bluuebunny/crossref_metadata_2025 huggingface dataset:
A Bayesian Deep Learning Approach to Near‐Term Climate Prediction
Authors: Luo Xihaier , Nadiga Balasubramanya T. , Park Ji Hwan , Ren Yihui , Xu Wei , Yoo Shinjae
Published: September 2022

Since model bias and associated initialization shock are serious shortcomings that reduce prediction skills in state‐of‐the‐art decadal climate prediction efforts, we pursue a complementary machine‐learning‐based approach to climate prediction. The example problem setting we consider consists of predicting natural variability of the North Atlantic sea surface temperature on the interannual timescale in the pre‐industrial control simulation of the Community Earth System Model. While previous works have considered the use of recurrent networks such as convolutional LSTMs and reservoir computing networks in this and other similar problem settings, we currently focus on the use of feedforward convolutional networks. In particular, we find that a feedforward convolutional network with a Densenet architecture is able to outperform a convolutional LSTM in terms of predictive skill. Next, we go on to consider a probabilistic formulation of the same network based on Stein variational gradient descent and find that in addition to providing useful measures of predictive uncertainty, the probabilistic (Bayesian) version improves on its deterministic counterpart in terms of predictive skill. Finally, we characterize the reliability of the ensemble of machine learning models obtained in the probabilistic setting by using analysis tools developed in the context of ensemble numerical weather prediction.
Effects of single- and multiple-dose oxytocin treatment on amygdala low-frequency BOLD fluctuations and BOLD spectral dynamics in autism
Authors: Alaerts Kaat , Bernaerts Sylvie , Wenderoth Nicole
Published: September 2022

Prior neuroimaging clinical trials investigating the neural effects of intranasal administration of the neuropeptide oxytocin demonstrated a key role of the amygdala in oxytocin’s neuromodulatory effects. These studies mostly demonstrated the acute effects of single-dose administrations, examining task-dependent effects of oxytocin on brain activity elicited during explicit experimental tasks or stimuli presentations. The increased consideration of oxytocin as a potential ameliorating treatment in autism spectrum disorder (ASD) requires a better understanding of how multiple-dose oxytocin administration affects intrinsic, task-free, amygdala function. In this double-blind, randomized, placebo-controlled trial with between-subject design, 38 adult men with ASD underwent resting-state fMRI scanning before and after oxytocin or placebo treatment. Effects were assessed either after a single-dose administration, consisting of 24 international units, or after multiple-dose treatment, consisting of 4 weeks of once-daily nasal spray administrations. Compared to placebo, oxytocin induced a decrease in intrinsic resting-state BOLD signal amplitudes of the bilateral amygdala (fractional amplitudes of low-frequency fluctuations) and modulated cross-frequency interactions between adjacent BOLD frequency components. The right amygdala showed a pattern of reduced cross-frequency harmonicity, while the left amygdala showed a relative increase in harmonic cross-frequency interactions after oxytocin treatment. Notably, the direction and magnitude of BOLD spectral changes induced after a single-dose were qualitatively similar to treatment effects induced after multiple-dose treatment. Furthermore, the identified spectral changes in amygdalar BOLD amplitude and cross-frequency harmonicity were associated with improved feelings of tension, reflecting oxytocin’s anxiolytic, stress-reducing neuromodulatory role. The observed effects of oxytocin on amygdalar BOLD spectral characteristics and associated behaviors contribute to a deeper mechanistic understanding of the intrinsic, task-free neuromodulatory dynamics that underlie single- and multiple-dose oxytocin treatment in ASD. European Clinical Trial Registry (Eudract 2014-000586-45).
An EGFR/HER2-targeted conjugate sensitizes gemcitabine-sensitive and resistant pancreatic cancer through different SMAD4-mediated mechanisms
Authors: Yao Hongjuan , Song Wenping , Cao Rui , Ye Cheng , Zhang Li , Chen Hebing , Wang Junting , Shi Yuchen , Li Rui , Li Yi , Liu Xiujun , Zhou Xiaofei , Shao Rongguang , Li Liang
Published: September 2022

Chemoresistance limits its clinical implementation for pancreatic ductal adenocarcinoma (PDAC). We previously generated an EGFR/HER2 targeted conjugate, dual-targeting ligand-based lidamycin (DTLL), which shows a highly potent antitumor effect. To overcome chemoresistance in PDAC, we aim to study DTLL efficacy when combined with gemcitabine and explore its mechanisms of action. DTLL in combination with gemcitabine show a superior inhibitory effect on the growth of gemcitabine-resistant/sensitive tumors. DTLL sensitizes gemcitabine efficacy via distinct action mechanisms mediated by mothers against decapentaplegic homolog 4 (SMAD4). It not only prevents neoplastic proliferation via ATK/mTOR blockade and NF-κB impaired function in SMAD4-sufficient PDACs, but also restores SMAD4 bioactivity to trigger downstream NF-κB-regulated signaling in SMAD4-deficient tumors and to overcome chemoresistance. DTLL seems to act as a SMAD4 module that normalizes its function in PDAC, having a synergistic effect in combination with gemcitabine. Our findings provide insight into a rational SMAD4-directed precision therapy in PDAC.
Adar-mediated A-to-I editing is required for embryonic patterning and innate immune response regulation in zebrafish
Authors: Niescierowicz Katarzyna , Pryszcz Leszek , Navarrete Cristina , Tralle Eugeniusz , Sulej Agata , Abu Nahia Karim , Kasprzyk Marta Elżbieta , Misztal Katarzyna , Pateria Abhishek , Pakuła Adrianna , Bochtler Matthias , Winata Cecilia
Published: September 2022

