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Study of Antimicrobial Resistant Gram Negative Bacteria in Chicken and Pork Meat Arou...
Sushma Paudel
Sumitra Tamang

Sushma Paudel

and 4 more

January 22, 2025
The increasing trend of multidrug resistance in Gram-negative bacteria (MDR-GNB) has been a major concern for the healthcare settings in Nepal and globally. In Nepal, previous studies on antimicrobial resistance (AMR) have received limited attention to animal-sourced food, which represents a significant route for the zoonotic transmission of antibiotic-resistant pathogens. This study aimed to assess antibiotic resistance, multidrug resistance patterns of Gram-negative bacteria isolated from intestinal and gizzard samples of chicken and pork meat collected from 5 municipalities in Kathmandu. From total of 13 samples collected, comprising 11 chicken and 2 pork intestinal and gizzard meat samples, 136 gram negative bacteria were isolated. Subsequently, the isolated bacteria underwent susceptibility testing against 16 different antibiotics. The bacterial isolates, representing eleven distinct types, were successfully identified: Escherichia coli(33.82%) and Shigella spp.(11.76%) were the predominant bactera followed by Yersinia(8.8%), Citrobacter(8.8%), Proteus(8.8%), Klebsiella(5.1%), and Plesiomonas(5.1%), among others. Notably, the prevalence of multidrug-resistant bacteria was alarmingly high, with half(50%) of the whole isolates exhibiting resistance to multiple classes of antibiotics and on comparative analysis of Chicken and Pork meat, the MDR was higher among the chicken sample than in the pork meat sample. Additionally, 73.9% of E. coli, 14.28% of Klebsiella, 58.33% of Yersinia and 41.67% of Citrobacter are found to be multidrug resistant. Thus, this study showed that the meat samples were loaded with multidrug-resistant gram-negative bacteria and there is the high risk of food-borne infection and contact-exposure transmission to slaughterhouse worker by pathogenic microbes calling for AMR monitoring and mitigation strategies.
Phylogenomic analyses and DNA barcoding development within Moraceae: insights into ge...
Li-Na Zhou
Xin-Jie Jin

Li-Na Zhou

and 5 more

January 22, 2025
Moraceae, with its seven tribes, 45 genera, and approximately 1,200 species, is of significant value in food, medicine, ecological restoration, and as a source of industrial raw materials. However, determination of the taxonomy and phylogeny of Moraceae species remains challenging due to their diverse morphological features. To address this issue, we sequenced seven complete plastomes and analyzed online datasets for other 42 species at the tribal level within Moraceae. Our analysis revealed that all the plastomes within this family had a typical quadripartite structure and ranged from 159,449 to 161,478 bp in length. Comparative plastome analyses revealed ten highly variable regions (ndhF-rpl32, rps4-trnT, rps15-ycf1, trnC-petN, ycf1, etc.). A total of 5,022 dispersed and tandem repeats along with 4,430 simple sequence repeats (SSRs), were identified, highlighting their potential for the development of molecular markers in Moraceae. While the evolutionary rates across the various tribes of Moraceae were found to be similar, the genes ndhK, ndhD, rps2, and rps12 displayed evidence of positive selection. Codon usage bias was shaped by mutation and selection, with significant natural selection observed on genes such as clpP, ndhC, ndhI, etc. Additionally, thirteen optimal codons were identified for 10 genes. This study confirms that the seven tribes within the Moraceae family are monophyletic, with divergence estimated to have occurred approximately 79.43 million years ago. This timing coincides with the formation of modern rainforests and a burst in angiosperm diversity towards the end of the Cretaceous period. Overall, our study provides a robust phylogeny and a temporal framework for further research on phylogeography and population genetics of Moraceae. Furthermore, our genomic resources will be available for genetic engineering and germplasm exploration within this versatile plant family.
Prolonged Pre-Eruptive Phase of Herpes Zoster Ophthalmicus in Immunocompetent Athlete...
Sharanya Kumar
Rahul Tuli

