bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimal cost and feasible design for grid-connected microgrid on campus area using the robust-intelligence method
Authors: Almas Prakasa Mohamad , Subiyanto Subiyanto 
Published: December 2021

Abstract
In this paper, a robust optimization and sustainable investigation are undertaken to find a feasible design for a microgrid in a campus area at minimum cost. The campus microgrid needs to be optimized with further investigation, especially to reduce the cost while considering feasibility in ensuring the continuity of energy supply. A modified combination of genetic algorithm and particle swarm optimization (MGAPSO) is applied to minimize the cost while considering the feasibility of a grid-connected photovoltaic/battery/diesel system. Then, a sustainable energy-management system is also defined to analyse the characteristics of the microgrid. The optimization results show that the MGAPSO method produces a better solution with better convergence and lower costs than conventional methods. The MGAPSO optimization reduces the system cost by up to 11.99% compared with the conventional methods. In the rest of the paper, the components that have been optimized are adjusted in a realistic scheme to discuss the energy profile and allocation characteristics. Further investigation has shown that MGAPSO can optimize the campus microgrid to be self-sustained by enhancing renewable-energy utilization.
A microgrid for the secluded Paana Theertham Kani settlement in India
Authors: Palanichamy C , Wen Tan Woan , Naveen P 
Published: December 2021

Abstract
Recognizing the importance of electricity as a driver of rapid economic growth and poverty alleviation, India aims to provide access to all households by 2030. Despite the best efforts of state and federal governments to meet consumers’ electrical needs, budget constraints, inefficient operations and massive loan burdens have hampered their efforts. Aside from these concerns, rural India, which accounts for 65% of the population, is plagued by a slew of issues, including low electricity demand, a low load factor and the expectation of cheap electricity. These concerns bind the authorities’ hands, preventing them from moving forward. As a result, this project aims to model an autonomous microgrid system that integrates three potential renewable-energy systems, namely wind, sun and hydrokinetic, to provide electricity for a remote society. It starts with assessing the region’s electricity needs with its inhabitants. The HOMER Pro platform creates a cost-effective microgrid based on the demand estimate. The components of the microgrid include 6.4-kW small wind turbine (SWT) groups, 4.4-kW solar photovoltaic (PV) panels, a 5-kW hydrokinetic water turbine, battery storage and a converter. The project is unique in that it considers site-specific initial capital costs, replacement costs, and operation and maintenance costs of the renewable-energy systems, and it does not include any environmentally hazardous energy system. The successful optimization results in terms of levelized energy costs are $0.0538, $0.0614 and $0.0427/kWh for wind, solar and hydrokinetic components, respectively, without any environmental issues.
Understanding risks and consequences of pathogen infections on the physiological performance of outmigrating Chinook salmon
Authors: Mauduit F , Segarra A , Mandic M , Todgham A E , Baerwald M R , Schreier A D , Fangue N A , Connon R E 
Published: December 2021

Abstract
The greatest concentration of at-risk anadromous salmonids is found in California (USA)—the populations that have been negatively impacted by the degradation of freshwater ecosystems. While climate-driven environmental changes threaten salmonids directly, they also change the life cycle dynamics and geographic distribution of pathogens, their resulting host-pathogen interactions and potential for disease progression. Recent studies have established the correlation between pathogen detection and salmonid smolt mortality during their migration to the ocean. The objective of the present study was to screen for up to 47 pathogens in juvenile Chinook salmon (Oncorhynchus tshawytscha) that were held in cages at two key sites of the Sacramento River (CA, USA) and measure potential consequences on fish health. To do so, we used a combination of transcriptomic analysis, enzymatic assays for energy metabolism and hypoxia and thermal tolerance measures. Results revealed that fish were infected by two myxozoan parasites: Ceratonova shasta and Parvicapsula minibicornis within a 2-week deployment. Compared to the control fish maintained in our rearing facility, infected fish displayed reduced body mass, depleted hepatic glycogen stores and differential regulation of genes involved in the immune and general stress responses. This suggests that infected fish would have lower chances of migration success. In contrast, hypoxia and upper thermal tolerances were not affected by infection, suggesting that infection did not impair their capacity to cope with acute abiotic stressors tested in this study. An evaluation of long-term consequences of the observed reduced body mass and hepatic glycogen depletion is needed to establish a causal relationship between salmon parasitic infection and their migration success. This study highlights that to assess the potential sublethal effects of a stressor, or to determine a suitable management action for fish, studies need to consider a combination of endpoints from the molecular to the organismal level.
Obesity increases heart failure incidence and mortality: observational and Mendelian randomization studies totalling over 1 million individuals
Authors: Benn Marianne , Marott Sarah C W , Tybjærg-Hansen Anne , Nordestgaard Børge G 
Published: December 2021

