bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the quality of comparative genomics data and results with the cogeqc R/Bioconductor package
Authors: Almeida‐Silva Fabricio , Van de Peer Yves 
Published: November 2023

Abstract

Comparative genomics has become an indispensable part of modern biology due to the advancements in high‐throughput sequencing technologies and the accumulation of genomic data in public databases. However, the quality of genomic data and the choice of parameters used in software tools used for comparative genomics can greatly impact the accuracy of results.

Here, we present cogeqc, an R/Bioconductor package that provides researchers with a toolkit to assess genome assembly and annotation quality, orthogroup inference, and synteny detection. The package offers context‐guided assessments of assembly and annotation statistics by comparing observed statistics to those of closely‐related species on NCBI. To assess orthogroup inference, cogeqc calculates a protein domain‐aware orthogroup score that aims at maximising the number of shared protein domains within the same orthogroup. The assessment of synteny detection consists in representing anchor gene pairs as a synteny network and analysing its graph properties, such as clustering coefficient, node count, and scale‐free topology fit.

The application of cogeqc to real datasets allowed for an evaluation of multiple parameter combinations for orthogroup inference and synteny detection, providing researchers in need for comparative genomics with guidelines to aid in the selection of the most appropriate tools and parameters for their specific data.

We demonstrate that the default parameters in orthogroup identification and synteny detection tools are not always the most suitable, highlighting the importance of performing assessments for each dataset. The assessment metrics provided by cogeqc will help researchers generate more accurate and reliable results.
A descriptive coronial study of heroin toxicity deaths in Australia, 2020–2022: Characteristics, toxicology and survival times
Authors: Darke Shane , Duflou Johan , Peacock Amy , Farrell Michael , Lappin Julia 
Published: November 2023

AbstractBackground and aimsMortality rates among people who use heroin are estimated to be 15 times that of the general population. The study aimed to determine (1) the case characteristics and circumstances of death of heroin‐related toxicity deaths in Australia, 2020–2022; (2) their toxicological profile and major autopsy findings; (3) the proportion of cases in which blood 6‐acetyl morphine (6AM) was detected, as a proxy measure of survival times; and (4) compare 6AM positive and negative cases on toxicology, circumstances of death and acute clinical presentation.DesignRetrospective study of heroin toxicity deaths in Australia, 2020–2022, retrieved from the National Coronial Information System.SettingThis study was conducted Australia‐wide.CasesThere were 610 cases of fatal heroin‐related drug toxicity.MeasurementsInformation was collected on characteristics, manner of death, toxicology and autopsy results.FindingsThe mean age was 42.6 years (range 18–73 years), 80.5% were male and 7.5% were enrolled in a drug treatment programme. The circumstances of death were as follows: unintentional drug toxicity (86.2%), combined unintentional drug toxicity/disease (11.3%) and intentional drug toxicity (2.5%). The median free morphine concentration was 0.17 mg/L (range 0.00–4.20 mg/L). Psychoactive drugs other than heroin were present in 95.2% (Confidence Interval 93.1%–96.8%), most commonly hypnosedatives (62.3%, 58.2%–66.4%) and psychostimulants (44.8%, 40.7%–49.1%). Major autopsy findings of clinical significance included acute bronchopneumonia (14.8%, 11.3%–18.8%), emphysema (16.9%, 13.2%–21.1%), cardiomegaly (30.1%, 12.7%–28.2%), coronary artery disease (27.4%, 23.0%–32.3%), coronary replacement fibrosis (13.4%, 10.1%–17.3%), hepatic cirrhosis (8.8%, 6.6%–12.2%) and renal fibrosis (10.3%, 7.3%–14.0%). In 47.0% (42.3%–51.2%), 6AM was present in blood.ConclusionsThe ‘typical’ heroin overdose case in Australia from 2020 to 2022 was a male who injected heroin, aged in the 40s, not enrolled in a treatment programme and had used multiple drugs. In over half of cases, there had been a sufficient survival time for 6‐acetyl morphine to have been metabolised, which may indicate times in excess of 20–30 min.
The effects of land direct payment program on farm income and production practices
Authors: Chang Hung‐Hao 
Published: November 2023

