bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated genome and metabolome mining unveiled structure and biosynthesis of novel lipopeptides from a deep‐sea Rhodococcus
Authors: Ragozzino Costanza , Palma Esposito Fortunato , Buonocore Carmine , Tedesco Pietro , Coppola Daniela , Paccagnella Davide , Ziemert Nadine , Della Sala Gerardo , de de Pascale Donatella 
Published: November 2024

AbstractMicrobial biosurfactants have garnered significant interest from industry due to their lower toxicity, biodegradability, activity at lower concentrations and higher resistance compared to synthetic surfactants. The deep‐sea Rhodococcus sp. I2R has been identified as a producer of glycolipid biosurfactants, specifically succinoyl trehalolipids, which exhibit antiviral activity. However, genome mining of this bacterium has revealed a still unexplored repertoire of biosurfactants. The microbial genome was found to host five non‐ribosomal peptide synthetase (NRPS) gene clusters containing starter condensation domains that direct lipopeptide biosynthesis. Genomics and mass spectrometry (MS)‐based metabolomics enabled the linking of two NRPS gene clusters to the corresponding lipopeptide families, leading to the identification of 20 new cyclolipopeptides, designated as rhodoheptins, and 33 new glycolipopeptides, designated as rhodamides. An integrated in silico gene cluster and high‐resolution MS/MS data analysis allowed us to elucidate the planar structure, inference of stereochemistry and reconstruction of the biosynthesis of rhodoheptins and rhodamides. Rhodoheptins are cyclic heptapeptides where the N‐terminus is bonded to a β‐hydroxy fatty acid forming a macrolactone ring with the C‐terminal amino acid residue. Rhodamides are linear 14‐mer glycolipopeptides with a serine‐ and alanine‐rich peptide backbone, featuring a distinctive pattern of acetylation, glycosylation and succinylation. These molecules exhibited biosurfactant activity in the oil‐spreading assay and showed moderate antiproliferative effects against human A375 melanoma cells.
Temporal Variability in Effective Size (N̂e$$ {\hat{N}}_e $$) Identifies Potential Sources of Discrepancies Between Mark Recapture and Close Kin Mark Recapture Estimates of Population Abundance
Authors: Ruzzante Daniel E. , McCracken Gregory R. , Fraser Dylan J. , MacMillan John , Buhariwalla Colin , Flemming Joanna Mills 
Published: November 2024

ABSTRACTAlthough efforts to estimate effective population size, census size and their ratio in wild populations are expanding, few empirical studies investigate interannual changes in these parameters. Hence, we do not know how repeatable or representative many estimates may be. Answering this question requires studies of long‐term population dynamics. Here we took advantage of a rich dataset of seven brook trout (Salvelinus fontinalis) populations, 5 consecutive years and 5400 individuals genotyped at 33 microsatellites to examine variation in estimates of effective and census size and in their ratio. We first estimated the annual effective number of breeders (b) using individuals aged 1+. We then adjusted these estimates using two life history traits, to obtain and subsequently, following Waples et al. (2013). was estimated for the years 2014 to 2019. Census size was estimated by mark recapture using double‐pass electrofishing () (years 2014–2018) as well as by the Close Kin Mark Recapture approach () (years 2015–2017). Within populations, annual variation in (ratio of maximum to minimum ) ranged from 1.6‐fold to 58‐fold. Over all 7 populations, the median annual variation in was around 5‐fold. These results reflect important interannual changes in the variance in reproductive success and more generally in population dynamics. Within population varied between years by a (median) factor of 2.7 with a range from 2 to 4.3. Thus, estimated effective size varied nearly twice as much as did estimated census size. Our results therefore suggest that, at least in small populations like those examined in the present study, any single annual estimate of is unlikely to be representative of long‐term dynamics. At least 3–4 annual estimates may be required for an estimate of contemporary effective size to be truly representative. We then compared to . For five of the seven populations, the estimates of population abundance based on mark recapture () were indistinguishable from those based on close kin mark recapture (). The two populations with discordant and exhibited extremely low ratios and the largest annual variation in (58‐fold and 35.4‐fold respectively). These results suggest that sampling effort in these two streams may have been insufficient to properly capture the genetic diversity of the entire population and that individuals sampled were not representative of the population. Our study further validates CKMR as a method for estimating abundance in wild populations and it demonstrates how knowledge of the temporal variation in can be used to identify potential sources of discrepancies between and .
metaRange: A framework to build mechanistic range models
Authors: Fallert Stefan , Li Lea , Cabral Juliano Sarmento 
Published: November 2024

Abstract

Mechanistic or process‐based models offer great insights into the range dynamics of species facing non‐equilibrium conditions, such as climate and land‐use changes or invasive species. Their consideration of underlying mechanisms relaxes the species‐environment equilibrium assumed by correlative approaches, while also generating conservation‐relevant indicators, such as range‐wide abundance time series and migration rates if demographically explicit. However, the computational complexity of mechanistic models limits their development and applicability to large spatiotemporal extents.

