bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Latitudinal Gradient of Reference Genomes
Authors: Linck Ethan B. , Cadena Carlos Daniel 
Published: October 2024

ABSTRACTGlobal inequality rooted in legacies of colonialism and uneven development can lead to systematic biases in scientific knowledge. In ecology and evolutionary biology, findings, funding and research effort are disproportionately concentrated at high latitudes, while biological diversity is concentrated at low latitudes. This discrepancy may have a particular influence in fields like phylogeography, molecular ecology and conservation genetics, where the rise of genomics has increased the cost and technical expertise required to apply state‐of‐the‐art methods. Here, we ask whether a fundamental biogeographic pattern—the latitudinal gradient of species richness in tetrapods—is reflected in the available reference genomes, an important data resource for various applications of molecular tools for biodiversity research and conservation. We also ask whether sequencing approaches differ between the Global South and Global North, reviewing the last 5 years of conservation genetics research in four leading journals. We find that extant reference genomes are scarce relative to species richness at low latitudes and that reduced representation and whole‐genome sequencing are disproportionately applied to taxa in the Global North. We conclude with recommendations to close this gap and improve international collaborations in biodiversity genomics.
Trypanosoma cruzi infection enhances olfactory response in Triatoma pallidipennis Stål (Hemiptera: Triatominae) to compounds potentially useful for insect control
Authors: Jiménez‐Santiago Berenice , Flores‐Villegas Any Laura , Cruz‐Esteban Samuel , Cabrera‐Bravo Margarita , Toriello Conchita 
Published: October 2024

AbstractIn Mexico, Triatoma pallidipennis is a major vector of Trypanosoma cruzi, the causative agent of Chagas disease. Current efforts are focused on developing attractants to control these vectors, using volatile substances derived from vertebrate hosts or compounds known to attract hematophagous insects. However, the efficacy of these compounds in attracting parasite‐infected triatomines remains to be evaluated. In this study, we assessed the attractant activity of octenol (1‐octen‐3‐ol), nonanal and a mixture of odorants consisting of ammonium hydroxide, lactic acid and hexanoic acid (in a ratio of 1:0.2:0.4 respectively), at concentrations of 1, 10 and 100 ng on the N3, N4 and N5 nymphal stages of T. pallidipennis, both infected and non‐infected with T. cruzi. We also evaluated the synergistic effect of the most effective compounds and doses. All experiments were performed in a laboratory using a Y‐type glass olfactometer. We found that both infected and non‐infected N3 and N4 nymphs were attracted to low doses of octenol, nonanal and the odorant mixture. Particularly noteworthy was the synergistic effect observed between the odorant mixture and nonanal, which significantly increased attraction of T. cruzi–infected individuals. These findings contribute to the development of baited traps utilising these compounds for monitoring triatomines in epidemiological studies or for mass trapping to control these vectors.
How do you assert a graph? Towards an account of depictions in scientific testimony
Authors: Dethier Corey 
Published: October 2024

AbstractI extend the literature on norms of assertion to the ubiquitous use of graphs in scientific papers and presentations, which I term “graphical testimony.” On my account, the testimonial presentation of a graph involves commitment to both (a) the in‐context reliability of the graph's framing devices and (b) the perspective‐relative accuracy of the graph's content. Despite apparent disagreements between my account and traditional accounts of assertion, the two are compatible and I argue that we should expect a similar pattern of commitments in a set of cases that extends beyond the graphical one. I end by demonstrating that the account resolves apparent tensions between the demands of honesty and the common scientific practice of presenting idealized or simplified graphs: these “distortions” can be honest so long as there's the right kind of alignment between the distortion and the background beliefs and values of the audience.
Wood nutrients: Underexplored traits with functional and biogeochemical consequences
Authors: Dalling James W. , Flores Manuel R. , Heineman Katherine D. 
Published: October 2024