AbstractMany countries of the world have implemented subsidy programs to maintain a minimum amount of farm production especially for rice. Agricultural support programs usually cause significant fiscal burdens on government budgets. These programs can be generally categorized into decoupled and coupled programs, and one longstanding research interest of previous literature is whether these programs are decoupled or coupled with farm production practices. In Taiwan, a unique land direct payment (LDP) program to rice farms was implemented to ease severe financial burden of the price support program with government purchase. In contrast to production control programs imposing quantity restrictions on farm production, this program is voluntary for rice farms, and participants are paid at a fixed rate per hectare of farmland. This paper examines the impacts of this program on farm income and farm production practices in Taiwan. The causal effect of the program is identified based on the exogenous rollout of the policy across multiple times and areas. We construct a dataset linking nationally representative rice farm surveys over several years and administrative records on program recipients to estimate the local average treatment effect of the program. We find that the effect is 4% of farm income. In addition, program participants rely less on price support programs and produce less rice and use less fertilizer, pesticide, and machinery. Although the LDP reduces rice production, we find that it causes overall government spending on the price support and direct payment programs to increase by 8.7% after the LDP.
Expanding clinical spectrum from Hashimoto's encephalopathy to anti‐NAE antibody‐associated disorders (NAEAD)
Authors: Matsunaga Akiko , Ikawa Masamichi , Yoneda Makoto 
Published: November 2023

AbstractUsing proteomic analysis, we identified anti‐NAE antibodies (autoantibodies against NH2‐terminal of alpha‐enolase) as a diagnostic marker for Hashimoto's encephalopathy (HE). As cases of HE with serum anti‐NAE antibodies accumulated, the clinical spectrum of HE with anti‐NAE antibodies became expanded. In addition, it is now known that antibodies can be detected in other diseases that differ from conventional HE. We recently reported the detection of anti‐NAE antibodies in patients with a clinical diagnosis of multiple system atrophy or corticobasal syndrome. These findings suggest that anti‐NAE antibodies indicate an immune mechanism in the pathogenesis of neurodegenerative diseases. We propose a novel disease concept for anti‐NAE antibody‐associated disorders (NAEAD). The clinical spectrum of NAEAD is not limited to HE but is a broad spectrum that partially shares several autoimmune neurological diseases, including autoimmune acute encephalopathy, autoimmune cerebellar ataxia, and autoimmune psychosis, and even extends to immune‐associated neurodegenerative diseases.
Scrutinizing the impact of policy instruments on adoption of agricultural conservation practices using Bayesian expert models
Authors: Dean Angela J , Eberhard Rachel , Baresi Umberto , Coggan Anthea , Deane Felicity , Hamman Evan , Helmstedt Kate J. , Loechel Barton , Jarvis Diane , Mayfield Helen , Stevens Lillian , Taylor Bruce , Vella Karen 
Published: November 2023

AbstractPolicy instruments—such as regulation, financial incentives, and agricultural extension—are commonly applied by governments to promote sustainable agricultural practices and tackle ecosystem degradation. Despite substantial investment, little data are available to gauge the impact of evolving policy mixes. We constructed a Bayesian network model to explore relationships between policy instruments, contextual factors, and adoption. Applying a series of scenarios, we present examples of how different instruments influence adoption and how their effectiveness is shaped by contextual factors. Scenarios highlight that the effect of policy instruments is often modest, and constrained by diverse practice and population characteristics. These findings allow us to reflect on the role of policy instruments, and the conditions necessary to support practice change. For example, our findings raise questions about the role of financial benefits versus financial capacity, and highlight the potential importance of concepts such as mental bandwidth in shaping both motivation and capacity to adopt.
Balancing development and sustainability: Assessing risks and protecting aquatic biodiversity on US college and university campuses
Authors: Sako Mikaela P. , McManamay Ryan A. 
Published: November 2023