We present the R package “metaRange”: a modular framework to build population‐based and metabolically constrained range models. We also provide a catalogue of biological functions to calculate niche‐based suitability, metabolic scaling, population dynamics, biotic interactions and kernel‐based dispersal, which may include directed movement. The framework's modularity enables the user to combine, extend, or replace these functions, making it possible to customize the model to the ecology of the study system. The package supports an unlimited number of static or dynamic environmental factors as input, including climate and land use.

As examples, we include one single‐species application to predict the range dynamics of the European wildcat (Felis silvestris) in Germany, and one theoretical study in which we simulated 100 virtual species in three scenarios: without competition, with competition, and with competition under a generalist‐specialist trade‐off. Due to the population‐level, the package can execute such extensive simulation experiments on regular end‐user hardware in a short amount of time. We provide detailed technical documentation, both for the individual functions in the package as well as instructions on how to set up different types of model structures and experimental designs.

The metaRange framework enables process‐based simulations of range dynamic of multiple interacting species on a high resolution and low computational demand. We believe that it allows for theoretical insights and hypotheses testing about future range dynamics of real‐world species, which may better support conservation policies targeting biodiversity loss mitigation.
Yes, they're all individuals: Hierarchical models for repeat survey data improve estimates of tree growth and size
Authors: O'Brien Tess , Warton David , Falster Daniel 
Published: November 2024

Abstract

Repeat measurement surveys of tree size are used in forests to estimate growth behaviour, biomass and population dynamics. Although size is measured with error and individuals vary in their growth trajectories, current size‐based growth modelling approaches do not usually or fully account for both of these features, and therefore under‐utilise available data.

We present a new method that leverages the auto‐correlation structure of repeat surveys into a hierarchical Bayesian longitudinal growth model. This new structure allows users to correct for measurement error and capture individual‐level variation in growth trajectories and parameters.

To demonstrate the new method we applied it to a sample of tropical tree survey data from long‐term monitoring sites at Barro Colorado Island. We were able to reduce estimated error in size and growth, and extract individual‐ and population‐level growth parameter estimates. We used simulation to evaluate the ability of the new method to improve estimates of growth rate and size, and estimate individual and species‐level parameters. Our method substantially improved the root mean squared error (RMSE) for growth by an average of 61% compared to existing approaches using pairwise differences and reduced RMSE in estimated size RMSE compared to ‘observed’ values in simulated data. Better numerical integration methods (Runge–Kutta fourth order in comparison to Euler and midpoint) provided better estimates of parameters, but did not improve the estimation of size and growth. The choice of a positive growth function eliminated all negative increments without data exclusion.

Overall, this study shows how we can gain new and improved insights on growth, using repeat forest surveys. Our new method offers improved biomass dynamics estimation through reduced error in sizes over time, coupled with novel information about within‐species variation in growth behaviour that is inaccessible with species average models, such as individual parameters for the growth function which allows for relationships between parameters to be considered for the first time.
Failure rate of the pulmonary embolism rule‐out criteria rule for adults 35 years or younger: Findings from the RIETE Registry
Authors: Jossein Thibaut , Mazzolai Lucia , Lorenzo Hernández Alicia , Otálora Valderrama Sonia , Zdraveska Marija , Rivas Guerrero Agustina , López Ruiz Antonio , Di Micco Pierpaolo , Monreal Manuel , Hugli Olivier ,   the RIETE Investigators
Published: November 2024

