bluuebunny/crossref_metadata_2025_split huggingface dataset:
A framework for rigorous evaluation of human performance in human and machine learning comparison studies
Authors: Cowley Hannah P. , Natter Mandy , Gray-Roncal Karla , Rhodes Rebecca E. , Johnson Erik C. , Drenkow Nathan , Shead Timothy M. , Chance Frances S. , Wester Brock , Gray-Roncal William 
Published: March 2022

AbstractRigorous comparisons of human and machine learning algorithm performance on the same task help to support accurate claims about algorithm success rates and advances understanding of their performance relative to that of human performers. In turn, these comparisons are critical for supporting advances in artificial intelligence. However, the machine learning community has lacked a standardized, consensus framework for performing the evaluations of human performance necessary for comparison. We demonstrate common pitfalls in a designing the human performance evaluation and propose a framework for the evaluation of human performance, illustrating guiding principles for a successful comparison. These principles are first, to design the human evaluation with an understanding of the differences between human and algorithm cognition; second, to match trials between human participants and the algorithm evaluation, and third, to employ best practices for psychology research studies, such as the collection and analysis of supplementary and subjective data and adhering to ethical review protocols. We demonstrate our framework’s utility for designing a study to evaluate human performance on a one-shot learning task. Adoption of this common framework may provide a standard approach to evaluate algorithm performance and aid in the reproducibility of comparisons between human and machine learning algorithm performance.
The coherence time of sunlight in the context of natural and artificial light-harvesting
Authors: Ricketti Berke Vow , Gauger Erik M. , Fedrizzi Alessandro 
Published: March 2022

AbstractThe suggestion that quantum coherence might enhance biological processes such as photosynthesis is not only of fundamental importance but also leads to hopes of developing bio-inspired ‘green’ quantum technologies that mimic nature. A key question is how the timescale of coherent processes in molecular systems compare to that of the driving light source—the Sun. Across the quantum biology literature on light-harvesting, the coherence time quoted for sunlight spans about two orders of magnitude, ranging from 0.6 to ‘10s’ of femtoseconds. This difference can potentially be significant in deciding whether the induced light-matter coherence is long enough to affect dynamical processes following photoexcitation. Here we revisit the historic calculations of sunlight coherence starting with the black-body spectrum and then proceed to provide values for the more realistic case of atmospherically filtered light. We corroborate these values with interferometric measurements of the complex degree of temporal coherence from which we calculate the coherence time of atmospherically filtered sunlight as $$1.12\pm {0.04}\,{\hbox { fs}}$$

1.12
±

0.04

fs

, as well as the coherence time in a chlorophyll analogous filtered case as $$4.87\pm {0.21}\,{\hbox { fs}}$$

4.87
±

0.21

fs

.
Methane emissions and rumen metabolite concentrations in cattle fed two different silages
Authors: Bica R. , Palarea-Albaladejo J. , Lima J. , Uhrin D. , Miller G. A. , Bowen J. M. , Pacheco D. , Macrae A. , Dewhurst R. J. 
Published: March 2022

AbstractIn this study, 18 animals were fed two forage-based diets: red clover (RC) and grass silage (GS), in a crossover-design experiment in which methane (CH4) emissions were recorded in respiration chambers. Rumen samples obtained through naso-gastric sampling tubes were analysed by NMR. Methane yield (g/kg DM) was significantly lower from animals fed RC (17.8 ± 3.17) compared to GS (21.2 ± 4.61) p = 0.008. In total 42 metabolites were identified, 6 showing significant differences between diets (acetate, propionate, butyrate, valerate, 3-phenylopropionate, and 2-hydroxyvalerate). Partial least squares discriminant analysis (PLS-DA) was used to assess which metabolites were more important to distinguish between diets and partial least squares (PLS) regressions were used to assess which metabolites were more strongly associated with the variation in CH4 emissions. Acetate, butyrate and propionate along with dimethylamine were important for the distinction between diets according to the PLS-DA results. PLS regression revealed that diet and dry matter intake are key factors to explain CH4 variation when included in the model. Additionally, PLS was conducted within diet, revealing that the association between metabolites and CH4 emissions can be conditioned by diet. These results provide new insights into the methylotrophic methanogenic pathway, confirming that metabolite profiles change according to diet composition, with consequences for CH4 emissions.
Investigation of Toxoplasma gondii in wastewater and surface water in the Qinghai-Tibet Plateau, China using real-time PCR and multilocus genotyping
Authors: Lass Anna , Kontogeorgos Ioannis , Ma Liqing , Zhang Xueyong , Li Xiuping , Karanis Panagiotis 
Published: March 2022

