bluuebunny/crossref_metadata_2025_split huggingface dataset:
Community biomass is driven by dominants and their characteristics – The insight from a field biodiversity experiment with realistic species loss scenario
Authors: Lisner Aleš , Konečná Marie , Blažek Petr , Lepš Jan 
Published: November 2022

Abstract

Revealing the role of biodiversity in ecosystem functioning (BEF) has been a major focus of ecological research over recent decades. In general, results from artificially assembled communities point to the important role of biodiversity showing that loss of species has a negative effect on various ecosystem functions (mostly assessed by above‐ground peak biomass). However, the evidence from manipulations of natural communities is scarce, and results are often contradictory between these two approaches. In particular, the importance of species dominance for ecosystem functioning remains poorly understood.

We created a gradient of plant species richness in a meadow community following a realistic species loss scenario (removal of less abundant species) to test the effect of diversity on community biomass and assess the importance of subordinate species compared with dominants in a 5‐year experiment.

Contrasting with results of BEF experiments with artificial assembly, we did not find any relationship between plant species diversity and above‐ground biomass across the timeframe of the experiment. We provide evidence that dominant species' identity and traits are the main drivers of community biomass because dominant species were able to maintain biomass production after substantial species loss. Furthermore, dominants prevented community biomass from declining and biomass was indirectly influenced not by species richness but through differences in functional diversity. Our results support the mass ratio hypothesis, showing much bigger effect of dominant species on community biomass production and hints to the rather minor importance of the complementarity effect between species. We emphasize that BEF research should more focus on the role of dominant species in maintaining various ecosystem functions.

Synthesis. Species diversity is a poor predictor of community above‐ground biomass production and dominant species can effectively compensate the total production after substantial loss of other species in a grassland community.
Stochastic and deterministic processes shape bioenergy crop microbiomes along a vertical soil niche
Authors: Benucci Gian Maria Niccolò , Beschoren da Costa Pedro , Wang Xinxin , Bonito Gregory 
Published: November 2022

AbstractSustainable biofuel cropping systems aim to address climate change while meeting energy needs. Understanding how soil and plant‐associated microbes respond to these different cropping systems is key to promoting agriculture sustainability and evaluating changes in ecosystem functions. Here, we leverage a long‐term biofuel cropping system field experiment to dissect soil and root microbiome changes across a soil‐depth gradient in poplar, restored prairie and switchgrass to understand their effects on the microbial communities. High throughput amplicon sequencing of the fungal internal transcribed spacer (ITS) and prokaryotic 16S DNA regions showed a common trend of root and soil microbial community richness decreasing and evenness increasing with depth. Ecological niche (root vs. soil) had the strongest effect on community structure, followed by depth, then crop. Stochastic processes dominated the structuring of fungal communities in deeper soil layers while operational taxonomic units (OTUs) in surface soil layers were more likely to co‐occur and to be enriched by plant hosts. Prokaryotic communities were dispersal limited at deeper depths. Microbial networks showed a higher density, connectedness, average degree and module size in deeper soils. We observed a decrease in fungal‐fungal links and an increase of bacteria–bacteria links with increasing depth in all crops, particularly in the root microbiome.
Effect of relative humidity on the quality and safety of peeled almond kernels (Prunus dulcis Mill.) during simulated maritime transport/storage
Authors: Fernandes Luana , Graeff Francieli , Jelassi Arij , Sulyok Michael , Garcia Carolina , Rodrigues Nuno , Pereira José Alberto , Bento Albino , Kanoun Alifa , Rodrigues Paula , Pereira Ermelinda Lopes , Ramalhosa Elsa 
Published: November 2022

AbstractLong‐term transport and storage of peeled almonds under unsuitable conditions may cause the product's rejection. To get knowledge in this topic, peeled almonds were stored at 25°C and 60, 70, and 80% relative humidity (RH). The maintenance of high RH (80%) caused some visual defects after 4 months. Even though the 60, 70, and 80% RH did not clearly affect the production of primary and secondary products formed in the lipid oxidation during the 6 months of storage, sometimes an increase in the values of the specific extinction at the wavelength of 268 nm (K268) was observed at 80% RH, suggesting the occurrence to some extent of secondary oxidation. Concerning microbial counts, the almonds stored at 60 and 70% RH presented a satisfactory microbial quality until 6 months; however, at 80% RH, the mold counts were higher than the reference values after 2 months. Several mycotoxins were detected at low levels, including aflatoxins B1 and G1, although some showed higher amounts at 80% RH. In general, it is recommended that almond producers and industrials should consider the use of low RH (< 80%) for maritime transport and long‐term storage of almond kernels.Practical ApplicationHigh levels of relative humidity during storage/transport of almond kernels favor fungal growth, mycotoxin production, and secondary oxidation (rancidity). It is recommended to keep the almond kernels under low RH (< 80%) in maritime transport and long storage, especially in tropical countries.
Limits to ecological forecasting: Estimating uncertainty for critical transitions with deep learning
Authors: Lapeyrolerie Marcus , Boettiger Carl 
Published: November 2022

