bluuebunny/crossref_metadata_2025_split huggingface dataset:
A genomic region associated with iteroparous spawning phenology is linked with age‐at‐maturity in female steelhead trout
Authors: Willis Stuart , Stephenson Jeff , Pierce Andrew , Medeiros Lea , Jenkins Laura , Hatch Douglas R. , Narum Shawn 
Published: December 2023

AbstractAge‐at‐maturity and iteroparity are two life history variations of steelhead trout (Oncorhynchus mykiss) that are believed to increase population resilience and stability. While repeat‐spawning individuals are thought to have historically made up a substantial portion of the reproductive population in the Columbia River and the majority of females still attempt outmigration as kelts, return rates of repeat‐spawner are low throughout the basin and below 1% for the furthest migrating stocks. Notably, outmigrating adults exhibit variation in rematuration phenology, displaying either “consecutive” (reproduce immediately the following season) or “skip” (delay spawning for future seasons) spawning patterns. Here, we use low coverage whole genome sequencing of consecutive versus skip spawning female Columbia River steelhead from two populations to test for genomic differences between these two iteroparous phenotypes. We identified genomic regions on several chromosomes which were associated with the phenology of iteroparity, including a region on chromosome 25 containing two genes, estradiol receptor beta (ERβ) and glycoprotein hormone beta‐5 (GPHB5), which, in mammals, are estrogen‐sensitive and expressed in reproductive tissues. Allele frequencies in this ERβ/GPHB5 region differed among female steelhead of different age at maturity, but not males. These genes also shared an island of linkage disequilibrium with the SIX6 gene, 600Kbp away on the same chromosome, a region of known association with age‐at‐maturity. These observations contribute to growing evidence that age‐at‐maturity and the phenology of iteroparity are determined by overlapping physiological processes and genetic pathways.
Dynamic nasopharyngeal collapse in horses: What we know so far
Authors: Jeong Sharon , Bond Stephanie L. , Sole‐Guitart Albert 
Published: December 2023

AbstractDynamic nasopharyngeal collapse (NPC) is an obstructive upper airway disease that affects mainly the inspiratory phase of respiration in horses undergoing strenuous exercise. It occurs when the neuromuscular activity of the nasopharynx is overwhelmed by the intense negative pressures generated during exercise. This leads to collapse of at least one of the four components of the nasopharynx which is comprised of the two lateral walls, the dorsal roof and the ventral soft palate. As a result, the airway diameter and thus airflow become compromised. Even small changes in the airway diameter produces profound increases in negative inspiratory pressure, perpetuating the cycle of collapse. Compared to other dynamic upper respiratory tract disorders, the amount of literature on NPC as a disease entity is limited. The exact pathophysiology of NPC is unknown; however, it impacts up to one quarter of high‐performance equine athletes presenting for poor performance. There is currently no definitive treatment for this severely performance‐limiting condition. Thus, the prognosis for future athletic prognosis is guarded, with most horses being retired from racing or athletic use in general. Further research is warranted in this field to reduce the impact of disease and in turn, reduce the turnover rate and economic loss by enhancing the career longevity of elite equine athletes diagnosed with NPC.
The impact of questioning strategies on target language production and learner confidence
Authors: Gardner Angela , Lichtman Karen 
Published: December 2023

AbstractThis study investigated how questioning strategies impact language learner performance. Specifically, it explored how questioning strategies influence (i) verb production and subject–verb agreement in the target language, and (ii) learner confidence in completing tasks without translation software. Sixty‐eight novice language learners enrolled in a high school Spanish I course participated. The students were divided into two groups. After a pretest, one group completed an activity with divergent (open‐ended) questions, while the other group did the same activity with contingent (either/or) questions. Participants then completed a posttest and rated their temptation to use translation software. Writing on the pre‐ and posttests was evaluated for verb production, verb conjugation, and subject–verb agreement. Results show that as compared with divergent questions, contingent questions (i) help students produce significantly more conjugated verbs and more accurate subject/verb agreement, and (ii) significantly reduce the temptation to rely on translation software.
Plant–soil synchrony in nutrient cycles: Learning from ecosystems to design sustainable agrosystems
Authors: Fontaine Sébastien , Abbadie Luc , Aubert Michaël , Barot Sébastien , Bloor Juliette M. G. , Derrien Delphine , Duchene Olivier , Gross Nicolas , Henneron Ludovic , Le Roux Xavier , Loeuille Nicolas , Michel Jennifer , Recous Sylvie , Wipf Daniel , Alvarez Gaël 
Published: December 2023

