bluuebunny/crossref_metadata_2025_split huggingface dataset:
On Multi‐Model Assessment of Complex Degradation Paths: The Fate of Diclofenac and Its Transformation Products
Authors: Ceresa Laura , Guadagnini Alberto , Rodríguez‐Escales Paula , Riva Monica , Sanchez‐Vila Xavier , Porta Giovanni M. 
Published: January 2023

AbstractWe present a methodology to quantify the impact of model structure and parametric uncertainty on formulations targeting biotransformation processes of Emerging Contaminants in subsurface water resources. The study is motivated by recognizing that modeling of bio‐mediated reactions of recalcitrant compounds in soil and aquifers is plagued by uncertainty. At the same time, process‐based models often require the parameterization of complex physico‐chemical processes, a situation which is exacerbated by the paucity of direct observations. Thus, assessment and formulation of modeling tools capable to balance complexity and reliability is a key challenge. The modeling strategy proposed here aims at pairing and applying a suite of quantitative tools starting from a prior diagnosis of multiple uncertainty sources and leading to parameter estimation and model selection in the presence of a limited number of observations. The methodology is illustrated through application to a multi‐step, reactive scenario involving biotransformation of the pharmaceutical diclofenac (DCF) in groundwater. Our framework includes four plausible models. These are obtained through successive simplifications of a recently developed highly complex model. Such simplifications are accomplished consistent with the results of a comprehensive Multi‐Model Global Sensitivity Analysis. The latter allows ranking the levels of influence of system processes on model outputs by incorporating the effects of model formulation and parametric uncertainties. The kinetic of the loop‐initiating process (DCF nitrosation, linked to the temporal evolution of N‐cycle components) is documented as dominating in explaining the variability of model outputs of environmental interest. Model discrimination criteria suggest that a simplified counterpart of the reference model is favored to interpret available data. Our modeling approach can assist interpretation and prototyping of a wide range of contaminant biotransformation models. The latter is a key objective also for the purpose of developing credible (environmental) risk assessment tools and designing experimental sampling campaigns.
Black phosphorous-based human-machine communication interface
Authors: Vaghasiya Jayraj V. , Mayorga-Martinez Carmen C. , Vyskočil Jan , Pumera Martin 
Published: January 2023

AbstractAssistive technology involving auditory feedback is generally utilized by those who are visually impaired or have speech and language difficulties. Therefore, here we concentrate on an auditory human-machine interface that uses audio as a platform for conveying information between visually or speech-disabled users and society. We develop a piezoresistive tactile sensor based on a black phosphorous and polyaniline (BP@PANI) composite by the facile chemical oxidative polymerization of aniline on cotton fabric. Taking advantage of BP’s puckered honeycomb lattice structure and superior electrical properties as well as the vast wavy fabric surface, this BP@PANI-based tactile sensor exhibits excellent sensitivity, low-pressure sensitivity, reasonable response time, and good cycle stability. For a real-world application, a prototype device employs six BP@PANI tactile sensors that correspond to braille characters and can convert pressed text into audio on reading or typing to assist visually or speech-disabled persons. Overall, this research offers promising insight into the material candidates and strategies for the development of auditory feedback devices based on layered and 2D materials for human-machine interfaces.
Southern hemisphere eastern boundary upwelling systems emerging as future marine heatwave hotspots under greenhouse warming
Authors: Wang Shengpeng , Jing Zhao , Wu Lixin , Sun Shantong , Peng Qihua , Wang Hong , Zhang Yu , Shi Jian 
Published: January 2023