AbstractBackgroundThe use of a computed tomography pulmonary angiogram to diagnose pulmonary embolism (PE) has increased, leading not only to higher PE diagnoses but also to overdiagnosis and unnecessary radiation exposure, even in young patients despite a lower PE incidence. The aim of this study was to assess the failure rate of the pulmonary embolism rule‐out criteria 35 (PERC‐35) rule developed to reduce unnecessary testing in individuals aged ≤35 years among patients included in the Registro Informatizado de la Enfermedad TromboEmbolica Venosa (RIETE) Registry.MethodsThis retrospective cohort study used data from the RIETE Registry, an ongoing, international prospective registry of patients with objectively confirmed venous thromboembolism. The primary outcome was the missed PE rate using PERC‐35 criteria. Secondary outcomes included the comparison of demographic and clinical characteristics, PE localization, treatment strategies, and outcomes between PERC‐negative (PERC‐35N) versus PERC‐positive (PERC‐35P) patients.ResultsOf 58,918 adult patients with acute PE, the PERC‐35 rule demonstrated a low missed PE rate of 0.35% (n = 204), with an upper 95% confidence interval [CI] of 0.40%. The missed rate was 7.0% (95% CI 6.0%–7.9%) in the 18‐ to 35‐year subgroup. Compared to PERC‐35P patients, PERC‐35N patients were younger (mean age 28.4 years), with a lower body mass index, and included a higher proportion of pregnant/postpartum women. PERC‐35N patients had a significantly lower rate of chronic diseases and presented less frequently with dyspnea or syncope but more often with chest pain. They showed lower rates of positive D‐dimer and troponin levels. PERC‐35N patients experienced fewer major bleeding episodes, similar recurrence rates of PE/deep vein thrombosis, and no deaths during anticoagulation.ConclusionsThe PERC‐35 rule demonstrated a low failure rate to exclude PE in patients aged 18–35 years and could reduce imaging and radiation exposure in young patients with a low PE pretest probability if confirmed prospectively.
Alcoholic beverage consumption and female breast cancer risk: A systematic review and meta‐analysis of prospective cohort studies
Authors: Sohi Ivneet , Rehm Jürgen , Saab Marian , Virmani Lavanya , Franklin Ari , Sánchez Gonzalo , Jhumi Mihojana , Irshad Ahmed , Shah Hiya , Correia Daniela , Ferrari Pietro , Ferreira‐Borges Carina , Lauby‐Secretan Beatrice , Galea Gauden , Gapstur Susan , Neufeld Maria , Rumgay Harriet , Soerjomataram Isabelle , Shield Kevin 
Published: November 2024

AbstractAlcohol consumption is an established cause of female breast cancer. This systematic review examines in detail the association between alcohol and female breast cancer overall and among the described subgroups, using all of the evidence to date. A systematic review of PubMed and Embase was performed according to the Preferred Reporting Items for Systematic Reviews and Meta‐Analyses guidelines. The search included articles published up to November 15, 2023. Meta‐analyses and regressions were performed for alcohol consumption of less than 1 standard drink (10 g of ethanol) per day and for a range of alcohol consumption categories in relation to breast cancer. Analyses by menopausal status, hormone receptor status, human epidermal growth factor receptor 2 status, and molecular subtype were performed. The search yielded 5645 publications, of which 23 publications of individual and pooled studies examined the association between overall alcohol consumption and breast cancer incidence. The meta‐regression showed a positive association; relative risks (RR) of breast cancer were 1.05 (95% CI: 1.04, 1.06), 1.10 (95% CI: 1.08, 1.12), 1.18 (95% CI: 1.15, 1.21), and 1.22 (95% CI: 1.19, 1.25) for 0.5, 1, 2, and 3 standard drinks per day compared with nondrinking, respectively. A meta‐analysis of nine studies indicated that for consumption of less than one standard drink per day, the RR estimate of breast cancer was 1.04 (95% CI: 1.01, 1.07) compared with nondrinking. Consumption of an additional 1 standard drink per day was associated with a higher risk of premenopausal (RR: 1.03 (95% CI: 1.01, 1.06)) and postmenopausal (RR: 1.10 (95% CI: 1.08, 1.12)) breast cancer. Alcohol consumption increases female breast cancer risk, even for women who consume one drink per day. Furthermore, alcohol consumption is associated with both pre‐ and postmenopausal breast cancer risk. These findings support evidence‐based cancer prevention guidelines to reduce alcohol‐related risks.
Lactobacillus rhamnosus GG attenuates depression‐like behaviour and cognitive deficits in chronic ethanol exposure mice by down‐regulating systemic inflammatory factors
Authors: Pan Xiaoyu , Guo Anqi , Guan Kaiyu , Chen Congcong , Xu Shengnan , Tang Yali , Li Xi , Huang Zhengwei 
Published: November 2024

