bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developmental plasticity of thermal performance curve for reproduction in Drosophila melanogaster
Authors: Klepsatel Peter , Knoblochová Diana , Dharanikota Malleswara , Vidlička Ľubomír , Gáliková Martina 
Published: September 2023

Abstract
In ectotherms, body temperature is a crucial determinant of performance and fitness, as captured by thermal performance curves (TPCs). Since survival in variable environments is often facilitated by phenotypic plasticity, to reliably assess an organism’s ability to cope with thermal changes, it is necessary to characterize not only TPCs but also their reaction norms. While previous studies have investigated plasticity in TPCs, these studies focus only on selected parameters and a few developmental temperatures. They may, therefore, overlook the complexity of developmental plasticity in TPCs. Here, we examined the full extent of thermal developmental plasticity in TPCs for fecundity and hatchability in Drosophila melanogaster. By employing a factorial design with ten developmental and twelve adult temperatures, our study enabled a comprehensive characterization of reaction norms of all key TPC parameters. We found that developmental temperature had a significant impact on the egg production rate, with minor effects on other TPC parameters. Nonoptimal developmental temperatures negatively affected most TPC parameters, whereas development at 22–26 °C maximized reproductive fitness. We also revealed that developmental plasticity for the maximum reproductive performance might be predominantly caused by developmentally-induced changes in ovariole number. Our results in conjunction with previous studies on intraspecific variation suggest that any changes in TPC for reproduction primarily involve the egg production rate, indicating that adaptive evolution and phenotypic plasticity followed the same pathway. Overall, our findings underscore the limitations of developmental plasticity in enhancing reproductive fitness, suggesting that while certain traits, such as egg production rate, may be relatively plastic, these changes may not be sufficient to enable effective adjustment to environmental shifts.
Genetic bases of resistance to the rice hoja blanca disease deciphered by a quantitative trait locus approach
Authors: Silva Alexander , Montoya María Elker , Quintero Constanza , Cuasquer Juan , Tohme Joe , Graterol Eduardo , Cruz Maribel , Lorieux Mathias 
Published: September 2023

Abstract
Rice hoja blanca (RHB) is one of the most serious diseases in rice-growing areas in tropical Americas. Its causal agent is RHB virus (RHBV), transmitted by the planthopper Tagosodes orizicolus Müir. Genetic resistance is the most effective and environment-friendly way of controlling the disease. So far, only 1 major quantitative trait locus (QTL) of Oryza sativa ssp. japonica origin, qHBV4.1, that alters the incidence of the virus symptoms in 2 Colombian cultivars has been reported. This resistance has already started to be broken, stressing the urgent need for diversifying the resistance sources. In the present study, we performed a search for new QTLs of O. sativa indica origin associated with RHB resistance. We used 4 F2:3-segregating populations derived from indica-resistant varieties crossed with a highly susceptible japonica pivot parent. Besides the standard method for measuring disease incidence, we developed a new method based on computer-assisted image processing to determine the affected leaf area (ALA) as a measure of symptom severity. Based on the disease severity and incidence scores in the F3 families under greenhouse conditions and SNP genotyping of the F2 individuals, we identified 4 new indica QTLs for RHB resistance on rice chromosomes 4, 6, and 11, namely, qHBV4.2WAS208, qHBV6.1PTB25, qHBV11.1, and qHBV11.2, respectively. We also confirmed the wide-range action of qHBV4.1. Among the 5 QTLs, qHBV4.1 and qHBV11.1 had the largest effects on incidence and severity, respectively. These results provide a more complete understanding of the genetic bases of RHBV resistance in the cultivated rice gene pool and can be used to develop marker-aided breeding strategies to improve RHB resistance. The power of joint- and meta-analyses allowed precise mapping and candidate gene identification, providing the basis for positional cloning of the 2 major QTLs qHBV4.1 and qHBV11.1.
Whole-genome sequence of the Cooley spruce gall adelgid, Adelges cooleyi (Hemiptera: Sternorrhyncha: Adelgidae)
Authors: Dial Dustin T , Weglarz Kathryn M , Brunet Bryan M T , Havill Nathan P , von Dohlen Carol D , Burke Gaelen R 
Published: September 2023

