bluuebunny/crossref_metadata_2025_split huggingface dataset:
Desert plants, arbuscular mycorrhizal fungi and associated bacteria: Exploring the diversity and role of symbiosis under drought
Authors: Chávez‐González Jose Daniel , Flores‐Núñez Víctor M. , Merino‐Espinoza Irving U. , Partida‐Martínez Laila Pamela 
Published: July 2024

AbstractDesert plants, such as Agave tequilana, A. salmiana and Myrtillocactus geometrizans, can survive harsh environmental conditions partly due to their symbiotic relationships with microorganisms, including arbuscular mycorrhizal fungi (AMF). Interestingly, some of these fungi also harbour endosymbiotic bacteria. Our research focused on investigating the diversity of these AMFs and their associated bacteria in these plants growing in arid soil. We found that agaves have a threefold higher AMF colonization than M. geometrizans. Metabarcoding techniques revealed that the composition of AMF communities was primarily influenced by the plant host, while the bacterial communities were more affected by the specific plant compartment or niche they inhabited. We identified both known and novel endofungal bacterial taxa, including Burkholderiales, and confirmed their presence within AMF spores using multiphoton microscopy. Our study also explored the effects of drought on the symbiosis between A. tequilana and AMF. We discovered that the severity of drought conditions could modulate the strength of this symbiosis and its outcomes for the plant holobiont. Severe drought conditions prevented the formation of this symbiosis, while moderate drought conditions promoted it, thereby conferring drought tolerance in A. tequilana. This research sheds light on the diversity of AMF and associated bacteria in Crassulacean Acid Metabolism (CAM) plants and underscores the crucial role of drought as a factor modulating the symbiosis between A. tequilana and AMF. Further research is needed to understand the role of endofungal bacteria in this response.
Robust point and variance estimation for meta‐analyses with selective reporting and dependent effect sizes
Authors: Yang Yefeng , Lagisz Malgorzata , Williams Coralie , Noble Daniel W. A. , Pan Jinming , Nakagawa Shinichi 
Published: July 2024

Abstract

Meta‐analysis produces a quantitative synthesis of evidence‐based knowledge, shaping not only research trends but also policies and practices in biology. However, two statistical issues, selective reporting and statistical dependence, can severely distort meta‐analytic parameter estimation and inference.

Here, we re‐analyse 448 meta‐analyses to demonstrate a new two‐step procedure to deal with two common challenges in biological meta‐analyses that often occur simultaneously: publication bias and non‐independence. First, we employ bias‐robust weighting schemes under the generalized least square estimator to obtain average effect sizes that are more robust to selective reporting. We then use cluster‐robust variance estimation to account for statistical dependence, reducing bias in estimating standard errors and ensuring valid statistical inference.

The first step of our approach demonstrates comparable performance in estimating average effect sizes to the existing publication‐bias adjustment methods in the presence of selective reporting. This equivalence holds across two publication bias selection processes. The second step achieves estimates of standard errors consistent with the multilevel meta‐analytic model, a benchmark method with adequate control of Type I error rates for multiple, statistically dependent effect sizes. Re‐analyses of 448 meta‐analyses show that ignoring these two issues tends to overestimate effect sizes by an average of 110% and underestimate standard errors by 120%.

To facilitate implementation, we have developed a website including a step‐by‐step tutorial. Complementing current meta‐analytic workflows with the proposed method as a sensitivity analysis can facilitate a transition to a more robust approach in quantitative evidence synthesis.
Recognize nuance when interpreting monitoring results
Authors: McClure Christopher J. W. , Rolek Brian W. 
Published: July 2024

Abstract

We recently published a study discussing the pitfalls of non‐probability sampling when selecting monitoring sites. We demonstrated that selecting sites based on abundance can often lead to biased inference, and we suggested that researchers use probability sampling. We also called for nuance when interpreting results of monitoring programs that use non‐probability sampling. We suggested that inference from sites of great abundance might still be useful for inference into population dynamics of long‐lived species such as raptors.