AbstractEthanol can directly or indirectly lead to cognitive and mental disorders. The long‐term intake of alcohol can directly affect the distribution of gut microbiota. Lactobacillus rhamnosus GG (LGG) is a natural bacterium isolated from healthy human intestines that has the function of preventing cytokine‐induced cell apoptosis and protecting cell barriers. However, the regulatory effect of LGG on cognitive and mental disorders caused by chronic ethanol exposure (CEE) is still unclear. In this study, we established a CEE mouse model through free alcohol consumption and added LGG or antibiotics in the later stages of the model. Sequencing analysis of the 16S rRNA gene showed that CEE resulted in a decrease in the abundance and diversity of mouse gut microbial communities accompanied by alterations in the relative abundance of multiple enterobacterial genera. The use of LGG and antibiotics alleviated the depression‐like behaviour and cognitive impairment of CEE‐induced mice, reduced expression of inflammatory factors such as interleukin (IL)‐6, IL‐1β and tumour necrosis factor (TNF)‐α in the ileum, serum and brain and increased the expression of synaptophysin (SYN), postsynaptic density protein‐95 (PSD‐95) and brain‐derived neurotrophic factor (BDNF) in the hippocampus. Together, LGG can alleviate depression‐like behaviour caused by CEE in mice while also improving cognitive and memory functions through reducing peripheral and nervous system inflammation factors and balancing gut microbiota.
The Case for Shared Decision‐making in Oncology and Why the Philippine Healthcare System is Primed for It
Authors: Bacorro Warren , Cairo Clarito , Baldivia Kathleen , Bautista Aida , Dancel Evelyn , Mariano Jocelyn , Gonzalez Gil , Ortin Teresa Sy , Canlas Rodel 
Published: November 2024

AbstractShared decision‐making is ethically imperative, and is a key component in cost‐effective, efficient and equitable cancer care. We review the recent advances in resources, training, tool development, and health policy, supporting the implementation of shared decision‐making, and how the Philippines is primed for it.
Association between self‐reported pain experiences in hospital and ratings of care, readmission and emergency department visits: a population‐based study from New South Wales, Australia
Authors: Prasad Narisha , Penm Jonathan , Watson Diane E. , Tran Bich N. H. , Dai Zhaoli , Tan Edwin C. K. 
Published: November 2024

SummaryIntroductionEvidence on patient experiences with pain in hospitals and its impact on post‐discharge outcomes is limited. This study investigated the prevalence of pain in hospitals, patient characteristics associated with pain management adequacy, and the link between pain experiences, care ratings, readmission and emergency department visits after discharge.MethodsWe conducted a retrospective cross‐sectional analysis of the 2019 Adult Admitted Patient Survey, focusing on self‐reported pain experiences, including presence, severity and management adequacy. The outcomes included self‐reported overall care ratings; readmission; and emergency department visits within one month of discharge. Multivariable logistic regression adjusted for population weight was used to estimate adjusted odds ratios.ResultsAmong 75 large public hospitals, 21,900 patients responded (35% response rate), with 51% of patients reporting pain (mean (SD) age 57 (8.8) y; 54.9% female), 38.3% of whom classified their pain as severe. Aboriginal and/or Torres Strait Islander people and patients who spoke a language other than English were less likely to report adequate pain management (aOR (95%CI) 0.74 (0.58–0.96) and 0.82 (0.70–0.96), respectively). Pain also correlated with poor to very poor care ratings (aOR (95%CI) 2.05 (1.42–2.95)). Those patients who experienced pain were twice as likely to be readmitted (aOR (95%CI) 1.92 (1.55–2.37)) or visit the emergency department after discharge (aOR (95%CI) 1.91 (1.58–2.32)). Conversely, adequate pain management was associated with a lower likelihood of readmission (aOR (95%CI) 0.69 (0.51–0.94)) and emergency department visits (aOR (95%CI) 0.62 (0.44–0.87)). Mediation analysis suggests adequate pain management significantly mediated the relationship between pain severity and hospital rating (50.8%), readmission (11.6%) and emergency department visits (5.9%), after adjusting for all available observed confounders.DiscussionThis study highlights the importance of adequate pain management in patients' perception of care and recovery outcomes, especially among culturally and linguistically diverse patients.
Hepatic Events During Immune Checkpoint Inhibitor Treatment Between Liver and Non‐Liver Malignancies in Hepatitis B Endemic Areas
Authors: Hung Yi‐Ping , Lee Pei‐Chang , Chang Yen‐Hwa , Yang Muh‐Hwa , Chiu Chao‐Hua , Chen Ming‐Huang , Lan Keng‐Hsin , Lee I‐Cheng , Hou Ming‐Chih , Chao Yee , Huang Yi‐Hsiang 
Published: November 2024