Abstract

Aims
Whether high body mass index (BMI) causally influences development and prognosis of heart failure has implications for clinical practice. We tested the hypotheses that high BMI causally influences heart failure incidence and mortality.

Methods and results
Using observational and Mendelian randomization causal, genetic analyses, we studied 106 121 individuals from the Copenhagen General Population Study, 18 407 from the Copenhagen City Heart Study, and 977 323 from publicly available databases. In observational analyses in the Copenhagen studies with 10 years of median follow-up, multivariable adjusted hazard ratios per 1 kg/m2 increment of BMI were 1.06 (95% confidence interval: 1.05–1.07; P &lt; 0.001; n = 124 528; events = 6589) for heart failure incidence, 1.04 (1.03–1.06; P &lt; 0.001; n = 124 528; events = 1237) for heart failure mortality, and 1.01 (1.00–1.01; P &lt; 0.001; n = 124 528; events = 24 144) for all-cause mortality. In genetic analyses in the Copenhagen studies, the age and sex adjusted causal risk ratios per 1 kg/m2 increment of BMI were 1.19 (1.05–1.36; P = 0.008; n = 118 200; events = 6541) for heart failure incidence, 1.27 (0.82–1.98; P = 0.28; n = 118 200; events = 889) for heart failure mortality, and 1.11 (1.02–1.22; P = 0.022; n = 118 200; events = 16 814) for all-cause mortality. Finally, combining genetic data from the Copenhagen studies, the Genetic Investigation of ANthropometric Traits, the Heart Failure Molecular Epidemiology for Therapeutic Targets, and the UK Biobank, the unadjusted causal risk ratios per 1 kg/m2 increment of BMI were 1.39 (1.27–1.52; P &lt; 0.001; n = 1 095 523; events = 53 850) for heart failure incidence, 1.18 (1.00–1.38; P = 0.05; n = 576 853; events = 2373) for heart failure mortality, and 1.02 (1.00–1.04; P = 0.03; n = 576 853; events = 44 734) for all-cause mortality.

Conclusion
High BMI causally increases the risk of both heart failure incidence and mortality.
Suppression of the Sugarcane Aphid, Melanaphis sacchari (Hemiptera: Aphididae), by Resident Natural Enemies on Susceptible and Resistant Sorghum Hybrids
Authors: Faris Ashleigh M , Elliott Norman C , Brewer Michael J 
Published: December 2021

Abstract
The sugarcane aphid, Melanaphis sacchari (Zehntner) (Hemiptera: Aphididae), is an invasive sorghum pest that has threatened over 90% of North American sorghum production. Resident parasitoids, coccinellids, syrphids, and lacewings prey on this aphid. Our objective was to compare and estimate parasitoid and predator suppression of sugarcane aphids placed on resistant and susceptible hybrids in a field setting using natural enemy exclusion cages. During 2018 and 2019 along the Texas Gulf Coast and Central Oklahoma, three natural enemy exclusion treatments—no exclusion (full access for parasitoids and predators), partial exclusion (access limited to parasitoids), and complete exclusion (excludes parasitoids and predators)—were used. The parasitoid Aphelinus nigritus Howard (Hymenoptera: Aphelinidae) accounted for 90% of recovered natural enemies. In 2018, aphid suppression attributable to A. nigritus was ca. 95% on the resistant hybrids and 80% on the susceptible hybrids when comparing aphid counts from complete and partial exclusion treatments, while few predators were observed. In 2019, aphid suppression was attributed to a combination of predation and parasitism. Relatively more predators were recorded at both sites, accounting for 14% to 33% of specimens recovered in the no exclusion treatment. Aphid suppression attributed to predators and parasitoids ranged from 85% on aphid-resistant hybrids and 27% on susceptible hybrids in south Texas and &gt;95% on both hybrids in Oklahoma when comparing aphid abundance in the complete and no exclusion treatments. Parasitism and predation contributed to aphid regulation on both hybrids, which may accrue multiple benefits leading to a more resilient sugarcane aphid management system.
Intersecting single-cell transcriptomics and genome-wide association studies identifies crucial cell populations and candidate genes for atherosclerosis
Authors: Slenders Lotte , Landsmeer Lennart P L , Cui Kai , Depuydt Marie A C , Verwer Maarten , Mekke Joost , Timmerman Nathalie , van den Dungen Noortje A M , Kuiper Johan , de Winther Menno P J , Prange Koen H M , Ma Wei Feng , Miller Clint L , Aherrahrou Redouane , Civelek Mete , de Borst Gert J , de Kleijn Dominique P V , Asselbergs Folkert W , den Ruijter Hester M , Boltjes Arjan , Pasterkamp Gerard , van der Laan Sander W , Mokry Michal 
Published: December 2021