AbstractExtensive urbanization impairs biological communities through landscape alteration and physiochemical changes to stream ecosystems. Analogous to urban development in cities, new building and facility expansion on university campuses can lead to dramatic changes in impervious cover and consequently, increased stormflow impacting downstream ecological communities. Here, we analyze the extent and relevance on a nationwide scale to determine campuses with the highest risk for ecological impairment. From the US‐wide analysis of 5761 college/university campuses, ~45% of campuses were within critical aquatic species watersheds, and >5% were identified as buffering critical habitat. The highest risk campus our study identified was selected to compare the impacts of planned, conventional development versus sustainable development on a sensitive aquatic species, the federally threatened Jollyville Plateau salamander (Eurycea tonkawae). Impervious cover, simulated increases in stormwater runoff, and total suspended solids (TSS) from the conventional expansion is estimated to lower salamander density. Conversely, an alternative campus expansion plan allowed for increased development but permitted provisions for reduced runoff and TSS, thereby maintaining current salamander densities. Our findings show that sustainable campus development plans have the potential to mitigate ecological disruption within watersheds, and that campus management and policies are critical for preserving biodiversity in the future.
Clinical relevance of the living kidney donor profile index in Korean kidney transplant recipients
Authors: Kim Hyun Jeong , Min Eunki , Yim Seung Hyuk , Choi Mun Chae , Kim Hyung Woo , Yang Jaeseok , Kim Beom Seok , Huh Kyu Ha , Kim Myoug Soo , Lee Juhan 
Published: November 2023

AbstractBackgroundThe Living Kidney Donor Profile Index (LKDPI) was developed in the United States to predict graft outcomes based on donor characteristics. However, there are significant differences in donor demographics, access to transplantation, proportion of ABO incompatibility, and posttransplant mortality in Asian countries compared with the United States.MethodsWe evaluated the clinical relevance of the LKDPI score in a Korean kidney transplant cohort by analyzing 1860 patients who underwent kidney transplantation between 2000 and 2019. Patients were divided into three groups according to LKDPI score: <0, 1–19.9, and ≥20.ResultsDuring a median follow‐up of 119 months, 232 recipients (12.5%) experienced death‐censored graft loss, and 98 recipients (5.3%) died. High LKDPI scores were significantly associated with increased risk of death‐censored graft loss independent of recipient characteristics (LKDPI 1–19.9: HR 1.389, 95% CI 1.036–1.863; LKDPI ≥20: HR 2.121, 95% CI 1.50–2.998). High LKDPI score was also significantly associated with increased risk of biopsy‐proven acute rejection and impaired graft renal function. By contrast, overall patient survival rates were comparable among the LKDPI groups.ConclusionHigh LKDPI scores were associated with an increased risk of death‐censored graft loss, biopsy‐proven acute rejection, and impaired graft renal function among a Korean kidney transplant cohort.
The utility of inpatient rehabilitation in heart transplantation: A review
Authors: Barker Kim , Rydberg Leslie , Lanphere Julie , Malmut Laura , Neal Jacqueline , Eickmeyer Sarah 
Published: November 2023

AbstractHeart transplantation is considered definitive treatment for patients with end‐stage heart failure. Unfortunately, medical and functional complications are common after heart transplantation for a variety of reasons, and these may impact the patients’ functional recovery. Rehabilitation is often needed post‐operatively to improve functional outcomes. This review article aims to discuss the transplanted heart exercise physiology that may affect the rehabilitation process and provide an overview of the functional benefits of inpatient rehabilitation for cardiac and surgical specialties who may be less familiar with post‐acute care rehabilitation options for their patients.
Larval nutritional effects on male and female survival and fecundity in Anastrepha ludens
Authors: Aceituno‐Medina Marysol , Hernández Emilio , Rincón‐Betancurt Olivia , García‐Fajardo Luz Verónica , Diego‐García Elia 
Published: November 2023

