bluuebunny/crossref_metadata_2025_split huggingface dataset:
Breath response following a nutritional challenge monitored by secondary electrospray ionization high-resolution mass spectrometry
Authors: Wüthrich Cedric , de Figueiredo Miguel , Burton-Pimentel Kathryn Jane , Vergères Guy , Wahl Fabian , Zenobi Renato , Giannoukos Stamatios 
Published: August 2022

Abstract
On-line breath analysis using secondary electrospray ionization coupled to high-resolution mass spectrometry (SESI-HRMS) is a sensitive method for biomarker discovery. The strengths of this technology have already been demonstrated in the clinical environment. For the first time, this study demonstrates the application of SESI-HRMS in the field of nutritional science using a standardized nutritional intervention, consisting of a high-energy shake (950 kcal, 8% protein, 35% sugar and 57% fat). Eleven subjects underwent the intervention on three separate days and their exhaled breath was monitored up to six hours postprandially. In addition, sampling was performed during equivalent fasting conditions for selected subjects. To estimate the impact of inter- and intra-individual variability, analysis of variance simultaneous component analysis was conducted, revealing that the inter-individual variability accounted for 30% of the data variation. To distinguish the effect of the intervention from fasting conditions, partial least squares discriminant analysis was performed. Candidate compound annotation was performed with pathway analysis and collision-induced dissociation (CID) experiments. Pathway analysis highlighted, among others, features associated with the metabolism of linoleate, butanoate and amino sugars. Tentative compounds annotated through CID measurements include fatty acids, amino acids, and amino acid derivatives, some of them likely derived from nutrients by the gut microbiome (e.g. propanoate, indoles), as well as organic acids from the Krebs cycle. Time-series clustering showed an overlap of observed kinetic trends with those reported previously in blood plasma.
Research on the exposure of workers in a courier company to the exhaust emissions of diesel engines
Authors: Haiducu M , Ștepa R A , Chiurtu E R , Scarlat I P 
Published: August 2022

Abstract
The paper presents the research on the development of a method for analysis of elemental carbon from diesel emissions in the workplace based on existing methods and studies on the exposure of workers in a courier company to emissions of diesel engines in the context of occupational exposure limit in Directive (EU) 2019/130 on the protection of workers from the risks related to exposure to carcinogens or mutagens at work. It is estimated that more than 3.6 million workers in Europe are exposed to diesel emissions. Occupational exposure takes place mainly in mining, construction, transport, agriculture and other activities using diesel vehicles and equipment. New data on the carcinogenicity of diesel engine emissions and the change in their classification from potentially carcinogenic (Group 2B) to carcinogenic (Group 1), as well as the high number of workers exposed to these types of chemical pollutants, highlighted the need to set occupational exposure limits for emissions diesel engines in the work environment.
Plant available potassium and phosphorus in arable soil: a comparative study on testing methods
Authors: Surleva A , Angelova L 
Published: August 2022

Abstract
Determination of soil fertility status is based on determination of plant available nutrients which occur in several forms. This strongly challenges the choice of extracting solution and detection technique. Deriving a mathematical model for data recalculation would allow relating the results of different methods without loss of agronomical validation data. This comparative study was aimed at assessing the relationship between two methods for determination of plant available potassium and phosphorus in arable soil. Soil K and P were extracted followed a diluted double acid (Mehlich 1) and an acetate/lactate methods (ALM). Potassium in the obtained extracts was determined by flame AES and phosphorus - by molybdenum blue spectrophotometry. To compare the results obtained by the both extraction methods, the uncertainty of measurement of each method was assessed following the single laboratory validation and quality control approach. The expended uncertainty was found to be 2 mg/100g as P2O5 and 7 mg/100g as K2O (at k=2). The results from the comparative analysis of 93 arable soil samples showed a correlation between Mehlich-1 and ALM extracted P and K within uncertainty limits (at k=3). Based on the recalculated values of extractable K and P, the fertility status of 60 % of soil samples were correctly classified, 30 % with acceptable error and 7 % could not be classified. The study showed that Mehlich-1 and ALM methods provided comparable results for studied range of soil samples. However, determination of soil fertility status based on recalculated results should be made with caution as it could be highly influenced by soil type.
Research on valorisation of spent garnets as addition in cementitious materials – preliminary experimental evaluation
Authors: Baeră C , Chendeş R , Gruin A , Perianu A , Vasile V , Varga L 
Published: August 2022