Abstract

In the current age of a rapidly changing environment, it is becoming increasingly important to study critical transitions and how to best anticipate them. Critical transitions pose extremely challenging forecasting problems, which necessitate informative uncertainty estimation rather than point forecasts. In this study, we apply some of the most cutting edge deep learning methods for probabilistic time series forecasting to several classic ecological models that examine critical transitions.

Our analysis focuses on three different simulated examples of critical transitions: a Hopf bifurcation, a saddle‐node bifurcation and a stochastic transition. For each scenario, we compare the forecasts from four deep learning models, long‐short term memory networks, gated recurrent unit networks, lock recurrent neural networks and transformers, to forecasts from an ARIMA model and a MCMC estimated model that is given the true transition dynamics.

We found that the deep learning models were able to perform comparably to the idealized MCMC model on the stochastic transition case, and generally in between the MCMC and ARIMA models on the Hopf and saddle‐node bifurcation examples.

Our results establish that deep learning methods warrant further exploration on the challenging class of critical transition forecasting problems.
Accuracy of “TICS” ultrasound protocol in detecting simple and complicated diverticulitis: A prospective cohort study
Authors: Shokoohi Hamid , Selame Lauren A. , Loesche Michael A. , Almulhim Abdullah , Al Saud Ahad A. , Goldsmith Andrew J. , Eke Onyinyechi F. , Springer Caitlin , Arru Chiara D. , Gullikson Jamie , McKaig Brenna N. , Liteplo Andrew S. , Huang Calvin K. 
Published: November 2022

AbstractBackgroundPoint‐of‐care ultrasound (US) has been suggested as the primary imaging in evaluating patients with suspected diverticulitis. Discrimination between simple and complicated diverticulitis may help to expedite emergent surgical consults and determine the risk of complications. This study aimed to: (1) determine the accuracy of an US protocol (TICS) for diagnosing diverticulitis in the emergency department (ED) setting and (2) assess the ability of TICS to distinguish between simple and complicated diverticulitis.MethodsPatients with clinically suspected diverticulitis who underwent a diagnostic computed tomography (CT) scan were identified prospectively in the ED. Emergency US faculty and fellows blinded to the CT results performed and interpreted US scans. The presence of simple or complicated diverticulitis was recorded after each US evaluation. The diagnostic ability of the US was compared to CT as the criterion standard. Modified Hinchey classification was used to distinguish between simple and complicated diverticulitis.ResultsA total of 149 patients (55% female, mean ± SD age 58 ± 16 years) were enrolled and included in the final analyses. Diverticulitis was the final diagnosis in 75 of 149 patients (50.3%), of whom 53 had simple diverticulitis and 22 had perforated diverticulitis (29.4%). TICS protocol's test characteristics for simple diverticulitis include a sensitivity of 95% (95% confidence interval [CI] 87%–99%), specificity of 76% (95% CI 65%–86%), positive predictive value of 80% (95% CI 71%–88%), and negative predictive value of 93% (95% CI 84%–98%). TICS protocol correctly identified 12 of 22 patients with complicated diverticulitis (sensitivity 55% [95% CI 32%–76%]) and specificity was 96% (95% CI 91%–99%). Eight of 10 missed diagnoses of complicated diverticulitis were identified as simple diverticulitis, and two were recorded as negative.ConclusionsIn ED patients with suspected diverticulitis, US demonstrated high accuracy in ruling out or diagnosing diverticulitis, but its reliability in differentiating complicated from simple diverticulitis is unsatisfactory.
Selection signatures for fiber production in commercial species: A review
Authors: Ghildiyal Kanika , Panigrahi Manjit , Kumar Harshit , Rajawat Divya , Nayak Sonali Sonejita , Lei Chuzhao , Bhushan Bharat , Dutt Triveni 
Published: November 2022

