bluuebunny/crossref_metadata_2025 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

Age‐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

Dynamic 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

This 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

Redesigning 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

Tropical 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.
PD‐L1 expression in vulvar cancer: a systematic review and meta‐analysis
Authors: Baandrup Louise , Sand Freja Lærke , Aalborg Gitte Lerche , Nøttrup Trine J , Fiehn Anne‐Marie K , Kjaer Susanne K
Published: December 2023

Programmed cell death ligand‐1 (PD‐L1) expression in cancer may predict clinical response to immunotherapeutic treatment with PD‐1/PD‐L1 inhibitors. Within the vulvar cancer field, PD‐L1 expression has only been assessed by a few studies. We conducted a meta‐analysis to examine the prevalence of PD‐L1 positivity in vulvar cancer. PubMed, Embase, and Cochrane were searched for articles reporting on PD‐L1 expression in vulvar cancer. Study selection and data extraction were performed independently by two authors. We extracted data on PD‐L1 prevalence in vulvar cancer according to combined positive score (CPS) and tumour proportion score (TPS). Cutoff values for positivity were ≥1 or ≥10 for CPS and ≥1% and ≥5% for TPS. Random‐effects models were used to estimate pooled PD‐L1 prevalence, with 95% confidence intervals (CIs). Tests of between‐study heterogeneity were evaluated by the I2 statistics. Sources of heterogeneity were explored by subgroup analyses and meta‐regression. In total, 19 studies were included. Pooled PD‐L1 prevalence in vulvar cancer was 83.4% (95% CI: 70.8–91.3; I2 = 80.0) and 53.9% (95% CI: 37.4–69.6; I2 = 93.0) according to CPS and TPS, respectively. Based on TPS, human papillomavirus (HPV)‐associated vulvar squamous cell carcinomas (SCC) showed a lower PD‐L1 prevalence (39.9%; 95% CI: 13.3–74.2) compared with HPV‐independent SCC (62.6%; 95% CI: 33.7–84.6), but meta‐regression showed no significant variation in PD‐L1 prevalence by HPV status. PD‐L1 prevalence was similar in advanced (44.9%; 95% CI: 29.8–61.1) and localized vulvar cancer (56.7%; 95% CI: 18.9–76.7). In conclusion, PD‐L1 expression in vulvar cancer is frequent but between‐study heterogeneity was high. Based on a subgroup of heterogenous studies, we found no strong variation in PD‐L1 prevalence according to HPV status and stage.
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

Aims

To 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 results

Clinical 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.

Conclusions

This 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

Objective

Hair 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.

Methods

The 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.

Results

We 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.

Conclusion

These 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

Introduction

Chronic 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 Methods

We 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.

Results

The 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%.

Conclusion

We 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

Germline 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

Aim

This study aimed to characterize the periodontal breakdown during supportive periodontal care (SPC) and to quantify the corresponding cost‐effectiveness of periodontal therapy.

Materials and Methods

Data 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.

Results

In 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.

Conclusions

The 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

Aim

Preeclampsia (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.

Methods

Placental 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.

Results

Our 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.

Conclusions

In 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

Antagonistic 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

As 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.
Long‐term safety of oral edaravone in Japanese patients with amyotrophic lateral sclerosis: Sub‐analysis of a global, open‐label, phase 3 study
Authors: Sun Xuezhu , Hirai Manabu , Tezuka Tomoaki , Hirota Shinya , Yuki Satoshi
Published: December 2023

Introduction/Aims

Patients with amyotrophic lateral sclerosis (ALS) experience a slower rate of physical function decline when treated with intravenous edaravone. The oral suspension formulation of edaravone (105 mg) has a similar pharmacokinetic profile to intravenous edaravone (60 mg/60 min). The long‐term safety of oral edaravone in Japanese patients with ALS has not been reported. Therefore, a sub‐analysis of Japanese patients in a global phase 3 study (NCT04165824) was conducted to evaluate the safety and tolerability of oral edaravone in Japanese patients with ALS.

Methods

This study was a global, open‐label, phase 3 study to evaluate the long‐term safety and tolerability of oral edaravone in patients with ALS. Patients with ALS received oral edaravone (105 mg/day) for 48 weeks. Adverse events in Japanese patients were assessed at week 48.

Results

Among the 185 patients enrolled globally, 65 patients were enrolled in Japan (mean age, 59.3 years; mean disease duration, 1.5 years). Most patients experienced treatment‐emergent adverse events (TEAEs) (84.6%), and the most common TEAEs by week 48 were constipation (15.4%), insomnia (12.3%), and back pain (10.8%). Two serious TEAEs were reported: atrial fibrillation and pleural effusion (both n = 1). Three adverse drug reactions (ADRs) were reported: diarrhea, abnormal hepatic function, and fatigue (all n = 1). There were no serious ADRs or TEAEs/ADRs that led to study drug discontinuation.