Abstract
Abrasive waterjet (AWJ) material processing represents a relatively new and extremely efficient method in the specific industries, implying various applicability areas, attributed to different materials, with different properties and domains of use. Besides numerous advantages of the AWJ cutting and generally of the material processing techniques, they also involve the waste generation: the abrasive sands are converted into sludge material, collected into recipients and further on, after natural drying, they become waste dumps randomly deserted. The enlargement of the AWJ techniques in the latest years determines the corresponding increase of the associated Garnet wastes (Spent Garnets, SG), thus leading towards the clear need of identifying opportunities for their recycling and valorisation. Aggregates are basic raw materials in the production of concrete, mortar and plasters, composite cementitious and/or cement-free materials (geopolymer concrete) in the building materials and generally, in the construction industry. The rapid growth of the population, recorded mainly in urban areas, determines an increasing demand on housing facilities and consequently, on concrete production and aggregates consumption. Aggregates and sand, mainly exploited from riverbeds or quarries, represent exhaustible natural resource for which substitution solutions need to be found, in order to control and reduce their extraction from the natural landscape. Considering the superposition of this independent cause and effect situations, the rapid growth of Spent Garnets (SG) landfills, generated by AWJ processes, and, on the other hand, the need to substitute the natural aggregate in construction industry, a reliable solution could emerge from the potential valorisation of SG wastes as partial or even complete substitution of sands / aggregates in the composition of construction materials. The present paper offers a preliminary overview regarding the possibility of incorporating SG wastes of local production in usual cement-based materials, as partial substitute of the aggregate, for the double purpose of waste management implementation and natural resources protection, on the transition path towards the implementing the Circular Economy (CE) concept in the Romanian industry.
Study of shoot-through control pulse generation for a Z-source converter with wind turbine energy system
Authors: Kumari Sweta , Mandal Rajib Kumar 
Published: August 2022

Abstract
In this paper, there is a discussion about different modulation schemes for a dc-to-ac ZSC, also named Z-source inverter (ZSI), for triggering the main switches of three-phase legs or poles of an inverter. A prototype of an 8.5-kilowatt wind turbine with a 5.8-kilowatt Permanent Magnet Synchronous Generator (PMSG) system employed with voltage-controlled ZSI is implemented in this paper. For voltage control of load side of a wind turbine generation system (WTGS), a Proportional Integral (PI) controller is used. Three types of PWM schemes namely simple boost pulse width modulation (SB-PWM), third harmonic injection boost control (THIBC-PWM) and the space vector pulse width modulation (SV-PWM) techniques are compared on the basis of total harmonic distortion of the output ac-waveform of the Z-source Converter (ZSC) to find out that, which modulation technique is the best fit for a ZSI integrated with WTGS. The pros and cons of these techniques are compared in terms of line-voltage harmonics, phase-voltage harmonics, phase-current harmonics and switching stress of switches with detailed simulation results. These different modulation techniques are implemented on the MATLAB-Simulink domain. From Total Harmonic Distortion (THD) analysis, simple boost control technique is found to be the most appropriate shoot-through control technique for a ZSI in collaboration with WTGS.
Low Na-β′′-alumina electrolyte/cathode interfacial resistance enabled by a hydroborate electrolyte opening up new cell architecture designs for all-solid-state sodium batteries
Authors: Bay Marie-Claude , Grissa Rabeb , Egorov Konstantin V , Asakura Ryo , Battaglia Corsin 
Published: August 2022