AbstractRedesigning agrosystems to include more ecological regulations can help feed a growing human population, preserve soils for future productivity, limit dependency on synthetic fertilizers, and reduce agriculture contribution to global changes such as eutrophication and warming. However, guidelines for redesigning cropping systems from natural systems to make them more sustainable remain limited. Synthetizing the knowledge on biogeochemical cycles in natural ecosystems, we outline four ecological systems that synchronize the supply of soluble nutrients by soil biota with the fluctuating nutrient demand of plants. This synchrony limits deficiencies and excesses of soluble nutrients, which usually penalize both production and regulating services of agrosystems such as nutrient retention and soil carbon storage. In the ecological systems outlined, synchrony emerges from plant–soil and plant–plant interactions, eco‐physiological processes, soil physicochemical processes, and the dynamics of various nutrient reservoirs, including soil organic matter, soil minerals, atmosphere, and a common market. We discuss the relative importance of these ecological systems in regulating nutrient cycles depending on the pedoclimatic context and on the functional diversity of plants and microbes. We offer ideas about how these systems could be stimulated within agrosystems to improve their sustainability. A review of the latest advances in agronomy shows that some of the practices suggested to promote synchrony (e.g., reduced tillage, rotation with perennial plant cover, crop diversification) have already been tested and shown to be effective in reducing nutrient losses, fertilizer use, and N2O emissions and/or improving biomass production and soil carbon storage. Our framework also highlights new management strategies and defines the conditions for the success of these nature‐based practices allowing for site‐specific modifications. This new synthetized knowledge should help practitioners to improve the long‐term productivity of agrosystems while reducing the negative impact of agriculture on the environment and the climate.
Too hot to handle? An urgent need to understand climate change impacts on the biogeochemistry of tropical coastal waters
Authors: Carreira Cátia , Joyce Patrick W. S. , Morán Xosé Anxelu G. , Carvalho Susana , Falkenberg Laura , Lønborg Christian 
Published: December 2023

AbstractTropical regions contain ecologically and socio‐economically important habitats, and are home to about 3.8 billion people, many of which directly depend on tropical coastal waters for their well‐being. At the basis of these ecosystems are biogeochemical processes. Climate change is expected to have a greater impact in the tropics compared to temperate regions because of the relatively stable environmental conditions found there. However, it was surprising to find only 660 research articles published focusing on the impact of climate change on the biogeochemistry of coastal tropical waters compared to 4823 for temperate waters. In this perspective, we highlight important topics in need of further research. Specifically, we suggest that in tropical regions compared to temperate counterparts climate change stressors will be experienced differently, that organisms have a lower acclimation capacity, and that long‐term baseline biogeochemical datasets useful for quantifying future changes are lacking. The low number of research papers on the impacts of climate change in coastal tropical regions is likely due to a mix of reasons including limited resources for research and limited number of long time series in many developing tropical countries. Finally, we propose some action points that we hope will stimulate more studies in tropical coastal waters.
The relationship between histopathological features, immunosuppression and outcome in patients undergoing native kidney biopsies
Authors: Kipgen David , Crosby Jana , Dey Vishal , Kelly Michael , McQuarrie Emily , Geddes Colin 
Published: December 2023