Adenosine deaminases (ADARs) catalyze the deamination of adenosine to inosine, also known as A-to-I editing, in RNA. Although A-to-I editing occurs widely across animals and is well studied, new biological roles are still being discovered. Here, we study the role of A-to-I editing in early zebrafish development. We demonstrate that Adar, the zebrafish orthologue of mammalian ADAR1, is essential for establishing the antero-posterior and dorso-ventral axes and patterning. Genome-wide editing discovery reveals pervasive editing in maternal and the earliest zygotic transcripts, the majority of which occurred in the 3’-UTR. Interestingly, transcripts implicated in gastrulation as well as dorso-ventral and antero-posterior patterning are found to contain multiple editing sites. Adar knockdown or overexpression affect gene expression by 12 hpf. Analysis ofadar-/- zygotic mutants further reveals that the previously described role of Adar in mammals in regulating the innate immune response is conserved in zebrafish. Our study therefore establishes distinct maternal and zygotic functions of RNA editing by Adar in embryonic patterning along the zebrafish antero-posterior and dorso-ventral axes, and in the regulation of the innate immune response, respectively.
Amyloidogenesis via interfacial shear in a containerless biochemical reactor aboard the International Space Station
Authors: McMackin Patrick , Adam Joe , Griffin Shannon , Hirsa Amir
Published: September 2022

Fluid interfaces significantly influence the dynamics of protein solutions, effects that can be isolated by performing experiments in microgravity, greatly reducing the amount of solid boundaries present, allowing air-liquid interfaces to become dominant. This investigation examined the effects of protein concentration on interfacial shear-induced fibrillization of insulin in microgravity within a containerless biochemical reactor, the ring-sheared drop (RSD), aboard the international space station (ISS). Human insulin was used as a model amyloidogenic protein for studying protein kinetics with applications to in situ pharmaceutical production, tissue engineering, and diseases such as Alzheimer’s, Parkinson’s, infectious prions, and type 2 diabetes. Experiments investigated three main stages of amyloidogenesis: nucleation studied by seeding native solutions with fibril aggregates, fibrillization quantified using intrinsic fibrillization rate after fitting measured solution intensity to a sigmoidal function, and gelation observed by detection of solidification fronts. Results demonstrated that in surface-dominated amyloidogenic protein solutions: seeding with fibrils induces fibrillization of native protein, intrinsic fibrillization rate is independent of concentration, and that there is a minimum fibril concentration for gelation with gelation rate and rapidity of onset increasing monotonically with increasing protein concentration. These findings matched well with results of previous studies within ground-based analogs.
Comparing the performance of Kernel PCA Mix Chart with PCA Mix Chart for monitoring mixed quality characteristics
Authors: Ahsan Muhammad , Mashuri Muhammad , Khusna Hidayatul
Published: September 2022

Along with the development of information and technology, the quality characteristics of a product cannot be monitored separately in the different types of control charts. In the past, conventional control charts were developed to monitor only one type of quality characteristic. The variable control charts are used to observe the variable or metric quality characteristics. Meanwhile, in monitoring non-metric characteristics or categorical data, attribute control charts are employed. To accommodate these two types of data, the PCA Mix control chart is suggested to simultaneously monitor these two types of data in one chart. However, some drawbacks occur when this chart is applied to monitor non-metric data which has an imbalanced proportion. Therefore, the Kernel PCA Mix control chart is created to overcome the gaps that occurred in the PCA Mix chart. Similar to the previous chart, this chart is also constructed using Hotelling’sT2statistics with Kernel Density Estimation control limit. Several simulations are used to evaluate the performance of the proposed control charts. The simulation results show that the proposed chart has a better result than the previous control chart, especially for a small mean shift with an imbalanced proportion of non-metric data. However, the PCA Mix chart has a similar performance to the proposed chart when it is applied to monitor the balanced proportion of categorical data with a large mean shift. The application with simulated data with various scenarios and the real-world case also shows that the Kernel PCA Mix chart performs better compared to the performance of the PCA Mix chart.
Adaptive SIR model with vaccination: simultaneous identification of rates and functions illustrated with COVID-19
Authors: Marinov Tchavdar T. , Marinova Rossitza S.
Published: September 2022

An Adaptive Susceptible-Infected-Removed-Vaccinated (A-SIRV) epidemic model with time-dependent transmission and removal rates is constructed for investigating the dynamics of an epidemic disease such as the COVID-19 pandemic. Real data of COVID-19 spread is used for the simultaneous identification of the unknown time-dependent rates and functions participating in the A-SIRV system. The inverse problem is formulated and solved numerically using the Method of Variational Imbedding, which reduces the inverse problem to a problem for minimizing a properly constructed functional for obtaining the sought values. To illustrate and validate the proposed solution approach, the present study used available public data for several countries with diverse population and vaccination dynamics—the World, Israel, The United States of America, and Japan.
Construction of a trio-based structural variation panel utilizing activated T lymphocytes and long-read sequencing technology
Authors: Otsuki Akihito , Okamura Yasunobu , Ishida Noriko , Tadaka Shu , Takayama Jun , Kumada Kazuki , Kawashima Junko , Taguchi Keiko , Minegishi Naoko , Kuriyama Shinichi , Tamiya Gen , Kinoshita Kengo , Katsuoka Fumiki , Yamamoto Masayuki
Published: September 2022