AbstractAimsGenome-wide association studies (GWASs) have discovered hundreds of common genetic variants for atherosclerotic disease and cardiovascular risk factors. The translation of susceptibility loci into biological mechanisms and targets for drug discovery remains challenging. Intersecting genetic and gene expression data has led to the identification of candidate genes. However, previously studied tissues are often non-diseased and heterogeneous in cell composition, hindering accurate candidate prioritization. Therefore, we analysed single-cell transcriptomics from atherosclerotic plaques for cell-type-specific expression to identify atherosclerosis-associated candidate gene–cell pairs.Methods and resultsWe applied gene-based analyses using GWAS summary statistics from 46 atherosclerotic and cardiovascular disease, risk factors, and other traits. We then intersected these candidates with single-cell RNA sequencing (scRNA-seq) data to identify genes specific for individual cell (sub)populations in atherosclerotic plaques. The coronary artery disease (CAD) loci demonstrated a prominent signal in plaque smooth muscle cells (SMCs) (SKI, KANK2, and SORT1) P-adj. = 0.0012, and endothelial cells (ECs) (SLC44A1, ATP2B1) P-adj. = 0.0011. Finally, we used liver-derived scRNA-seq data and showed hepatocyte-specific enrichment of genes involved in serum lipid levels.ConclusionWe discovered novel and known gene–cell pairs pointing to new biological mechanisms of atherosclerotic disease. We highlight that loci associated with CAD reveal prominent association levels in mainly plaque SMC and EC populations. We present an intuitive single-cell transcriptomics-driven workflow rooted in human large-scale genetic studies to identify putative candidate genes and affected cells associated with cardiovascular traits. Collectively, our workflow allows for the identification of cell-specific targets relevant for atherosclerosis and can be universally applied to other complex genetic diseases and traits.
NanoLuc luciferase as a quantitative yeast two-hybrid reporter
Authors: Heintz Veronica J , Wang Ling , LaCount Douglas J 
Published: December 2021

ABSTRACT
The yeast two-hybrid (Y2H) assay is a powerful technique to identify protein-protein interactions. However, the auxotrophic markers that are the most common Y2H reporters take several days to yield data and require subjective assessment of semiquantitative data to identify interactions. Several reporters have been developed to overcome these disadvantages, but there is still a need for a Y2H reporter that is objective, fast and able to be performed with common laboratory equipment. In this report, we replaced the ADE2 reporter in BK100 with NanoLuc luciferase to yield BK100Nano. We developed an optimized assay to measure NanoLuc activity in 96-well plates and analyzed a set of 74 pairs identified in Y2H library screens, which revealed 44 positive interactions using an unbiased cutoff based on the mean luminescence of negative control samples. The same set was also tested for growth on Y2H selection medium via expression of the HIS3 reporter. We found 91% agreement between the two assays, with discrepancies attributed to weak interactions that displayed variable growth on Y2H medium. Overall, the new BK100Nano strain establishes a quantitative and convenient method to identify Y2H interactions and has potential to be applied to a high throughput manner.
Long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears (Ursus arctos)
Authors: Tseng Elizabeth , Underwood Jason G , Evans Hutzenbiler Brandon D , Trojahn Shawn , Kingham Brewster , Shevchenko Olga , Bernberg Erin , Vierra Michelle , Robbins Charles T , Jansen Heiko T , Kelley Joanna L 
Published: December 2021

