bluuebunny/crossref_metadata_2025_split huggingface dataset:
High thermostability improves neutralizing antibody responses induced by native-like HIV-1 envelope trimers
Authors: del Moral-Sánchez Iván , Russell Rebecca A. , Schermer Edith E. , Cottrell Christopher A. , Allen Joel D. , Torrents de la Peña Alba , LaBranche Celia C. , Kumar Sanjeev , Crispin Max , Ward Andrew B. , Montefiori David C. , Sattentau Quentin J. , Sliepen Kwinten , Sanders Rogier W. 
Published: February 2022

AbstractSoluble HIV-1 envelope glycoprotein (Env) immunogens are a prime constituent of candidate vaccines designed to induce broadly neutralizing antibodies. Several lines of evidence suggest that enhancing Env immunogen thermostability can improve neutralizing antibody (NAb) responses. Here, we generated BG505 SOSIP.v9 trimers, which displayed virtually no reactivity with non-neutralizing antibodies and showed increased global and epitope thermostability, compared to previous BG505 SOSIP versions. Chemical crosslinking of BG505 SOSIP.v9 further increased the melting temperature to 91.3 °C, which is almost 25 °C higher than that of the prototype SOSIP.664 trimer. Next, we compared the immunogenicity of a palette of BG505-based SOSIP trimers with a gradient of thermostabilities in rabbits. We also included SOSIP.v9 proteins in which a strain-specific immunodominant epitope was masked by glycans to redirect the NAb response to other subdominant epitopes. We found that increased trimer thermostability correlated with increased potency and consistency of the autologous NAb response. Furthermore, glycan masking steered the NAb response to subdominant epitopes without decreasing the potency of the autologous NAb response. In summary, SOSIP.v9 trimers and their glycan masked versions represent an improved platform for HIV-1 Env based vaccination strategies.
A near-natural experiment on factors influencing larval drift in Salamandra salamandra
Authors: Schafft Malwina , Wagner Norman , Schuetz Tobias , Veith Michael 
Published: February 2022

AbstractThe larval stage of the European fire salamander (Salamandra salamandra) inhabits both lentic and lotic habitats. In the latter, they are constantly exposed to unidirectional water flow, which has been shown to cause downstream drift in a variety of taxa. In this study, a closed artificial creek, which allowed us to keep the water flow constant over time and, at the same time, to simulates with predefined water quantities and durations, was used to examine the individual movement patterns of marked larval fire salamanders exposed to unidirectional flow. Movements were tracked by marking the larvae with VIAlpha tags individually and by using downstream and upstream traps. Most individuals showed stationarity, while downstream drift dominated the overall movement pattern. Upstream movements were rare and occurred only on small distances of about 30 cm; downstream drift distances exceeded 10 m (until next downstream trap). The simulated flood events increased drift rates significantly, even several days after the flood simulation experiments. Drift probability increased with decreasing body size and decreasing nutritional status. Our results support the production hypothesis as an explanation for the movements of European fire salamander larvae within creeks.
Tunable x-ray free electron laser multi-pulses with nanosecond separation
Authors: Decker Franz-Josef , Bane Karl L. , Colocho William , Gilevich Sasha , Marinelli Agostino , Sheppard John C. , Turner James L. , Turner Joshua J. , Vetter Sharon L. , Halavanau Aliaksei , Pellegrini Claudio , Lutman Alberto A. 
Published: February 2022

AbstractX-ray Free Electron Lasers provide femtosecond x-ray pulses with narrow bandwidth and unprecedented peak brightness. Special modes of operation have been developed to deliver double pulses for x-ray pump, x-ray probe experiments. However, the longest delay between the two pulses achieved with existing single bucket methods is less than 1 picosecond, thus preventing the exploration of longer time-scale dynamics. We present a novel two-bucket scheme covering delays from 350 picoseconds to hundreds of nanoseconds in discrete steps of 350 picoseconds. Performance for each pulse can be similar to the one in a single pulse operation. The method has been experimentally tested with the Linac Coherent Light Source (LCLS-I) and the copper linac with LCLS-II hard x-ray undulators.
Small intestinal viability assessment using dielectric relaxation spectroscopy and deep learning
Authors: Hou Jie , Strand-Amundsen Runar , Tronstad Christian , Tønnessen Tor Inge , Høgetveit Jan Olav , Martinsen Ørjan Grøttem 
Published: February 2022

