bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenetic diversity of genes with copy number variations among natural populations of the three‐spined stickleback
Authors: Chain Frédéric J. J. , Meyer Britta S. , Heckwolf Melanie J. , Franzenburg Sören , Eizaguirre Christophe , Reusch Thorsten B. H. 
Published: July 2024

AbstractDuplicated genes provide the opportunity for evolutionary novelty and adaptive divergence. In many cases, having more gene copies increases gene expression, which might facilitate adaptation to stressful or novel environments. Conversely, overexpression or misexpression of duplicated genes can be detrimental and subject to negative selection. In this scenario, newly duplicate genes may evade purifying selection if they are epigenetically silenced, at least temporarily, leading them to persist in populations as copy number variations (CNVs). In animals and plants, younger gene duplicates tend to have higher levels of DNA methylation and lower levels of gene expression, suggesting epigenetic regulation could promote the retention of gene duplications via expression repression or silencing. Here, we test the hypothesis that DNA methylation variation coincides with young duplicate genes that are segregating as CNVs in six populations of the three‐spined stickleback that span a salinity gradient from 4 to 30 PSU. Using reduced‐representation bisulfite sequencing, we found DNA methylation and CNV differentiation outliers rarely overlapped. Whereas lineage‐specific genes and young duplicates were found to be highly methylated, just two gene CNVs showed a significant association between promoter methylation level and copy number, suggesting that DNA methylation might not interact with CNVs in our dataset. If most new duplications are regulated for dosage by epigenetic mechanisms, our results do not support a strong contribution from DNA methylation soon after duplication. Instead, our results are consistent with a preference to duplicate genes that are already highly methylated.
Pitfalls and windfalls of detecting demographic declines using population genetics in long‐lived species
Authors: Clark Meaghan I. , Fitzpatrick Sarah W. , Bradburd Gideon S. 
Published: July 2024

AbstractDetecting recent demographic changes is a crucial component of species conservation and management, as many natural populations face declines due to anthropogenic habitat alteration and climate change. Genetic methods allow researchers to detect changes in effective population size (Ne) from sampling at a single timepoint. However, in species with long lifespans, there is a lag between the start of a decline in a population and the resulting decrease in genetic diversity. This lag slows the rate at which diversity is lost, and therefore makes it difficult to detect recent declines using genetic data. However, the genomes of old individuals can provide a window into the past, and can be compared to those of younger individuals, a contrast that may help reveal recent demographic declines. To test whether comparing the genomes of young and old individuals can help infer recent demographic bottlenecks, we use forward‐time, individual‐based simulations with varying mean individual lifespans and extents of generational overlap. We find that age information can be used to aid in the detection of demographic declines when the decline has been severe. When average lifespan is long, comparing young and old individuals from a single timepoint has greater power to detect a recent (within the last 50 years) bottleneck event than comparing individuals sampled at different points in time. Our results demonstrate how longevity and generational overlap can be both a hindrance and a boon to detecting recent demographic declines from population genomic data.
Modeling food web and fisheries dynamics in Lake Baringo, Kenya
Authors: Walumona Jacques Riziki , Kaunda‐Arara Boaz , Ogombe Odoli Cyprian , Masilya Mulungula Pascal , Philip Raburu , Kondowe Benjamin Nelson , Kobingi Nyakeya , Murakaru Mugo James , Mulongaibalu Mbalassa , Amisi Muvundja Fabrice 
Published: July 2024