AbstractToxoplasma gondii is a protozoan parasite, causing one of the most prevalent parasitic infections in the world. In the present study water sources of the Qinghai-Tibet Plateau (QTP), China, where the hygienic infrastructure is still developing, were investigated. A total of 214 water samples of 10 L volume, were collected from wastewater treatment plants (WWTPs), a slaughterhouse and rivers. The samples were filtered and then analysed using real-time PCR and multilocus genotyping. T. gondii DNA was found in four (1.9%) samples representing T. gondii type I; in one of them T. gondii-like oocysts were also confirmed microscopically. The approximate level of contamination of positive samples ranged between 30 and 2300 T. gondii sporozoites. The results of this study confirmed that T. gondii is present in wastewater in the greater metropolitan area of Xining and a neighbouring county. Contamination of wastewater at this level constitutes rather a moderate source of Toxoplasma infections in humans and animals. It suggests, however, a link between environmental exposure of animals, meat processing facilities and WWTPs. To our knowledge, this is the first investigation describing T. gondii detection in wastewater and environmental water samples collected from the territory of P.R. China using sensitive molecular tools.
Tuning of composition and morphology of LiFePO4 cathode for applications in all solid-state lithium metal batteries
Authors: Erabhoina Harimohan , Thelakkat Mukundan 
Published: March 2022

AbstractAll solid-state rechargeable lithium metal batteries (SS-LMBs) are gaining more and more importance because of their higher safety and higher energy densities in comparison to their liquid-based counterparts. In spite of this potential, their low discharge capacities and poor rate performances limit them to be used as state-of-the-art SS-LMBs. This arise due to the low intrinsic ionic and electronic transport pathways within the solid components in the cathode during the fast charge/discharge processes. Therefore, it is necessary to have a cathode with good electron conducting channels to increase the active material utilization without blocking the movement of lithium ions. Since SS-LMBs require a different morphology and composition of the cathode, we selected LiFePO4 (LFP) as a prototype and, we have systematically studied the influence of the cathode composition by varying the contents of active material LFP, conductive additives (super C65 conductive carbon black and conductive graphite), ion conducting components (PEO and LiTFSI) in order to elucidate the best ion as well as electron conduction morphology in the cathode. In addition, a comparative study on different cathode slurry preparation methods was made, wherein ball milling was found to reduce the particle size and increase the homogeneity of LFP which further aids fast Li ion transport throughout the electrode. The SEM analysis of the resulting calendered electrode shows the formation of non-porous and crack-free structures with the presence of conductive graphite throughout the electrode. As a result, the optimum LFP cathode composition with solid polymer nanocomposite electrolyte (SPNE) delivered higher initial discharge capacities of 114 mAh g-1 at 0.2C rate at 30 °C and 141 mAh g-1 at 1C rate at 70 °C. When the current rate was increased to 2C, the electrode still delivered high discharge capacity of 82 mAh g-1 even after 500 cycle, which indicates that the optimum cathode formulation is one of the important parameters in building high rate and long cycle performing SS-LMBs.
A union of deep learning and swarm-based optimization for 3D human action recognition
Authors: Basak Hritam , Kundu Rohit , Singh Pawan Kumar , Ijaz Muhammad Fazal , Woźniak Marcin , Sarkar Ram 
Published: March 2022