AbstractThe three major macronutrients – proteins (P), carbohydrates (C), and lipids (L) – constitute the fundamental nutrient niche. In order to meet their nutritional requirements, organisms need to assess their nutritional state, select suitable foods, and regulate the amount of food eaten. The objective of this study was to determine whether larval nutrition could have a differential effect on female and male survival and fecundity by manipulating the P:C:L ratios in diet environments. We manipulated food availability during the larval stages, subjecting the larvae to food regimes with different P:C:L ratios. Upon adult emergence, we examined the fecundity, fertility, survival, and longevity of the various larval nutrition treatments. We then assessed the reproductive performance (fecundity and egg hatching) under an ad libitum food regime. We found that the concentration of macronutrients in the larval hemolymph indicates that the P:C:L ratio in the larval diet affects the assignment of macronutrients, and this effect is carried over to males and females differently. A larval diet with high carbohydrate content affects the carryover of macronutrients and male and female fitness. According to the life‐history traits, an adult that emerged from a larva with high lipid content in the hemolymph could suggest better health status. Insects with high cold tolerance have high body lipids content. Interactions between lipids, carbohydrates, and proteins suggest that their relative ratios must be taken into consideration in the design and improvement of artificial diets.
Extreme thrombocytosis with an aggressive evolution harboring a novel variant of calreticulin (CALR) in exon 3
Authors: Bonnet Sarah , Carillo Serge , Legrand Baptiste , Burroni Barbara , Lavabre‐Bertrand Thierry , Requirand Guilhem , Robert Nicolas , Fornero Lea , Al Mansoori Ahmed , Moreaux Jérôme , Cartron Guillaume , Gabellier Ludovic , Herbaux Charles 
Published: November 2023

AbstractWe describe the case of a patient with extreme thrombocytosis whose evolution was rapidly fatal. No cause of secondary thrombocytosis was found. There was no sign of myelofibrosis but the megakaryocytes were small and dysplastic. The patient presented a calreticulin (CALR) variant in exon 3 (C105S), as well as concomitant mutations of ASXL1, U2AF1, and EZH2. This variant of CALR has never been described before, and after sorting, all identified mutations were found in myeloid cells but not in lymphoid cells. Therefore, the diagnosis of a frontier case of myelodysplastic syndrome/myeloproliferative neoplasm (MDS/MPN) was made. A treatment with hydroxycarbamide was started because of a high risk of thrombosis. Upon worsening of the hematological status two new mutations appeared, SETBP1 and ETV6, and the CALR mutation was still detectable, as well as the three other mutations found in the chronic stage. Our results show that this variant could contribute to MDS/MPN pathogenesis in that patient.
Syndemics of the sea: Adverse disease interactions and the stressors of fisher livelihoods
Authors: Singer Merrill 
Published: November 2023

AbstractThe occupation of commercial fishing is recognized as a comparatively stressful and hazardous job characterized by a myriad of risks to health, including high rates of job‐related injury, morbidity, and mortality. Nonetheless, systematic study of fisher health is limited. This paper examines a particularly understudied aspect of illness among fishers: the physical and social contexts, pathways, and potential for adverse disease interactions. The focus of the paper is on a biosocial disease process called syndemics, which increases the health burdens of this population. The paper is presented as an initial testing of the hypothesis that a “lens” of syndemics improves occupational health research and advocacy for commercial fishermen who face a substantial burden of biosocial challenges.
PVA/essential oil‐based active food packaging films functionalised with halloysite nanotubes and cellulose nanocrystals as filler materials for the shelf‐life extension of papaya fruits
Authors: V Dharini , Biswal Abhishek , Sellamuthu Periyar Selvam , J Jayaramudu , Sadiku Emmanuel R. 
Published: November 2023

SummaryThis study investigates the development of polyvinyl alcohol (PVA) and essential oil‐based biocomposite films incorporating halloysite nanotubes (HNTs) and cellulose nanocrystals (CNCs) as reinforcement materials for the packaging of papaya fruits to extend their postharvest shelf‐life. The fabrication process involves the dispersion of filler materials within the PVA polymer matrix, followed by the casting of the films using the solvent‐evaporation technique. The CNC isolated from the papaya peel exhibited rod‐like structures that were confirmed in the morphological studies. The films reinforced with HNT and CNC (5 wt%) had enhanced mechanical properties and exhibited a tensile strength of ~64.40 MPa. The findings of the study demonstrate that the fruits packed with biocomposite materials containing HNTs and CNCs as reinforcements and lemongrass essential oil as active material showed better performance when compared to the control. The edible quality and the storage life of the papaya fruits (TSS, firmness and weight loss %) under investigation were extended by 14 days at ambient temperature (25 °C ± 2 °C) and relative humidity (80%–85%), thus improving the postharvest shelf‐life of harvested papayas. Therefore, PVA‐based active packaging film prepared with lemongrass essential oil, HNTs and CNCs has great potential for the preservation of papaya during postharvest storage.
Quality monitoring during sufu fermented process and establishment of random forest prediction model
Authors: Wang Xiaodan , Chang Ping , Wang Cuilian , Zhu Shijie , Wu Duo , Jiang Shaoping , Tian Jiaxue 
Published: November 2023