AbstractLakes are important in supporting ecosystem services and livelihoods. However, their food webs and ecological functioning are continuously threatened by anthropogenic influences. Food web models have been widely used in studying trophodynamics, fisheries impacts, and ecological functioning of temperate lakes, but less often in Afrotropical lake systems. We used Ecopath mass‐balanced trophic models annually in 1999, 2010, and 2020 to assess trends in ecosystem function, and the impact of fisheries on the Lake Baringo Ecosystem, a shallow freshwater lake in Kenya. Pre‐balance (PREBAL) and Pedigree analyses supplemented Ecopath models. Model input data were from field sampling, published and gray literature. Food web trophic models indicated a bottom‐up grazer and detrital food chains in all 3 years. Odum's ecosystem development indicators (total productivity to total biomass and total respiration ratios; TPP/TB and TPP/TR) showed that the lake was in a low to intermediate developmental stage, with room for bio‐manipulation, and a highly reduced mean transfer efficiency (TE) (6.4%–0.49%) indicated low trophic transfer of internal production. System omnivory (SOI) and connectance (CI) indices that varied among years indicated temporal variation in food web complexity. Indices of system resilience (overhead and ascendency) indicated an increasing potential for the lake to recover from perturbations. The mean trophic level of the catch (MTLc) increased from 1999 to 2010 and decreased in 2020, by fishing down the food chain as fishing pressure increased. Oreochromis niloticus, an endemic cichlid, was the keystone species (KSi >0) controlling community structure, while the lungfish Protopterus aethiopicus, the top predator in the lake, was not a keystone species (KSi <0). We recommend an integrated approach to lake management that incorporates watershed regulations, regulates fishing effort on the keystone species (O. niloticus), and monitors water quality for sustainable management of the Lake Baringo ecosystem.
Disentangling ecological drivers of interspecific achromatic plumage variation in birds
Authors: Wu Su , Zhang Kai , Wang Bin , Que Pinjia , Yang Biao , Xu Yu 
Published: July 2024

AbstractAimUnderstanding the ecological determinants of interspecific achromatic (light‐to‐dark) plumage variation in birds is crucial yet challenging due to the complex interplay of climatic, habitat‐related, and morphological influences. This study aimed to disentangle the effects of temperature, precipitation, habitat openness, body mass and hand‐wing index (HWI, a widely used single‐parameter proxy for the extent to which a species relies on flight) on shaping achromatic plumage variation among bird species.LocationGlobal.Time PeriodContemporary.Major Taxa StudiedBirds.MethodsBased on data from over 8000 sessile bird species globally, we employed phylogenetic linear regressions to account for achromatic plumage colour in relation to temperature, precipitation, habitat openness, body mass and HWI, while correcting for phylogenetic non‐independence between species. Furthermore, we conducted phylogenetic path analyses to decompose direct from indirect effects.ResultsWe found that temperature, precipitation, habitat openness and body mass exerted separate but interactive effects on the variation in achromatic colour across species. Species inhabiting cold, wet or densely vegetated environments were darker coloured, while smaller species were lighter. Darker plumage was more strongly related to higher precipitation in colder regions for nocturnal species. For diurnal species, darker plumage was more closely associated with higher precipitation in more open habitats, whereas lighter plumage was more linked to lower mass in denser habitats. Noteworthy was the identification of a substantial correlation between achromatic colour and HWI. Diurnal species that are more aerial were lighter. Conversely, nocturnal flyers, especially females, tended to be darker.Main ConclusionsThe findings highlight the multifaceted nature of plumage coloration evolution, with adaptations for thermal efficiency, crypsis, signalling, waterproofing or protection against bacteria. However, the variable relative importance of these factors among groups emphasizes the significance of each factor in different contexts.
Sustainable hybrid snack product: impact of dual fortification with Gracillaria seaweed and pressure‐cooked milkfish broth by‐products on nutritive, physical, texture, and sensory properties
Authors: Mindarwati Endang , Sedayu Bakti Berlyanto , Suryaningrum Th. Dwi , Mardiyana Indri , Prodiana Natalia , Supriyanto Agus , Suwarti  , Raharjo Susilo , Nuridha Ahmad , Trisnoharjono Dwi Budiyanto , Pari Rizfi Fariz , Ramadhan Wahyu 
Published: July 2024