AbstractNatural fibers derived from diverse animal species have gained increased attention in recent years due to their favorable environmental effects, long‐term sustainability benefits, and remarkable physical and mechanical properties that make them valuable raw materials used for textile and non‐textile production. Domestication and selective breeding for the economically significant fiber traits play an imperative role in shaping the genomes and, thus, positively impact the overall productivity of the various fiber‐producing species. These selection pressures leave unique footprints on the genome due to alteration in the allelic frequencies at specific loci, characterizing selective sweeps. Recent advances in genomics have enabled the discovery of selection signatures across the genome using a variety of methods. The increased demand for ‘green products’ manufactured from natural fibers necessitates a detailed investigation of the genomes of the various fiber‐producing plant and animal species to identify the candidate genes associated with important fiber attributes such as fiber diameter/fineness, color, length, and strength, among others. The objective of this review is to present a comprehensive overview of the concept of selection signature and selective sweeps, discuss the main methods used for its detection, and address the selection signature studies conducted so far in the diverse fiber‐producing animal species.
Does the type of pushing at delivery influence pelvic floor function at 2 months postpartum? A pragmatic randomized trial—The EOLE study
Authors: Barasinski Chloé , Debost‐Legrand Anne , Savary Denis , Bouchet Pamela , Curinier Sandra , Vendittelli Françoise 
Published: November 2022

AbstractIntroductionMaternal pushing techniques during the second stage of labor may affect women's pelvic floor function. Our main objective was to assess the impact of the type of pushing used at delivery on the mother's medium‐term pelvic floor function.Material and methodsThis is a secondary analysis of a randomized clinical trial (clinicaltrials.gov: NCT02474745) that took place in four French hospitals from 2015 through 2017 (n = 250). Women in labor with a singleton fetus in cephalic presentation at term who had undergone standardized training in both of these types of pushing were randomized after cervical dilation ≥7 cm. The exclusion criteria were a previous cesarean, a cesarean delivery in this pregnancy or a fetal heart rate anomaly. In the intervention group, open‐glottis (OG) pushing was defined as a prolonged exhalation contracting the abdominal muscles to help move the fetus down the birth canal. Closed‐glottis (CG) pushing was defined as Valsalva pushing. The principal outcome was the stage of pelvic organ prolapse (POP) assessed by the Pelvic Organ Prolapse‐Quantification 2 months after delivery. A secondary outcome was incidence of urinary incontinence (UI). The results of our multivariable, modified intention‐to‐treat analysis are reported as crude relative risks (RRs) with their 95% confidence intervals.ResultsOur analysis included 207 women. Mode of birth was similar in both groups. The two groups did not differ for stage II POP: 10 of 104 (9.4%) in the OG group compared with 7 of 98 (7.1%) in the CG group, for a RR 1.32, 95% confidence interval [CI] 0.52–3.33, and an adjusted RR of 1.22, 95% CI 0.42–3.6. Similarly, the incidence of UI did not differ: 26.7% in the OG group and 28.6% in the CG group (aRR 0.81, 95% CI 0.42–1.53). Subgroup analysis suggests that for secundiparous and multiparous women, OG pushing could have a protective effect on the occurrence of UI (RR 0.33, 95% CI 0.13–0.80).ConclusionsThe type of directed pushing used at delivery did not impact the occurrence of pelvic organ prolapse 2 months after delivery. OG pushing may have a protective effect against UI among secundiparous and multiparous women.
Transcriptomics of acute myeloid leukaemia core bone marrow biopsies reveals distinct therapy response‐specific osteo‐mesenchymal profiles
Authors: Treaba Diana O. , Bonal Dennis M. , Chorzalska Anna , Castillo‐Martin Mireia , Oakes Alissa , Pardo Makayla , Petersen Max , Schorl Christoph , Hopkins Kelsey , Melcher Dean , Zhao Ting C. , Liang Olin , So Eui‐Young , Reagan John , Olszewski Adam J. , Butera James , Anthony Douglas C. , Rintels Peter , Quesenberry Peter , Dubielecka Patrycja M. 
Published: November 2022