AbstractMarine heatwaves (MHWs) exert devastating impacts on ecosystems and have been revealed to increase in their incidence, duration, and intensity in response to greenhouse warming. The biologically productive eastern boundary upwelling systems (EBUSs) are generally regarded as thermal refugia for marine species due to buffering effects of upwelling on ocean warming. However, using an ensemble of state-of-the-art high-resolution global climate simulations under a high carbon emission scenario, here we show that the MHW stress, measured as the annual cumulative intensity of MHWs, is projected to increase faster in the Southern Hemisphere EBUSs (Humboldt and Benguela current systems) than in their adjacent oceans. This is mainly because the additional warming caused by the weakened eastern boundary currents overwhelms the buffering effect of upwelling. Our findings suggest that the Southern Hemisphere EBUSs will emerge as local hotspots of MHWs in the future, potentially causing severe threats to the ecosystems.
The rapid and highly parallel identification of antibodies with defined biological activities by SLISY
Authors: Lu Steve , Mattox Austin K. , Aitana Azurmendi P. , Christodoulou Ilias , Wright Katharine M. , Popoli Maria , Chen Zan , Sur Surojit , Li Yana , Bonifant Challice L. , Bettegowda Chetan , Papadopoulos Nickolas , Zhou Shibin , Gabelli Sandra B. , Vogelstein Bert , Kinzler Kenneth W. 
Published: January 2023

AbstractThe therapeutic applications of antibodies are manifold and the emergence of SARS-CoV-2 provides a cogent example of the value of rapidly identifying biologically active antibodies. We describe an approach called SLISY (Sequencing-Linked ImmunoSorbent assaY) that in a single experiment can assess the binding specificity of millions of clones, be applied to any screen that links DNA sequence to a potential binding moiety, and requires only a single round of biopanning. We demonstrate this approach using an scFv library applied to cellular and protein targets to identify specific or broadly reacting antibodies. For a cellular target, we use paired HLA knockout cell lines to identify a panel of antibodies specific to HLA-A3. For a protein target, SLISY identifies 1279 clones that bound to the Receptor Binding Domain of the SARS-CoV-2 spike protein, with >40% of tested clones also neutralizing its interaction with ACE2 in in vitro assays. Using a multi-comparison SLISY against the Beta, Gamma, and Delta variants, we recovered clones that exhibited broad-spectrum neutralizing potential in vitro. By evaluating millions of scFvs simultaneously against multiple targets, SLISY allows the rapid identification of candidate scFvs with defined binding profiles facilitating the identification of antibodies with the desired biological activity.
Increased adipose catecholamine levels and protection from obesity with loss of Allograft Inflammatory Factor-1
Authors: Chinnasamy Prameladevi , Casimiro Isabel , Riascos-Bernal Dario F. , Venkatesh Shreeganesh , Parikh Dippal , Maira Alishba , Srinivasan Aparna , Zheng Wei , Tarabra Elena , Zong Haihong , Jayakumar Smitha , Jeganathan Venkatesh , Pradan Kith , Aleman Jose O. , Singh Rajat , Nandi Sayan , Pessin Jeffrey E. , Sibinga Nicholas E. S. 
Published: January 2023

AbstractRecent studies implicate macrophages in regulation of thermogenic, sympathetic neuron-mediated norepinephrine (NE) signaling in adipose tissues, but understanding of such non-classical macrophage activities is incomplete. Here we show that male mice lacking the allograft inflammatory factor-1 (AIF1) protein resist high fat diet (HFD)-induced obesity and hyperglycemia. We link this phenotype to higher adipose NE levels that stem from decreased monoamine oxidase A (MAOA) expression and NE clearance by AIF1-deficient macrophages, and find through reciprocal bone marrow transplantation that donor Aif1-/- vs WT genotype confers the obesity phenotype in mice. Interestingly, human sequence variants near the AIF1 locus associate with obesity and diabetes; in adipose samples from participants with obesity, we observe direct correlation of AIF1 and MAOA transcript levels. These findings identify AIF1 as a regulator of MAOA expression in macrophages and catecholamine activity in adipose tissues – limiting energy expenditure and promoting energy storage – and suggest how it might contribute to human obesity.
The effect of DNA polymorphisms and natural variation on crossover hotspot activity in Arabidopsis hybrids
Authors: Szymanska-Lejman Maja , Dziegielewski Wojciech , Dluzewska Julia , Kbiri Nadia , Bieluszewska Anna , Poethig R. Scott , Ziolkowski Piotr A. 
Published: January 2023

