid , Alabduljabbar Hisham , Khedher Khaled Mohamed 
Published: June 2021

AbstractToday, it’s getting harder to find natural resources for concrete production. Utilization of the waste materials not just helps in getting them used in concrete, cement, and other construction materials, but also has various secondary advantages, for example, saving in energy, decrease in landfill cost, and protecting climate from pollution. Considering this in the development of modern structural design, utilizing waste materials instead of natural aggregate is a good option to make concrete that is sustainable and eco-friendly. The present research aims to find the impact of adding glass fiber into sustainable concrete made with silica fume, as a partial replacement of cement, and coconut shell added with different ratios as a replacement of coarse aggregate, on concrete mechanical and durability aspects. Various blends were made, with coconut shell as a substitution of coarse aggregates with different ratios. Portland cement was substituted with silica fume at 5%, 10%, 15%, and 20% by cement weight in all concrete blends. The volume ratios of glass fibers utilized in this study were 0.5%, 1.0%, 1.5% and 2.0%. Adding glass fibers increases concrete density to some extent and then marginally reduces the density of coconut shell concrete. When the percentage of glass fibers increases, the compressive, flexural and split tensile strength of coconut shell concrete also increases. From the lab results and SEM images of the present research display that glass fibers might be utilized in coconut shell concrete to enhance its mechanical and durability attributes, to accomplish sustainable concrete with acceptable strength with ease.
Comparison of endogenously expressed fluorescent protein fusions behaviour for protein quality control and cellular ageing research
Authors: Schneider Kara L. , Wollman Adam J. M. , Nyström Thomas , Shashkova Sviatlana 
Published: June 2021

AbstractThe yeast Hsp104 protein disaggregase is often used as a reporter for misfolded or damaged protein aggregates and protein quality control and ageing research. Observing Hsp104 fusions with fluorescent proteins is a popular approach to follow post stress protein aggregation, inclusion formation and disaggregation. While concerns that bigger protein tags, such as genetically encoded fluorescent tags, may affect protein behaviour and function have been around for quite some time, experimental evidence of how exactly the physiology of the protein of interest is altered within fluorescent protein fusions remains limited. To address this issue, we performed a comparative assessment of endogenously expressed Hsp104 fluorescent fusions function and behaviour. We provide experimental evidence that molecular behaviour may not only be altered by introducing a fluorescent protein tag but also varies depending on such a tag within the fusion. Although our findings are especially applicable to protein quality control and ageing research in yeast, similar effects may play a role in other eukaryotic systems.
Air pollution and retinal vessel diameter and blood pressure in school-aged children in a region impacted by residential biomass burning
Authors: Korsiak Jill , Perepeluk Kay-Lynne , Peterson Nicholas G. , Kulka Ryan , Weichenthal Scott 
Published: June 2021

AbstractLittle is known about the early-life cardiovascular health impacts of fine particulate air pollution (PM2.5) and oxidant gases. A repeated-measures panel study was used to evaluate associations between outdoor PM2.5 and the combined oxidant capacity of O3 and NO2 (using a redox-weighted average, Ox) and retinal vessel diameter and blood pressure in children living in a region impacted by residential biomass burning. A median of 6 retinal vessel and blood pressure measurements were collected from 64 children (ages 4–12 years), for a total of 344 retinal measurements and 432 blood pressure measurements. Linear mixed-effect models were used to estimate associations between PM2.5 or Ox (same-day, 3-day, 7-day, and 21-day means) and retinal vessel diameter and blood pressure. Interactions between PM2.5 and Ox were also examined. Ox was inversely associated with retinal arteriolar diameter; the strongest association was observed for 7-day mean exposures, where each 10 ppb increase in Ox was associated with a 2.63 μm (95% CI − 4.63, − 0.63) decrease in arteriolar diameter. Moreover, Ox modified associations between PM2.5 and arteriolar diameter, with weak inverse associations observed between PM2.5 and arteriolar diameter only at higher concentrations of Ox. Our results suggest that outdoor air pollution impacts the retinal microvasculature of children and interactions between PM2.5 and Ox may play an important role in determining the magnitude and direction of these associations.
Superconductor qubits hamiltonian approximations effect on quantum state evolution and control
Authors: Sharifi Javad 
Published: June 2021