SummaryThe liquid by‐products obtained from the fisheries industry are usually discarded after primary processing. In this study, by‐products of pressure‐cooked milkfish broth were utilised and combined with Gracilaria sp. to create sustainable seaweed stick snacks. By utilising the by‐products of liquid waste from pressurised milkfish processing, combined with the addition of Gracilaria seaweed in snack development, it is expected to obtain a snack products with increased protein and fibre level. This endeavour contributes to the achievement of the Sustainable Development Goals (SDGs), particularly in promoting good health and well‐being, as well as responsible consumption and production. Comprehensive analyses were performed, covering proximate composition, dietary fibre, functional group, thermal properties, colour, microstructure, pore size, viscosity, texture, and sensory evaluation through hedonic testing and check‐all‐that‐apply sensory (CATA) profiling. The FTIR results showed that the inclusion of seaweed and fish broth was recognised and presented in the specific characteristic bands, especially the stretching band in the polysaccharide fingerprint region, and with protein vibration bands blending with the inclusion of broth. The seaweed had an impact on the dough viscosity and product's texture, increasing the firmness, and the amino acids in the broth enhanced the taste of the resulting snack, positively influencing the panellists' preferences. The smoothness, moistness, roughness, and overall texture attributes of the snack were altered by the combination of seaweed and broth additions. According to the sensory, physical properties, and nutrient results, the optimal snack formulations included the addition of 36% seaweed and 4% broth (S36B4). The prominent sensory attributes of the product were also described in the CATA sensory evaluation. Additionally, the inclusion of Gracilaria sp. increased the dietary fibre content, while milkfish broth contributed to higher levels of amino acids, improving the nutritional profile of the snacks. Therefore, this study promoting a new source of protein could be synergistically combined with marine plant‐based fibre to produce hybrid nutrient‐dense snack products, addressing the growing demand for sustainable food trends.
Accelerate Senescence Reversed CO2‐Fertilization Effect under Elevated CO2 in Potato: A Weak Relationship with Nitrogen Acquisition
Authors: Yi Yan , Yano Katsuya 
Published: July 2024

ABSTRACTAccelerated senescence under elevated CO2 (eCO2) has not received sufficient attention, and its impact on the effect of CO2‐fertilization is unclear. To investigate the relationship between plant senescence and CO2 concentration, a pot experiment was conducted in four potato genotypes under low CO2 (LC), medium CO2 (MC) and high CO2 (HC) conditions. Nitrogen (N) uptake and cumulative transpiration were analysed to clarify whether eCO2‐induced senescence could be explained by low N uptake due to reduced transpiration. Compared to LC, the lifespan of potato plants under MC and HC was reduced by 3%–6% and 12%–32%, respectively, depending on the genotype. Biomass accumulation at full senescence was reduced when lifespan was shortened by approximately 5% and 10% under MC and HC, respectively. Cumulative transpiration was less affected by eCO2 during early developmental stages but decreased under eCO2 as plants aged. Plant water use decreased with a shortened lifespan under eCO2, but there was no reduction in N uptake, which was attributed to the high N uptake per unit of water used. The results of this study indicate that senescence in potato genotypes is non‐linearly related to CO2 concentration and cannot be explained by reduced N acquisition via reduced transpiration. The positive effect of CO2 fertilization can be reversed by accelerated senescence under eCO2.
Yield Trait and Stability of Chickpea Genotypes for Intensification of Drought‐Prone Rice Fallows of South Asia
Authors: Nath C. P. , Jha U. C. , Kumar Narendra , Singh Raghavendra , Kumar Yogesh , Dixit G. P. , Hazra K. K. , Srivastava A. K. 
Published: July 2024

ABSTRACTThere is a need for increasing cropping intensity in South Asia including India to ensure food security of burgeoning population. Accordingly, increasing cropping intensity in rainfed rice fallows can be a futuristic strategy. Identification of suitable cultivar and exploration of genetic variability of specific crops/traits are imperative for genetic improvement, drought resistance and yield gain in rice fallows. We evaluated the morphophysiological, yield traits and stability of 15 chickpea genotypes in randomised complete block design for three consecutive years on a drought‐prone rainfed condition of Fluvisol in Kanpur, India. Among genotypes, ‘IPC 2014‐55’, ‘IPC 2015‐44’ and ‘IPC 2011‐92’ had 2%–10% higher relative water content (RWC) over ‘ICC‐92944’ (check cultivar). These genotypes did not differ for total chlorophyll content, root dry weight and nodule dry weight with ‘ICC‐92944’ and ‘KWR 108’ (wider adaptable cultivar of the region). The nitrogen balance index was higher in ‘IPC 2011‐92’, ‘IPC 2014‐88’ and ‘IPC 2014‐55’ by 5%–44% over check cultivar (p < 0.05). The membrane stability index was higher for ‘IPC 2014‐55’ (30%, p < 0.05) and ‘IPC 2011‐92’ (17%, p < 0.05) than ‘ICC‐92944’. ‘IPC 2011‐92’, ‘IPC 2014‐88’ and ‘IPC 2014‐55’ (3 years mean) had 3%–24% higher plant dry weight than ‘ICC‐92944’. Notably, ‘IPC 2014‐55’, ‘IPC 2015‐44’, ‘IPC 2014‐88’ and ‘IPC 2011‐92’ had higher yield attributes such as pods plant−1 by 9%, grain weight plant−1 by 13% and 100‐seed weight by 3% than ‘ICC‐92944’ and ‘KWR 108’ (mean of years). These genotypes had higher mean seed yield than ‘ICC‐92944’ by 23%–42% and ‘KWR 108’ by 7%–23% (p < 0.05). The yield of ‘IPC 2014‐55’, ‘IPC 2015‐44’, ‘IPC 2014‐88’ and ‘IPC 2011‐92’ were stable over years across variable soil and environmental condition as indicated by the genotype × year biplot. Membrane stability index, pods plant−1 and 100‐seed weight were the determinants for increased seed yield of chickpea under drought‐prone condition. Evidently, genotype ‘IPC 2014‐55’, ‘IPC 2015‐44’, ‘IPC 2014‐88’ and ‘IPC 2011‐92’ were better under rainfed rice fallows. These genotypes could be tested under specific drought condition for developing varieties and promoted in rice fallows of South Asia for yield advantage and drought resistance.
Influence of in‐office whitening on the color matching and surface characteristics of single‐shade resin composites
Authors: Sugimura Runa , Takamizawa Toshiki , Aoki Ryota , Muto Rei , Hirokane Eizo , Kurokawa Hiroyasu , Kitahara Nobuya , Miyazaki Masashi 
Published: July 2024