Long-read sequencing technology enable better characterization of structural variants (SVs). To adapt the technology to population-scale analyses, one critical issue is to obtain sufficient amount of high-molecular-weight genomic DNA. Here, we propose utilizing activated T lymphocytes, which can be established efficiently in a biobank to stably supply high-grade genomic DNA sufficiently. We conducted nanopore sequencing of 333 individuals constituting 111 trios with high-coverage long-read sequencing data (depth 22.2x, N50 of 25.8 kb) and identified 74,201 SVs. Our trio-based analysis revealed that more than 95% of the SVs were concordant with Mendelian inheritance. We also identified SVs associated with clinical phenotypes, all of which appear to be stably transmitted from parents to offspring. Our data provide a catalog of SVs in the general Japanese population, and the applied approach using the activated T-lymphocyte resource will contribute to biobank-based human genetic studies focusing on SVs at the population scale.
A sample-to-answer DNA detection microfluidic system integrating sample pretreatment and smartphone-readable gradient plasmonic photothermal continuous-flow PCR
Authors: Zhang Zengming , Zhao Shuhao , Jiang Lei , Wu Junjun , Zhao Wenhan , Guo Xiaoniu , Peng Niancai , Hu Fei
Published: September 2022

We report a microfluidic system integrating sample pretreatment and smartphone-readable gradient plasmonic photothermal continuous-flow PCR, paving the way for low-cost and rapid implementation of PCR diagnostics.
Chemical proteomic analysis of bile acid-protein targets in Enterococcus faecium
Authors: Yang Xinglin , Zhao Xiaohui , Chen Victor , Hang Howard C.
Published: September 2022

Chemoproteomics of bile acid-protein targets reveals a bile salt hydrolase in Enterococcus faecium.
Novel crystal forms of Entresto: a supramolecular complex of trisodium sacubitril/valsartan hemi-pentahydrate
Authors: Shaikh Tabrez R. , George Christy P. , Bhukya Priyanka , Shelke Nikita , Pawar Komal , Garai Abhijit , Dandela Rambabu , Gonnade Rajesh G. , Nangia Ashwini K.
Published: September 2022

The synthesis of Entresto, a multidrug cocrystal from sacubitril sodium and valsartan disodium using different conditions yielded six novel crystal forms. Stability studies showed higher stability of Form-I and III over the other crystal forms.
Machine learning of phase diagrams
Authors: Lund J. , Wang H. , Braatz R. D. , García R. E.
Published: September 2022

A ML strategy is presented to infer the free energy state functions by using phase diagram images as input, resulting in optimized properties 3–5 orders of magnitude faster and dramatically increased accuracy as compared to current approaches.
Polymer-grafted ZnO nanorods enhance optical nonlinearity of oligothiophene-doped liquid crystals
Authors: Mejia Jose Carlos , Matsumoto Kohsuke , Ogata Kaho , Taguchi Daisuke , Nakano Kaho , Kubo Shoichi , Shishido Atsushi
Published: September 2022

The photoinduced molecular reorientation of nonlinear optical materials is a promising approach to cause the nonlinear optical effect used for developing next-generation self-modulating and optical switching devices.
STM-induced ring closure of vinylheptafulvene molecular dipole switches on Au(111)
Authors: Au-Yeung Kwan Ho , Kühne Tim , Aiboudi Oumaima , Sarkar Suchetana , Guskova Olga , Ryndyk Dmitry A. , Heine Thomas , Lissel Franziska , Moresco Francesca
Published: September 2022

Ring-closure reaction of a single vinylheptafulvene adsorbed on the Au(111) surface induced by voltage pulses from the tip of a scanning tunneling microscope.
Structural, optical and magnetic properties of pure and 3d metal dopant-incorporated SnO2 nanoparticles
Authors: K K Supin , George Anson , Kumar Y. Ranjith , K. K. Thejas , Mandal Guruprasad , Chanda Anupama , Vasundhara M.
Published: September 2022

We focused on the systematic study of the effect of Fe, Co and Ni substitution on the structural, optical and magnetic properties of SnO2 nanoparticles.
Indirect aqueous carbonation of CaSO4·2H2O with aspartic acid as a recyclable additive
Authors: Gong Yuan , Zhu Xuechen , Yang Zhuo , Zhang Xin , Li Chunlei
Published: September 2022

Aspartic acid was employed as a recyclable additive during the indirect aqueous carbonation of CaSO4·2H2O. The multiple roles of aspartic acid were found to be Ca2+ leaching agent, CO2 absorbent, and CaCO3 polymorph regulator.
MultiShapeC, an algorithm to assess concentration in multi-shape nanoparticle samples: nanosilver, a case study
Authors: Núñez Rodrigo Nicolás , Veglia Alicia Viviana , Pacioni Natalia Lorena
Published: September 2022

An algorithm to include multi-shape and polydispersity in the nanoparticle concentration calculation is presented.
Diamond-rich crystalline nanosheets seeded with a Langmuir monolayer of arachidic acid on water
Authors: Tanaka Toshihiko , Miura Yasuhiro F. , Aoyama Tetsuya , Miyamoto Kazunori , Akagi Yoshiya , Uchiyama Masanobu , Osawa Eiji
Published: September 2022