Discussion

Oral edaravone had a similar safety profile to intravenous edaravone in Japanese patients, and good tolerability over 48 weeks. No new safety concerns were observed in this population.
Local distribution of manganese to leaf sheath is mediated by OsNramp5 in rice
Authors: Huang Sheng , Konishi Noriyuki , Yamaji Naoki , Ma Jian Feng
Published: December 2023

To play essential roles of manganese (Mn) in plant growth and development, it needs to be transported to different organs and tissues after uptake. However, the molecular mechanisms underlying Mn distribution between different tissues are poorly understood.

We functionally characterized a member of rice natural resistance‐associated macrophage protein (NRAMP) family, OsNramp5 in terms of its tissue specificity of gene expression, cell‐specificity of protein localization, phenotypic analysis of leaf growth and response to Mn fluctuations.

OsNramp5 is highly expressed in the leaf sheath. Immunostaining revealed that OsNramp5 is polarly localized at the proximal side of xylem parenchyma cells of the leaf sheath. Both the gene expression and protein abundance of OsNramp5 are unaffected by different Mn concentrations. Knockout of OsNramp5 decreased the distribution of Mn to the leaf sheath, but increased the distribution to the leaf blade at both low and high Mn supplies, resulting in reduced growth of leaf sheath. Furthermore, expression of OsNramp5 under the control of root‐specific promoter in osnramp5 mutant complemented Mn uptake, but could not complement Mn distribution to the leaf sheath.

These results indicate that OsNramp5 expressed in the leaf sheath plays an important role in unloading Mn from the xylem for the local distribution in rice.
Segregation of neuronal and vascular retinal damage in patients with hypertension and diabetes
Authors: Chua Jacqueline , Wong Damon , Yow Ai Ping , Tan Bingyao , Liu Xinyu , Ismail Munirah Binte , Chin Calvin Woon Loong , Lamoureux Ecosse , Husain Rahat , Schmetterer Leopold
Published: December 2023

This study aimed to examine the impact of diabetes and hypertension on retinal nerve fiber layer (RNFL) thickness components. Optical coherence tomography (OCT) measurements do not consider blood vessel contribution, which this study addressed. We hypothesized that diabetes and/or hypertension would lead to thinner RNFL versus controls due to the vascular component. OCT angiography was used to measure the RNFL in 121 controls, 50 diabetes patients, 371 hypertension patients, and 177 diabetes patients with hypertension. A novel technique separated the RNFL thickness into original (vascular component) and corrected (no vascular component) measurements. Diabetes‐only (98 ± 1.7 µm; p = 0.002) and diabetes with hypertension (99 ± 0.8 µm; p = 0.001) patients had thinner original RNFL versus controls (102 ± 0.8 µm). No difference was seen between hypertension‐only patients (101 ± 0.5 µm; p = 0.083) and controls. After removing the blood vessel component, diabetes/hypertension groups had thinner corrected RNFL versus controls (p = 0.024). Discrepancies in diabetes/hypertension patients were due to thicker retinal blood vessels within the RNFL thickness (p = 0.002). Our findings suggest that diabetes and/or hypertension independently contribute to neurodegenerative thinning of the RNFL, even in the absence of retinopathy. The differentiation of neuronal and vascular components in RNFL thickness measurements provided by the novel technique highlights the importance of considering vascular changes in individuals with these conditions.
DNA metabarcoding uncovers dispersal‐constrained arthropods in a highly fragmented restoration setting
Authors: Contos Peter , Gibb Heloise , Jellinek Sacha , Murphy Nicholas P.
Published: December 2023