Abstract
The adelgids (Adelgidae) are a small family of sap-feeding insects, which, together with true aphids (Aphididae) and phylloxerans (Phylloxeridae), make up the infraorder Aphidomorpha. Some adelgid species are highly destructive to forest ecosystems such as Adelges tsugae, Adelges piceae, Adelges laricis, Pineus pini, and Pineus boerneri. Despite this, there are no high-quality genomic resources for adelgids, hindering advanced genomic analyses within Adelgidae and among Aphidomorpha. Here, we used PacBio continuous long-read and Illumina RNA-sequencing to construct a high-quality draft genome assembly for the Cooley spruce gall adelgid, Adelges cooleyi (Gillette), a gall-forming species endemic to North America. The assembled genome is 270.2 Mb in total size and has scaffold and contig N50 statistics of 14.87 and 7.18 Mb, respectively. There are 24,967 predicted coding sequences, and the assembly completeness is estimated at 98.1 and 99.6% with core BUSCO gene sets of Arthropoda and Hemiptera, respectively. Phylogenomic analysis using the A. cooleyi genome, 3 publicly available adelgid transcriptomes, 4 phylloxera transcriptomes, the Daktulosphaira vitifoliae (grape phylloxera) genome, 4 aphid genomes, and 2 outgroup coccoid genomes fully resolves adelgids and phylloxerans as sister taxa. The mitochondrial genome is 24 kb, among the largest in insects sampled to date, with 39.4% composed of noncoding regions. This genome assembly is currently the only genome-scale, annotated assembly for adelgids and will be a valuable resource for understanding the ecology and evolution of Aphidomorpha.
No Signs of Adaptations for High Flight Intensity in the Mitochondrial Genome of Birds
Authors: Claramunt Santiago , Haddrath Oliver 
Published: September 2023

Abstract
Mitochondrial genomes are expected to show adaptations for optimizing aerobic respiration in birds that make intense use of flight. However, there is limited empirical evidence of such a relationship. We here examine correlates of several mitochondrial genome characteristics and flight use across a diverse sample of 597 bird species. We developed an index of flight use intensity that ranged from 0 in flightless species to 9 in migratory hummingbirds and examined its association with nucleobase composition, amino acid class composition, and amino acid site allelic variation using phylogenetic comparative methods. We found no evidence of mitochondrial genome adaptations to flight intensity. Neither nucleotide composition nor amino acid properties showed consistent patterns related to flight use. While specific sites in mitochondrial genes exhibited variation associated with flight intensity, there was limited association between specific amino acid residues and flight intensity levels. Our findings suggest a complex genetic architecture for aerobic performance traits, where multiple genes in both mitochondria and the nucleus may contribute to overall performance. Other factors, such as gene expression regulation and anatomical adaptations, may play a more significant role in influencing flight performance than changes in mitochondrial genes. These findings highlight the need for comprehensive genomic analyses to unravel the intricate relationship between genetic variants and aerobic performance in birds.
Ohnologs and SSD Paralogs Differ in Genomic and Expression Features Related to Dosage Constraints
Authors: Vance Zoe , McLysaght Aoife 
Published: September 2023

Abstract
Gene duplication is recognized as a critical process in genome evolution; however, many questions about this process remain unanswered. Although gene duplicability has been observed to differ by duplication mechanism and evolutionary rate, there is so far no broad characterization of its determinants. Many features correlate with this difference in duplicability; however, our ability to exploit these observations to advance our understanding of the role of duplication in evolution is hampered by limitations within existing work. In particular, the existence of methodological differences across studies impedes meaningful comparison. Here, we use consistent definitions of duplicability in the human lineage to explore these associations, allow resolution of the impact of confounding factors, and define the overall relevance of individual features. Using a classifier approach and controlling for the confounding effect of duplicate longevity, we find a subset of gene features important in differentiating genes duplicable by small-scale duplication from those duplicable by whole-genome duplication, revealing critical roles for gene dosage and expression costs in duplicability. We further delve into patterns of functional enrichment and find a lack of constraint on duplicate retention in any context for genes duplicable by small-scale duplication.
OmicsSuite: a customized and pipelined suite for analysis and visualization of multi-omics big data
Authors: Miao Ben-Ben , Dong Wei , Gu Yi-Xin , Han Zhao-Fang , Luo Xuan , Ke Cai-Huan , You Wei-Wei 
Published: September 2023