Crystalline nanosheets with thickness of ∼25 nm were grown from a Langmuir monolayer of arachidic acid at the interface between air and a dilute aqueous nanodiamond (ND) solution. They are hydrated colloidal crystals of homogeneous ND particles.
A Cu(ii) complex supported on Fe3O4@SiO2 as a magnetic heterogeneous catalyst for the reduction of environmental pollutants
Authors: Khalaj Mehdi , Zarandi Maryam
Published: September 2022

Nitro-aromatic-pollutants are hazardous to people and the environment. In this work, the catalytic potential of CM@SS-BBTU-Cu(ii) has been investigated for reduction of nitro group in aqueous media by NaBH4.
Implications of the unfolded state in the folding energetics of heterogeneous-backbone protein mimetics
Authors: Santhouse Jacqueline R. , Leung Jeremy M. G. , Chong Lillian T. , Horne W. Seth
Published: September 2022

Biophysical experiments and atomistic simulation reveal impacts of protein backbone alteration on the ensemble that defines the unfolded state. These effects have implications on folded stability of protein mimetics.
An electrochemically deposited ordered hierarchical metal–organic framework-based dual-module sensor for decoding organic vapors
Authors: Qin Sijia , Chen Min , Wu Limin
Published: September 2022

A dual-module lanthanide MOF film with three-dimensional ordered macro-microporous structure was fabricated to discriminate six amines, enabling a multi-analyte recognition decoding scheme.
Electroreduction of CO2to CO over wide potential window byin situelectrodeposited CdCO3/Cd-CP electrocatalysts
Authors: Yang Jie , Yang Han , Zhang Renjie , Zhou Guangying , Li Hongping , Yang Dexin
Published: September 2022

The electrodeposited CdCO3/Cd-CP-xelectrocatalysts exhibited outstanding catalytic performance for CO2electroreduction in both pure CO2and low CO2concentration.
Balancing the trade-off between the mechanical and electrical properties of conjugated polymer blend films for organic field-effect transistors
Authors: Ren Hang , Tong Yanhong , Ouyang Mingzhao , Wang Jiake , Zhang Lei , Fu Yuegang , Tang Qingxin
Published: September 2022

A balance between the mechanical and electrical performance is achieved in conjugated polymer blend films with an optimal blend ratio.
Doubly 1,3-butadiyne-bridged ditwistacene with enhanced ultrafast broadband reverse saturable absorption
Authors: Han Yanbing , Xiao Jinchong , Wu Xingzhi , Wang Yuxiao , Zhang Xueru , Song Yinglin
Published: September 2022

The introduction of a double 1,3-butadiyne bridge greatly enhances the ultrafast broadband reverse saturable absorption of twistacene.
The influence of axial fluorination of SubPc on the photoresponse performances of small-molecule organic photodiodes
Authors: Fang Feifei , Minami Daiki , Yun Sungyoung , Heo Chul-Joon , Shibuya Hiromasa , Hong Hyerim , Choi Byoungki , Park Kyung-Bae
Published: September 2022

The accelerated photoresponse of OPD devices for axial fluorinated SubPc was confirmed by photovoltaic analysis and theoretical simulations.
The Association between Breast Cancer Related Lymphedema and Area Deprivation Index
Authors: Chiang Sarah N. , Finnan Michael J. , Varagur Kaamya , Skolnick Gary B. , Sacks Justin M. , Christensen Joani M.
Published: September 2022

Background Lymphedema affects up to 34% of patients after breast cancer treatment but remains underdiagnosed and undertreated. Here, we use area deprivation index (ADI), a measure of neighborhood socioeconomic disadvantage, to determine how socioeconomic status may affect risk for and diagnosis of breast cancer-related lymphedema.

Methods Records of patients who underwent surgical treatment of breast cancer between 2017–2020 were examined. Patients' nine-digit ZIP codes were utilized to determine their deprivation level as a national ADI percentile, and those fitting into the most and least deprived quartiles were compared with evaluate lymphedema risk factors and incidence.

Results A total of 1,333 breast cancer patients were included, 812 (61%) of whom resided within the most disadvantaged ADI quartile nationally, and 521 within the least disadvantaged quartile. The most deprived group had higher rates of diabetes, obesity, and regional breast cancer, and received more extensive surgeries (7.5% modified radical mastectomy vs 1.9%, p < 0.001) and chemotherapy compared with the least disadvantaged quartile. The most disadvantaged cohort were more often at extreme risk of lymphedema utilizing the Risk Assessment Tool Evaluating Lymphedema Risk (9.1% versus 2.5%, p < 0.001); however, the incidence of lymphedema diagnoses was not significantly higher (13% vs 12%, p > 0.9). Logistic regression showed that the most deprived ADI quartile had 44% lower odds of a lymphedema diagnosis in comparison to the least deprived quartile.