AbstractMicrowave IQ-mixer controllers are designed for the three approximated Hamiltonians of charge, phase and flux qubits and the controllers are exerted both on approximate and precise quantum system models. The controlled qubits are for the implementation of the two quantum-gates with these three fundamental types of qubits, Quantum NOT-gate and Hadamard-gate. In the charge-qubit, for implementation of both gates, in the approximated and precise model, we observed different controlled trajectories. But fortunately, applying the controller designed for the approximated system over the precise system leads to the passing of the quantum state from the desired state sooner that the expected time. Phase-qubit and flux qubit have similar behaviour under the control system action. In both of them, the implementation of NOT-gate operation led to same trajectories which arrive at final goal state at different times. But in both of those two qubits for implementation of Hadamard-gate, desired trajectory and precise trajectory have some angle of deviation, then by exerting the approximated design controller to precise system, it caused the quantum state to approach the goal state for Hadamard gate implementation, and since the quantum state does not completely reach the goal state, we can not obtain very high gate fidelity.
Association between sanitary toilet coverage rate and intestinal infectious disease in Jiangsu Province, China
Authors: Chen TingTing , Kallawicha Kraiwuth 
Published: June 2021

AbstractIntestinal infectious disease is one of the most common diseases in China and is prevalent worldwide. The Chinese government launched a toilet improvement campaign to improve sanitation and reduce the incidence of diseases. This study determined the association between sanitary toilet use and intestinal infectious disease incidence in Jiangsu Province, China during 2011–2019. This study adopted an ecological retrospective research design. All secondary data were obtained through government websites and government information disclosure channels. Multiple linear regression was employed to analyze the association between the incidence of intestinal infectious diseases and sanitary toilet coverage rate and other potential predictors. Data suggested that the aggregate annual incidence of Type A and B intestinal infectious diseases showed a downward trend, the aggregate annual incidence of other infectious diarrhea continued to increase, and hand–foot–mouth disease occurred every other year with the highest annual incidence rate. The incidence was higher in coastal cities. Multiple regression results indicated that the usage of three types of sanitary toilets, compliance rate of water quality, and average ambient temperature have an impact on intestinal infectious diseases. The aggregate annual incidence of Type A and B intestinal infectious disease was negatively correlated with the cumulative use of sanitary toilets (β = − 0.036) and surface water quality (β =  − 0.135; p < 0.05). Increase in sanitary toilet use and water quality control can reduce the number of new cases, which will be beneficial for the population in the province. Moreover, the toilet improvement interventions should continue to maintain high-quality construction.
Kinetic mechanism of Na+-coupled aspartate transport catalyzed by GltTk
Authors: Trinco Gianluca , Arkhipova Valentina , Garaeva Alisa A. , Hutter Cedric A. J. , Seeger Markus A. , Guskov Albert , Slotboom Dirk J. 
Published: June 2021

AbstractIt is well-established that the secondary active transporters GltTk and GltPh catalyze coupled uptake of aspartate and three sodium ions, but insight in the kinetic mechanism of transport is fragmentary. Here, we systematically measured aspartate uptake rates in proteoliposomes containing purified GltTk, and derived the rate equation for a mechanism in which two sodium ions bind before and another after aspartate. Re-analysis of existing data on GltPh using this equation allowed for determination of the turnover number (0.14 s−1), without the need for error-prone protein quantification. To overcome the complication that purified transporters may adopt right-side-out or inside-out membrane orientations upon reconstitution, thereby confounding the kinetic analysis, we employed a rapid method using synthetic nanobodies to inactivate one population. Oppositely oriented GltTk proteins showed the same transport kinetics, consistent with the use of an identical gating element on both sides of the membrane. Our work underlines the value of bona fide transport experiments to reveal mechanistic features of Na+-aspartate symport that cannot be observed in detergent solution. Combined with previous pre-equilibrium binding studies, a full kinetic mechanism of structurally characterized aspartate transporters of the SLC1A family is now emerging.