Perret et al. seem to misinterpret our call for nuance as advocating for non‐probability sampling. They state that we concluded the general recommendation of using probability sampling should be revised. We did not conclude this. In fact, we agree with their recommendation.

Perret et al. implemented simulations that are unrealistic within the context of our study. We use empirical data for 12 raptor species to demonstrate that our previous results are valid and that simulations implemented by Perret et al. do not reflect the biology of long‐lived raptors. The time series simulated by Perret et al. fluctuated greatly in abundance with populations often more than doubling within a year. This is extremely unlikely for populations of long‐lived species having high site fidelity.

Many historical programs monitor sites of great abundance and thus risk biased results. We demonstrate that this risk is minimal under some important conditions and our results likely apply to other long‐lived species. Acknowledging this nuance could rescue many long‐term monitoring programs and their data thereby preserving efforts of costly conservation programs. Consistent with our original study, these exceptions do not invalidate the general recommendation to avoid non‐probability sampling; however, they do support our call for nuance when interpreting results of studies that monitored animals at sites of great abundance.
FLApy: A Python package for evaluating the 3D light availability heterogeneity within forest communities
Authors: Wang Bin , Proctor Cameron , Yao Zhiliang , Li Ninglv , Chen Qifei , Liu Wenjun , Ma Suhui , Jing Chuanbao , Zhou Zhaoyu , Liu Weihong , Ma Yufeng , Wang Zimu , Zhang Zhiming , Lin Luxiang 
Published: July 2024

Abstract

Light availability (LAv) dictates a variety of biological and ecological processes across a range of spatiotemporal scales. Quantifying the spatial pattern of LAv in three‐dimensional (3D) space can promote the understanding of microclimates that are critical to fine‐scale species distribution. However, there is still a lack of tools that are robust to evaluate spatiotemporal heterogeneity of LAv in forests.

Here, we propose the Forest Light Analyzer python package (FLApy), an open‐source computational tool designed for the analysis of intra‐forest LAv variation across multiple spatial scales. FLApy is freely invoked by Python, facilitating the processing of LiDAR point cloud data into a 3D data container constructed by voxels, as well as traversal calculations related to the LAv regime by high performance synthetic hemispherical algorithm. Furthermore, FLApy incorporates 37 indicators, enabling users to expediently export and visualize LAv patterns and the evaluation of heterogeneity of LAv at two scales (voxel scale and 3D‐cluster scale) for a range of fine‐scale ecological study purposes.

To validate the efficacy of the FLApy, we employed a simulated point cloud dataset that simulates forests (varying in canopy closure). Furthermore, to evaluate real world forest, we executed the standard workflow of FLApy utilizing drone‐derived data from three subtropical evergreen broad‐leaved forest dynamics plots within the Ailao Mountain Reserve. Our findings underscore that a series of indices derived from FLApy provide a robust characterization of light availability heterogeneity within diverse forest settings. Additionally, when juxtaposed with conventional monitoring techniques, the metrics offered by FLApy demonstrated better generality in our field assessments.

FLApy offers ecologists a solution for rapid quantification of understory light 3D‐regimes across multiple scales, addressing the disparity between traditional manual approaches and the precision required for contemporary ecological studies. Moreover, FLApy provides robust support for the establishment and expansion of heterogeneity indices based on 3D micro‐environments, enhancing our understanding of the largely uncharted 3D structural patterns. Anticipated outcomes suggest that FLApy will enhance our knowledge concerning the intra‐forest climatic conditions into a 3D context, proving pivotal in the delineation of microhabitats and the development of detailed 3D‐scale species distribution models.
A probabilistic time geographic approach to quantifying seabird‐vessel interactions
Authors: Rutter J. D. , Borrelle S. B. , Bose S. , Carneiro A. P.B. , Clark B. L. , Debski I. , Elliott G. , Fischer J. H. , Walker K. , Pittman S. J. 
Published: July 2024