AbstractHuman Action Recognition (HAR) is a popular area of research in computer vision due to its wide range of applications such as surveillance, health care, and gaming, etc. Action recognition based on 3D skeleton data allows simplistic, cost-efficient models to be formed making it a widely used method. In this work, we proposeDSwarm-Net, a framework that employs deep learning and swarm intelligence-based metaheuristic for HAR that uses 3D skeleton data for action classification. We extract four different types of features from the skeletal data namely: Distance, Distance Velocity, Angle, and Angle Velocity, which capture complementary information from the skeleton joints for encoding them into images. Encoding the skeleton data features into images is an alternative to the traditional video-processing approach and it helps in making the classification task less complex. The Distance and Distance Velocity encoded images have been stacked depth-wise and fed into a Convolutional Neural Network model which is a modified version of Inception-ResNet. Similarly, the Angle and Angle Velocity encoded images have been stacked depth-wise and fed into the same network. After training these models, deep features have been extracted from the pre-final layer of the networks, and the obtained feature representation is optimized by a nature-inspired metaheuristic, called Ant Lion Optimizer, to eliminate the non-informative or misleading features and to reduce the dimensionality of the feature set. DSwarm-Net has been evaluated on three publicly available HAR datasets, namely UTD-MHAD, HDM05, and NTU RGB+D 60 achieving competitive results, thus confirming the superiority of the proposed model compared to state-of-the-art models.
Association of the new zero-tolerance drinking and driving law with hospitalization rate due to road traffic injuries in Brazil
Authors: Souza Cássia Rebeca de Lima , Russo Letícia Xander , da Silva Everton Nunes 
Published: March 2022

AbstractWe investigated the association of the new zero-tolerance drinking and driving law (Law 12,760, Dec. 2012) with hospital admissions due to road traffic injuries in Brazil by using interrupted time series from 2008 to 2019. We used linear regression designed to adjust for autocorrelation and Cumby–Huizinga test for residual autocorrelation. Newey–West standard errors was used to handle heteroscedasticity. We used ICD-10 codes for land transport accidents (V01–V89). The hospitalization rate was calculated per 100,000 inhabitants. The sources were the Hospital Information System and the Brazilian Institute for Geography and Statistics. Pre- and postintervention consist of 59 and 85 months, respectively. For Brazil, the hospitalization rate was associated with a reduction of 0.34 (p = 0.097; 95% CI − 0.74 to 0.06) in the first month of the intervention (Dec. 2012), followed by a significant change in the hospitalization trend. Compared to the period prior to the intervention, the monthly trend was associated with a reduction of 0.05 (p < 0.01; 95% CI − 0.06 to − 0.04) in the post period. These results stand in agreement with subgroup analyses for the Brazilian regions, although North and Northeast regions did not immediately reduce hospitalization rates (level change). Our results suggested that 440,599 hospitalizations for land transport accidents would be averted by the new zero-tolerance drinking and driving law from Dec. 2012 to Dec. 2019 in Brazil. Even using a quasi-experimental approach, our findings must be interpreted with caution due to observational design and registration flaws surrounding our data.
Analytic simulation of thermophoretic second grade fluid flow past a vertical surface with variable fluid characteristics and convective heating
Authors: Shah Nehad Ali , Yook Se-Jin , Tosin Oreyeni 
Published: March 2022

AbstractThe study considers the effect of thermophoresis particle deposition on the flow properties of second grade fluid with variable viscosity, variable thermal conductivity and variable concentration diffusivity subjected to a convective boundary condition. To further describe the transport phenomenon, the special case of assisting and opposing flows is explored. Using similarity transformations, the governing equations of the fluid model are transformed and parameterized into a system of nonlinear ordinary differential equations. The approximate analytic solution of a dimensionless system is obtained through the Optimal Homotopy Analysis Method (OHAM). It is observed that velocity and temperature distributions are decreasing functions of the second grade parameter for both assisting and opposing flows. When the thermophoretic parameter is increased, the concentration distributions at the first and fourth orders of chemical reaction decrease. For both opposing and assisting flows, velocity distributions are enhanced due to larger temperature-dependent viscous parameters.
A clinically relevant heterozygous ATR mutation sensitizes colorectal cancer cells to replication stress
Authors: Egger Tom , Bordignon Benoît , Coquelle Arnaud 
Published: March 2022