Sharanya Kumar

and 4 more

January 22, 2025
Introduction:The varicella-zoster virus (VZV) causes Chickenpox and herpes zoster (HZ), commonly referred to as shingles. VZV reactivation occurs within the dorsal ganglion, typically prompted by a compromised immune system. Herpes zoster ophthalmicus (HZO) represents about 10-20% of all HZ cases and occurs secondary to involvement of the ophthalmic nerve, particularly within the V1 distribution. Symptoms manifest with eye pain, tearing, vision loss, and headaches, however more permanent visual deficits can occur if not promptly treated. These symptoms commonly occur 48-72 hours prior to eruption of typical vesicular rash, known as the pre-eruptive phase. Diagnosis in the pre-eruptive phase may be challenging, resulting in increased morbidity.Case Presentation:We present the case of a healthy marathon runner with no medical history who presented with seven days of intractable headache and unilateral eye pain, resulting in profound insomnia and physical debility. The severity of pain caused immense distress and a rapid decrease in functional status for this previously healthy patient. Despite undergoing various pain management interventions and evaluations by both neurology and ophthalmology with unremarkable results, symptoms remained debilitating. The patient eventually developed a small vesicular rash ten days after symptom onset, resulting in diagnosis of HZO. Antiviral therapy led to rapidly improved symptoms. Conclusion:The significance of considering HZO as a differential diagnosis in patients with intractable pain syndromes cannot be overstated, as overlooking this condition may lead to permanent ophthalmologic consequences including vision loss and blindness. Awareness of the prolonged pre-eruptive phase can lead to earlier consideration of HZO, and prompt antiviral therapy. 
Physics-Informed Intelligent Islanding Detection Method (PI-IIDM) for Cyber-Physical...
Arif Hussain

Arif Hussain

and 1 more

January 31, 2025
With the increasing integration of distributed energy resources (DER) into the distributed power system, the security of the power system from cyber-attacks is paramount. Cyber attacks make unintentional islanding detection challenging within the networked DER-integrated microgrid system. This study proposes a physics-informed approach for feature extraction and dimension reduction, leveraging principles from physics and domain-specific knowledge to analyze three-phase voltage and current signals. Moreover, a recurrent neural network (RNN) based gated recurrent unit (GRU), is introduced to fortify networked DER-integrated microgrids against cyber-physical threats, particularly focusing on unintentional islanding triggered by cyber-attacks at the point of common coupling (PCC). The most essential and difficult stage in an intelligent islanding detection system (IIDM) is feature extraction and selection, for which a physics-informed wavelet scattering network (WSN) and minimum redundancy maximum relevance (MRMR) algorithm are proposed. The WSN facilitates enhanced signal representation by capturing low and high-frequency information simultaneously, ensuring translation-invariant and deformationstable signal representations. The MRMR algorithm is applied for dimension reduction, ensuring that the reduced feature space retains the most informative and physically relevant features while minimizing redundancy. Finally, GRU network is proposed for islanding detection. We developed an API integrated with RT-Lab to generate a diverse dataset for islanding, faults, and nonislanding scenarios to gather PCC voltage and current signals. The proposed method is assessed under various islanding, faults, and non-islanding scenarios, also considering the non-detection zone (NDZ), a critical factor affecting islanding conditions using an OPAL-RT real-time digital simulator. The proposed method is also validated using accuracy, selectivity, and sensitivity performance indices, demonstrating the effectiveness of physicsinformed feature extraction/selection and GRU-based islanding detection (PI-IIDM), ensuring accurate islanding detection.
First Arab Cohort of DCDC2-Related Neonatal Sclerosing Cholangitis: Expanding the Cli...
Muad Abdi Hassan
Ahmed Saeed