Degraded areas are often restored through active revegetation; however, recolonization by animals is rarely engineered. Recolonization may be rapid for species with strong dispersal abilities. However, poor dispersers, such as many flightless arthropods, may struggle to recolonize newly restored sites. Actively reintroducing or “rewilding” arthropods may therefore be necessary to facilitate recolonization and restoration of arthropod communities and the ecological functions they perform. However, active interventions are rare. The purpose of this study was twofold. First, we asked whether potential source remnant arthropod communities were dispersal‐constrained and struggling to recolonize restoration sites. Second, we tested whether reintroducing entire arthropod communities from remnant populations would help dispersal‐constrained species establish during farmland ecological restoration in southern Australia. Rewilding was conducted in summer 2018 by transplanting leaf litter, soil, and entire communities contained within it from remnant source populations into geographically isolated restoration sites, which were paired with untreated controls (n = 6 remnant, rewilding transplant, and control sites). We collected leaf litter and extracted arthropod communities 19 months after the initial rewilding event, then sequenced mite, springtail, and insect communities using a metabarcoding approach. Within all groups, community similarity decreased with spatial distance between sites, suggesting significant dispersal barriers. However, only mite communities showed a strong response to rewilding, which was expressed as increased compositional similarity toward remnant sites and greater species richness relative to controls. Our results demonstrate that many arthropod species may struggle to recolonize geographically isolated restoration sites and that full community restoration requires active interventions via rewilding.
Zeolites synthesized from agro‐industrial residues applied in agriculture: A review and future prospects
Authors: de Carvalho Izidoro Juliana , Fungaro Denise Alves , Cataldo Eleonora
Published: December 2023

Zeolites have been widely applied as catalysts, wastewater treatment agents, gas adsorbents and fertilizers, among others. However, the use of natural zeolites or those synthesized from oversaturated commercial solutions are more explored commercially than the zeolites synthesized from residues. Therefore, the aim of this review is to highlight the importance of zeolites synthesized from agro‐industrial residues and their use in agriculture. This review has been divided into three different sections, that is, zeolites, agriculture applications, synthesis of zeolites from residues and their application in plant growth. In the first section, the definition, types and the critical properties of zeolites are explained. The second section gives a brief review of the application of zeolites in agriculture. Finally, the synthesis of zeolites from residues, such as coal ash, rice husk ash and sugarcane ash, with special attention to renewable sources is presented. The optimization of the synthesis of zeolites from residues with the incorporation of specific nutrients necessary for the cultivation of soybeans, corn and sugarcane (considered the most significant crops in Brazilian agriculture in terms of the planted area) can significantly contribute to the concept of circular economy at the industries and the fulfilment of sustainable development objectives, especially, the number 12 (SDO—12—Responsible consumption and production).
A vesicular Warburg effect: Aerobic glycolysis occurs on axonal vesicles for local NAD+ recycling and transport
Authors: Mc Cluskey Maximilian , Dubouchaud Hervé , Nicot Anne‐Sophie , Saudou Frédéric
Published: December 2023

In neurons, fast axonal transport (FAT) of vesicles occurs over long distances and requires constant and local energy supply for molecular motors in the form of adenosine triphosphate (ATP). FAT is independent of mitochondrial metabolism. Indeed, the glycolytic machinery is present on vesicles and locally produces ATP, as well as nicotinamide adenine dinucleotide bonded with hydrogen (NADH) and pyruvate, using glucose as a substrate. It remains unclear whether pyruvate is transferred to mitochondria from the vesicles as well as how NADH is recycled into NAD+ on vesicles for continuous glycolysis activity. The optimization of a glycolytic activity test for subcellular compartments allowed the evaluation of the kinetics of vesicular glycolysis in the brain. This revealed that glycolysis is more efficient on vesicles than in the cytosol. We also found that lactate dehydrogenase (LDH) enzymatic activity is required for effective vesicular ATP production. Indeed, inhibition of LDH or the forced degradation of pyruvate inhibited ATP production from axonal vesicles. We found LDHA rather than the B isoform to be enriched on axonal vesicles suggesting a preferential transformation of pyruvate to lactate and a concomitant recycling of NADH into NAD+ on vesicles. Finally, we found that LDHA inhibition dramatically reduces the FAT of both dense‐core vesicles and synaptic vesicle precursors in a reconstituted cortico‐striatal circuit on‐a‐chip. Together, this shows that aerobic glycolysis is required to supply energy for vesicular transport in neurons, similar to the Warburg effect.
Proximity proteomic analysis of the NRF family reveals the Parkinson’s disease protein ZNF746/PARIS as a co-complexed repressor of NRF2
Authors: LaPak Kyle M. , Saeidi Soma , Bok Ilah , Wamsley Nathan T. , Plutzer Isaac B. , Bhatt Dhaval P. , Luo Jingqin , Ashrafi Ghazaleh , Ben Major M.
Published: December 2023