AbstractIntestinal ischemia is a serious condition where the surgeon often has to make important but difficult decisions regarding resections and resection margins. Previous studies have shown that 3 h (hours) of warm full ischemia of the small bowel followed by reperfusion appears to be the upper limit for viability in the porcine mesenteric ischemia model. However, the critical transition between 3 to 4 h of ischemic injury can be nearly impossible to distinguish intraoperatively based on standard clinical methods. In this study, permittivity data from porcine intestine was used to analyze the characteristics of various degrees of ischemia/reperfusion injury. Our results show that dielectric relaxation spectroscopy can be used to assess intestinal viability. The dielectric constant and conductivity showed clear differences between healthy, ischemic and reperfused intestinal segments. This indicates that dielectric parameters can be used to characterize different intestinal conditions. In addition, machine learning models were employed to classify viable and non-viable segments based on frequency dependent dielectric properties of the intestinal tissue, providing a method for fast and accurate intraoperative surgical decision-making. An average classification accuracy of 98.7% was obtained using only permittivity data measured during ischemia, and 96.2% was obtained with data measured during reperfusion. The proposed approach allows the surgeon to get accurate evaluation from the trained machine learning model by performing one single measurement on an intestinal segment where the viability state is questionable.
A comparison of approaches to improve worst-case predictive model performance over patient subpopulations
Authors: Pfohl Stephen R. , Zhang Haoran , Xu Yizhe , Foryciarz Agata , Ghassemi Marzyeh , Shah Nigam H. 
Published: February 2022

AbstractPredictive models for clinical outcomes that are accurate on average in a patient population may underperform drastically for some subpopulations, potentially introducing or reinforcing inequities in care access and quality. Model training approaches that aim to maximize worst-case model performance across subpopulations, such as distributionally robust optimization (DRO), attempt to address this problem without introducing additional harms. We conduct a large-scale empirical study of DRO and several variations of standard learning procedures to identify approaches for model development and selection that consistently improve disaggregated and worst-case performance over subpopulations compared to standard approaches for learning predictive models from electronic health records data. In the course of our evaluation, we introduce an extension to DRO approaches that allows for specification of the metric used to assess worst-case performance. We conduct the analysis for models that predict in-hospital mortality, prolonged length of stay, and 30-day readmission for inpatient admissions, and predict in-hospital mortality using intensive care data. We find that, with relatively few exceptions, no approach performs better, for each patient subpopulation examined, than standard learning procedures using the entire training dataset. These results imply that when it is of interest to improve model performance for patient subpopulations beyond what can be achieved with standard practices, it may be necessary to do so via data collection techniques that increase the effective sample size or reduce the level of noise in the prediction problem.
The elimination of stressed induced light leakage for in-plane-switching LCD
Authors: Wang Feifei , Zhan Hongming , Ji Lintao , Yang Tao , Meng Qingyong , Li Yajun , Li Bowen , Zang Yuansheng , Chen Junsheng , Huang Yinhu , Wang Kaixuan , Lin Lifeng , Shao Xibin 
Published: February 2022

AbstractAs the mainstream display mode of LCD, IPS is overwhelmingly used in many fields of flat displays. However, due to the stress sensitivity of glass, the stressed light leakage is a bottleneck for achieving perfect dark state performance. The conventional scheme of using a compensation polarizer outside the cell has no effect on this light leakage. Although many studies have been conducted to overcome this limitation, the proposed methods have limited effects. Our research team has proposed a novel light leakage compensation mechanism by introducing a positive A plate that is sandwiched between the glass and the LC layer, therefore the light leakage which is caused by the combined effect of the phase retardations from the stressed glasses and the LC layer can be eliminated. In addition to theoretically analyzing the compensation principles of the novel light leakage compensation mechanism, we also use the developed positive A material to prepare light leakage compensation demos. And then the electric-optical characteristics and light leakage compensation effects of the demos are evaluated. While maintaining excellent optical and electrical characteristics, this technology effectively solves the problem of stressed light leakage of glass-based IPS, improves the dark-state image quality, and breaks the application of IPS in products such as curve products.
Microfluidic channel sensory system for electro-addressing cell location, determining confluency, and quantifying a general number of cells
Authors: Rapier Crystal E. , Jagadeesan Srikanth , Vatine Gad , Ben-Yoav Hadar 
Published: February 2022