Conclusion Residing in more socioeconomically disadvantaged neighborhoods is associated with lower odds of a lymphedema diagnosis, despite higher rates of risk factors for lymphedema, suggesting significant underdiagnosis in this population.
Campsiandra laurifolia Reduces Oxidative Stress and Inflammation in Rats with Ulcerative Colitis
Authors: da Fonseca Sandielly Rebeca Benitez , de Souza Lucas Petitemberte , Fillmann Henrique Sarubbi , Hartmann Renata Minuzzo , Colares Josieli Raskopf , Schemitt Elizângela Gonçalves , Brasil Marilda da Silva , Suyenaga Edna Sayuri , Marroni Norma Anair Possa
Published: September 2022

Ulcerative colitis (UC) affects the mucosa and submucosa of the large intestine. One of the mechanisms involved in its etiology is oxidative stress (OS), directly involved in the inflammatory process characteristic of UC. The Campsiandra laurifolia, known as acapurana, was described as possessing antioxidant properties. We used 24 male Wistar rats, divided into control (CO), control + acapurana (CO + A), colitis (CL), and colitis + acapurana (CL + A) groups. This study performed histological analysis, measuring anal sphincter pressure (ASP) and lipoperoxidation (LPO). The activity of the antioxidant enzyme superoxide dismutase (SOD) and glutathione (GSH) levels were evaluated. The expression of the nuclear factor kappa B (NFκB) and inducible nitric oxide synthase (iNOS) was analyzed by immunohistochemistry. The statistical analysis used was the one-way analysis of variance (ANOVA), followed by the Student-Newman-Keuls test; values were expressed as mean ± standard error, and the significance level was p < 0.05. In the animals of the CL group, we observed the destruction of the crypts and the presence of mucosal ulcers, edema, and submucosal inflammatory infiltrate, as well as increased damage to the intestinal mucosa, reduced ASP, increased LPO and SOD activity, reduced GSH levels, and increased expression of NFκB and iNOS. The administration of C. laurifolia in the CL + A group was shown to cause regeneration of crypts, reduction of inflammatory infiltrate, reduction of damage to the intestinal mucosa, increase in ASP, and reduction in LPO with the restoration of SOD activity and GSH levels. The immunohistochemistry of NFκB and iNOS was significantly reduced. Therefore, the C. laurifolia aqueous extract appears to exert an antioxidant and anti-inflammatory effect in rats with AA-induced colitis.
Correlation between Central Obesity and Liver Function in Young Adults—A Cross-Sectional Study
Authors: Alvin John , KM Damodara Gowda
Published: September 2022

Background Visceral fat is a more accurate predictor of metabolic and cardiovascular disease risk than body fat alone. Although the liver function is associated with waist-to-hip ratio (WHR) in studies, this correlation is not well established in young central obese individuals. In this study, we examined the correlation between liver function parameters and central obesity in young obese subjects.

Methods Subjects with central obesity among the student and staff community between 18 and 40 years were recruited for the study after their written and informed consent. Male subjects whose WHR is above 0.90 and females above 0.85 were included. The liver function was assessed by estimating alanine transaminase (ALT), aspartate transaminase (AST), albumin, globulin, albumin:globulin ratio (A:G ratio), total bilirubin, direct bilirubin, and Gamma-glutamyl transferase (GGT). The data were analyzed using Pearson correlation to find the statistical significance between lung function parameters in centrally obese individuals with their WHR using SPSS version-16. A p-value less than 0.05 was considered the level of significance.

Results The results showed an insignificant correlation between the liver function parameters (p > 0.05) and WHR except for serum albumin (p < 0.021). The level of AST, ALT, total protein, globulin, A:G ratio, GGT, total Bilirubin, and direct bilirubin in young male and female central obese subjects have not deviated from the normal physiological range.

Conclusion The serum albumin level estimation will be considered an early indicator of metabolic disorder due to central obesity.
Clinical Score Application for Abdominopelvic Computed Tomography Used in the Diagnosis of Renal Colic Patients
Authors: Gönüllü Gizem , Selvi Fatih , Bedel Cihan
Published: September 2022

Background To develop risk scoring for the use of computed tomography (CT) imaging using the visual analog scale (VAS), physical examination, and laboratory findings of renal colic patients admitted to the emergency department (ED).

Materials and Methods This is prospective observational study. Among the patients who presented to the ED with abdominal or flank pain, patients who were scheduled for CT imaging for urolithiasis were included in the study. The mean VAS pain scores, physical examination findings, laboratory parameters, and macroscopic and microscopic values in urinalysis were compared between the two groups with and without stones on CT.

Results Of the 196 urolithiasis patients included in the study, 165 had ureteral stones, 76 had renal stones, and 45 had renal and ureteral stones. While the difference between the urine erythrocyte averages of the two groups was borderline significant (p = 0.04), there was a high difference between the urinary hemoglobin amounts (p < 0.001). In patients with urinary system stone disease, hydronephrosis, and ureteral dilatation, hemoglobin ++ and above were more significant (p < 0.001). For ureteral stones, pain intensity increased as the size increased (r = 0.34 p < 0.001). White blood cells > 10,000 103/mL, and C-reactive protein (CRP) ≤ 5 mg/L were more significant in patients with acute renal colic.

Conclusions Although we cannot develop a clinical scoring system for renal colic patients, the meaningful results we found for urinary stone disease can be used in a newly developed scoring system. It can be used in new scoring systems in the ED using a high VAS score, presence and amount of urine hemoglobin, CRP) ≤ 5 mg/L, and creatinine value.
A connectivity-based approach to evaluating port importance in the global container shipping network
Authors: Jarumaneeroj Pisit , Ramudhin Amar , Barnett Lawton Jorge
Published: September 2022