Abstract
Development of low-resistance electrode/electrolyte interfaces is key for enabling all-solid-state batteries with fast-charging capabilities. Low interfacial resistance and high current density were demonstrated for Na-β′′-alumina/sodium metal interfaces, making Na-β′′-alumina a promising solid electrolyte for high-energy all-solid-state batteries. However, integration of Na-β′′-alumina with a high-energy sodium-ion intercalation cathode remains challenging. Here, we report a proof-of-concept study that targets the implementation of a Na-β′′-alumina ceramic electrolyte with a slurry-casted porous NaCrO2 cathode with infiltrated sodium hydroborates as secondary electrolyte. The hydroborate Na4(B12H12)(B10H10) possesses similar sodium-ion conductivity of 1 mS cm−1 at room temperature as Na-β′′-alumina and can be fully densified by cold pressing. Using the Na4(B12H12)(B10H10) secondary electrolyte as interlayer between Na-β′′-alumina and NaCrO2, we obtain a cathode-electrolyte interfacial resistance of only 25 Ω cm2 after cold pressing at 70 MPa. Proof-of-concept cells with a sodium metal anode and a NaCrO2 cathode feature an initial discharge capacity of 103 mAh g−1 at C/10 and 42 mAh g−1 at 1 C with an excellent capacity retention of 88% after 100 cycles at 1 C at room temperature. Ion-milled cross-sections of the cathode/electrolyte interface demonstrate that intimate contact is maintained during cycling, proving that the use of hydroborates as secondary electrolyte and as an interlayer is a promising approach for the development of all-solid-state batteries with ceramic electrolytes.
Genome-wide alignment-free phylogenetic distance estimation under a no strand-bias model
Authors: Balaban Metin , Bristy Nishat Anjum , Faisal Ahnaf , Bayzid Md Shamsuzzoha , Mirarab Siavash 
Published: August 2022

Abstract

Summary: While alignment has been the dominant approach for determining homology prior to phylogenetic inference, alignment-free methods can simplify the analysis, especially when analyzing genome-wide data. Furthermore, alignment-free methods present the only option for emerging forms of data, such as genome skims, which do not permit assembly. Despite the appeal, alignment-free methods have not been competitive with alignment-based methods in terms of accuracy. One limitation of alignment-free methods is their reliance on simplified models of sequence evolution such as Jukes–Cantor. If we can estimate frequencies of base substitutions in an alignment-free setting, we can compute pairwise distances under more complex models. However, since the strand of DNA sequences is unknown for many forms of genome-wide data, which arguably present the best use case for alignment-free methods, the most complex models that one can use are the so-called no strand-bias models. We show how to calculate distances under a four-parameter no strand-bias model called TK4 without relying on alignments or assemblies. The main idea is to replace letters in the input sequences and recompute Jaccard indices between k-mer sets. However, on larger genomes, we also need to compute the number of k-mer mismatches after replacement due to random chance as opposed to homology. We show in simulation that alignment-free distances can be highly accurate when genomes evolve under the assumed models and study the accuracy on assembled and unassembled biological data.

Availability and implementation
Our software is available open source at https://github.com/nishatbristy007/NSB.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
Detecting and quantifying antibody reactivity in PhIP-Seq data with BEER
Authors: Chen Athena , Kammers Kai , Larman H Benjamin , Scharpf Robert B , Ruczinski Ingo 
Published: August 2022

AbstractSummaryBecause of their high abundance, easy accessibility in peripheral blood, and relative stability ex vivo, antibodies serve as excellent records of environmental exposures and immune responses. Phage Immuno-Precipitation Sequencing (PhIP-Seq) is the most efficient technique available for assessing antibody binding to hundreds of thousands of peptides at a cohort scale. PhIP-Seq is a high-throughput approach for assessing antibody reactivity to hundreds of thousands of candidate epitopes. Accurate detection of weakly reactive peptides is particularly important for characterizing the development and decline of antibody responses. Here, we present BEER (Bayesian Enrichment Estimation in R), a software package specifically developed for the quantification of peptide reactivity from PhIP-Seq experiments. BEER implements a hierarchical model and produces posterior probabilities for peptide reactivity and a fold change estimate to quantify the magnitude. BEER also offers functionality to infer peptide reactivity based on the edgeR package, though the improvement in speed is offset by slightly lower sensitivity compared to the Bayesian approach, specifically for weakly reactive peptides.Availability and implementationBEER is implemented in R and freely available from the Bioconductor repository at https://bioconductor.org/packages/release/bioc/html/beer.html.
Estimating the Period Prevalence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection During the Omicron (BA.1) Surge in New York City (NYC), 1 January to 16 March 2022
Authors: Qasmieh Saba A , Robertson McKaylee M , Teasdale Chloe A , Kulkarni Sarah G , Nash Denis 
Published: August 2022