The nuclear factor erythroid 2-related factor 2 (NRF2) transcription factor activates cytoprotective and metabolic gene expression in response to various electrophilic stressors. Constitutive NRF2 activity promotes cancer progression, whereas decreased NRF2 function contributes to neurodegenerative diseases. We used proximity proteomic analysis to define protein networks for NRF2 and its family members NRF1, NRF3, and the NRF2 heterodimer MAFG. A functional screen of co-complexed proteins revealed previously uncharacterized regulators of NRF2 transcriptional activity. We found that ZNF746 (also known as PARIS), a zinc finger transcription factor implicated in Parkinson’s disease, physically associated with NRF2 and MAFG, resulting in suppression of NRF2-driven transcription. ZNF746 overexpression increased oxidative stress and apoptosis in a neuronal cell model of Parkinson’s disease, phenotypes that were reversed by chemical and genetic hyperactivation of NRF2. This study presents a functionally annotated proximity network for NRF2 and suggests a link between ZNF746 overexpression in Parkinson’s disease and inhibition of NRF2-driven neuroprotection.
Deubiquitinase USP1 regulates sarbecovirus ORF6 protein function
Authors: Gao Wenying , Wang Liuli , Cui Wenzhe , Wang Hongfei , Huang Guofeng , Li Zhaolong , Li Guangquan , Zhang Wenyan
Published: December 2023

SARS-CoV-2 belongs to the subgenus
Sarbecovirus
, which universally encodes the accessory protein ORF6. SARS-CoV-2 ORF6 is an antagonist of the interferon (IFN)-mediated antiviral response and plays an important role in viral infections. However, the mechanism by which the host counteracts the function of ORF6 to restrict viral replication remains unclear. In this study, we found that most ORF6 proteins encoded by sarbecoviruses could be ubiquitinated and subsequently degraded via the proteasome pathway. Through extensive screening, we identified that the deubiquitinase USP1, which effectively and broadly deubiquitinates sarbecovirus ORF6 proteins, stabilizes ORF6 proteins, resulting in enhanced viral replication. Therefore, ubiquitination and deubiquitination of ORF6 are important for antagonizing IFN-mediated antiviral signaling and influencing the virulence of SARS-CoV-2. These findings highlight an essential molecular mechanism and may provide a novel target for therapeutic interventions against viral infections.

IMPORTANCE

The ORF6 proteins encoded by sarbecoviruses are essential for effective viral replication and infection and are important targets for developing effective intervention strategies. In this study, we confirmed that sarbecovirus ORF6 proteins are important antagonists of the host immune response and identified the regulatory mechanisms of ubiquitination and deubiquitination of most sarbecovirus ORF6 proteins. Moreover, we revealed that DUB USP1 prevents the proteasomal degradation of all ORF6 proteins, thereby promoting the virulence of SARS-CoV-2. Thus, impeding ORF6 function is helpful for attenuating the virulence of sarbecoviruses. Therefore, our findings provide a deeper understanding of the molecular mechanisms underlying sarbecovirus infections and offer potential new therapeutic targets for the prevention and treatment of these infections.
Fecal and skin microbiota of two rescued Mediterranean monk seal pups during rehabilitation
Authors: Dosi Aggeliki , Meziti Alexandra , Tounta Eleni , Koemtzopoulos Kimon , Komnenou Anastasia , Dendrinos Panagiotis , Kormas Konstantinos
Published: December 2023

The role of animal host-associated microbiomes is becoming more apparent and defined for wild animals, especially for the species under conservation strategies. This study investigated the succession of fecal and skin bacterial microbiota of two rescued female Mediterranean monk seal (
Monachus monachus
) pups for most of their rehabilitation period. Bacterial species richness and diversity were assessed by high-throughput sequencing of nine freshly collected fecal samples and four skin swabs per individual. Both the fecal and skin microbiota highly overlapped in their containing operational taxonomic units (OTUs) and abundance patterns. The fecal microbiota was separated in two distinct periods and was dominated by OTUs related to the
Shigella
,
Streptococcus
,
Enterococcus
,
Lactobacillus,
and
Escherichia
genera in the first period, while in the second period, the dominating genera were the
Clostridium, Blautia, Fusobacterium, Edwardsiella,
and
Bacteroides
. The skin microbiota was highly similar between the two individuals in each sampling and was dominated by
Psychrobacter-, Elizabethkingia-,
and
Bergeyella
-related OTUs. The provided antibiotic treatment, along with the provided probiotics and nutritional supplements, resulted in a major turnover of the bacterial microbiota with the potentially detrimental OTUs being eliminated toward the end of the rehabilitation period, prior to the release of the pups in the wild.