Abstract
With the advancements in high-throughput sequencing technologies such as Illumina, PacBio, and 10X Genomics platforms, and gas/liquid chromatography-mass spectrometry, large volumes of biological data in multiple formats can now be obtained through multi-omics analysis. Bioinformatics is constantly evolving and seeking breakthroughs to solve multi-omics problems; however, it is challenging for most experimental biologists to analyse data using command-line interfaces, coding, and scripting. Based on experience with multi-omics, we have developed OmicsSuite, a desktop suite that comprehensively integrates statistics and multi-omics analysis and visualization. The suite has 175 sub-applications in 12 categories, including Sequence, Statistics, Algorithm, Genomics, Transcriptomics, Enrichment, Proteomics, Metabolomics, Clinical, Microorganism, Single Cell, and Table Operation. We created the user interface with Sequence View, Table View, and intelligent components based on JavaFX and the popular Shiny framework. The multi-omics analysis functions were developed based on BioJava and 300+ packages provided by the R CRAN and Bioconductor communities, and it encompasses over 3000 adjustable parameter interfaces. OmicsSuite can directly read multi-omics raw data in FastA, FastQ, Mutation Annotation Format, mzML, Matrix, and HDF5 formats, and the programs emphasize data transfer directions and pipeline analysis functions. OmicsSuite can produce pre-publication images and tables, allowing users to focus on biological aspects. OmicsSuite offers multi-omics step-by-step workflows that can be easily applied to horticultural plant breeding and molecular mechanism studies in plants. It enables researchers to freely explore the molecular information contained in multi-omics big data (Source: https://github.com/OmicsSuite/, Website: https://omicssuite.github.io, v1.3.9).
Planes, Trains, and Armored Mobiles: Introducing a Dataset of the Global Distribution of Military Capabilities
Authors: Gannon J Andrés 
Published: September 2023

Abstract
This article introduces a dataset on disaggregated national military capabilities from 1970 to 2014, drawn from the International Institute for Strategic Studies Military Balance. While practitioners have long recognized the importance of what weapons states own, scholars have largely examined surrounding questions in piecemeal fashion due to data limitations. The Distribution of Military Capabilities dataset identifies the weapons portfolios of states over the past half century at various levels of aggregation suitable to a wide variety of research questions. This paper begins by explaining the value of data on disaggregated national military capabilities, the data’s scope, and the data collection process, including the creation of a new modular typology of weapons categories consistent across time and space. I then identify some initial trends about changes in the distribution of military capabilities and their implications for China’s military rise. These data allow scholars to better investigate important questions concerning power projection, military innovation, conflict outcomes, the use of force decisions, and interest group lobbying.
Time- and temperature-dependent postmortem ∆9-tetrahydrocannabinol concentration changes in rabbits following controlled inhaled cannabis administration
Authors: Cliburn Kacey D , Kemp Philip M , Huestis Marilyn A , Wagner Jarrad R , Payton Mark , Liu Lin , Liang Yurong , Maxwell Lara K 
Published: September 2023