Muad Abdi Hassan

and 3 more

January 22, 2025
A document by Muad Abdi Hassan . Click on the document to view its contents.
Rapidly Progressing Radicular Cyst in an Endodontically Treated Tooth: Diagnosis,...
saeed asgary
Nafise Shamloo

saeed asgary

and 1 more

January 22, 2025
A document by saeed asgary. Click on the document to view its contents.
Polidocanol sclerotherapy in Hereditary Hemorrhagic Teleangiectasia patients – out...
ELSA-LEEA KOTOLA
Johanna Wikstén

ELSA-LEEA KOTOLA

and 2 more

January 22, 2025
ABSTRACT INTRUDUCTION: Hereditary Hemorrhagic Telangiectasia (HHT) is an inherited condition causing mucosal telangiectasia and visceral arteriovenous malformations. Troublesome nosebleeds affect almost all HHT patients. Different treatments to control nosebleeds have been applied, but no clear consensus exists on the most effective one. Sclerotherapy with polidocanol is one option and previous studies have reported promising results. However, no data on the effect of sclerotherapy on epistaxis-related visits and procedures exists. The aim of our study was to investigate the impact of polidocanol sclerotherapy on epistaxis-related emergency department and outpatient visits and emergency procedures in HHT patients. MATERIAL AND METHODS: We retrospectively collected data on Helsinki University Hospital’s HHT-patients receiving polidocanol sclerotherapy. We analyzed the number of outpatient and emergency department visits in our Otorhinolaryngology unit as well as measures to control the nosebleeds, especially emergency operating room procedures. We compared the number of visits and procedures before and after initiating polidocanol sclerotherapy. RESULTS: Of the 145 HHT patients identified, 29 HHT patients received polidocanol sclerotherapy in our unit and had sufficient follow-up data. The number of emergency department visits on average per year increased from 0.21 to 0.32 and the number of outpatient visits changed from 1.30 to 1.64 after initiation of sclerotherapy. No statistically significant changes were observed. Emergency operating room procedures were not observed during the study period in this patient group. CONCLUSION: Previous studies have shown sclerotherapy to decrease the severity of nosebleeds in HHT patients. However, we did not observe changes in the numbers of epistaxis-related visits before and after initiation sclerotherapy. More studies are needed to assess the efficacy of sclerotherapy for HHT-related nosebleeds. Keywords: osler, epistaxis, nose bleed, injection, lauromacrogol
Proton Pump Inhibitor-Resistant Gastric Ulcer Caused by Eosinophilic Gastroenteritis:...
丹 孙
Quan Ren

丹 孙

and 2 more

January 22, 2025
Proton Pump Inhibitor-Resistant Gastric Ulcer Caused by Eosinophilic Gastritis:A Case ReportDan Sun, Quan Ren, Xianfei, WangGastroenterology and Digestive Endoscopy Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
Spatiotemporal Evolution of the Himalayan Ladybird Scymnus Coincide with the “Stepwis...
feng peng
Xiaoning Zhang

feng peng

and 6 more

January 22, 2025
The Himalaya Mountains are a biodiversity hotspot, boasting one of the world’s richest insect biotas. However, the primary mechanisms driving such high mountain biodiversity remain unclear. To address this, we use Scymnus, the largest genus of ladybirds, to explore the biogeographic origin and spatiotemporal evolution of the eastern Himalayan insect fauna for understanding the biological response to orogenic movement. Combining mitochondrial genomes and two nuclear genes (18S and 28S), we reconstructed the first highly supported and dated backbone phylogeny of Scymnus. Our findings strongly support the monophyly of Scymnus and identify seven major lineages within the genus. However, the subgenus Scymnus, Orthoscymnus and Pullus were found to be polyphyletic. We conclude that most extant Himalayan species originated through in situ speciation, with the Himalayan Scymnus lineage originating during the late Eocene and undergoing rapid diversification in the early Miocene. This diversification was likely triggered by the rapid uplift of the Himalayas and aligns with the recently proposed stepwise hypothesis of Himalayan orogenesis. Our findings, combined with net diversification rate analysis, indicate that new niche opportunities created by mountain uplift govern the diversification of the genus Scymnus. Furthermore, we found that the significantly higher diversity of Scymnus in mountains regions is driven by a combination of ecological factors, primarily the intensification of the Asian monsoon during the Miocene, which further strengthened the diversification of Scymnus in Himalayas. Our study provides a framework for biogeographic and evolutionary studies in eastern Himalayan Mountains, contributing to the understanding of the mechanism underlying.
A method for the evaluation of crack-tip opening loads based on strip yield modelling...
Aditya Khanna
James Vidler