SummaryResource storage is a critical component of plant life history. While the storage of nonstructural carbohydrates in wood has been studied extensively, the multiple functions of mineral nutrient storage have received much less attention. Here, we highlight the size of wood nutrient pools, a primary determinant of whole‐plant nutrient use efficiency, and a substantial fraction of ecosystem nutrient budgets, particularly tropical forests. Wood nutrient concentrations also show exceptional interspecific variation, even among co‐occurring plant species, yet how they align with other plant functional traits and fit into existing trait economic spectra is unclear. We review the chemical forms and location of nutrient pools in bark and sapwood, and the evidence that nutrient remobilization from sapwood is associated with mast reproduction, seasonal leaf flush, and the capacity to resprout following damage. We also emphasize the role wood nutrients are likely to play in determining decomposition rates. Given the magnitude of wood nutrient stocks, and the importance of tissue stoichiometry to forest productivity, a key unresolved question is whether investment in wood nutrients is a relatively fixed trait, or conversely whether under global change plants will adjust nutrient allocation to wood depending on carbon gain and nutrient supply.
Carotenoid‐carbohydrate crosstalk: evidence for genetic and physiological interactions in storage tissues across crop species
Authors: Villwock Seren S. , Li Li , Jannink Jean‐Luc 
Published: October 2024

SummaryCarotenoids play essential roles in photosynthesis, photoprotection, and human health. Efforts to increase carotenoid content in several staple crops have been successful through both conventional selection and genetic engineering methods. Interestingly, in some cases, altering carotenoid content has had unexpected effects on other aspects of plant metabolism, impacting traits like sugar content, dry matter percentage, fatty acid content, stress tolerance, and phytohormone concentrations. Studies across several diverse crop species have identified negative correlations between carotenoid and starch contents, as well as positive correlations between carotenoids and soluble sugars. Collectively, these reports suggest a metabolic interaction between carotenoids and carbohydrates. We synthesize evidence pointing to four hypothesized mechanisms: (1) direct competition for precursors; (2) physical interactions in plastids; (3) influences of sugar or apocarotenoid signaling networks; and (4) nonmechanistic population or statistical sources of correlations. Though the carotenoid biosynthesis pathway is well understood, the regulation and interactions of carotenoids, especially in nonphotosynthetic tissues, remain unclear. This topic represents an underexplored interplay between primary and secondary metabolism where further research is needed.
What do they look for and what do they find? A coproduced qualitative study on young people's experiences of searching for mental health information online
Authors: Loades M. E. , Higson‐Sweeney N. , Teague B. , Leas J. , Payne‐Cook C. , Slastikova A. V. , Peel H. , Chamberlain G. , Ferguson L. , Janes K. , Rhodes T. , Roupa E. C. , Biddle L. 
Published: October 2024

AbstractBackgroundMany young people (YP) struggle with their mental health and look online for help. To capitalise on their digital presence, we need to better understand how and where they seek information online and what they think of what they find.MethodWe recruited 24 YP (aged 13–18 years). Online interviews were co‐conducted by research team members and trained young researchers. We presented a persona with depression symptoms and asked about potential sources of information/support they might seek. They were also asked to think aloud while searching online and reviewing mental health resources (NHS, Young Minds). We used reflexive thematic analysis.ResultsAnalysis generated four themes: (1) the online help‐seeking process, showcasing where YP look for information and why; (2) the mismatch between the information YP expected to find and the reality; (3) the strategies YP employed to determine a source's trust and credibility and (4) individual differences that can influence help‐seeking.ConclusionParticipants initiated their online search by Googling symptoms. They trusted NHS websites for basic medical information, while charities provided detailed content. Despite scepticism about content, social media offered validation. Online resources should prioritise visual appeal, user‐friendliness, age‐appropriate and personalised content and peer insights. Codesign is imperative to ensure high‐quality, impactful research.
Improving photosynthetic efficiency of rice via over‐expressing a ferredoxin‐like protein gene from Methanothermobacter thermautotrophicus
Authors: Yan Xin , Si FengFeng , Zhu Danpeng , Chen Qiusheng , Hu Zhao , Wang Ting , Ying Suping , Tang Yunting , Yang Jing , Ding Xia , Li Yu , Liu Yizhen , Wang Zhaohai , Peng Xiaojue 
Published: October 2024