AbstractMicrofluidics is a highly useful platform for culturing, monitoring, and testing biological cells. The integration of electrodes into microfluidic channels extends the functionality, sensing, and testing capabilities of microfluidic systems. By employing an electrochemical impedance spectroscopy (EIS) technique, the non-invasive, label-free detection of the activities of cells in real-time can be achieved. To address the movement toward spatially resolving cells in cell culture, we developed a sensory system capable of electro-addressing cell location within a microfluidic channel. This simple system allows for real-time cell location, integrity monitoring (of barrier producing cells), and confluency sensing without the need for frequent optical evaluation—saving time. EIS results demonstrate that cells within microfluidic channels can be located between various pairs of electrodes at different positions along the length of the device. Impedance spectra clearly differentiates between empty, sparse, and confluent microfluidic channels. The system also senses the level of cell confluence between electrode pairs—allowing for the relative quantification of cells in different areas of the microfluidic channel. The system’s electrode layout can easily be incorporated into other devices. Namely, organ-on-a-chip devices, that require the monitoring of precise cell location and confluency levels for understanding tissue function, modeling diseases, and for testing therapeutics.
Agent based simulation with data driven parameterization for evaluation of social acceptance of a geothermal development: a case study in Tsuchiyu, Fukushima, Japan
Authors: Masuda Shuntaro , Bahr Kyle , Tsuchiya Noriyoshi , Takemori Tatsuya 
Published: February 2022

AbstractDevelopment of geothermal power plants and local geothermal energy initiatives have lagged due to the social problems such as conflicts with stakeholders such as Onsen (Hot Spa) owners, despite the abundant geothermal resources. Study area was Tsuchiyu Onsen in Fukushima prefecture, Tohoku (Northeast) District, Japan, where the Great East Japan Earthquake and Fukushima Nuclear Accident occurred in 2011, and the reconstruction and local initiatives of geothermal energy were still unclear. Agent-based modeling is an effective methodology for modeling and analysis of opinion formation. Parameter estimation method was proposed to extract appropriate parameters from various factors through a Bayesian Network. The characteristics of stakeholders and communities that affected opinion formation in the survey area were successfully extracted. Here we show the sufficient methodology to quantify the characteristics of each person using survey data, and to extract the parameters of the agent by data-driven inverse analysis. By using this methodology, we could reproduce opinion diversity, which is a property of opinion formation in real communities. This result suggests that the model replicates the actual formation of opinion in Tsuchiyu, where the economy was boosted by the construction of a binary cycle power plant.
Technological creep masks continued decline in a lobster (Homarus gammarus) fishery over a century
Authors: Kleiven Alf Ring , Espeland Sigurd Heiberg , Stiansen Stian , Ono Kotaro , Zimmermann Fabian , Olsen Esben Moland 
Published: February 2022

AbstractFishery-dependent data are frequently used to inform management decisions. However, inferences about stock development based on commercial data such as Catch-Per-Unit-Effort (CPUE) can be severely biased due to a phenomenon known as technological creep, where fishing technology improves over time. Here we show how trap improvement over nine decades has driven technological creep in a European lobster (Homarus gammarus) fishery. We combined fishing data, experimental fishing with contemporary and older trap types, and information on depletion effects during fishing seasons. The resulting standardized CPUE time series indicates a 92% decline in lobster abundance between 1928 and 2019 compared to 70% if technological creep is not corrected for. Differences are most pronounced within the last 40 years when the most substantial shift in gear technology occurred: an uncorrected CPUE index suggests an 8% increase in lobster abundance during this period, while the corrected CPUE index declined by 57%. We conclude that technological creep has masked a continuous stock decline, particularly in recent decades and largely driven by the shift from one- to two-chambered traps, as well as the ability of newer trap designs to capture larger lobsters. Our study confirms the importance of adequate standardization, including technological development, when using fishery dependent CPUE for monitoring and management of data-limited fisheries.
The role of the anterior insula during targeted helping behavior in male rats
Authors: Cox Stewart S. , Kearns Angela M. , Woods Samuel K. , Brown Brogan J. , Brown Samantha J. , Reichel Carmela M. 
Published: February 2022