AbstractAccounting for uncertainty is essential for precautionary approaches to managing seabird bycatch in commercial fisheries. However, there is no existing mechanism to explicitly quantify the uncertainty of seabird‐vessel interactions (i.e. co‐occurrence in space and time). Here we develop a time geographic method to measure the probability of individual birds encountering (co‐occurring within 30 km) and attending (within 5 km) individual fishing vessels. The approach involves creating voxel‐based probabilistic space–time prisms (PSTPs) to model the movements of individual birds and vessels, with trajectory data from bird‐borne GPS devices and vessel Automatic Identification Systems (AIS). We intersected these PSTPs to quantify the probability of interaction between bird‐vessel pairs over time and space. We demonstrate the approach with a case study of interactions of Endangered Toroa (Antipodean Albatross; Diomedea antipodensis antipodensis) with pelagic longline vessels in part of the South Pacific high seas. We found 15 vessels within 150 km and 3 h of two birds, yet interaction occurred with only two of those vessels. We visualised the probability of encounter and attendance over time and space and determined that interactions lasted several hours each (up to 6.2–14.1 h attendance, 20.8–26.1 h encounter for one bird‐vessel pair). Our time geographic approach adds to existing tools to quantify seabird bycatch risk by providing an explicit measure of uncertainty of seabird‐vessel interactions. We provide a flexible methodological pathway and R scripts, the application of which would allow managers to estimate interaction probability for multiple marine species and fisheries, including those with lower‐resolution positional datasets.
Ruellia blechum: A new case of cleistogamy in Acanthaceae
Authors: Bonzanini Olavo Honório Corrêa , Soares Milena Rodrigues , da Silva Devando Rosa , Matias Raphael 
Published: July 2024

AbstractCleistogamy is characterized by the presence of flowers that are permanently closed, yet they still produce fruits and seeds through autonomous self‐pollination. Populations with cleistogamous flowers can also have flowers that open, called chasmogamous, which promote cross‐pollination and genetic variability. Acanthaceae is among the families with the highest frequency of cleistogamy, observed mainly in Ruellia. This study aimed to assess cleistogamy in Ruellia blechum for the first time. In a population in Central Brazil, we analysed the production of cleistogamous and chasmogamous flowers, their fruiting, differences in flower bud size, self‐pollination in cleistogamous flowers and visitors in chasmogamous flowers. Of the flower buds observed, 35.29% remained closed (cleistogamous flowers), with 31.25% of them forming fruit. In contrast, 60.24% of the flowers that opened (chasmogamous) developed fruit. The length of cleistogamous flowers was shorter than that of chasmogamous floral buds in pre‐anthesis. On average, 24.45 pollen grains were self‐deposited on the stigma of a cleistogamous flower. The chasmogamous flowers were visited mainly by small bees. This study is the first to confirm the presence of cleistogamous flowers in R. blechum. However, their co‐occurrence with chasmogamous flowers suggests a fitness advantage for maintaining a mixed mating strategy.
Discrimination experiences and problematic alcohol and cannabis use in young adulthood
Authors: Perez Lilian G. , Troxel Wendy M. , Tucker Joan S. , Dunbar Michael S. , Rodriguez Anthony , Klein David J. , D'Amico Elizabeth J. 
Published: July 2024

AbstractBackground and ObjectivesLimited research has examined how discrimination in young adulthood relates to substance use. We examined how multiple and specific types (e.g., race‐based) of experiences of unfair treatment are related to problematic alcohol and cannabis use.MethodsWe analyzed cross‐sectional data from a diverse cohort of young adults (mean age 24.7) predominantly residing in southern California (n = 2303) to examine associations of multiple (count) and specific experiences (race‐, sexual orientation‐, gender‐based) of perceived everyday discrimination with self‐reported alcohol and cannabis use outcomes (consequences, use disorders, and solitary use). We also tested interactions between the three specific discrimination experiences and sociodemographic characteristics (e.g., race‐based discrimination × race/ethnicity).ResultsIn this diverse sample (e.g., 47% Latinx/o and 22% Asian; 22% sexual/gender diverse; 56% female) of young adults, about 46% reported up to four different discrimination experiences and 27% reported race‐, 26% gender‐, and 5% sexual orientation‐based discrimination. Race‐ and gender‐based discrimination and experiencing more types of discrimination were associated with worse cannabis use outcomes. Race‐based discrimination was associated with fewer alcohol consequences and lower Alcohol Use Disorders Identification Test (AUDIT) scores. Associations with sexual orientation‐based discrimination and the interactions were not significant.Discussion and ConclusionsFindings build on limited research on associations of discrimination with cannabis use in young adults. More work is needed to understand the mechanisms by which discrimination influences drinking behaviors.Scientific SignificanceThis study advances the field by examining the unique contributions of specific and multiple types of discrimination experiences in young adulthood, a critical developmental period in which substance use peaks.
The impact of impaired intrauterine growth on male fertility: A systematic review and meta‐analysis
Authors: Meng Fucheng , Yao Minglan , Li Sujuan , Tian Anran , Zhang Cai , Luo Xiaoping 
Published: July 2024