This paper proposes a framework for evaluating the strategic importance of container ports based on their connectivity. The Container Port Connectivity Index is computed and decomposed into components according to the Liner Shipping Connectivity Index—each reflecting its contribution to the overall port importance score. The framework produces separate scores for each component, thus allowing port stakeholders to better comprehend why a particular port has become important, and for what reasons. The decomposition approach also allows more detailed analyses, and explanations of the impacts of major economic phenomena—i.e., the expansion of Panama Canal or the crumbling of Hanjin shipping—on the relative importance of ports within the Global Container Shipping Network, as more explanatory variables become available. Our computational results indicate that, while the connectivity of ports related to these events is impacted, changes on connectivity rankings could be adequately explained by the proposed decomposition scheme. The inbound connectivity of New York, for example, was slightly improved after the Panama Canal expansion—from the 29th place in Q1/2016 to the 24th place in Q2/2016—due mainly to the rise in the larger capacity of ships calling. However, in Q3/2016, its inbound rank returned to the 29th place, which was mainly due to the decline in the number of liner services available, number of liner companies, and number of ships calling. The effects of Hanjin’s bankruptcy, on the contrary, were more localized and relatively brief.
Study on phase demodulation algorithm of fiber optic pressure sensor based on nonlinear differential equation
Authors: Feng Fei , Jia Qi , Liu Chunhua , Yue Kaibai
Published: September 2022

Fiber optic Fabry–Pérot sensors have been widely developed with unique advantages, such as ease of reuse, resistance to electromagnetic interference, light weight, and their ability to work in extreme environments. There are many demodulation methods that can be applied to fiber optic Fabry–Pérot sensors, including the intensity demodulation method, spectral demodulation, and the phase carrier method, but these demodulation methods cannot meet the requirements that take into account range, speed, and dynamic and static demodulation capabilities. In view of these problems, this paper uses nonlinear differential equations to solve the problem of simultaneous measurement of a large number of ranges and dynamic and static parameters. The measuring interferometer in the demodulation module was built using a polarizing interferometer, which avoids the difficulty in optical wedge processing when using a Fizeau interferometer. Regarding the problems of high and low signal-to-noise ratios of the generated signal, for the problem that the introduction of dispersion in the crystal causes the demodulation result of the traditional demodulation method to be wrong, a nonlinear differential equation is proposed to achieve the correct demodulation of the fiber optic sensor: the slow demodulation speed problem. This paper designs the acquisition, transmission, and processing system based on digital signal processing and a field-programmable gate array, which provide a hardware platform for real-time demodulation. Finally, experiments to test the resolution, linearity, stability, and repeatability of the interferometer were carried out on the designed demodulation system.
Charge dissociation in organic solar cells—from Onsager and Frenkel to modern models
Authors: Liraz Dan , Tessler Nir
Published: September 2022

Organic-based solar cells have developed for the last three decades. Moving forward generally requires the assistance of useful models that are adapted to currently used materials and device architectures. The least understood part of the charge generation is the first step of the exciton dissociation, and new or refined models are being suggested. However, many of today's questions have been asked before, going back almost an entire century. We have gone to the 1930s and attempted to critically review significant contributions on equal footing. We find that Onsager's and Frenkel's models have a similar foundation but were developed to suit very different materials (ions in solutions vs electrons in semiconductors). The contribution by Braun or the Onsager–Braun model can be considered wrong, yet it was instrumental for the field's development. The community practically ignores one of the most promising models (Arkhipov–Baranovskii). Hot exciton dissociation has many faces due to “hot” being a relative term and/or the heat being stored in different ways (electronic, vibronic, etc.). Entropy considerations are instrumental in simplifying the picture, yet they add no physics compared to the full-3D models. We hope that by emphasizing the physical picture of the various models and the underlying assumptions, one could use them as a stepping stone to the next generation models.
Modeling results on the dust charge distribution in a plasma afterglow
Authors: Denysenko I. B. , Mikikian M. , Azarenkov N. A.
Published: September 2022

Discharging of dust particles in an argon plasma afterglow is investigated using different approaches. First, the dust charge distribution function (DCDF) is obtained by solving numerically the master equation describing dust discharging as a one-step stochastic process. Second, the DCDF is calculated as a Gaussian distribution with mean dust charge and variance, which are functions of time. Additionally, the time-dependencies for the mean dust charge are obtained assuming that the charge changes continuously in the afterglow plasma. Calculation results are compared with available experimental data and are found to be in good qualitative agreement if the dust discharging model accounts for the emission of electrons in the collisions of excited argon atoms with dust particles. This study is carried out taking into account the transition from ambipolar to free diffusion as well as multistep ionization, excitation, and deexcitation of argon atoms in the plasma afterglow.
Resonant alpha particle loss in stellarators
Authors: White Roscoe
Published: September 2022

Particle resonances in stellarators can produce islands in the space of passing particle orbits without the presence of an unstable Alfvén mode, provided the period of the resonance matches the period of the equilibrium magnetic field. In this case, the equilibrium itself plays the role of a mode amplitude, and the islands appear on surfaces where the orbital helicity matches the field period. At low energy, these surfaces are given by the field line helicity, but at higher energy, cross field drift causes them to move. The resonances are also felt by trapped particles bouncing back and forth on surfaces with matching helicity. The periodic variation of B along these orbits produces local wells, giving loss due to drift while trapped in a well. Stellarator designs that have equilibrium-induced resonance islands exhibit anomalous alpha particle loss and are unsuitable for reactors.
Tunable magnon antibunching via degenerate three-wave mixing in a hybrid ferromagnet–superconductor system
Authors: Li Xiyun , Cheng Guang-Ling , Yang Wen-Xing
Published: September 2022