AbstractEmpathy, the understanding of the emotional state of others, can be examined across species using the Perception Action Model, where shared affect promotes an action by “Observers” to aid a distressed “Target”. The anterior insula (AI) has garnered interest in empathic behavior due to its role integrating sensory and emotional information of self and other. In the following studies, the AI was inhibited pharmacologically and chemogenetically during targeted helping. We demonstrate the insula is active during, and is necessary for the maintenance of, targeted helping. Analysis of ultrasonic vocalizations revealed distress calls from Targets increased when Observers’ helping was attenuated due to insula inhibition. Targets’ elevated distress was directly correlated to Observers’ diminished helping behavior, suggesting emotional transfer between Observer and Target is blunted following Observer AI inhibition. Finally, the AI may selectively blunt targeted helping, as social exploration did not change in a social reward place conditioning task. These studies help further establish the anterior insula as a critical node in the empathic brain during targeted helping, even in the absence of direct social contact.
Phylogenetic analyses of Eurasian lynx (Lynx lynx Linnaeus, 1758) including new mitochondrial DNA sequences from Iran
Authors: Behzadi Farshad , Malekian Mansoureh , Fadakar Davoud , Adibi Mohammad Ali , Bärmann Eva V. 
Published: February 2022

AbstractThe Eurasian lynx (Lynx lynx) is one of the widespread felids in Eurasia; however, relatively little is known about the Asian subspecies, and especially the Iranian populations, which comprise the most southwestern part of its range. The current study aimed to assess the phylogenetic status of Iranian populations relative to other populations of Eurasia, by sequencing a 613 bp fragment of the mitochondrial control region. In total, 44 haplotypes were recorded from 83 sequences throughout Eurasia, two of which were found in Iran. The haplotype (H1) is dominant in all Iranian lynx populations and identical to specimens from SW Russia and central China. The second haplotype (H2) is unique and was recorded only from Ghazvin Province in the central Alborz Mountains. Both haplotypes occur in Ghazvin Province. The phylogenetic tree and a median-joining network identified four clades (i.e., East, West 1, West 2, and South). These results are congruent with previous studies and suggest that Eurasian lynx was restricted to the southern part of its range during the glacial maxima and expanded from there to East Asia and to Europe during several independent re-colonization events. The Caucasus region most like plays an important role as a refugium during glacial cycles.
Seasonal variation of pesticides in surface water and drinking water wells in the annual cycle in western Poland, and potential health risk assessment
Authors: Kruć-Fijałkowska Roksana , Dragon Krzysztof , Drożdżyński Dariusz , Górski Józef 
Published: February 2022

AbstractDrinking water wells on a riverbank filtration sites are exposed to contamination from farmlands (like pesticides) that had migrated from the contaminated river. In this study, pesticide contamination of the Warta River and riverbank filtration water at the Mosina-Krajkowo well field (Poland) were examined during the annual cycle. Among the 164 pesticides analysed, 25 were identified. The highest concentrations occurred in the river water and decreased along the flow path from the river to wells. Only the most persistent substances were detected at the farthest points. During the study, seasonal changes in pesticide concentrations and differences in the types of occurring substances were observed. Most substances and the highest concentrations were detected in May 2018, while the lowest number and the lowest concentrations were detected in February 2018. Spring is the period of increased exposure of water to pollution, which is correlated with increased pesticides use and increased rainfall. Seven toxic and persistent pesticides were found with the highest concentrations in water: isoproturon, nicosulfuron, imidacloprid, terbuthylazine, chlorotoluron, S-metalachlor, and prometryn. Pesticides are widely used in the study area; therefore, a potential health risk assessment was performed. The hazard quotient (HQ) values did not exceed one, which indicated a less significant health risk.
Integrated analysis of the transcriptome, sRNAome, and degradome reveals the network regulating fruit skin coloration in sponge gourd (Luffa cylindrica)
Authors: Sun Yuyan , Zhang Huiqing , Dong Wenqi , He Shengmi , Qiao Shuting , Qi Xingjiang , Hu Qizan 
Published: February 2022