Abstract
Understanding hibernation in brown bears (Ursus arctos) can provide insight into some human diseases. During hibernation, brown bears experience periods of insulin resistance, physical inactivity, extreme bradycardia, obesity, and the absence of urine production. These states closely mimic aspects of human diseases such as type 2 diabetes, muscle atrophy, as well as renal and heart failure. The reversibility of these states from hibernation to active season enables the identification of mediators with possible therapeutic value for humans. Recent studies have identified genes and pathways that are differentially expressed between active and hibernation seasons in bears. However, little is known about the role of differential expression of gene isoforms on hibernation physiology. To identify both distinct and novel mRNA isoforms, full-length RNA-sequencing (Iso-Seq) was performed on adipose, skeletal muscle, and liver from three individual bears sampled during both active and hibernation seasons. The existing reference genome annotation was improved by combining it with the Iso-Seq data. Short-read RNA-sequencing data from six individuals were mapped to the new reference annotation to quantify differential isoform usage (DIU) between tissues and seasons. We identified differentially expressed isoforms in all three tissues, to varying degrees. Adipose had a high level of DIU with isoform switching, regardless of whether the genes were differentially expressed. Our analyses revealed that DIU, even in the absence of differential gene expression, is an important mechanism for modulating genes during hibernation. These findings demonstrate the value of isoform expression studies and will serve as the basis for deeper exploration into hibernation biology.
Expanding the Menu: Are Polyphagy and Gene Family Expansions Linked across Lepidoptera?
Authors: Breeschoten Thijmen , van der Linden Corné F H , Ros Vera I D , Schranz M Eric , Simon Sabrina 
Published: December 2021

AbstractEvolutionary expansions and contractions of gene families are often correlated with key innovations and/or ecological characteristics. In butterflies and moths (Lepidoptera), expansions of gene families involved in detoxification of plant specialized metabolites are hypothesized to facilitate a polyphagous feeding style. However, analyses supporting this hypothesis are mostly based on a limited number of lepidopteran species. We applied a phylogenomics approach, using 37 lepidopteran genomes, to analyze if gene family evolution (gene gain and loss) is associated with the evolution of polyphagy. Specifically, we compared gene counts and evolutionary gene gain and loss rates of gene families involved in adaptations with plant feeding. We correlated gene evolution to host plant family range (phylogenetic diversity) and specialized metabolite content of plant families (functional metabolite diversity). We found a higher rate for gene loss than gene gain in Lepidoptera, a potential consequence of genomic rearrangements and deletions after (potentially small-scale) duplication events. Gene family expansions and contractions varied across lepidopteran families, and were associated to host plant use and specialization levels. Within the family Noctuidae, a higher expansion rate for gene families involved in detoxification can be related to the large number of polyphagous species. However, gene family expansions are observed in both polyphagous and monophagous lepidopteran species and thus seem to be species-specific in the taxa sampled. Nevertheless, a significant positive correlation of gene counts of the carboxyl- and choline esterase and glutathione-S-transferase detoxification gene families with the level of polyphagy was identified across Lepidoptera.
Destructive outbreaks of the corallivorous starfish Acanthaster cf. solarisspare coral assemblages in the shallowest reef flat areas in New Caledonia
Authors: Dumas Pascal , Peignon Christophe , Dumas Mahé , Bourgeois Bertrand , Gossuin Hugues , Fiat Sylvie 
Published: December 2021

Abstract
Outbreaks of the corallivorous starfish Acanthaster cf. solaris (COTS) are not fully understood, especially in the shallowest areas behind the reef crests where limited COTS impacts are often reported. Here, we investigated the outbreak occurrence and compared post-outbreak habitat impacts in reef flats vs. upper fore reefs at 13 sites in New Caledonia. In this Pacific territory so far considered marginally affected by COTS, we documented wide occurrences of aggregations, combining massive population increases (maximum 605 COTS per swim, abundances &gt;100 COTS recorded in 46% of the sites) with limited spatiotemporal boundaries. Abundance levels met the highest values in the literature, but were restricted to relatively small, isolated mid-shelf reefs. Typical residence time was short (&lt; two years), with at least one site where COTS seemingly disappeared within seven months. The spread of COTS population and subsequent impacts appeared self-contained, and never affected the reef flats (0.5–1.5 m). The transition to severely affected fore reefs was abrupt, with live coral cover divided by nine and morphological diversity halved within a very few meters (3–5 m). We suggest that these differential impacts likely result from harsh environmental conditions making shallow, coral-rich areas less suitable for COTS, thereby pushing predation pressure further downwards.
Incorporating spatial heterogeneity and environmental impacts into stock-recruitment relationships for Gulf of Maine lobster
Authors: Mazur Mackenzie D , Tanaka Kisei R , Shank Burton , Chang Jui-Han , Hodgdon Cameron T , Reardon Kathleen M , Friedland Kevin D , Chen Yong 
Published: December 2021