Abstract
In a population-based survey of adults in New York City, we assessed positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) tests (including via exclusive at-home testing) and possible cases among untested respondents. An estimated 27.4% (95% confidence interval [CI]: 22.8%–32.0%) or 1.8 million adults (95% CI: 1.6–2.1 million) had SARS-CoV-2 infection between 1 January and 16 March 2022.
Management and Control Issues Related to Two Mumps Outbreaks in Houston: Future Implications
Authors: Schulte Joann , Short Kirstin , Persse David 
Published: August 2022

Abstract

Background
Mumps is a highly contagious disease spread by airborne droplets, making control especially difficult in congregate, crowded settings such as shelters and jails. A mumps outbreak in Honduras, starting in 2018 among adults who were unvaccinated, spread northward with Central Americans migrating to the United States. We describe 2 mumps outbreaks in Houston during 2019 among migrants at the Houston Contract Detention Facility (HCDF) and among inmates at the Harris County Jail (HCJ).

Methods
We investigated cases of acute onset parotitis. Three or more mumps cases in a facility was considered an outbreak. Confirmed cases had positive polymerase chain reactions (PCR). Probable cases were linked epidemiologically to a confirmed case in the same unit and a positive serology for serum anti-mumps immunoglobulin M (IgM) antibody. Outbreak control measures included enhanced surveillance, isolation of housing units, educational outreach, and immunization with Measles, Mumps, Rubella (MMR) vaccine.

Results
At HCDF, during a 10-month period, we investigated 42 possible cases. Of the possible cases, 28 were lab-confirmed with 9 probable, 4 ruled out, and 1 vaccine reaction. All were migrants. At HCJ, during a 3-month period, we investigated 60 suspect cases; 20 cases were lab-confirmed, 13 probable and 27 ruled out. All but 2 were inmates. Only about a third of those offered MMR vaccination accepted.

Conclusions
Successful outbreak resolution required close cooperation with HCDF and HCJ with ongoing surveillance, isolation of units with cases and MMR vaccination. Such facilities will have outbreaks; regular communications with local public health could improve response.
Maintenance of quantitative genetic variance in complex, multitrait phenotypes: the contribution of rare, large effect variants in 2 Drosophila species
Authors: Hine Emma , Runcie Daniel E , Allen Scott L , Wang Yiguan , Chenoweth Stephen F , Blows Mark W , McGuigan Katrina 
Published: August 2022

Abstract
The interaction of evolutionary processes to determine quantitative genetic variation has implications for contemporary and future phenotypic evolution, as well as for our ability to detect causal genetic variants. While theoretical studies have provided robust predictions to discriminate among competing models, empirical assessment of these has been limited. In particular, theory highlights the importance of pleiotropy in resolving observations of selection and mutation, but empirical investigations have typically been limited to few traits. Here, we applied high-dimensional Bayesian Sparse Factor Genetic modeling to gene expression datasets in 2 species, Drosophila melanogaster and Drosophila serrata, to explore the distributions of genetic variance across high-dimensional phenotypic space. Surprisingly, most of the heritable trait covariation was due to few lines (genotypes) with extreme [&gt;3 interquartile ranges (IQR) from the median] values. Intriguingly, while genotypes extreme for a multivariate factor also tended to have a higher proportion of individual traits that were extreme, we also observed genotypes that were extreme for multivariate factors but not for any individual trait. We observed other consistent differences between heritable multivariate factors with outlier lines vs those factors without extreme values, including differences in gene functions. We use these observations to identify further data required to advance our understanding of the evolutionary dynamics and nature of standing genetic variation for quantitative traits.
Extraoral Taste Buds on the Paired Fins of Damselfishes
Authors: Hardy Adam R , Hale Melina E 
Published: August 2022