AbstractObjectiveThe color matching of single‐shade resin composites after in‐office whitening was investigated.Materials and MethodsFour single‐shade resin composites were used. A total of 35% hydrogen peroxide was used as the whitening agent. The resin composite was placed in a cavity of an artificially discolored bovine tooth. The color differences between the restoration and surrounding enamel before and after whitening were determined based on ΔE*ab, ΔE00, and ΔWID. The color stability, surface roughness (Sa), and surface gloss (GU) of the resin composite alone were also evaluated. Statistical analyses were performed using repeated‐measures analysis of variance with the Tukey–Kramer test.ResultsBased on the 50:50% of perceptibility and acceptability thresholds of ΔE*ab and ΔE00, none of the resin composite restorations were clinically acceptable before or after whitening. Regarding ΔWID, although all resin composites showed “acceptable match” in the baseline, they showed “mismatch” after the third session of whitening. Most of the resin composites alone were stable in color against whitening.ConclusionsAlthough the single‐shade resin composites failed to achieve the expected color matching on discolored teeth either before or after the whitening, the impact of the whitening on the color of the resin composite alone may be negligible.
A fatty acid elongase complex regulates cell membrane integrity and septin‐dependent host infection by the rice blast fungus
Authors: Su Jia , Xu Youpin , Lei Mingliang , Meng Yingying , Zhang Siqi , Liu Hongrui , Zhu Caicun , Chen Jinhua , Zhang Tianxin , Liu Jiawei , Lin Yunxiang , Yan Zhaorui , Li Weitao , Wang Jing , Chen Xuewei , He Min 
Published: July 2024

AbstractVery‐long‐chain fatty acids (VLCFAs) regulate biophysical properties of cell membranes to determine growth and development of eukaryotes, such as the pathogenesis of the rice blast fungus Magnaporthe oryzae. The fatty acid elongase Elo1 regulates pathogenesis of M. oryzae by modulating VLCFA biosynthesis. However, it remains unknown whether and how Elo1 associates with other factors to regulate VLCFA biosynthesis in fungal pathogens. Here, we identified Ifa38, Phs1 and Tsc13 as interacting proteins of Elo1 by proximity labelling in M. oryzae. Elo1 associated with Ifa38, Phs1 and Tsc13 on the endoplasmic reticulum (ER) membrane to control VLCFA biosynthesis. Targeted gene deletion mutants Δifa38, Δphs1 and Δtsc13 were all similarly impaired as Δelo1 in vegetative growth, conidial morphology, stress responses in ER, cell wall and membrane. These deletion mutants also displayed severe damage in cell membrane integrity and failed to organize the septin ring that is essential for penetration peg formation and pathogenicity. Our study demonstrates that M. oryzae employs a fatty acid elongase complex to regulate VLCFAs for maintaining or remodelling cell membrane structure, which is important for septin‐mediated host penetration.
Pneumocephalus caused by Enterobacter cloacae meningoencephalitis following cerebral infarction
Authors: Senda Mayumi , Harada Nozomi , Kanda Konoka , Kako Tetsuharu , Urano Makoto , Ito Mizuki 
Published: July 2024