AbstractBackgroundAdverse intrauterine environment was believed to have deleterious effects on the gonadal function. However, the association between impaired intrauterine growth and fertility in adult males has not been established.ObjectivesTo compare the reproductive rates of males born small for gestational age (SGA), with low birth weight (LBW) or very low birth weight (VLBW) with control groups.MethodsThe Preferred Reporting Items for Systematic reviews and Meta‐Analyses (PRISMA) statement was followed to search PubMed, Web of Science, Cochrane Library, and Embase databases from inception to June 16, 2023. Cohort studies investigating the reproductive rates of males born SGA, with LBW or VLBW were included. A random or fixed effects model was used for different exposures.ResultsA total of 10 studies out of 3,801 records were included. Males born SGA showed a higher risk of infertility than the control group (odds ratio, OR = 0.91, 95% confidence interval, 95% CI 0.89–0.93, p = 0.000). The reproductive rates of individuals born with LBW or VLBW were lower than the control group (OR = 0.86, 95% CI 0.78–0.94, p = 0.001; OR = 0.57, 95% CI 0.40–0.81, p = 0.002, respectively). Participants were further divided into two age groups of 18–35 and 35–45 years. In both subgroups, the reproductive rates were lower in males born SGA, with LBW or VLBW compared with controls. Sensitivity analysis showed the robustness of the pooled estimates among LBW and VLBW.ConclusionIn summary, SGA, LBW, and VLBW were associated with a higher risk of male infertility in both early and middle adulthood. Achieving optimal intrauterine growth would be helpful to prevent male infertility.
Editorial: Treatments for inflammatory bowel disease across the age‐spectrum—Are they the same?
Authors: Ho Agnes Hiu Yan , Mak Joyce Wing Yan 
Published: July 2024

LINKED CONTENTThis article is linked to Nordestgaard et al papers. To view these articles, visit https://doi.org/10.1111/apt.18106 and https://doi.org/10.1111/apt.18163
Evaluation of the short‐term complications of intracorporeal anastomosis in right‐sided colectomy
Authors: Nakagawa Masataka , Kochi Masatoshi , Teshima Marino , Kitasaki Nao , Abe Tomoyuki , Hotta Ryuichi , Inoue Masashi , Shimohana Junichi , Toyota Kazuhiro 
Published: July 2024

AbstractIntroductionThe benefits of intracorporeal anastomosis in laparoscopic colorectal cancer surgery remain unclear. Therefore, we aimed to investigate the short‐term postoperative outcomes of intracorporeal anastomosis.MethodsWe retrospectively analyzed 87 patients who underwent laparoscopic surgery for right‐sided colon tumors using a colon database.ResultsOf the 87 patients, 23 underwent intracorporeal anastomosis and 64 underwent extracorporeal anastomosis. Intraoperative bleeding, wound length, exhaust gas, preoperative white blood cell count, and C‐reactive protein (postoperative day 1) were higher in the extracorporeal anastomosis group than in the intracorporeal anastomosis group. The incidence of wound infection was higher in the intracorporeal anastomosis group than in the extracorporeal anastomosis group. In the irrigation water bacterial culture collected after anastomosis, the positive group had a higher white blood cell count on postoperative day 1 and higher C‐reactive protein levels on postoperative day 3 than did the negative group. Patients who underwent chemical preparation had lower C‐reactive protein levels on postoperative day 1 than did the group who did not undergo chemical preparation.ConclusionDespite the advantages of intracorporeal anastomosis in terms of wound length and intraoperative bleeding, the risk of infection may increase during the introduction phase. Fever and inflammatory responses are significantly elevated in culture‐positive cases.
A highly selective inhibitor of discoidin domain receptor‐1 (DDR1‐IN‐1) protects corneal epithelial cells from YAP/ACSL4‐mediated ferroptosis in dry eye
Authors: Dai Yiqin , Li Yue , Xu Jianjiang , Zhang Jing 
Published: July 2024