AbstractFerredoxins (Fds) are crucial in various essential plant metabolic processes, including photosynthesis, fermentation and aerobic nitrogen fixation, due to their role in electron transport rate (ETR). However, the full scope of ferredoxin's function across prokaryotes and eukaryotic plants remains less understood. This study investigated the effect of MtFd from Methanothermobacter thermoautotrophicus on rice photosynthetic efficiency. We found that MtFd was localized in the chloroplasts of rice protoplasts. Transgenic analysis showed that MtFd significantly enhanced the photosynthetic capacity compared to the wild‐type plants. This enhancement was evident through increased ETR, NADPH content and net photosynthetic rates, as well as decreased non‐photochemical quenching (NPQ). Despite similar biomass to wild type plants, MtFd transgenic plants exhibited a marked increase in grain size and the 1000‐grian weight. The elevated ETR and surplus free electrons in transgenic plants result in a considerable rise in cellular ROS content, which in turn enhances the enzymatic activity of the antioxidant system. In summary, our findings suggest that introducing the Fd protein from M. thermoautotrophicus into transgenic rice improves photosynthetic efficiency by accelerating ETR, which triggers the cellular oxidative stress response.
Reduced diffusional limitations in carnation stems facilitate higher photosynthetic rates and reduced photorespiratory losses compared with leaves
Authors: Yiotis Charilaos , Chondrogiannis Christos 
Published: October 2024

AbstractGreen stem photosynthesis has been shown to be relatively inefficient but can occasionally contribute significantly to the carbon budget of desert plants. Although the possession of green photosynthetic stems is a common trait, little is known about their photosynthetic characteristics in non‐desert species. Dianthus caryophyllus is a semi‐woody species with prominent green stems, which show similar photosynthetic anatomy with leaves. In the present study, we used a combination of gas exchange and chlorophyll fluorescence measurements, some of which were taken under varying O2 and CO2 partial pressures, to investigate whether the apparent anatomical similarities between the species' leaves and stems translate into similar photosynthetic physiology and capacity for CO2 assimilation. Both organs displayed high photosynthetic electron transport rates (ETR) and similar values of steady‐state non‐photochemical quenching (NPQ), albeit leaves could attain them faster. The analysis of OJIP transients showed that the quantum efficiencies and energy fluxes along the photosynthetic electron transport chain are largely similar between leaves and stems. Stems displayed higher total conductance to CO2 diffusion, similar biochemical properties, significantly higher photosynthetic rates and lower water use efficiency than leaves. Leaf ETR was more sensitive to sub‐ambient O2 and super‐ambient CO2 partial pressures, while leaves also displayed a higher relative rate of Rubisco oxygenation. We conclude that the highly responsive NPQ and the enhanced photorespiration and WUE in leaves represent photoprotective and water‐conserving adaptations to the high incident light intensities they experience naturally, at the expense of higher CO2 assimilation rates, which the vertically orientated stems can readily attain.
Conversion of lipids into carbohydrates rescues energy insufficiency in rapeseed germination under waterlogging stress
Authors: Yang Haiyun , Bai Chenyang , Ai Xueying , Yu Haiqiu , Xu Zhenghua , Wang Jing , Kuai Jie , Zhao Jie , Wang Bo , Zhou Guangsheng 
Published: October 2024

AbstractWaterlogging stress, particularly during seed germination, significantly affects plant growth and development. However, the physiological and molecular mechanisms underlying waterlogging stress responses during rapeseed germination remain unclear. In this study, two rapeseed cultivars, Xiangzayou518 (waterlogging‐sensitive) and Dadi199 (waterlogging‐tolerant), were used to explore the physiological mechanisms underlying rapeseed response to waterlogging stress during germination. Our results showed that waterlogging significantly decreased the emergence percentage and seedling growth rate. During the radicle elongation period (from 48 to 96 h post‐germination), the most sensitive period to waterlogging during germination, sugar content, and glycolysis efficiency were significantly decreased, but anaerobic fermentation was enhanced. In tolerant cultivars, when the energy supply was insufficient, the conversion efficiency of lipids into sugar increased, and the activities of isocitrate lyase, malate synthase, and fructose‐1, 6‐diphosphatase were enhanced by 11.63, 19.06, and 20.37%, respectively, at 72 h post‐germination under waterlogging stress. Transcriptome data showed that the differentially expressed genes were significantly enriched in glucose and lipid metabolism pathways when comparing waterlogged stress and normal conditions. These results indicate that waterlogging affects seed germination in rapeseed by inhibiting carbohydrate metabolism, and the conversion capacity of lipids into sugar under waterlogging stress was stronger in tolerant cultivars than in sensitive cultivars, thus rescuing the insufficient energy supply in seed germination and seedling growth. This study reveals the physiological mechanism of rapeseed response to waterlogging stress during seed germination and provides a valuable reference for improving waterlogging tolerance.
Potency evaluation of different GNRH analogues on ovulation induction and reproductive performance of doe rabbit
Authors: Viudes‐de‐Castro M. P. , Marco‐Jiménez F. , Miralles‐Bover H. , Vicente J. S. 
Published: October 2024