Abstract
ostmortem redistribution (PMR), a well-known phenomenon in forensic toxicology, can result in substantial changes in drug concentrations after death, depending on the chemical characteristics of the drug, blood collection site, storage conditions of the body and postmortem interval (PMI). Limited PMR data are available for ∆9-tetrahydrocannabinol (THC), the primary psychoactive component in Cannabis sativa. PMR was evaluated after controlled cannabis inhalation via a smoking machine and exposure chamber in New Zealand white rabbits. Necropsies were performed on five control rabbits immediately after euthanasia, whereas 27 others were stored at room temperature (21°C) or refrigerated conditions (4°C) until necropsy at 2, 6, 16, 24 or 36 h after death. THC and its Phase I and glucuronidated Phase II metabolites were quantified in blood, vitreous humor, urine, bile and tissues by liquid chromatography–tandem mass spectrometry (LC–MS-MS). Under refrigerated temperature, heart blood THC concentrations significantly increased at PMI 2 h in rabbits, whereas peripheral blood THC concentrations showed a significant increase at PMI 16 h. Central:peripheral blood and liver:peripheral blood ratios for THC ranged from 0.13 to 4.1 and 0.28 to 8.9, respectively. Lung revealed the highest THC concentrations, while brain and liver exhibited the most stable THC concentrations over time. This report contributes much needed data to our understanding of postmortem THC behavior and can aid toxicologists in the interpretation of THC concentrations in medicolegal death investigations.
Complete Salvage of Third-degree Burn of Ear by Repairing Gel-PRP-Fibrin Glue, A Case Report
Authors: Tavousi Seyed Hasan , Safari Hosein , Kouchaki Amir , Emadi Elaheh , Hamidi Alamdari Daryoush 
Published: September 2023

Abstract
The ear is a very important facial feature and enhances the overall look of the face. Usually, patients with entire ear burns also have large areas of burn in their bodies. To save the patient, skin grafting to reduce the injured body surface area is prioritized and the treatment of the ears may be inevitably delayed, which results in minor to very severe cosmetic deformity. This has a deep effect on the life quality of a patient who survives a burn injury. Therefore, any step that decreases ear deformity or loss is very crucial for the patient. There are different challenging procedures for ear reconstruction which are very tedious works. In this study, for one patient, repairing gel–platelet-rich plasma-fibrin glue was applied for the treatment of a deep dermal burned ear as a novel, non-invasive, and simple approach to give a normal shape to the ear to prevent extensive morbidity during the acute phase and deformities later as a consequence of burns. No keloid is observed after treatment.
Experiment and particle flow simulation on mechanical properties and crack evolution mechanism of Brazilian discs containing two flaws
Authors: Bai Yao , Sun Peng , Dou Haoyu , Ma Tiancheng , Wang Yujing , Liu Pengqian 
Published: September 2023

Abstract
The mechanical behavior of fractured rock in tensile stress environment is a hot topic in underground mining engineering. Here, real surrounding rock of coal mine roadway was simulated by using rock-like materials and the tensile failure behavior of Brazilian discs with intermittent double fissures was investigated experimentally. The deformation response, fracture evolution, and failure mode of rock were analyzed. The fissured disc specimen's discrete element model was proposed in particle flow code (PFC2D). The microforce field, crack, and energy evolution processes of model specimens were discussed. The results showed that the load-displacement curves exhibit single-peak and double-peak types, corresponding to the splitting penetration and wing crack penetration damage modes of the specimen. The fissure angle or rock bridge angle showed a great influence on the evolution of main cracks and secondary cracks. The double-fissured Brazilian disc failed due to the initiation and transfer of microcracks in the stress concentration zone, combined with the continuous propagation and convergence of those microcracks. The splitting failure of the Brazilian disc is a continuous process of strain energy accumulation from the early stage of loading and instantaneous release of strain energy after obtaining the peak strength as the dissipative energy sharply rises.
Phenomenological Interview and Gender Dysphoria: A Third Pathway for Diagnosis and Treatment
Authors: Dierckxsens Geoffrey , Baron Teresa R 
Published: September 2023