Aditya Khanna

and 4 more

January 13, 2025
Based on the strip-yield model for propagating cracks, the current paper proposes a new method for the evaluation of crack-tip opening loads. It is based on the theoretical analysis of shapes of the compliance offset curves for various applied stress levels and R-ratios, which indicates that the inflection point of the curve is a good approximation of the initiation of the crack tip opening. The method avoids uncertainties and drawbacks associated with the selection of empirical thresholds or criteria to identify the value of opening load, which is often utilised to calculate the effective stress intensity factor range or fatigue crack driving force. Careful experimental studies also confirm the ability of this proposed method to negate R-ratio effect on fatigue crack growth rates for a wide range of loading conditions.
Recurrence of atrial fibrillation after cryoballoon ablation in women is less pulmona...
Maxime Tijskens
Juan Pablo Abugattas

Maxime Tijskens

and 4 more

January 22, 2025
Background: Data on sex-related outcomes of pulmonary vein isolation (PVI) of cryoballoon ablation (CBA) in atrial fibrillation (AF) are sparse. Aim: To compare sex-differences in PV reconnection, strategy and outcome of repeat ablations after CBA. Methods: Repeat procedures were performed using radiofrequency ablation guided by 3D mapping. PV reconnection characteristics were compared in 229 patients (77 (33.6%) females). In durable PVI patients, we compared left atrial voltage maps, ablation strategy and 1-year outcome. Clinical success was defined as freedom of documented AF or atrial tachycardia (AT) >30s. Results: Female patients had a lower overall number of PV reconnections (0.8±0.9 vs 1.2±1.0, P<0.001) driven by less reconnected left PVs: 13/77 (16.9%) vs 51/152 (33,6%), P=0.008 and 7/77 (9.1%) vs 39/152 (25.7%), P=0.003 for LSPV and LIPV, respectively. Durable PVI was more frequent in women (34/77 (44.1%) vs 37/152 (24.4%), P=0.001). Female sex was the only independent predictor for durable PVI (HR=2.003; 95%CI 1.090-3.682; P=0.025). In durable PVI patients, substrate ablation was more frequently performed in women (21/35 (60%) vs 13/35 (37.1%), P=0.044), mainly targeting the higher prevalent atrial low-voltage zones (21/35 (60.0%) vs 12/36 (33.3%), P=0.017). At 1 year, recurrence of AF/AT did not differ between sexes: 6/35 (17.1%) vs. 8/35 (22.9%), P=0.591. Conclusions: The higher persistence of durable PVI in women points to a sex difference in AF recurrence driver after CBA. In durable PVI patients, a higher prevalence of low-voltage regions results in more substrate ablation in women. Despite sex differences in ablation strategy, 1-year outcome was similar.
A 3 months old infant with extralobar subdiaphragmatic bronchopulmonary sequestration...
somayeh sheidaei
Mahdi naeimaei aali

somayeh sheidaei

and 3 more

January 22, 2025
A 3 months old infant with extralobar subdiaphragmatic bronchopulmonary sequestration: A case report
Thermal mismatch in a host-parasitoid interaction is likely mediated by a viral symbi...
Katherine Malinski
Olivia Madalone