AbstractGonadotropin‐releasing hormone (GnRH) ‐supplemented extenders have emerged as a welfare‐orientated method to induce ovulation in the artificial insemination (AI) of rabbits. The main factor that limits the bioavailability of GnRH analogue on intravaginal administration is the proteolytic activity of enzymes present in rabbit seminal plasma. The use of GnRH analogues with higher biological potency would allow us to decrease their concentration in the seminal dose without compromising effectiveness. The current study was designed to assess the efficacy of various GnRH analogues concerning their ability to induce ovulation in rabbit AI. The base solution used for experimental extenders contained an aminopeptidase inhibitor. Four experimental groups were used, females from the Control group were induced to ovulate with an intramuscular administration of 1 μg of buserelin, while in the other three groups females received an intravaginal administration of 3.5 μg of buserelin (BUS), deslorelin (DES) or fertirelin (FER) within the seminal dose. Results showed that the ovulation frequency was similar in all groups studied. A concentration of 3.5 μg of the different GnRH analogues tested in this study showed similar potency in inducing ovulation in non‐lactating females, yielding comparable results in terms of pregnancy rate at birth and prolificacy.
Seasonality analysis on cryopreserved doses from the autochthonous cattle breeds Asturiana de la Montaña and Asturiana de los Valles
Authors: Tamargo Carolina , Salman Amer , Fernández‐Alegre Estela , Fueyo Carmen , Arija Cristina , Fernández Ángel , Merino María J. , Martínez‐Pastor Felipe , Caamaño J. Néstor , Hidalgo Carlos O. 
Published: October 2024

AbstractGermplasm banking is a fundamental tool for the preservation of autochthonous breeds. Semen cryopreservation is effective for this task, but protocols are adapted to commercial species, and post‐thawing sperm quality could be sensitive to environmental cues. We compared the post‐thawing sperm quality in doses from the CBA‐SERIDA bank in northern Spain for the Asturiana de la Montaña (AM) and Asturiana de los Valles (AV) autochthonous cattle breeds. Doses from 23 AM and 16 AV bulls (ejaculates from at least three different seasons) were assessed for motility (computer‐assisted sperm analysis), physiology and chromatin status (flow cytometry) after thawing and after 5 h at 38°C. Data were analysed using linear mixed‐effects and cosinor models for seasonal and breed effects and by correlations with the association of sperm quality with temperature‐humidity index (THI), considering the interval of spermatogenesis plus maturation. The breed affected sperm quality, with higher motility for AV and higher apoptotic ratio, mitochondrial activity, reactive oxygen species, DNA fragmentation and chromatin immaturity for AM. However, seasonality effects were minimal, and THI was not associated with sperm quality. In summary, the season seems to be a minor factor in the post‐thawing quality of the AM and AV autochthonous breeds, well‐adapted to their local environment.
Development of an equine endometrial histology scoring system to complement the Kenney–Doig scale
Authors: Martínez‐Bartolomé I. , Masot J. , Serres C. 
Published: October 2024