AimsTo assess retrospectively the association between histopathological lesions on renal biopsy and subsequent impairment of renal function across the spectrum of kidney diseases and to explore the influence of immunosuppressive therapy within the first 6 months after biopsy on this association.Methods and resultsClinical data from 488 adult patients having a renal biopsy reported at a single centre from 2017 to 2019 were obtained during a median follow‐up period of 786 days. Seventeen semi‐quantitative histology parameters were recorded at the time of biopsy, 14 of which were suitable for assessment of association with loss of eGFR by multivariable Cox regression analysis, measurement of eGFR slope and measurement of eGFR 12 months after biopsy. A widely used histopathological chronicity score was also assessed. Clinical baseline variables including prescription of immunosuppression were recorded. Seven of 14 histology parameters: mesangial matrix expansion, global glomerulosclerosis, tubular atrophy, interstitial fibrosis, arteriolosclerosis, mesangial hypercellularity and acute tubular injury; and the chronicity score, predicted loss of kidney function by all three measures. Prescription of immunosuppression was more likely in patients with active inflammatory pathology and less likely in patients with chronic fibrotic pathology, and was associated with reduced risk of loss of eGFR.ConclusionsThis retrospective study demonstrates the prognostic significance and complex relationship with immunosuppression of routinely reported histopathological variables in patients having native kidney biopsies, across the spectrum of kidney diseases. It provides useful information for renal biopsy prognostication and design of retrospective studies, including machine learning models.
Age‐related hair denaturation related to protein carbonyls
Authors: Fuse Naoya , Morita Shigeaki , Matsue Yukako 
Published: December 2023

AbstractObjectiveHair ageing is accompanied by hair fibres becoming irregularly shaped causing them to stick out in irregular directions or have more curliness and being spread out. This is believed to be due to changes within the hair fibre structure which occur with ageing, and one of the causes of these changes could be an increase in the number of protein carbonyl groups present in the hair. The aim of this study is to investigate the internal denaturation of hair related to protein carbonyls in attempt to gain new insight into age‐related changes that occur in hair.MethodsThe degree of carbonylation of the hair structural protein as determined by fluorescent labelling and Western blotting analysis was used to investigate the primary structure of hair protein. The amount of helix, a common conformation in the secondary structure of proteins, in hair in groups of women with different ages was also analysed using infrared microscopy coupled with multivariate curve resolution (MCR). From the results of this, an image of the two‐dimensional distribution of the α‐helices was generated for the hair taken from each age group. Also, high‐pressure differential scanning calorimetry (HPDSC) of the hair in water was performed on the hair taken from each age group to determine the peak temperature of endothermic effect and the enthalpy of denaturation.ResultsWe found that the amino group content in hair proteins decreased and Type II keratin, one of the subunits of intermediate filament, was more carbonylated with age. The results of the MCR indicated eight separate components, including components of the secondary structure of proteins, such as α helices and β sheets. Two‐dimensional images of the hair cross‐sections revealed that the presence of α helices decreased with age. In addition, data from the HPDSC showed that the enthalpy associated with the denaturing temperature also significantly decreased with age.ConclusionThese results suggest that there is a negative correlation between age and structural integrity of the helix segment in intermediate filament. The results of this study also show that there is a positive correlation between age‐related hair denaturation and protein carbonyls.
Detection of dysplasia in peripheral blood: Proposal of an algorithm to detect myelodysplastic syndromes and chronic myelomonocytic leukemias on a high‐speed technical platform using the Sysmex XN™ analyser
Authors: Bouriche Lakhdar , Fuster Léa , Laurent Hugo , Soler Christophe , Benhabib Sofiane 
Published: December 2023

AbstractIntroductionChronic Myelomonocytic Leukemia (CMML) and Myelodysplastic Syndromes (MDS) are increasingly represented in the general population. We propose a screening strategy based on algorithms calculated from quantitative and analytical data from the XN analyser.Materials and MethodsWe tested the performance of previously published MDS and CMML scores on an evaluation cohort of 749 individual eligible patients over 50 years of age. These patients were classified into 3 groups as follows: 713 patients without MDS or CMML, 18 patients with MDS, and finally 18 patients with CMML. In a second step, a routine cohort of 37 828 samples was studied to evaluate the impact of this approach.ResultsThe concordance rate between cytology and the two scores is 92.1%. The sensitivity and specificity of the CMML score are 100% and 96.2%, respectively. For the MDS score, they are 83.3% and 89.6% respectively. The ratio of platelets measured by fluorescence on board (PLT‐F) as reflex tests generated is 1.5% after 6 months. The additional smear ratio for suspected MDS is calculated at 0.6%.ConclusionWe propose a flowchart using embedded artificial intelligence to help the cytologist in an optimized smear review and thus improve guidance to the clinician and the patients in the diagnosis process. This strategy permits a more comprehensive approach to MDS and CMML detection fitting with the new definition of CMML according to the recommendations of the World Health Organization (WHO) published in 2022.
Human STAT1 gain of function with chronic mucocutaneous candidiasis: A comprehensive review for strengthening the connection between bedside observations and laboratory research
Authors: Asano Takaki , Noma Kosuke , Mizoguchi Yoko , Karakawa Shuhei , Okada Satoshi 
Published: December 2023