ABSTRACTFunctional stock-recruitment relationships (SRRs) are often difficult to quantify and can differ over space. Additionally, climate change adds to the complexity of recruitment dynamics. This paper's aim was to incorporate spatial heterogeneity and environmental effects on productivity in SRRs with American lobster in the Gulf of Maine (GOM) as a case study. GOM lobster recruitment has substantially increased since the mid-2000s, due to improved survival rates of pre-recruits and increased spawning stock biomass (SSB). GOM bottom water temperatures have increased at a rate of 0.2ºC per decade, which caused lobster settlement area to expand and improved survival rates. We first estimated local SSB using bottom trawl survey data and a geostatistical model. Using estimated SSB, recruitment data from a ventless trap survey, and an interpolated bottom water temperature field, we developed modified Ricker stock-recruitment models accounting for spatial heterogeneity and temperature impacts with varying coefficient generalized additive models. Results showed that temperature significantly impacted recruitment. Changes in temperature mediated productivity differed between the eastern and western GOM. Our study demonstrated that the incorporation of spatial heterogeneity and environmental effects impacts our understanding of SRRs. These methods can be applied to other species to understand recruitment dynamics influenced by climate change.
Validation of the 3M™ Molecular Detection Assay 2 - STEC Gene Screen (stx) for the Detection of Shiga Toxin Gene (stx1 and/or stx2) in Fresh Raw Ground Beef and Fresh Spinach: AOAC Performance Tested MethodSM 071903
Authors: Rosauer Micki L , Barnes Christina , Silbernagel Karen M , Koch Kateland M 
Published: December 2021

Abstract

Background
The 3M™ Molecular Detection Assay 2 - STEC Gene Screen (stx) method is based on gene amplification by the use of real time loop-mediated isothermal amplification when used with the 3M Molecular Detection System for the rapid and specific detection of Shiga toxin gene (stx1 and/or stx2) from Shiga toxin-producing Escherichia coli (STEC) in enriched foods. The stx assay does not differentiate between stx1 and stx2 but detects the presence of stx1 and/or stx2.

Objective
The 3M Molecular Detection Assay 2 - STEC Gene Screen (stx) method was evaluated for AOAC® Performance Tested MethodsSM certification.

Methods
Matrix studies, inclusivity/exclusivity, robustness testing, product stability, and lot-to-lot variability testing were conducted to assess the method’s performance.

Results
The 3M Molecular Detection Assay 2 - STEC Gene Screen (stx) demonstrated equivalent results to the United States Department of Agriculture/Food Safety and Inspection Service Microbiology Laboratory Guidebook Chapter 5C.00 reference method for fresh raw ground beef, and the U.S. Food and Drug Administration Bacteriological Analytical Manual Chapter 4A reference method for fresh spinach. The 3M Molecular Detection Assay 2 - STEC Gene Screen (stx) detected all STEC E. coli strains (E. coli strains with stx1 and/or stx2 genes) and did not detect any of the 45 strains from the exclusivity panel. Robustness testing indicated that small variations in critical test parameters did not adversely affect the assay’s performance. Product consistency and stability testing demonstrated no differences between the lots evaluated.

Conclusion
The data collected in these studies demonstrate that the 3M Molecular Detection Assay 2 - STEC Gene Screen (stx) is a reliable method for the rapid and specific detection of Shiga toxin-producing E. coli in raw ground beef and spinach.

Highlights
The 3M Molecular Detection Assay 2 - STEC Gene Screen (stx) method is suitable for the rapid and specific detection of Shiga toxin-producing E. coli in fresh raw ground beef, and spinach.