ABSTRACTBackgroundNotable advances have been made in immune checkpoint inhibitors (ICIs) for cancer treatment. However, the adverse effects of ICIs, especially hepatotoxicity, remain a challenging problem. Whether patients in hepatitis B virus (HBV)‐endemic areas are prone to developing hepatic adverse events during ICI treatment warrants further exploration.MethodsFrom 2014 to 2020, the data of all patients with cancer who received ICI treatment at Taipei Veterans General Hospital were retrospectively reviewed. The incidence of and risk factors for hepatic adverse events, including hepatitis flare, immune‐related hepatitis (irHepatitis) and HBV reactivation (HBVr), were analysed through a Cox proportional hazard regression model.ResultsA total of 1283 patients with cancer (190 hepatocellular carcinoma [HCC] patients and 1093 patients with non‐HCC malignancies) were eligible for analysis, of whom 283 (22.1%) were HBsAg‐positive. The incidence of hepatitis flare events of any grade was significantly higher in HCC patients than in non‐HCC patients (45.8% vs. 25.6%, p < 0.001). HCC and baseline alanine aminotransferase (ALT) > 40 U/L were independent risk factors for ≥ grade 3 hepatitis flare events. No difference was observed in irHepatitis risk between HCC patients and non‐HCC patients. ALT > 40 U/L was an independent risk factor for irHepatitis. Among 283 HBsAg‐positive patients, six patients (2.1%) experienced HBVr. HCC patients had a higher risk of HBVr than non‐HCC patients (4.4% vs. 0.6%). No specific risk factor for HBVr could be identified. However, none of the patients under nucleos/tide analogue (NUC) prophylaxis experienced HBVr in this study.ConclusionsUnder ICI treatment, HCC patients had a higher risk of hepatitis flare events than non‐HCC patients. Abnormal baseline ALT levels are a risk factor for hepatic adverse events. NUC prophylaxis can minimise the risk of HBVr.
The financial impact of robotic surgery on hospital gross profits in Japan compared to laparoscopic surgery
Authors: Sakai Yoshiharu , Morishita Tsutomu 
Published: November 2024

AbstractRobotic surgery is gaining traction in Japan due to its technological advancements, but its financial viability for hospitals remains uncertain. This study investigates the impact of robotic surgery on hospital gross profits, comparing it to laparoscopic surgery using data from surgeries performed at Red Cross Hospital Osaka. The study spans multiple surgical fields, including gastrointestinal, urology, gynecology, and thoracic surgery. While the number of robotic surgeries has increased, they consistently generate lower gross profits for hospitals compared with laparoscopic surgeries, primarily due to the high costs of robotic instruments and maintenance. Certain procedures, such as hernia repair, proximal gastrectomy, and distal pancreatectomy, result in negative profits when performed robotically. This article highlights the financial challenges hospitals face under Japan's current healthcare reimbursement system, where the fees for robotic and laparoscopic surgeries are largely the same. Policy adjustments may be necessary to ensure the financial sustainability of robotic surgery.
Neurophysiological markers in myelodysplastic syndromes: Insights into peripheral neuropathy
Authors: Möhn Nora 
Published: November 2024

In their paper, Papantoniou et al. present relevant findings on the prevalence and characteristics of peripheral neuropathy in patients with myelodysplastic syndromes (MDS), underscoring the necessity for a more nuanced understanding of neurophysiological involvement in this complex haematological disorder. Their study not only reveals a higher frequency of neuropathy in MDS patients than previously reported but also illuminates specific neurophysiological patterns that may redefine clinical expectations and diagnostic practices in MDS‐associated peripheral neuropathy.Commentary on: Papantoniou et al. Clinical and neurophysiological aspects of peripheral neuropathy in patients with myelodysplastic syndromes. Br J Haematol 2024 (Online ahead of print). doi: 10.1111/bjh.19901.