SummaryGermline human heterozygous STAT1 gain‐of‐function (GOF) variants were first discovered a common cause of chronic mucocutaneous candidiasis (CMC) in 2011. Since then, numerous STAT1 GOF variants have been identified. A variety of clinical phenotypes, including fungal, viral, and bacterial infections, endocrine disorders, autoimmunity, malignancy, and aneurysms, have recently been revealed for STAT1 GOF variants, which has led to the expansion of the clinical spectrum associated with STAT1 GOF. Among this broad range of complications, it has been determined that invasive infections, aneurysms, and malignancies are poor prognostic factors for STAT1 GOF. The effectiveness of JAK inhibitors as a therapeutic option has been established, although further investigation of their long‐term utility and side effects is needed. In contrast to the advancements in treatment options, the precise molecular mechanism underlying STAT1 GOF remains undetermined. Two primary hypotheses for this mechanism involve impaired STAT1 dephosphorylation and increased STAT1 protein levels, both of which are still controversial. A precise understanding of the molecular mechanism is essential for not only advancing diagnostics but also developing therapeutic interventions. Here, we provide a comprehensive review of STAT1 GOF with the aim of establishing a stronger connection between bedside observations and laboratory research.
Periodontitis stage and grade modifies the benefit of regular supportive periodontal care in terms of need for retreatment and mean cumulative cost
Authors: Saleh Muhammad H. A. , Decker Ann , Ravidà Andrea , Wang Hom‐lay , Tonetti Maurizio 
Published: December 2023

AbstractAimThis study aimed to characterize the periodontal breakdown during supportive periodontal care (SPC) and to quantify the corresponding cost‐effectiveness of periodontal therapy.Materials and MethodsData were obtained from charts of patients who received active periodontal therapy (APT) with a minimum follow‐up of ≥10 years. Analysis was done to identify factors associated with the incidence of additional sub‐gingival instrumentation (SGI) and/or surgery (SUR) during SPC and mean cumulative cost of recurrence was calculated. All relevant data were collected.ResultsIn all, 442 patients were included. Over the follow‐up period, 62% of Stage I and II patients and 72% of Stage III and IV patients required further treatment following the APT; 56.5% of SGI patients and 78.6% of SUR patients received a second intervention. SUR patients received more SUR during the follow‐up period (p = .035). Stage III and IV patients received more SUR during SPC than Stage I and II patients (p = .001). Grade C patients received more SUR during the follow‐up period (p < .05). During the 5‐year period preceding retreatment, the mean SPC visits were lower for patients who did not require retreatment (p < .001). Risk factors such as regularity of maintenance, smoking and diabetes were related to a higher chance of receiving SUR during the follow‐up period (p < .05). The mean cumulative costs indicated less recurrence cost for compliers in Stage III and IV or Grade B and C but not for those in Stage I and II or Grade A.ConclusionsThe risk of relapse in the maintenance population may be correlated with higher stage and grade, patient compliance, modifiable risk factors and the nature of the treatment provided during APT. The total cost of treatment of recurrences was lower for compliers in Stage III/IV and Grade B/C compared with erratic compliers with the same severity and risk.
Suppression of circular RNA serum and glucocorticoid‐induced kinase 1 elevates antioxidant molecules and angiogenesis in trophoblast cells to attenuate preeclampsia via microRNA‐508‐3p to target and restrain PUM homolog 1
Authors: Lu CaiXia , Zheng FuMin , Pan LiXiao , Han QingFang , Wu JiXia , Zhang WenKe 
Published: December 2023