Katherine Malinski

and 3 more

January 22, 2025
High temperature events can disrupt species interactions, resulting in ecological shifts as climate change continues. Current understanding of the molecular processes underlying these disruptions is lacking, especially in complex networks of multiple interacting species. Here we investigate the impact of a high temperature event on the transcriptomic and immunological interactions among an insect host, Manduca sexta, its insect parasitoid, Cotesia congregata, and the parasitoid’s symbiotic virus. High temperatures are lethal to developing parasitoids, but not hosts. Using parasitoid egg in vitro experiments, immunological assays, and RNAseq, we evaluated whether parasitoid mortality at high temperatures is associated with A) increased thermal sensitivity of parasitoid eggs, and/or B) altered functionality and expression of the parasitoid’s symbiotic virus inside the host. High temperatures did not significantly increase mortality of parasitoid eggs in vitro, suggesting that direct temperature effects are not sufficient for causing parasitoid mortality. In contrast, high temperatures disrupted viral suppression of the host insect’s immune responses. At the transcriptomic level, viral genes displayed patterns of expression dependent on their location on the viral circular genome: genes on viral circles not previously shown to integrate into host DNA showed reduced expression, with the opposite for circles that integrate. These results suggest that the genomic structure of the parasitoid’s symbiont may impose constraints on the parasitoid’s thermal tolerance, limiting the ecological functioning of a host-parasitoid system at high temperatures. This research provides a framework for understanding how molecular processes can contribute to ecological outcomes in complex species networks under high temperature events.
Prediction of Received Power in Low-Power and Lossy Networks Deployed in Rough Enviro...
Waltenegus Dargie

Waltenegus Dargie

January 22, 2025
Cost-efficient and low-power sensing nodes enable to monitor various physical environments. Some of these impose extreme operating conditions, subjecting the nodes to excessive heat or rainfall or motion. Rough operating conditions affect the stability of the wireless links the nodes establish and cause a significant amount of packet loss. Adaptive transmission power control (ATPC) enables nodes to adapt to extreme conditions and maintain stable wireless links and often rely on knowledge of the received power as a closed-feedback system to adjust the power of outgoing packets. However, in the presence of a significant packet loss, this knowledge may not reflect the current state of the receiver. In this paper we propose a lightweight nstep predictor which enables transmitters to adapt transmission power in the presence of lost packets. Through extensive practical deployments and testing we demonstrate that the predictor avoids expensive computation and still achieves an average prediction accuracy exceeding 90% with a low-power radio that supports a transmission rate of 250 kbps (CC2538) and 85% with a lowpower radio that supports 50 kbps (CC1200).
Functional abundance of species -- a new concept in study of trait variability
Evsey Kosman
Jukka Jokela

Evsey Kosman

and 1 more

January 22, 2025
1. A new concept of functional abundance of species is presented. The absolute and relative functional abundance is mainly aimed at analyzing functional variability of communities based on intraspecific trait variation. 2. Functional abundance of species in a given community was estimated for two models of proportional and nonproportional random sampling of individuals of each species for determining trait profiles of the selected individuals. The intraspecific trait variabilities obtained for each separate species were incorporated together with taxonomic abundance of those species to assess species functional abundance. 3. Two examples demonstrate the pipeline of calculations of the functional abundance for the two corresponding models. Possible applications of the functional abundance and related technical issues are briefly discussed.
Teacher Characteristics as Predictors of Emotion-Focused Teaching Practices: A Stu...
Jiayi Li

Jiayi Li

January 22, 2025
Preschool teachers are regarded as important socializers for young children’s social-emotional development. Moreover, preschool teachers’ emotion-focused teaching practices have gained increasing attention. This study examined relations between three sets of teacher characteristics (i.e., professional background, emotion-focused teaching beliefs, and psychological skills) and teachers’ emotion-focused teaching practices. Based on data collected from 287 Chinese preschool teachers, this study revealed that teachers’ emotion-related teaching beliefs and certain psychological skills (i.e., emotional intelligence and self-efficacy) positively predicted their emotion-focused teaching practices. However, having more years of teaching experience was related to poorer emotion-focused teaching practices. The findings advance the understanding of antecedent factors of emotion-focused teaching in the Chinese preschool contexts by highlighting the significance of teachers’ emotion-focused beliefs, emotional intelligence, and self-efficacy in promoting their teaching practices related to emotion socialization. Professional development programs may endeavor to cultivate positive emotion-oriented teaching beliefs and augment teachers’ emotional intelligence and self-efficacy.
Prevalence and risk factors of postpartum depression among mothers who gave birth wit...
Leticia Tornyevah
Samuel Bosomprah