AbstractPneumocephalus develops due to various reasons; however, pneumocephalus caused by factors other than head trauma is rare, and a few cases of infections have been reported. We encountered a case of pneumocephalus caused by Enterobacter cloacae meningoencephalitis following cerebral infarction. Although we could not perform cerebrospinal fluid analysis and culture, E. cloacae was cultured from blood. We conducted an autopsy and confirmed meningoencephalitis in the cerebral infarction lesion. Thus, we considered that E. cloacae meningoencephalitis caused the pneumocephalus. Because bacterial meningoencephalitis is a treatable disease, we should strictly consider that meningoencephalitis due to bacteria such as E. cloacae causes pneumocephalus.
Observational study on the identification of left atrial tachycardia circuits using Local Activation Time Histogram
Authors: Yamagishi Daisuke , Kanazawa Koichi , Saito Kazuki , Kono Tsunesuke 
Published: July 2024

AbstractBackgroundMapping of atypical atrial arrythmias arising in the left atrium is often challenging. The Local Activation Time (LAT) Histogram, a new function of the 3D color mapping system CARTO version 7, may help improve identification of atrial tachycardia circuits. We aimed to assess the effectiveness of the LAT Histogram for identification of left atrial tachycardia circuits.MethodsThis retrospective study compared 25 consecutive cases of left atrial tachycardia that were treated before use of LAT Histogram (unused group) and 25 consecutive cases that were treated after introduction of LAT Histogram (used group) at Nagano Chuo Hospital. We evaluated whether we could identify the circuit of left atrial tachycardia from the electrophysiology lab data during ablation and the CARTO system data and whether we could perform effective ablation.ResultsDoor‐to‐door time, skin‐to‐skin time, and fluoroscopy time (p ≤ .011) were all shorter in the LAT Histogram used group versus unused group, while mapping analysis times were longer in the used group (p ≤ .019). A significantly greater number of cases in the LAT Histogram used compared with the unused group had ablation for entrance or exit points (19 vs. 10 cases; p = .001 for first map). Ablation resulted in a return to sinus rhythm and changed cycle length at the first mapping in 20 cases (80%) in the LAT Histogram unused group and in 24 cases (96%) in the used group.ConclusionsLAT Histogram may provide a simple and effective method to identify entrance and exit locations in left atrial tachycardia.
Detection of tomato brown rugose fruit virus in environmental residues: The importance of contextualizing test results
Authors: Giesbers Anne K. J. , Vogel Elise , Skelton Anna , Zisi Zafeiro , Wildhagen Mandy , Loh Yue Lin , Ghijselings Lucas , Groothuismink Johanne , Westenberg Marcel , Matthijnssens Jelle , Roenhorst Annelien , Vos Christine , Fox Adrian , Botermans Marleen 
Published: July 2024

AbstractTomato brown rugose fruit virus (ToBRFV) is regulated as a quarantine pest in many countries worldwide. To assess whether ToBRFV is present in cultivations, plants or seed lots, testing is required. The interpretation of test results, however, can be challenging. Reverse transcription‐quantitative (real‐time) PCR results, even though considered “positive”, may not always signify plant infection or indicate the presence of infectious virus, but could be due to the presence of viral residues in the environment. Here, case studies from the Netherlands, Belgium, and the United Kingdom address questions regarding the detection of ToBRFV in various settings, and the infectiousness of ToBRFV‐positive samples. These exploratory analyses demonstrate widespread detection of ToBRFV in diverse samples and environments. ToBRFV was detected inside and around greenhouses with no prior history of ToBRFV infection, and on different materials and surfaces, including those that were untouched by individuals, plants or objects. This suggested the dispersal of viral residues through aerosols. ToBRFV or its residues were more often detected in regions with nearby tomato production, yet were also found in a wider environment extending beyond infected crops. ToBRFV originating from environmental contamination may or may not be infectious, adding complexity to decision‐making in response to positive test results. Contextual information, such as the origin of the sample and the likelihood of residues from prior cultivations and/or the broader environment, is important for interpreting test results. A nuanced approach is crucial to correctly interpret ToBRFV test results, necessitating further research to support risk assessment.