IMPORTANCE

This study showed that during the rehabilitation of two rescued Mediterranean monk seal pups (
Monachus monachus
), the skin and fecal bacterial communities showed similar succession patterns between the two individuals. This finding means that co-housed pups share their microbiomes, and this needs to be considered in cases of infection outbreaks and their treatment. The housing conditions, along with the feeding scheme and care protocols, including the admission of antibiotics as prophylaxis, probiotics, and essential food supplements, resulted in bacterial communities with no apparent pathogenic bacteria. This is the first contribution to the microbiome of the protected seal species of
M. monachus
and contributes to the animal’s conservation practices through its microbiome.
Early Cambrian Cambroclavus is a scleritomous eumetazoan unrelated to bryozoan or dasyclad algae
Authors: Xiang Kai , Yin Zongjun , Liu Wei , Zhao Fangchen , Zhu Maoyan
Published: December 2023

The origin of Bryozoa has long been an intriguing mystery, largely due to the dearth of unambiguous bryozoan fossils within Cambrian strata. The earliest bryozoan thus far identified, Protomelission, an early Cambrian microfossil from Australia and China, was recently contested and proposed to be dasyclad algae. Our reanalysis of micro-computed tomography data from Protomelission specimens, however, unveils previously unrevealed structures, indicating Protomelission to be neither bryozoan nor alga, but a scleritome of Cambroclavus, an early Cambrian microfossil typically found as disarticulated sclerites. The long-sought scleritomes suggest that enigmatic cambroclaves likely represent an extinct group of epitheliozoan-grade eumetazoan, with spiny sclerites covering their epidermis for defense. The prevalence of bizarre animals like cambroclaves, lacking modern analogues, implies a greater disparity of animal body plans during the Cambrian explosion than previously recognized. Our findings underscore the absence of definitive early Cambrian bryozoan fossils, further highlighting the dilemma of the origin of Bryozoa.
Genetic Diversity of the Amur Tiger (Panthera tigris altaica): Are There Differences between the 20th and the Early 21st Centuries?
Authors: Sorokin P. A. , Yudin V. G. , Naidenko S. V. , Hernandez-Blanco J. A. , Chistopolova M. D. , Rozhnov V. V.
Published: December 2023

Polymorphism of nine microsatellite loci in the Sikhote-Alin tiger population was analyzed in the modern and recent historical periods, using blood, excrement, and museum bone samples. Tests for excess heterozygosity to determine whether the population went through a period of low abundance and a low value of the Garza–Williamson coefficient indicated that such events were highly probable to occur in both recent and earlier history. The mean effective population size Ne of a current sample was 34.4 (95% confidence interval 17–106.8). This fact is of great interest in the contest of conservation and restoration of endangered large cat species.
Transport Properties of the Magnetic Topological Insulators Family (MnBi2Te4)(Bi2Te3)m (m = 0, 1, …, 6)
Authors: Zverev V. N. , Abdullayev N. A. , Aliyev Z. S. , Amiraslanov I. R. , Otrokov M. M. , Mamedov N. T. , Chulkov E. V.
Published: December 2023

Systematic studies of magneto-transport properties of the whole (MnBi2Te4)(Bi2Te3)m family of magnetic topological insulators ($$m = 0,1,...,6)$$ have been carried out. Temperature dependences of the resistivity, magnetoresistance and the Hall effect at low temperatures have been studied. When m increases, i.e., when the separation between 2D MnBi2Te4 magnetic layers becomes larger, the transition from antiferromagnetic to ferromagnetic state takes place. We have found that ferromagnetic state survives even in the samples with $$m = 6$$, when 2D magnets are separated by six non-magnetic Bi2Te3 blocks.
Crohn’s disease and intestinal tuberculosis: challenging from every angle
Authors: Guimarães Andreia , Gama João , Curvo-Semedo Luis , Manso António Canaveira
Published: December 2023

A woman in her 20s with a recent diagnosis of Crohn’s disease (CD) affecting the ileocaecal valve was started on adalimumab, after routine tuberculosis (TB) tests were negative. Her abdominal symptoms got worse and she started presenting respiratory distress and fever. Tomography revealed a left pleural effusion, pneumonia and peritonitis with pelvic abscess. The diagnosis of disseminated TB with digestive involvement was suggested and sputum cultures were positive forMycobacterium tuberculosis. Treatment for TB was started and immunosuppressants discontinued, leading to respiratory improvement. Abdominal imaging was repeated, showing worsening signs of multisegmental ileal wall thickening, ileocaecal valve obstruction and a persistent pelvic abscess. She was then submitted to a laparoscopic ileocaecal resection for suspicion of worsening CD. Histopathology showed chronic ileocolitis compatible with CD and ganglionic tuberculosis, revealing the diagnosis of intestinal tuberculosis superimposed in CD. Recovery was uneventful.