AbstractIn hybrid organisms, genetically divergent homologous chromosomes pair and recombine during meiosis; however, the effect of specific types of polymorphisms on crossover is poorly understood. Here, to analyze this in Arabidopsis, we develop the seed-typing method that enables the massively parallel fine-mapping of crossovers by sequencing. We show that structural variants, observed in one of the generated intervals, do not change crossover frequency unless they are located directly within crossover hotspots. Both natural and Cas9-induced deletions result in lower hotspot activity but are not compensated by increases in immediately adjacent hotspots. To examine the effect of single nucleotide polymorphisms on crossover formation, we analyze hotspot activity in mismatch detection-deficient msh2 mutants. Surprisingly, polymorphic hotspots show reduced activity in msh2. In lines where only the hotspot-containing interval is heterozygous, crossover numbers increase above those in the inbred (homozygous). We conclude that MSH2 shapes crossover distribution by stimulating hotspot activity at polymorphic regions.
Initial study on quantitative electroencephalographic analysis of bioelectrical activity of the brain of children with fetal alcohol spectrum disorders (FASD) without epilepsy
Authors: Bauer Waldemar , Dylag Katarzyna Anna , Lysiak Adam , Wieczorek-Stawinska Wiktoria , Pelc Mariusz , Szmajda Miroslaw , Martinek Radek , Zygarlicki Jaroslaw , Bańdo Bożena , Stomal-Slowinska Monika , Kawala-Sterniuk Aleksandra 
Published: January 2023

AbstractFetal alcohol spectrum disorders (FASD) are spectrum of neurodevelopmental conditions associated with prenatal alcohol exposure. The FASD manifests mostly with facial dysmorphism, prenatal and postnatal growth retardation, and selected birth defects (including central nervous system defects). Unrecognized and untreated FASD leads to severe disability in adulthood. The diagnosis of FASD is based on clinical criteria and neither biomarkers nor imaging tests can be used in order to confirm the diagnosis. The quantitative electroencephalography (QEEG) is a type of EEG analysis, which involves the use of mathematical algorithms, and which has brought new possibilities of EEG signal evaluation, among the other things—the analysis of a specific frequency band. The main objective of this study was to identify characteristic patterns in QEEG among individuals affected with FASD. This study was of a pilot prospective study character with experimental group consisting of patients with newly diagnosed FASD and of the control group consisting of children with gastroenterological issues. The EEG recordings of both groups were obtained, than analyzed using a commercial QEEG module. As a results we were able to establish the dominance of the alpha rhythm over the beta rhythm in FASD-participants compared to those from the control group, mostly in frontal and temporal regions. Second important finding is an increased theta/beta ratio among patients with FASD. These findings are consistent with the current knowledge on the pathological processes resulting from the prenatal alcohol exposure. The obtained results and conclusions were promising, however, further research is necessary (and planned) in order to validate the use of QEEG tools in FASD diagnostics.
Screening fundus photography predicts and reveals risk factors for glaucoma conversion in eyes with large optic disc cupping
Authors: Kim Yong Woo , Yun Young In , Choi Hyuk Jin 
Published: January 2023

AbstractThis study aimed to investigate the risk factors for glaucoma conversion and progression in eyes with large optic disc cupping without retinal nerve fiber layer defect (RNFLD). Five hundred forty-two eyes of 271 subjects who had a vertical cup-to-disc ratio (CDR) ≥ 0.6 without RNFLD were enrolled. Characteristics for optic disc configuration (including CDR, vertical cupping, ISNT rule, disc ovality, peripapillary atrophy [PPA]-to-disc area [DA] ratio, and lamina cribrosa pore visibility) and blood vessels (including central retinal vessel trunk [CRVT] nasalization, bayoneting of vessels, baring of circumlinear vessels, history of disc hemorrhage [DH] and vessel narrowing/sclerotic change) were evaluated. From a median follow-up of 11.3 years, 26.6% of eyes (n = 144) developed RNFLD within a median of 5.1 years. Baseline factors, including vertical CDR ≥ 0.7 (hazard ratio [HR] = 2.12), vertical cupping (HR = 1.93), ISNT rule violation (HR = 2.84), disc ovality ≥ 1.2 (HR = 1.61), PPA-to-DA ratio ≥ 0.4 (HR = 1.77), CRVT nasalization ≥ 60% (HR = 1.77), vessel narrowing/sclerotic change (HR = 2.13), DH history (HR = 5.60), and baseline intraocular pressure ≥ 14 mmHg (HR = 1.70) were significantly associated with glaucoma conversion (all Ps < 0.05). An HR-matched scoring system based on initial fundus photography predicted glaucoma conversion with specificity of 90.4%. Careful examination of the optic nerve head and vascular structures can help to predict the risk of glaucoma conversion in eyes with large optic disc cupping.
New plant immunity elicitors from a sugar beet byproduct protect wheat against Zymoseptoria tritici
Authors: Mejri Samara , Ghinet Alina , Magnin-Robert Maryline , Randoux Béatrice , Abuhaie Cristina-Maria , Tisserant Benoit , Gautret Philippe , Rigo Benoit , Halama Patrice , Reignault Philippe , Siah Ali 
Published: January 2023