Leticia Tornyevah

and 4 more

January 22, 2025
Objective: To identify risk factors of postpartum depression (PPD) and explore lived experiences to understand the social, psychological, and emotional mechanisms explaining being at higher likelihood of PPD. Design: Mixed method, cross-sectional study design. Setting: Three hospitals in Ho, Ghana. Population: 399 postpartum women aged 18 years and above. Methods: We used multivariable binomial generalized linear models to identify factors independently associated with PPD. We used thematic analysis to identify themes that highlight pathways through which these risk factors influence PPD. Main outcome measure: Screened positive for PPD. Results: Overall, 117 (29.3%) screened positive for PPD. Being unmarried (adjusted prevalence ratio, aPR, 1.33, 95% CI 1.02-1.72), lack of partner support (aPR 1.60, 95% CI 1.21-2.12), history of depressive or psychiatric disorders (aPR 2.44, 95% CI 1.84-3.25), unplanned pregnancy (aPR 1.63, 95% CI 1.18-2.25), low self-esteem (aPR 2.38, 95% CI 1.79-3.16), and low birthweight (aPR 1.87, 95% CI 1.33-2.65) were independently associated with PPD. The thematic analysis revealed four key themes: 1) social isolation and limited support, 2) emotional stress and vulnerability, 3) self-image and identity challenges, and 4) resilience resources. Conclusion: Our findings stress the urgent need for targeted interventions that address individual and structural factors to promote early screening, accessible mental health care, and programs that encourage partner involvement, and support unmarried mothers to enhance maternal well-being.
Knowledge Management in Software Development Outsourcing: A systematic literature rev...
Solomon Abebe Nurye

Solomon Abebe Nurye

January 22, 2025
Knowledge management is widely recognized as a means of improving software development outsourcing (SDO) success due to the high failure rate and knowledge-intensive nature of SDO projects. However, how knowledge is effectively managed in SDO arrangements remains a challenge. This study aims to systematically review knowledge management studies linked with SDO success and analyze 32 research articles published in peer-reviewed journals from 2001 to 2023. Furthermore, the study strives to uncover gaps and research opportunities in SDO from the perspective of knowledge management. The main findings of this study reveal that knowledge categories in SDO are based on traditional tacit and explicit dichotomies, and an outsourcing partner does not have the full range of knowledge needed for developing the software. Most studies show one-way knowledge flow, with knowledge transfer being the most researched knowledge management process. Additionally, the vendors’ perspective of SDO success is the most researched (47%), followed by clients’ (36%), and client-vendor (17%) perspectives, respectively. Furthermore, data collection from vendors and clients is primarily sourced from senior and middle-level business and IT/IS managers, while project managers are the primary focus from the client-vendor perspective. The study also demonstrates the specific knowledge items needed in the SDO context, the modes of knowledge flows, the key knowledge management processes, and SDO success dimensions from the perspectives of clients, vendors, and both. Then, it develops a holistic knowledge management-based SDO success framework. It suggests ample avenues for future research to improve SDO success from the perspective of knowledge management.
Leaf nutrients, but not genome size, modulate plant photosynthesis