SummaryWhile the bone marrow (BM) microenvironment is significantly remodelled in acute myeloid leukaemia (AML), molecular insight into AML‐specific alterations in the microenvironment has been historically limited by the analysis of liquid marrow aspirates rather than core biopsies that contain solid‐phase BM stroma. We assessed the effect of anthracycline‐ and cytarabine‐based induction chemotherapy on both haematopoietic and non‐haematopoietic cells directly in core BM biopsies using RNA‐seq and histological analysis. We compared matched human core BM biopsies at diagnosis and 2 weeks after cytarabine‐ and anthracycline‐based induction therapy in responders (<5% blasts present after treatment) and non‐responders (≥5% blasts present after treatment). Our data indicated enrichment in vimentin (VIM), platelet‐derived growth factor receptor beta (PDGFRB) and Snail family transcriptional repressor 2 (SNAI2) transcripts in responders, consistent with the reactivation of the mesenchymal population in the BM stroma. Enrichment of osteoblast maturation‐related transcripts of biglycan (BGN), osteopontin (SPP1) and osteonectin (SPARC) was observed in non‐responders. To the best of our knowledge, this is the first report demonstrating distinct osteogenic and mesenchymal transcriptome profiles specific to AML response to induction chemotherapy assessed directly in core BM biopsies. Detailing treatment response‐specific alterations in the BM stroma may inform optimised therapeutic strategies for AML.
Can allogeneic haematopoietic cell transplantation be curative in classical Crohn's disease?
Authors: McLaughlin Laura , DeZoeten Edwin , Verneris Michael R. 
Published: November 2022

SummaryThe article by Moser et al. details the outcomes of 11 patients with inflammatory bowel disease (IBD) as the main manifestation of their immune deficiency syndrome who are treated with allogeneic transplantation. The authors report low rates of complications (including graft‐versus‐host disease) and resolution of symptoms. Here we outline whether allogeneic transplantation should be considered more broadly for IBD.Commentary on: Moser et al. Treatment of inborn errors of immunity patients with inflammatory bowel disease phenotype by allogeneic stem cell transplantation. Br J Haematol 2023;200:595‐607.
Allicin ameliorates imiquimod‐induced psoriasis‐like skin inflammation via disturbing the interaction of keratinocytes with IL‐17A
Authors: Zhang Lu , Ma Xuehong , Shi Rongmei , Zhang Libo , Zhao Ruolin , Duan Ran , Qin Yuanyuan , Gao Sijia , Li Xinxia , Duan Jingjing , Li Jianguang 
Published: November 2022

Background and PurposePsoriasis is an inflammatory skin disease of chronic recurrence mediated by the interaction between IL‐17 and keratinocytes, which sustains a vicious circle of inflammation. Safe and effective natural medicine is a potential strategy for the clinical treatment of psoriasis. Given its prominent anti‐proliferative and anti‐inflammatory properties, we investigated the actions of allicin in improving psoriasis.Experimental ApproachPharmacodynamic studies were carried out in mice after topical administration of allicin against psoriasis‐like lesions induced by imiquimod. Skin sensitization tests were evaluated on guinea pigs. Toxicological studies and skin irritation tests were assessed by consecutive topical allicin alone on the skin of rabbits. RNA‐seq probed transcriptomic changes following allicin. Western blot explored the actions of allicin on the interaction between IL‐17A and keratinocytes. Changes in inflammatory factor expression were analysed by qPCR and immunohistochemistry.Key ResultsAllicin significantly improved the epidermal structure by inhibiting the excessive proliferation and reduced apoptosis of keratinocytes. Furthermore, allicin reduced the secretion of inflammatory cytokines (IL‐17A/F, IL‐22, IL‐12, and IL‐20), chemokines (CXCL2, CXCL5, and CCL20), and anti‐bacterial peptides (S100a8/9). Mechanistically, allicin directly inhibited the IL‐17‐induced TRAF6/MAPK/NF‐κB and STAT3/NF‐κB signalling cascades in keratinocytes, thus breaking the positive inflammatory feedback and alleviating imiquimod‐induced psoriasis‐like dermatitis in mice. Importantly, topical administration of allicin did not cause skin allergy, and the safety and adaptability of long‐term application were verified.Conclusions and ImplicationsInterfering with IL‐17 signalling in keratinocytes with allicin is a promising strategy for treating psoriasis, given its safety and effectiveness.
Circadian rhythms and glial cells of the central nervous system
Authors: Brécier Aurélie , Li Vina W. , Smith Chloé S. , Halievski Katherine , Ghasemlou Nader 
Published: November 2022