AbstractThe current worldwide context promoting agroecology and green agriculture require the discovery of new ecofriendly and sustainable plant protection tools. Plant resistance inducers, called also elicitors, are one of the most promising alternatives fitting with such requirements. We produced here a set of 30 molecules from pyroglutamic acid, bio-sourced from sugar beet byproducts, and examined for their biological activity on the major agro-economically pathosystem wheat-Zymoseptoria tritici. Foliar application of the molecules provided significant protection rates (up to 63% disease severity reduction) for 16 among them. Structure–activity relationship analysis highlighted the importance of all chemical groups of the pharmacophore in the bioactivity of the molecules. Further investigations using in vitro andin plantaantifungal bioassays as well as plant molecular biomarkers revealed that the activity of the molecules did not rely on direct biocide activity towards the pathogen, but rather on the activation of plant defense mechanisms dependent on lipoxygenase, phenylalanine ammonia-lyase, peroxidase, and pathogenesis-related protein pathways. This study reports a new family of bio-sourced resistance inducers and provides new insights into the valorization of agro-resources to develop the sustainable agriculture of tomorrow.
Novel indicator for the spread of new coronavirus disease 2019 and its association with human mobility in Japan
Authors: Kawakami Yuta , Nojiri Shuko , Nakamoto Daisuke , Irie Yoshiki , Miyazawa Satoshi , Kuroki Manabu , Nishizaki Yuji 
Published: January 2023

AbstractThe Japanese government adopted policies to control human mobility in 2020 to prevent the spread of severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19). The present study examined the impact of human mobility on COVID-19 cases at the prefectural level in Japan by devising an indicator to have a relationship between the number of infected people and on human mobility. We calculated origin–destination travel mobility within prefectures in Japan from March 1st to December 31st, 2020, using mobile phone data. A cross-correlation function (CCF) was used to examine the relationship between human mobility and a COVID-19 infection acceleration indicator (IAI), which represents the rate of change in the speed of COVID-19 infection. The CCF of intraprefectural human mobility and the IAI in Tokyo showed a maximum value of 0.440 at lag day 12, and the IAI could be used as an indicator to predict COVID-19 cases. Therefore, the IAI and human mobility during the COVID-19 pandemic were useful for predicting infection status. The number of COVID-19 cases was associated with human mobility at the prefectural level in Japan in 2020. Controlling human mobility could help control infectious diseases in a pandemic, especially prior to starting vaccination.
Machine learning for knowledge acquisition and accelerated inverse-design for non-Hermitian systems
Authors: Ahmed Waqas W. , Farhat Mohamed , Staliunas Kestutis , Zhang Xiangliang , Wu Ying 
Published: January 2023

AbstractNon-Hermitian systems offer new platforms for unusual physical properties that can be flexibly manipulated by redistribution of the real and imaginary parts of refractive indices, whose presence breaks conventional wave propagation symmetries, leading to asymmetric reflection and symmetric transmission with respect to the wave propagation direction. Here, we use supervised and unsupervised learning techniques for knowledge acquisition in non-Hermitian systems which accelerate the inverse design process. In particular, we construct a deep learning model that relates the transmission and asymmetric reflection in non-conservative settings and propose sub-manifold learning to recognize non-Hermitian features from transmission spectra. The developed deep learning framework determines the feasibility of a desired spectral response for a given structure and uncovers the role of effective gain-loss parameters to tailor the spectral response. These findings offer a route for intelligent inverse design and contribute to the understanding of physical mechanism in general non-Hermitian systems.
An urban take on sustainable development policies and corresponding positioning strategies
Authors: Wittwer Stefan , Hofer Katrin , Kaufmann David 
Published: January 2023