We propose a scheme for achieving magnon antibunching in a hybrid ferromagnet–superconductor system, where the magnons excited in two yttrium iron garnet (YIG) spheres couple the different levels of a cyclic three-level superconducting qubit by eliminating two perpendicular microwave cavity modes. With the aid of the three-level system, we find that the magnon antibunching can be achieved in a weak coupling regime via the degenerate three-wave mixing process. Moreover, it is found that the magnon antibunching inside a YIG2 sphere can be effectively regulated by manipulating the YIG1 sphere, for instance, the coupling strength of the YIG1 sphere and qubit and the driving strengths of the system. This work provides an alternative scheme for constructing the single magnon source based on the ferromagnet–superconductor technology and is conducive to studying the quantum properties of magnons.
A liquid–solid mixed robot based on ferrofluid with high flexibility and high controllability
Authors: Zhang Yicheng , Qin Ling , Wang Jiyao , Xu Wei
Published: September 2022

A magnetically actuated robot, which could be divided into two categories, a solid-particle magnetic robot and a ferrofluid-based robot, has the potential application in rescuing, bioengineering, and medication. However, the solid-particle magnetic robot is limited by the pre-designed location of magnetization, which limits the flexibility of the robot. Here, this paper proposed a liquid–solid mixed and ferrofluid-based robot, which could overcome the weakness of the magnetic solid particle robot. In addition, topology optimization is used in the design process of the robot to obtain the logical structure for minimizing flow loss. The feasibility of the robot is validated in the COMSOL simulation model. Experimental results demonstrate that the robot possesses large flexibility and high controllability and can be adapted to various environmental situations.
Low-temperature preparation and electrical properties of CaBi2Nb2O9 piezoelectric ceramic by addition of B2O3
Authors: Pan C. B. , Zhao G. C. , Li S. M. , Wang X. L. , Wang J. M. Z. , Tao M. , Yin L. H. , Song W. H. , Zhu X. B. , Yang J. , Sun Y. P.
Published: September 2022

CaBi2Nb2O9 ceramics were fabricated via the solid-state reaction method by the addition of B2O3 as a sintering aid at lower sintering temperatures than that prepared without B2O3. Ferroelectricity, piezoelectricity, and resistivity can be still greatly enhanced when the sintering temperature is decreased from 1075 °C for CaBi2Nb2O9 to 975 °C for CaBi2Nb2O9–0.25 wt. % B2O3. The high resistivity and weak c-axis texture ensure that the ceramics can be fully polarized in a high enough electric field. The increased spontaneous ferroelectric and remanent polarization result in a significant enhancement in the piezoelectric properties of CaBi2Nb2O9–0.25 wt. % B2O3. The sample sintered at 975 °C possesses a high piezoelectric coefficient d33 of ∼15.0 pC/N and resistivity of 1.4 × 106 Ω cm (at 600 °C) along with a high ferroelectric Curie temperature TC of ∼954 °C. This work is beneficial for the preparation of high-temperature piezoelectric ceramics with excellent electrical properties at a low sintering temperature.
Non-contact optical thermometry via non-thermally coupled levels in upconverting glass
Authors: Kesarwani Vishab , Rai Vineet Kumar
Published: September 2022

This research article reports the non-contact optical thermometric study using the UC emission intensity ratio of thermally and non-thermally coupled levels. Tm3+/Er3+/Yb3+ codoped TeO2-WO3-Bi2O3 (TWBi) glass have been synthesized using melt-quenching technique. After analyzing the optical absorption and UC emission spectra at room temperature, the temperature-dependent study of UC emission spectra has been performed in the 303–523 K range. First, the optical temperature sensing using the luminescence intensity ratio of thermally coupled levels of Er3+ ion has been studied. The maximum value of absolute and relative sensitivities has been found to be ∼0.0088 K−1 at 483 K and ∼0.0120 K−1 at 303 K, respectively. Furthermore, the luminescence intensity ratio approach has been employed to study non-contact temperature sensing in non-thermally coupled levels. While employing the ratiometric approach involving non-thermally coupled levels, a simultaneous improvement in absolute and relative sensitivities has been witnessed. There, the maximum value of absolute and relative sensitivities has been found as high as ∼0.7143 K−1 at 523 K and ∼0.0249 K−1 at 483 K, respectively. It has been found that the relative sensitivity in the case of non-thermally coupled levels (NTCLs) clearly dominates the relative sensitivity of TCLs.
Perspective: Mechanistic investigations of photocatalytic processes with time-resolved optical spectroscopy
Authors: Wang Chen , Malinoski Aaron
Published: September 2022

Rational design and optimization of photocatalytic systems can only be achieved through understanding the reaction mechanisms involved. Time-resolved optical spectroscopy has been employed to resolve the complexities involved in photocatalytic reaction systems by identifying transient reaction intermediates and measuring the key kinetic parameters. In this Perspective, we showcase three systems that were systematically investigated as examples to demonstrate that well-designed time-resolved spectroscopic experiments can play a vital role in mechanistic investigations of photocatalytic systems while it is necessary to combine them with other analytical methods to fully resolve the complexities in these reaction processes. We summarize the commonly used methodologies and indicate the critical dynamic information that should be addressed in spectroscopic analysis. We also discuss the utilization of mechanistic insights to improve reaction performances and inspire the invention of novel photocatalysts. We foresee that the close collaboration of physical, synthetic, and materials chemists will mutually promote progress in the rapidly developing fields of photocatalysis and spectroscopy.
Translaboration
Authors: Zwischenberger Cornelia , Alfer Alexa
Published: September 2022