SummaryMicroscopic, mechanical, physiochemical and colour changes of sufu during fermentation (10, 20, 30, 40, 50, 60 days) were analysed to predict sufu quality objectively and accurately. Fourier transform infrared spectroscopy (FT‐IR) and scanning electron microscopy (SEM) showed that the absorption peaks at 702, 1454, 1652, 2926 and 3281 cm−1 increased in intensity, and sufu was altered from a granular colloidal protein structure to a smooth and uniform shape. Analysis of mechanical, physiochemical and colour properties demonstrated the growth of mucor, the addition of salt and dressing mixture had a significant impact on the changes of indexes of sufu with extension of fermentation time. Besides, a random forest (RF) sufu quality prediction model with 90% accuracy was established by selecting forest quality evaluation indicators using RF and setting the model parameters mtry and ntree to 5 and 900, respectively.
Matrix‐Variate Time Series Analysis: A Brief Review and Some New Developments
Authors: Tsay Ruey S. 
Published: November 2023

SummaryThis paper briefly reviews the recent research in matrix‐variate time series analysis, discusses some new developments, especially for seasonal time series, and demonstrates some applications. A general matrix autoregressive moving‐average model is introduced. The paper narrates a simple approach for understanding the model, identifiability issues, and estimation. Real examples are used to illustrate the theory.
COLOR AND APPEARANCE—BRIDGING THE GAP FROM CONCEPT TO PRODUCT
Authors: STYNE ALEXANDER F. 
Published: November 2023

ABSTRACTThis paper explains the principle of the “Universal Color Language,” published by Kenneth L. Kelly in 1965 after many years' development, as a specification concept that can he applied to practically all situations where color ideas and facts must be communicated and specified. Geometric configuration is discussed as a specific influence on the appearance of color in materials and products.
THE EFFECT OF ROD ACTIVITY ON LARGE FIELD COLOUR MATCHING
Authors: TREZONA P. W. 
Published: November 2023

ABSTRACTColorimetric standards, such as the CIE 1931 System for a 2° field, and the 1964 System for a (large) 10° field, depend on the additivity principle both for their derivation and use. Tests have shown that while the principle can fairly safely be applied in the former case, this is not true of the latter, where for some colour combinations large discrepancies occur. The fact that deviations have been shown by many workers to apply specifically to the blue matching stimulus leads to a suggestion for a physiological model.A quite different aspect to the model is the question of how to remove these deviations, i.e., to find an additive system of large field colorimetry. The reason for the deviations is the presence of rod activity in all fields subtending more than 2°: the large field trichromatic match is distorted, causing additivity deviations, because this rod activity has not been equated. To do so an extra matching stimulus is required, resulting in a tetrachromatic colour match. The method proposed for achieving this match is the two luminance level, convergent technique. This has been shown to give a unique match which is generally valid. The tetrachromatic match obeys the additivity principle under conditions where the trichromatic does not: it is quick enough to perform and precise enough to form a starting point for large field additive colorimetry.
Role of nano‐zones in enhancing the performance of YSZ coatings under thermal shock conditions
Authors: Ashofteh Afshin , Seifollahpour Sana 
Published: November 2023

AbstractThermal barrier coatings have been widely employed in high‐temperature turbine blades to enhance their resistance against corrosion, oxidation, and foreign object damage. Yttria‐stabilized zirconia (YSZ) coatings, both conventional and nano‐structured, exhibit distinct characteristics. Notably, nano‐structured coatings demonstrate remarkable reductions in oxygen permeability and thermally grown oxide (TGO) layer thickness owing to the presence of nano‐zones (NZs). This paper focuses on elucidating the formation mechanisms, dispersion patterns, and behavior of NZs under varying conditions. Furthermore, it investigates the shock resistance performance of YSZ coatings subjected to furnace heating and water quenching. The findings reveal that the incorporation of NZs effectively restricts oxygen penetration and TGO growth and significantly enhances the overall performance of the coatings.