ABSTRACTGlial cells are the most abundant cells in the central nervous system and play crucial roles in neural development, homeostasis, immunity, and conductivity. Over the past few decades, glial cell activity in mammals has been linked to circadian rhythms, the 24‐h chronobiological clocks that regulate many physiological processes. Indeed, glial cells rhythmically express clock genes that cell‐autonomously regulate glial function. In addition, recent findings in rodents have revealed that disruption of the glial molecular clock could impact the entire organism. In this review, we discuss the impact of circadian rhythms on the function of the three major glial cell types – astrocytes, microglia, and oligodendrocytes – across different locations within the central nervous system. We also review recent evidence uncovering the impact of glial cells on the body's circadian rhythm. Together, this sheds new light on the involvement of glial clock machinery in various diseases.
Impacts of paediatric chronic pain on parents: A qualitative study
Authors: Ngo Danny , Aouad Phillip , Goodison‐Farnsworth Meg , Gorrie Andrew , Kenmuir Tracey , Jaaniste Tiina 
Published: November 2022

AbstractBackgroundPaediatric chronic pain adversely impacts the child's functioning, health‐related quality of life and development. However, there is a need for a holistic assessment of parental impacts of caring for a child with chronic pain. This qualitative study aimed to investigate the possible psychosocial, functional and work impacts of caring for a child with chronic pain on parents, including any positive effects of the experience.MethodsTen parents (eight mothers and two fathers), whose child attended the Sydney Children's Hospital Interdisciplinary Chronic and Complex Pain Clinic, participated in semi‐structured interviews exploring the impact of caring for a child with chronic pain. Interviews were audio‐recorded, transcribed, coded (with good inter‐coder agreement) and analysed using thematic analysis.ResultsThe parental experience of caring for a child with chronic pain was encapsulated by four overarching themes: (1) ‘the constant and all‐consuming nature of pain’ – parents described the unpredictable, yet constant nature of chronic pain, contributing to wide‐reaching impacts in various areas of their life; (2) ‘dealing with uncertainty’ – their experience was commonly characterized by a sense of uncertainty, stress, hopelessness and fear; (3) ‘importance of support and self‐care’ – strong support networks and prioritizing self‐care were crucial in alleviating the negative effects of paediatric chronic pain; and (4) ‘a revitalized and optimistic view on life and relationships’ – some parents identified unique and positive effects, such as stronger relationships, personal growth and a reformed view on life.ConclusionsThis study provided rich data on the various impacts of caring for a child with chronic pain, highlighting the need for the development of holistic, family‐centred interventions addressing both child and parental functioning.
Ginsenoside Rg1 promotes astrocyte‐to‐neuron transdifferentiation in rat and its possible mechanism
Authors: Shen Kelv , Wu Duanrong , Sun Baihan , Zhu Yin , Wang Hao , Zou Wenjun , Ma Yuhang , Lu Zhengfeng 
Published: November 2022

AbstractIntroductionNeuronal loss caused by spinal cord injury (SCI) usually contributes to irreversible motor dysfunction. Promoting neuronal regeneration and functional recovery is vital to the repair of SCI.AimsAstrocytes, activated by SCI with high proliferative capacity and proximity to neuronal lineage, are considered ideal cells for neuronal regeneration. As previous studies identified several small molecules for the induction of astrocyte‐to‐neuron, we confirmed that ginsenoside Rg1, a neuroprotective herb, could promote the direct transdifferentiation of astrocyte‐to‐neuron in rat.Methods and ResultsImmunofluorescence staining showed that 26.0 ± 1.5% of the induced cells exhibited less astroglial properties and more neuronal markers with typical neuronal morphologies, reflecting 20.6 ± 0.9% of cholinergic neurons and 22.3 ± 1.9% of dopaminergic neurons. Western blot and qRT‐PCR revealed that the induced cells had better antiapoptotic ability and Rg1‐promoted neuronal transdifferentiation of reactive astrocytes might take effect through suppressing Notch/Stat3 signal pathway. In vivo, a revised SCI model treated by Rg1 was confirmed with faster functional recovery and less injury lesion cavity.ConclusionIn summary, our study provided a novel strategy of direct transdifferentiation of endogenous rat reactive astrocytes into neurons with Rg1 and promotion of neuronal regeneration after SCI.