AbstractKenney–Doig scale is considered the international standard method for classifying uterine biopsies in mares; however, its objectivity has been questioned by various studies. In the present study, we analysed the degree of agreement between two pathologists when assessing the same set of 201 uterine biopsies, obtaining a slight to moderate level of agreement (κ = .34/κw = .57). Subsequently, we developed a numerical scale based on the evaluation of histological parameters, including inflammation, fibrosis, glandular density and lymphatic lacunae. Partial scores were summed to obtain a fifth parameter called Summation. The correlation between both scales was demonstrated (p < .0001), and their combined use resulted in a notable increase in the degree of agreement between the two pathologists (κ = .53/κw = .67).
Methodological approaches in vitrification: Enhancing viability of bovine oocytes and in vitro‐produced embryos
Authors: Mogas Teresa , García‐Martínez Tania , Martínez‐Rodero Iris 
Published: October 2024

AbstractCryopreservation of bovine oocytes and embryos is essential for long‐term preservation and widespread distribution of genetic material, particularly in bovine in vitro embryo production, which has witnessed substantial growth in the past decade due to advancements in reproductive biotechnologies. Among current cryopreservation methods, vitrification has emerged as the preferred cryopreservation technique over slow freezing for preserving oocytes and in vitro‐produced (IVP) embryos, as it effectively addresses membrane chilling injury and ice crystal formation. Nonetheless, challenges remain and a simple and robust vitrification protocol that guarantees the efficiency and viability after warming has not yet been developed. Furthermore, although slow cooling can easily be adapted for direct transfer, an easier and more practical vitrification protocol for IVP embryos is required to allow the transfer of IVP embryos on farms using in‐straw dilution. In addition, the susceptibility of bovine oocytes and embryos to cryoinjuries highlights the need for novel strategies to improve their cryotolerance. This manuscript examines various methodological approaches for increasing the viability of bovine oocytes and IVP embryos during vitrification. Strategies such as modifying lipid content or mitigating oxidative damage have shown promise in improving cryotolerance. Additionally, mathematical modelling of oocyte and embryo membrane permeability has facilitated the rational design of cryopreservation protocols, optimizing the exposure time and concentration of cryoprotectants to reduce cytotoxicity.
High cooling rate of 60°C/min around ice nucleation during cryopreservation compromises chicken sperm viability
Authors: Toledano‐Díaz Adolfo , Robledo Rosalina , Alba Esther , Fernández‐Alaez Pablo , García‐Casado Pedro , Bernal Berenice , Castaño Cristina , Torres Olga , Rauw Wendy M. , Santiago‐Moreno Julián 
Published: October 2024

AbstractThe present study compares two protocols for the cryopreservation of chicken semen. Both protocols had an initial low cooling rate in the first step, followed by higher cooling rates around ice nucleation (Protocol 1) or following the dissipation of the latent heat of fusion (Protocol 2) in the second step. Semen ejaculates obtained from 12 roosters were diluted with Rootex with 6% dimethylformamide and frozen following either Protocol 1 (from +5°C to −10°C at 5°C/min and from −10°C to −130°C at 60°C/min) or Protocol 2 (from +5°C to −35°C at 7°C/min and from −35°C to −140°C at 60°C/min). Compared with fresh semen, following both protocols, cryopreservation resulted in reduced post‐thaw sperm quality (p < .001). Post‐thaw percentage of sperm with an intact plasma membrane was greater using Protocol 2 than Protocol 1 (p < .05). The results suggest that high cooling rates around the time of ice nucleation are not recommendable.
Effective use of artificial insemination as an ex situ conservation method for the capercaillie
Authors: O'Brien Emma , Sabater Alexia Siegmund , Toledano‐Díaz Adolfo , Castaño Cristina , de Pedro Aguilar Gabriel , Cubero David , Łukaszewicz Ewa , Santiago‐Moreno Julián 
Published: October 2024

AbstractWith the threat of extinction looming over many species, the development of assisted reproduction techniques for use in conservation programmes is imperative. This work explores the feasibility and efficacy of artificial insemination in the capercaillie (Tetrao urogallus), a species in critical danger of extinction. Nine young, male birds were used as sperm donors for five young females. Three of the females laid 19 viable eggs, of which 13 were fertilized (68%). This research contributes to the scientific understanding of the capercaillie's reproductive biology and provides practical insights that could be instrumental in the conservation and recovery of the species.