Background and PurposeThis study investigated the involvement of discoidin domain receptor (DDR) in dry eye and assessed the potential of specific DDR inhibitors as a therapeutic strategy for dry eye by exploring the underlying mechanism.Experimental ApproachDry eye was induced in Wistar rats by applying 0.2% benzalkonium chloride (BAC), after which rats were treated topically for 7 days with DDR1‐IN‐1, a selective inhibitor of DDR1. Clinical manifestations of dry eye were assessed on Day‐7 post‐treatment. Histological evaluation of corneal damage was performed using haematoxylin and eosin (H&E) staining. In vitro, immortalized human corneal epithelial cells (HCECs) exposed to hyperosmotic stress (HS) were treated with varying doses of DDR1‐IN‐1 for 24 h. The levels of lipid peroxidation in dry eye corneas or HS‐stimulated HCECs were assessed. Protein levels of DDR1/DDR2 and related pathways were detected by western blotting. The cellular distribution of acyl‐CoA synthetase long chain family member 4 (ACSL4) and Yes‐associated protein (YAP) was evaluated using immunohistochemistry or immunofluorescent staining.Key ResultsIn dry eye corneas, only DDR1 expression was significantly up‐regulated compared with normal controls. DDR1‐IN‐1 treatment significantly alleviated dry eye symptoms in vivo. The treatment remarkably reduced lipid hydroperoxide (LPO) levels and suppressed the expression of ferroptosis markers, particularly ACSL4. Overexpression or reactivation of YAP diminished the protective effects of DDR1‐IN‐1, indicating the involvement of the Hippo/YAP pathway in DDR1‐targeted therapeutic effects.Conclusions and ImplicationsThis study confirms the significance of DDR1 in dry eye and highlights the potential of selective DDR1 inhibitor(s) for dry eye treatment.
Protocol for a national, multicentre study of post‐endoscopy colorectal and upper gastrointestinal cancers: The POET study
Authors: Xu William , McGuinness Matthew James , Wells Cameron , Varghese Chris , Elliott Brodie , Paterson Luke , Collins Ray , Lill Marianne , Windsor John , Koea Jonathan , Panoho Joy , Walmsley Russell , Wright Deborah , Parry Susan , Harmston Christopher ,   the STRATA Collaborative
Published: July 2024

AbstractAimThe primary aim of the study is to define the post‐colonoscopy colorectal cancer (PCCRC) three‐year rate and the post‐endoscopy upper gastrointestinal cancer (PEUGIC) three‐year rate across public hospitals in Aotearoa New Zealand.MethodThis retrospective cohort study will be conducted via the trainee‐led STRATA Collaborative network. All public hospitals in Aotearoa New Zealand will be eligible to participate. Data will be collected on all adult patients who are diagnosed with colorectal adenocarcinoma within 6 to 48 months of a colonoscopy and all adult patients diagnosed with gastroesophageal cancer within 6 to 48 months of an upper gastrointestinal endoscopy. The study period will be from 2010 to 2022. The primary outcome is the PCCRC 3‐year rate and the PEUGIC 3‐year rate. Secondary aims are to define and characterize survival after PCCRC or PEUGIC, the cause of PCCRC as based on the World Endoscopy Organization System of Analysis definitions, trends over time, and centre level variation.ConclusionThis protocol describes the methodology for a nationwide retrospective cohort study on PCCRC and PEUGIC in Aotearoa New Zealand. These data will lay the foundation for future studies and quality improvement initiatives.