AbstractColorectal cancer (CRC) ranks third among the most frequent malignancies and represents the second most common cause of cancer-related deaths worldwide. By interfering with the DNA replication process of cancer cells, several chemotherapeutic molecules used in CRC therapy induce replication stress (RS). At the cellular level, this stress is managed by the ATR-CHK1 pathway, which activates the replication checkpoint. In recent years, the therapeutic value of targeting this pathway has been demonstrated. Moreover, MSI + (microsatellite instability) tumors frequently harbor a nonsense, heterozygous mutation in the ATR gene. Using isogenic HCT116 clones, we showed that this mutation of ATR sensitizes the cells to several drugs, including SN-38 (topoisomerase I inhibitor) and VE-822 (ATR inhibitor) and exacerbates their synergistic effects. We showed that this mutation bottlenecks the replication checkpoint leading to extensive DNA damage. The combination of VE-822 and SN-38 induces an exhaustion of RPA and a subsequent replication catastrophe. Surviving cells complete replication and accumulate in G2 in a DNA-PK-dependent manner, protecting them from cell death. Together, our results suggest that RPA and DNA-PK represent promising therapeutic targets to optimize the inhibition of the ATR-CHK1 pathway in oncology. Ultimately, ATR frameshift mutations found in patients may also represent important prognostic factors.
Excess mortality in Belarus during the COVID-19 pandemic as the case study of a country with limited non-pharmaceutical interventions and limited reporting
Authors: Kirpich Alexander , Shishkin Aleksandr , Weppelmann Thomas A. , Tchernov Alexander Perez , Skums Pavel , Gankin Yuriy 
Published: March 2022

AbstractPublic health intervention to contain the ongoing COVID-19 pandemic significantly differed by country since the SARS-CoV-2 spread varied regionally in time and in scale. Since vaccinations were not available until the end of 2020 non-pharmaceutical interventions (NPIs) remained the only strategies to mitigate the pandemic spread at that time. Belarus in Europe is one of a few countries with a high Human Development Index where no lockdowns have ever been implemented and only limited NPIs have taken place for a period of time. Therefore, the Belarusian case was evaluated and compared in terms of the mortality burden. Since the COVID-19 mortality was low, the excess overall mortality was studied for Belarus. Since no overall mortality data have been reported past June 2020 the analysis was complemented by the study of Google Trends funeral-related search queries up until August 2021. Depending on the model, the Belarusian mortality for June of 2020 was 29 to 39% higher than otherwise expected with the corresponding estimated excess death was from 2953 to 3690 while the reported COVID-19 mortality for June 2020 was only 157 cases. The Belarusian excess mortality for June 2020 was higher than for all neighboring countries with an excess of 5% for Poland, 5% for Ukraine, 8% for Russia, 11% for Lithuania and 11% for Latvia. The relationship between Google Trends and mortality time series was studied using Granger’s test and the results were statistically significant. The results for Google Trends searches did vary by key phrase with the largest excess of 138% for April 2020 and 148% for September 2020 was observed for a key phrase “coffin”, while the largest excess of 218% for January 2021 was observed for “funeral services”. In summary, there are indications of the excess overall mortality in Belarus, which is larger than the reported COVID-19-related mortality.
Four novel candidate causal variants for deficient homozygous haplotypes in Holstein cattle
Authors: Häfliger Irene M. , Spengeler Mirjam , Seefried Franz R. , Drögemüller Cord 
Published: March 2022