SynopsisSome fish species have taste buds on the surface of their bodies and fins, as well as in the oral cavity. The extraoral taste system of fish has traditionally been studied in species that inhabit environments and/or employ feeding strategies where vision is limited. Here we examined taste sensation in a new ecological context by investigating the paired fins of damselfish (Pomacentridae), a group of diurnal midwater fishes that inhabit the light-rich waters of coral reefs. Immunohistochemistry demonstrated the presence of taste buds on the paired fins of Chromis viridis, including on the distal tips of elongate leading-edge pelvic fin rays, where they are particularly densely packed, suggesting specialization for chemosensation. Similar anatomical results were also recorded from two other species, Pomacentrus amboinensis and Pomacentrus coelestis. We found that afferent pectoral fin nerves of C. viridis responded to a food-derived stimulus. By investigating the extraoral taste system in a new phylogenetic and ecological context, these results show that taste buds on fins are more widespread amongst fish than previously known and are present even in highly visual environments.
Technical note: Evaluation of sampling methods for methane concentration from in vitro fermentation
Authors: D’Souza Genevieve M , Norris Aaron B , Tedeschi Luis O 
Published: August 2022

Abstract
The objectives of this multipart study were 1) to assess the efficacy of sampling methods of methane concentration ([CH4]) of headspace gas produced during in vitro gas production (IVGP) fermentation, 2) to verify whether headspace [CH4] sampled from an exetainer has the same [CH4] as the headspace of IVGP bottles, 3) to measure relative humidity (RH) within an IVGP bottle, and 4) to compare [CH4] on a dry-gas (DG) basis when accounting for water vapor pressure (Pw). The original IVGP protocol recommends placing bottles on ice (0 °C) for 30 min to stop fermentation (ICE). A laboratory protocol recommends placing the bottles in the refrigerator (4 to 6 °C) to slow fermentation for 48 h and subsequently allowing the bottles to return to ambient temperature before sampling (FRIDGE). This study evaluated the previous methods against a direct sampling of the headspace gas after incubation (DIRECT). Rumen inoculum from four rumen-cannulated beef steers was combined and homogenized before incubating the fermentable substrate of ground alfalfa hay. After 48 h of IVGP incubation, each bottle was randomly assigned to a treatment protocol. The pressure (P), volume (V), and temperature (T) of headspace gas in each bottle were recorded. Headspace gas was then thoroughly mixed, and 12 mL gas was removed into an evacuated exetainer for [CH4] sampling via gas chromatography (EXET; Objective 1). Eight bottles from ICE and FRIDGE were randomly selected to follow EXET, whereas the remaining bottles had [CH4] directly measured from their headspace (BOTT; Objective 2). Five diets of differing feed composition and nutrient densities were used with a blank to test the RH of the IVGP slurry (Objective 3). Using RH, [CH4] was transformed to a DG basis to account for Pw (Objective 4). Statistical analysis was completed using a random coefficients model. There were no differences between EXET and BOTT (P = 0.28). The RH of the IVGP slurry was 100% (P = 1.00), confirming that IVGP gas is saturated with water vapor. The P, V, and T differed among treatments (P &lt; 0.01). The [CH4] of DIRECT, ICE, and FRIDGE were different (P &lt; 0.01). Dry-gas P, V, and [CH4] differed among treatments (P &lt; 0.01). As the methods differ in their assessment of [CH4], there is no clear recommendation. Instead, to present a more accurate [CH4], P, V, and T should be measured when sampling headspace gas and equations presented should be used to remove volume inflation due to water vapor and present [CH4] on a DG basis.