Translaboration, a concept derived from blending ‘translation’ and ‘collaboration,’ has the concept of labour at its core. This paper investigates the dimension of labour in online collaborative translation, relates translational labour to Arendt’s categories of work and action, and proceeds to broaden the discussion to the labour involved in translation more generally. It also considers what effect the application of these concepts has on the interests of translators and other stakeholders. Probing the labour of translation has a profound bearing on framings of both voluntary and professional translation practices and potentially reshapes discussions of the translation concept as such. Rather than pitting ‘work’ and ‘labour’ as competing concepts, this paper shows that labour, work, and action all apply to translation and can be brought into productive dialogue in the translaborative space.
Exposure to animal feeding operations including concentrated animal feeding operations (CAFOs) and environmental justice in Iowa, USA
Authors: Son Ji-Young , Bell Michelle L
Published: September 2022

Health consequences of intensive livestock industry and implications for environmental justice are of great concern in Iowa, USA, which has an extensive history of animal feeding operations (AFOs). We examined disparities in exposure to AFOs including concentrated AFOs (CAFOs) with several environmental justice metrics and considered exposure intensity based on animal units (AUs). Using data on permitted AFOs from the Iowa Department of Natural Resources, we evaluated environmental disparities by multiple environmental justice metrics (e.g. race/ethnicity, socio-economic status (SES), income inequality (Gini index), racial isolation, and educational isolation) using 2010 Census tract-level variables. We used an exposure metric incorporating the density and intensity as the sum of AUs within each Census tract. We investigated exposure disparities by comparing distributions of environmental justice metrics based on operation type (e.g. confinement, open feedlot, large CAFOs), animal type, and Census tract-level AFOs exposure intensity categories (i.e. from low exposure (quartile 1) to high exposure (quartile 4)). AFOs in Iowa were located in areas with lower percentages of racial/ethnic minority persons and high SES communities. For example, the percent of the population that is non-Hispanic Black was over 9 times higher in Census tracts without AFOs than tracts with AFOs (5.14% vs. 0.55%). However, when we considered AFO exposure intensity within the areas having AFO exposure, areas with higher AFO exposure had higher percentages of racial/ethnic minority persons (e.g. Hispanic) and low SES communities (e.g. higher educational isolation) compared to areas with lower AFO exposure. Findings by AFO type (e.g. large CAFO, medium CAFO) showed similar patterns of the distribution of environmental justice metrics as the findings for AFOs overall. We identified complex disparities with higher exposure to non-disadvantaged subpopulations when considering areas with versus without AFOs, but higher exposure to disadvantaged communities within areas with AFOs.
MERRIN: MEtabolic regulation rule INference from time series data
Authors: Thuillier Kerian , Baroukh Caroline , Bockmayr Alexander , Cottret Ludovic , Paulevé Loïc , Siegel Anne
Published: September 2022

Motivation

Many techniques have been developed to infer Boolean regulations from a prior knowledge network (PKN) and experimental data. Existing methods are able to reverse-engineer Boolean regulations for transcriptional and signaling networks, but they fail to infer regulations that control metabolic networks.

Results

We present a novel approach to infer Boolean rules for metabolic regulation from time-series data and a PKN. Our method is based on a combination of answer set programming and linear programming. By solving both combinatorial and linear arithmetic constraints, we generate candidate Boolean regulations that can reproduce the given data when coupled to the metabolic network. We evaluate our approach on a core regulated metabolic network and show how the quality of the predictions depends on the available kinetic, fluxomics or transcriptomics time-series data.

Availability and implementation

Software available at https://github.com/bioasp/merrin.

Supplementary information

Supplementary data are available at https://doi.org/10.5281/zenodo.6670164.
Design centering enables robustness screening of pattern formation models
Authors: Solomatina Anastasia , Cezanne Alice , Kalaidzidis Yannis , Zerial Marino , Sbalzarini Ivo F
Published: September 2022

Motivation

Access to unprecedented amounts of quantitative biological data allows us to build and test biochemically accurate reaction–diffusion models of intracellular processes. However, any increase in model complexity increases the number of unknown parameters and, thus, the computational cost of model analysis. To efficiently characterize the behavior and robustness of models with many unknown parameters remains, therefore, a key challenge in systems biology.

Results

We propose a novel computational framework for efficient high-dimensional parameter space characterization of reaction–diffusion models in systems biology. The method leverages the Lp-Adaptation algorithm, an adaptive-proposal statistical method for approximate design centering and robustness estimation. Our approach is based on an oracle function, which predicts for any given point in parameter space whether the model fulfills given specifications. We propose specific oracles to efficiently predict four characteristics of Turing-type reaction–diffusion models: bistability, instability, capability of spontaneous pattern formation and capability of pattern maintenance. We benchmark the method and demonstrate that it enables global exploration of a model’s ability to undergo pattern-forming instabilities and to quantify robustness for model selection in polynomial time with dimensionality. We present an application of the framework to pattern formation on the endosomal membrane by the small GTPase Rab5 and its effectors, and we propose molecular mechanisms underlying this system.

Availability and implementation

Our code is implemented in MATLAB and is available as open source under https://git.mpi-cbg.de/mosaic/software/black-box-optimization/rd-parameter-space-screening.

Supplementary information

Supplementary data are available at Bioinformatics online.