AbstractMendelian variants can determine both insemination success and neonatal survival and thus influence fertility and rearing success of cattle. We present 24 deficient homozygous haplotype regions in the Holstein population of Switzerland and provide an overview of the previously identified haplotypes in the global Holstein breed. This study encompasses massive genotyping, whole-genome sequencing (WGS) and phenotype association analyses. We performed haplotype screenings on almost 53 thousand genotyped animals including 114 k SNP data with two different approaches. We revealed significant haplotype associations to several survival, birth and fertility traits. Within haplotype regions, we mined WGS data of hundreds of bovine genomes for candidate causal variants, which were subsequently evaluated by using a custom genotyping array in several thousand breeding animals. With this approach, we confirmed the known deleterious SMC2:p.Phe1135Ser missense variant associated with Holstein haplotype (HH) 3. For two previously reported deficient homozygous haplotypes that show negative associations to female fertility traits, we propose candidate causative loss-of-function variants: the HH13-related KIR2DS1:p.Gln159* nonsense variant and the HH21-related NOTCH3:p.Cys44del deletion. In addition, we propose the RIOX1:p.Ala133_Glu142del deletion as well as the PCDH15:p.Leu867Val missense variant to explain the unexpected low number of homozygous haplotype carriers for HH25 and HH35, respectively. In conclusion, we demonstrate that with mining massive SNP data in combination with WGS data, we can map several haplotype regions and unravel novel recessive protein-changing variants segregating at frequencies of 1 to 5%. Our findings both confirm previously identified loci and expand the spectrum of undesired alleles impairing reproduction success in Holstein cattle, the world's most important dairy breed.
Ammonium removal by erythrocyte-bioreactors based on glutamate dehydrogenase from Proteus sp. jointly with porcine heart alanine aminotransferase
Authors: Borsakova Daria V. , Koleva Larisa D. , Protasov Evgeniy S. , Ataullakhanov Fazoil I. , Sinauridze Elena I. 
Published: March 2022

AbstractExcessive ammonium blood concentration causes many serious neurological complications. The medications currently used are not very effective. To remove ammonium from the blood, erythrocyte-bioreactors containing enzymes that processing ammonium have been proposed. The most promising bioreactor contained co-encapsulated glutamate dehydrogenase (GDH) and alanine aminotransferase (ALT). However, a low encapsulation of a commonly used bovine liver GDH (due to high aggregation), makes clinical use of such bioreactors impossible. In this study, new bioreactors containing ALT and non-aggregating GDH at higher loading were first produced using the flow dialysis method and the new bacterial GDH enzyme fromProteussp. The efficacy of these erythrocyte-bioreactors and their properties (hemolysis, osmotic fragility, intracellular and extracellular activity of included enzymes, erythrocyte indices, and filterability) were studied and compared with native cells during 1-week storage. The ammonium removal rate in vitro by such erythrocyte-bioreactors increased linearly with an increase in encapsulated GDH activity. Alanine in vitro increased in accordance with ammonium consumption, which indicated the joint functioning of both included enzymes. Thus, novel bioreactors for ammonium removal containing GDH fromProteussp. are promising for clinical use, since they have a more efficient GDH encapsulation and their properties are not inferior to previously obtained erythrocyte-bioreactors.
Efficient targeted transgenesis of large donor DNA into multiple mouse genetic backgrounds using bacteriophage Bxb1 integrase
Authors: Low Benjamin E. , Hosur Vishnu , Lesbirel Simon , Wiles Michael V. 
Published: March 2022

AbstractThe development of mouse models of human disease and synthetic biology research by targeted transgenesis of large DNA constructs represent a significant genetic engineering hurdle. We developed an efficient, precise, single-copy integration of large transgenes directly into zygotes using multiple mouse genetic backgrounds. We used in vivo Bxb1 mediated recombinase-mediated cassette exchange (RMCE) with a transgene “landing pad” composed of dual heterologous Bxb1 attachment (att) sites in cis, within the Gt(ROSA)26Sor safe harbor locus. RMCE of donor was achieved by microinjection of vector DNA carrying cognate attachment sites flanking the donor transgene with Bxb1-integrase mRNA. This approach achieves perfect vector-free integration of donor constructs at efficiencies > 40% with up to ~ 43 kb transgenes. Coupled with a nanopore-based Cas9-targeted sequencing (nCATS), complete verification of precise insertion sequence was achieved. As a proof-of-concept we describe the development of C57BL/6J and NSG Krt18-ACE2 models for SARS-CoV2 research with verified heterozygous N1 animals within ~ 4 months. Additionally, we created a series of mice with diverse backgrounds carrying a single att site including FVB/NJ, PWK/PhJ, NOD/ShiLtJ, CAST/EiJ and DBA/2J allowing for rapid transgene insertion. Combined, this system enables predictable, rapid development with simplified characterization of precisely targeted transgenic animals across multiple genetic backgrounds.