AbstractSponge gourd fruit skin color is an important quality-related trait because it substantially influences consumer preferences. However, little is known about the miRNAs and genes regulating sponge gourd fruit skin coloration. This study involved an integrated analysis of the transcriptome, sRNAome, and degradome of sponge gourd fruit skins with green skin (GS) and white skin (WS). A total of 4,331 genes were differentially expressed between the GS and WS, with 2,442 down-regulated and 1,889 up-regulated genes in WS. The crucial genes involved in chlorophyll metabolism, chloroplast development, and chloroplast protection were identified (e.g.,HEMA,CHLM,CRD1,POR,CAO,CLH,SGR,CAB,BEL1-like,KNAT,ARF, and peroxidase genes). Additionally, 167 differentially expressed miRNAs were identified, with 70 up-regulated and 97 down-regulated miRNAs in WS. Degradome sequencing identified 125 differentially expressed miRNAs and their 521 differentially expressed target genes. The miR156, miR159, miR166, miR167, miR172, and miR393 targeted the genes involved in chlorophyll metabolism, chloroplast development, and chloroplast protection. Moreover, a flavonoid biosynthesis regulatory network was established involving miR159, miR166, miR169, miR319, miR390, miR396, and their targetsCHS,4CL,bHLH, andMYB. The qRT-PCR data for the differentially expressed genes were generally consistent with the transcriptome results. Subcellular localization analysis of selected proteins revealed their locations in different cellular compartments, including nucleus, cytoplasm and endoplasmic reticulum. The study findings revealed the important miRNAs, their target genes, and the regulatory network controlling fruit skin coloration in sponge gourd.
Dietary salt with nitric oxide deficiency induces nocturnal polyuria in mice via hyperactivation of intrarenal angiotensin II-SPAK-NCC pathway
Authors: Sekii Y. , Kiuchi H. , Takezawa K. , Imanaka T. , Kuribayashi S. , Okada K. , Inagaki Y. , Ueda N. , Fukuhara S. , Imamura R. , Negoro H. , Nonomura N. 
Published: February 2022

AbstractNocturnal polyuria is the most frequent cause of nocturia, a common disease associated with a compromised quality of life and increased mortality. Its pathogenesis is complex, and the detailed underlying mechanism remains unknown. Herein, we report that concomitant intake of a high-salt diet and reduced nitric oxide (NO) production achieved through Nω-Nitro-L-arginine methyl ester hydrochloride (L-NAME) administration in mice resulted in nocturnal polyuria recapitulating the clinical features in humans. High salt intake under reduced NO production overactivated the angiotensin II-SPAK (STE20/SPS1-related proline–alanine-rich protein kinase)-NCC (sodium chloride co-transporter) pathway in the kidney, resulting in the insufficient excretion of sodium during the day and its excessive excretion at night. Excessive Na excretion at night in turn leads to nocturnal polyuria due to osmotic diuresis. Our study identified a central role for the intrarenal angiotensin II-SPAK-NCC pathway in the pathophysiology of nocturnal polyuria, highlighting its potential as a promising therapeutic target.
A machine learning inversion scheme for determining interaction from scattering
Authors: Chang Ming-Ching , Tung Chi-Huan , Chang Shou-Yi , Carrillo Jan Michael , Wang Yangyang , Sumpter Bobby G. , Huang Guan-Rong , Do Changwoo , Chen Wei-Ren 
Published: February 2022

AbstractSmall angle scattering techniques have now been routinely used to quantitatively determine the potential of mean force in colloidal suspensions. However the numerical accuracy of data interpretation is often compounded by the approximations adopted by liquid state analytical theories. To circumvent this long standing issue, here we outline a machine learning strategy for determining the effective interaction in the condensed phases of matter using scattering. Via a case study of colloidal suspensions, we show that the effective potential can be probabilistically inferred from the scattering spectra without any restriction imposed by model assumptions. Comparisons to existing parametric approaches demonstrate the superior performance of this method in accuracy, efficiency, and applicability. This method can effectively enable quantification of interaction in highly correlated systems using scattering and diffraction experiments.