January 22, 2025
The extreme variability of genome size (GS) across plant species results in morphological and physiological constraints leading to ecological and evolutionary consequences. Previous studies pointed out that plants with larger GS have lower photosynthetic rates. Plants with larger GS, however, also have higher foliar concentrations of nitrogen (N) and phosphorus (P), which positively correlate with photosynthetic rates following the assumptions of the leaf economics spectrum. Nonetheless, the interplay between GS, leaf photosynthetic rates (Amax), N and P concentrations across a relevant phylogenetic scale remains elusive. We address this question by compiling a global dataset of GS, Amax, leaf concentrations of N and P and environmental information for 376 plant species. Our results indicate that the evolutionary history is a direct factor affecting GS, Amax, foliar N and P. Larger GS were found in plants with high foliar P and living over acidic soils. Amax was higher in P and N-rich plants, but we did not find evidence suggesting that photosynthetic capacity is constrained by their GS. Our results suggest that GS-driven evolutionary limitation does not pivot around a constraint imposed on the photosynthetic capacity of plant species.
Mitigation of volatile chemicals' effect on adjacent microtiter plate wells
Svetlana Avlasevich
Erica Briggs

Svetlana Avlasevich

and 7 more

January 22, 2025
New approach methodologies (NAMs) used to assess chemicals for biological effects are typically designed to limit the amount of test article required, and to promote efficiencies such as compatibility with liquid handlers, etc. This is certainly true in the case of genetic toxicology, where many methods have been and continue to be developed with 96- or 384-well plate processing in mind. However, one recognized concern with microwell plates is that the volatility of test substances and/or their metabolites and/or their degradation products may affect adjacent wells. Here, we describe an approach that combines breathable membranes as well as activated carbon filters to mitigate volatility issues in 96 well plates. These experiments were performed with cyclophosphamide-exposed TK6 cells, and utilized the biomarkers micronuclei, p53, gammaH2AX, phospho-histone H3, and nuclei to counting bead ratios to both demonstrate volatility impact, and to assess the effectiveness of the solution described herein.
Genomic analysis revealed a long-lived clonal population of Typha latifolia and its s...
Chichi Zhao
Ziyu Wang

Chichi Zhao

and 5 more

January 22, 2025
A sexual reproduction is an important mode of plant reproduction, and plants can form large clonal populations through continuous asexual reproduction. Determining the duration of asexual reproduction and the size of clonal populations is essential for our deeper understanding of plant survival and adaptation strategies. Advances in sequencing technology and improved methods for analyzing genomic data have made it possible to measure the size or age of clonal populations accurately. So far, such studies have been limited to only a few cases in seagrasses and trees, not herbaceous clonal plants on the continent with high habitat heterogeneity. This study focused on Typha latifolia, a rhizomatous herbaceous perennial. A 103.2 ha population of T. latifolia was found in an alpine wetland in Sichuan, China. We first constructed a gap-free genome as a reference. We then performed genomic analysis on 72 samples across the wetland based on high-depth resequencing data and identified this population as a clonal population. We further estimated the age of the clonal population to be over 2000 years, based on a somatic genetic clock and radiocarbon dating of Typha pollen-bearing sediments. We also examined the pattern of somatic mutations in the population and found that 71% of somatic mutations occurred in transposable elements, which make up 34% of the genome, and that high percentages of somatic mutations occurred at an allele frequency of 1.0 and under positive selection. Overall, this work advances our understanding of asexual reproduction in plants and somatic mutation accumulation in continuously clonally-reproducing herbaceous plants.
Is it safe to reserve uterus after live-birth following fertility-sparing treatment o...
Yiqin Wang
Yuanyuan Liu