Abstract
Gender dysphoria (GD) is marked by an incongruence between a person’s biological sex at birth, and their felt gender (or gender identity). There is continuing debate regarding the benefits and drawbacks of physiological treatment of GD in children, a pathway, beginning with endocrine treatment to suppress puberty. Currently, the main alternative to physiological treatment consists of the so-called “wait-and-see” approach, which often includes counseling or other psychotherapeutic treatment. In this paper, we argue in favor of a “third pathway” for the diagnosis and treatment of GD in youths. To make our case, we draw on a recent development in bioethics: the phenomenological approach. Scholars such as Slatman and Svenaeus have argued that the extent to which the body can (or should be) manipulated or reconstructed through medical intervention is not only determined by consideration of ethical frameworks and social and legal norms. Rather, we must also take account of patients’ personal experience of their body, the personal and social values associated with it, and their understanding of its situation in their life: their narrative identities. We apply this phenomenological approach to medicine and nursing to the diagnosis and treatment of GD in youth. In particular, we discuss Zahavi and Martiny’s conception of the phenomenological interview, in order to show that narrative techniques can assist in the process of gender identification and in the treatment of youth presenting with GD. We focus on two case studies that highlight the relevance of a narrative-based interview in relations between patients, HCPs, and family, to expose the influence of social ideologies on how young people presenting with GD experience their bodies and gender.
The intricate role of CCL5/CCR5 axis in Alzheimer disease
Authors: Ma Weijiang , Liu Aihua , Wu Xinya , Gao Li , Chen Jingjing , Wu Hanxin , Liu Meixiao , Fan Yuxin , Peng Li , Yang Jiaru , Kong Jing , Li Bingxue , Ji Zhenhua , Dong Yan , Luo Suyi , Song Jieqin , Bao Fukai 
Published: September 2023

Abstract
The morbidity and mortality associated with Alzheimer disease (AD), one of the most common neurodegenerative diseases, are increasing each year. Although both amyloid β and tau proteins are known to be involved in AD pathology, their detailed functions in the pathogenesis of the disease are not fully understood. There is increasing evidence that neuroinflammation contributes to the development and progression of AD, with astrocytes, microglia, and the cytokines and chemokines they secrete acting coordinately in these processes. Signaling involving chemokine (C-C motif) ligand 5 (CCL5) and its main receptor C-C chemokine receptor 5 (CCR5) plays an important role in normal physiologic processes as well as pathologic conditions such as neurodegeneration. In recent years, many studies have shown that the CCL5/CCR5 axis plays a major effect in the pathogenesis of AD, but there are also a few studies that contradict this. In short, the role of CCL5/CCR5 axis in the pathogenesis of AD is still intricate. This review summarizes the structure, distribution, physiologic functions of the CCL5/CCR5 axis, and the progress in understanding its involvement in the pathogenesis of AD.
Hemorrhage and Massive Transfusion Protocols
Authors: Heine Christopher , Brown Tod 
Published: September 2023

Abstract
Acute, major hemorrhage, like that seen in the setting of a traumatic injury, carries a high risk of morbidity and mortality. This is the result of the inciting injury, the treatment with intravenous infusions and transfusions, and the body’s subsequent response to both. While the ultimate treatment of the insult is either surgery or conservative critical care, the resuscitation is often managed by paramedics and other first responders, emergency rooms, and potentially anesthetists if the patient is brought to the operating room. Proper use of blood products, protocols, pharmacologic and nonpharmacologic therapy, and testing can help mitigate the damage caused by the trauma and the therapy. The principles of damage control surgery and resuscitation allow for the care team to initially stabilize the patient in the operating room and then the critical care team to further resuscitate and treat coagulopathies before returning for the definitive repair hours or days later.
Anaphylaxis
Authors: Sutaria Richa , Guta Cosmin 
Published: September 2023

Abstract
Anaphylaxis is a life-threatening, type 1 hypersensitivity reaction that occurs with reexposure to an antigen, eliciting an IgE-mediated response, which triggers a widespread mediator release of mast cells and basophils. The top causative agents of anaphylaxis during the perioperative period are neuromuscular blockers, antibiotics, and latex. However, with the increased use of sugammadex, the overall incidence of anaphylaxis in patients under general anesthesia has been reported to be increased by one-third. Symptoms can progress rapidly and involve multiple organ systems. During the perioperative period, anaphylaxis can be more severe with higher mortality rates as patients are unable to report their symptoms. For many cases, the initial detection of anaphylaxis occurs with severe airway obstruction and/or cardiovascular collapse. The symptoms of anaphylaxis can be more difficult to recognize in sedated or anesthetized patients, requiring vigilant oversight by the anesthetic provider. Prompt recognition of these symptoms and initiating treatment of anaphylaxis is key as clinical deterioration can occur rapidly. It is of utmost importance to initiate early cardiopulmonary resuscitation with epinephrine administration and fluid resuscitation. Obtaining serum tryptase levels in a timely fashion can confirm the diagnosis.