AbstractCities have emerged as policy actors of global relevance in sustainable development, and their strengthened position challenges the primacy of national states in this area. To account for this shift and for potential emerging contestations between cities and national states, we propose a framework to understand national–urban relations in sustainable development policy-making. Based on a selection of twelve case study vignettes from European cities, we identify and discuss four ideal types of urban sustainable development policy, which are classified depending on their congruence with the national policy agenda and the scale of the issue at hand. Building on this typology, we reflect on positioning strategies that cities can develop to support, promote or defend these policies. We argue that accounting for these different positioning strategies is important for understanding how cities seek to put specifically urban takes of sustainable development on global agendas.
Mid-Miocene sea level altitude of the Qaidam Basin, northern Tibetan Plateau
Authors: Sun Yuanyuan , Liang Yu , Liu Hu , Liu Jun , Ji Junliang , Ke Xue , Liu Xiaobo , He Yuxin , Wang Huanye , Zhang Bin , Zhang Yongsu , Zhuang Guangsheng , Pei Junling , Li Yongxiang , Quan Cheng , Li Jianxing , Aitchison Jonathan C. , Liu Weiguo , Liu Zhonghui 
Published: January 2023

AbstractA detailed uplift history of the Tibetan Plateau is essential for disentangling the proposed geodynamical models and assessing its impacts on climate and biodiversity. However, when and how the plateau formed remains highly controversial. Here, we present unusual geochemical indicators of marine signatures in the Cenozoic terrestrial strata of the Qaidam Basin, northern Tibetan Plateau, with strong implications for the basin altitude. Our investigations across the basin reveal typical marine alkenones and anomalously high carbonate carbon isotopic values during the mid-Miocene, but not at earlier stages, which are accompanied by a divergent trend in the paired carbonate oxygen and leaf wax hydrogen isotopic records. We infer an incursion of seawater into the Qaidam Basin, thus constraining the mid-Miocene basin altitude close to sea level. Hence, much of the substantial northern plateau uplift afterwards appears to be associated with the outward growth of the Tibetan Plateau.
Remdesivir improves biomarkers associated with disease severity in COVID-19 patients treated in an outpatient setting
Authors: Pan David Z. , Odorizzi Pamela M. , Schoenichen Andre , Abdelghany Mazin , Chen Shuguang , Osinusi Anu , Patterson Scott D. , Downie Bryan , Juneja Kavita , Wallin Jeffrey J. 
Published: January 2023

Abstract
Background
Remdesivir (RDV) is an intravenous antiviral with activity against SARS-CoV-2 for treatment of hospitalized COVID-19 patients with moderate-to-severe disease. Biomarkers associated with clinical outcomes have been identified for COVID-19, but few evaluated in context of antiviral treatment. Here, we assessed baseline (day 1, prior to first RDV dose) biomarkers and the impact of RDV treatment on longitudinal biomarker readouts.

Methods
Recently, RDV was evaluated in high-risk, non-hospitalized patients with confirmed SARS-CoV-2 infection and was highly effective at preventing disease progression. The randomized, double-blind, placebo-controlled Phase 3 study included 562 participants who received at least 1 dose of study drug, of which 312 consented for longitudinal biomarker assessments at baseline, day 3, and day 14. We assessed sixteen baseline biomarkers and the impact of RDV treatment on longitudinal biomarker readouts.

Results
Six well-known, inflammation-associated biomarkers are elevated at baseline in participants meeting the primary endpoint of hospitalization or death by day 28. Moreover, in comparison to placebo, biomarkers in RDV-treated participants show accelerated improvement, including reduction of soluble angiopoietin-2, D-dimer, and neutrophil-to-lymphocyte ratio, as well as an increase in lymphocyte counts.

Conclusions
Overall, the findings in this study suggest that RDV treatment may accelerate the improvement of multiple biomarkers of COVID-19 severity, which are associated with better clinical outcomes during infection. These findings have implications for better understanding the activity of antiviral treatments in COVID-19.