Yiqin Wang

and 5 more

January 22, 2025
Objective To assess the safety of continuous uterus-preserving in endometrial cancer (EC) and atypical endometrial hyperplasia (AEH) patients who gave birth after fertility-sparing treatment (FST). Design A retrospective study conducted between January 2005 and June 2020. Setting Peking University People’s Hospital, China. Population A total of 212 EC/AEH patients undergoing FST. Methods Patients were stratified as patients with a live-birth (n=73) outcome and those without (n=139). Main Outcomes Measures Risk factors for disease recurrence were analyzed for all patients undergoing FST and postpartum recurrence was analyzed for those with live-birth after FST. Results Live-birth significantly reduced the risk of disease recurrence (HR 0.326, P=0.011), while insulin resistance is an adverse factor (HR 3.216, P=0.014). Exceprt for two patients who underwent hysterectomy, for the 71 patients with uterus-preserving after live-birth, five (7%) patients occurred disease relapse (one EC and four AEH), after a median follow-up of 26 (11, 47.5) months. While there were another eight patients (11.3%) experiencing hyperplasia without atypical (EH). Risk factors for postparturm EC/AEH/EH included irregular menstrual period (75% vs. 36.8%, P=0.028), abnormal echo of ultrasound (53.8% vs. 13.7%, P=0.005) and a thicker endometrium (0.76cm vs. 0.53cm, P=0.003) . While maintenance treatment after birth (38.5% vs. 62.5%, P=0.129) tended to have a protective effect. Conclusions Alough live-birth for EC/AEH patients who underwent FST has benefit on recurrence-free survival, there still exists a postpartum risk of disease recurrence, with irrregular menstruation, thicker endometrium and abnormal ultrasound as risk factors.
Mapping species birth across the recombination landscapes of marine snails
Emily Giles
Romuald Laso-Jadart

Emily Giles

and 8 more

January 22, 2025
Understanding the drivers of heterogenous genomic divergence is essential for uncovering the mechanisms that generate and constrain biodiversity. The extent to which adaptation and speciation are facilitated by reorganization of the recombination landscape remains untested in many systems. Marine ecosystems, with their dynamic and fluid habitats, offer a compelling context to investigate genomic divergence. In this study we mapped genomic divergence and selection across recombination landscapes of parapatric marine snail sister species that we show have recently undergone secondary contact. Regions of reduced recombination were enriched for genes exhibiting signatures of negative selection, whereas regions of high recombination were associated with genes under putative positive selection. Notably, the recombination landscape of the population in parapatry of one species (Scurria viridula) differs markedly from that of the other population within this same species, highlighting the role of introgression in reshaping recombination landscapes. In the other species (Scurria zebrina), conservation of the recombination landscape and divergent selection among populations suggest trapping of beneficial allele combinations in regions of low recombination maintain the identity of this species. Among species, signals of divergence with gene flow consistently cluster within specific genomic regions characterized by high recombination rate variation among the populations of S. viridula. These results challenge theoretical expectations of recombination evolution by showing that the causes of genomic divergence can be population- specific. This study demonstrates that recombination landscapes are key modulators of genomic divergence, with contemporary evolutionary shifts that could enable populations to adapt to distinct environments. Our findings provide new insights into the interplay between recombination, selection, and gene flow during speciation, underscoring the complexity of evolutionary trajectories in marine systems.
Integrated Machine Learning and Multivariate Analyses to Apportion the Different Orga...
Yeganeh Mirzaei
Cameron Skinner

Yeganeh Mirzaei

and 2 more

February 10, 2025
Understanding the key parameters in apportioning the contribution of organic matter (OM) sources in diverse settings, such as costal sediments, is critical due to its implications for carbon cycling, Earth’s archival record, ecosystem dynamics, and land-sea interactions. This study applies integrated machine learning (ML) and multivariant analyses to overcome the limitations of traditional single-variable proxies in OM source apportionment, focusing on the natural laboratory of the St. Lawrence Estuary and Gulf, the largest semi-enclosed estuarine system on Earth. Using principal component analysis (PCA), random forest (RF), and partial least squares regression (PLSR), we investigate the complex relationships between biomarkers distributions (C17-C27 n-alkanes), elemental concentrations (C and N), and both bulk and compound specific δ13C isotope values. While PCA effectively helps visualizing compositional differences, its predictive capability for continuous estimates of the contribution from each OM fraction was limited. In contrast, supervised regression models, particularly PLSR, excelled at quantifying the proportional contributions of OM sources in regions of high collinearity and linear mixing. Our results reveal a gradient of increasing marine OM dominance along the estuarine continuum, driven by reduced terrestrial inputs and elevated marine productivity. This study highlights the effectiveness of ML-based multivariate approaches in improving source characterization and feature selection, enhancing our understanding of organic carbon dynamics in challenging sedimentary environments.
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