AbstractAimPreeclampsia (PE) is a pregnancy‐specific syndrome characterized by hypertension and proteinuria. Recently, multiple circular RNAs (circRNAs) were considered latent clinical diagnostic markers or therapeutic targets. This study was to explore the impact of circRNA serum and glucocorticoid‐induced kinase 1 (SGK1) on PE via influencing the microRNA (miR)‐508‐3p/PUM homolog 1 (PUM1) axis.MethodsPlacental tissues of 34 pregnant women with PE and 34 normal pregnant women were collected to measure circRNA SGK1 (circSGK1), miR‐508‐3p, and PUM1. Human placental trophoblasts HTR‐8/SVneo were transfected with plasmids, thereafter to observe proliferation, migration, invasion, and apoptosis, analyze antioxidant molecules Troxerutin (TXN), Glutamate‐cysteine ligase catalytic subunit (GCLC), NAD (P) H‐quinone oxidoreductase 1 (NQO1), and determine angiogenesis. After the construction of the PE rat model, antioxidant molecules TXN, GCLC, and NQO1, vascular‐associated factor vascular endothelial growth factor A (VEGF‐A), and histopathological conditions were tested. Examination of the binding of circSGK1 and miR‐508‐3p with PUM1 was performed.ResultsOur data showed that circSGK1 expression was elevated in the placenta of patients with PE. Silenced circSGK1 or elevated miR‐508‐3p promoted the growth and antioxidant molecules and angiogenesis in trophoblast cells; CircSGK1 combined with miR‐508‐3p, and miR‐508‐3p targeted PUM1.ConclusionsIn summary, suppression of circSGK1 augments antioxidant molecules and angiogenesis in trophoblast cells to attenuate PE via miR‐508‐3p to target PUM1.
Two‐speed genomes of Epichloe fungal pathogens show contrasting signatures of selection between species and across populations
Authors: Treindl Artemis D. , Stapley Jessica , Croll Daniel , Leuchtmann Adrian 
Published: December 2023

AbstractAntagonistic selection between pathogens and their hosts can drive rapid evolutionary change and leave distinct molecular footprints of past and ongoing selection in the genomes of the interacting species. Despite an increasing availability of tools able to identify signatures of selection, the genetic mechanisms underlying coevolutionary interactions and the specific genes involved are still poorly understood, especially in heterogeneous natural environments. We searched the genomes of two species of Epichloe plant pathogen for evidence of recent selection. The Epichloe genus includes highly host‐specific species that can sterilize their grass hosts. We performed selection scans using genome‐wide SNP data from seven natural populations of two co‐occurring Epichloe sibling species specialized on different hosts. We found evidence of recent (and ongoing) selective sweeps across the genome in both species. However, selective sweeps were more abundant in the species with a larger effective population size. Sweep regions often overlapped with highly polymorphic AT‐rich regions supporting the role of these genome compartments in adaptive evolution. Although most loci under selection were specific to individual populations, we could also identify several candidate genes targeted by selection in sweep regions shared among populations. The genes encoded small secreted proteins typical of fungal effectors and cell wall‐degrading enzymes. By investigating the genomic signatures of selection across multiple populations and species, this study contributes to our understanding of complex adaptive processes in natural plant pathogen systems.
A hierarchical control approach for virtual coupling in metro trains
Authors: Liu Hongjie , Luo Xiaolin , Tang Tao , Zhang Yang , Chai Ming 
Published: December 2023

AbstractAs an emerging technology, virtual coupling improves the efficiency and flexibility of metro services by forming multiple trains (units) as a virtually coupled train set (VCTS) without mechanical couplers. However, to realize the desired VCTS operation in practical metro services, a significant gap to be filled is that the implicit and nonlinear safety constraints are hard to be addressed in real‐time control. Thus, this paper proposes a hierarchical control approach with a two‐layer framework. In the upper layer, a trajectory planning method is designed, which addresses the safety constraints and prescribes a reference trajectory for each unit. In the lower layer, a model predictive control approach is constructed, by which each unit accurately tracks its reference trajectory in real time. Afterward, the proposed hierarchical control approach is employed to realize VCTS inter‐station operation in field tests. The average tracking error of speed is around 8 cm/s and the stopping error is less than 12 cm. The following distance between two units in VCTS is reduced to less than 105 m at the speed of 80 km/h, which is a breakthrough in the development of VCTS.