bluuebunny/crossref_metadata_2025_split huggingface dataset:
Natal origin and dispersal of problem saltwater crocodiles in the Darwin Harbor, Australia
Authors: Fukuda Yusuke , Moritz Craig , FitzSimmons Nancy N. , Jang Namchul , Webb Grahame , Lindner Garry , Campbell Hamish , Christian Keith , Leeder Steven , Banks Sam 
Published: November 2023

AbstractManagement programs that successfully recovered wild saltwater crocodile (Crocodylus porosus) populations in the Northern Territory of Australia did so with an expanding commitment to maintaining public safety. One aspect of the program is the ongoing removal of resident and immigrant crocodiles within Darwin Harbor (since 1979), the main urban center. We determined the likely sources of crocodiles caught as problem animals between 2015–2017 by comparing recently developed methods for population assignment. Depending on the assignment model used, we estimated that between 30% and 50% of crocodiles in Darwin Harbor originated from the Adelaide and Mary rivers, and the Kakadu region east of Darwin, and between 20% and 30% of crocodiles originated from the Finniss, Reynolds, and Daly rivers southwest of Darwin. Saltwater crocodiles occur at particularly high densities in these catchments. The remainder came from a mixture of different sources across the Northern Territory. The most common animals captured were immature (150–180 cm) males that have traveled 100–200 km. We did not identify any relationships between the distance from the inferred origin to Darwin Harbor and the size and sex of the crocodiles, or the year of capture. The targeted removal of crocodiles from specific sites such as Darwin Harbor, near where most people live, improves public safety in the highest risk areas, without compromising abundant source populations in most areas.
Lesser prevalence of polyps/WNT‐dysregulation and concomitant upregulation of gamma‐catenin/MYC point to alternate pathways in colorectal cancer in India
Authors: Vishnubhotla Ravikanth , Avanthi Steffie , Mitnala Sasikala , Guduru Venkat Rao , Rebala Pradeep , Patil Sanjeev M. , Shetty Mahesh , Sekaran Anuradha , Duvvur Nageshwar Reddy 
Published: November 2023

AbstractColorectal cancer (CRC) is known to follow adenoma carcinoma sequence (ACS) in majority of the tumors and the driver variants and associated pathways are well delineated. However, most of the published data are from the west and information in other ethnicities is sparse. We therefore comprehensively evaluated the CRC tumors from Indian ethnicity for the prevalence of ACS. In this cohort study, clinical data of 100,497 patients who attended hospital between 2013 and 2018 were accessed. Tumors from patients (n = 130) with CRC who were treated primarily by surgery were included. DNA and RNA were isolated to assess variants (direct sequencing) and WNT‐pathway dysregulation in genes related to ACS. Global gene expression was generated and analyzed on microarrays (Affymetrix; N = 10) and next generation sequencing platforms (Illumina; N = 25). Gene expression at mRNA (qRT‐PCR) and protein level (IHC) of JUP/CTNNB1/MYC were assessed. Correlation between expression of JUP and MYC was evaluated by Karl Pearson's correlation coefficient. The prevalence of polyps was 16.75%, while 18.26% variants in APC/CTNNB1, 20.00% in KRAS, and 18.33% WNT dysregulation were noted. Interestingly, 29/60 (48.33%) tumors showed only MYC upregulation with normal APC/CTNNB1 expression. Global gene expression and validation in an independent tumor cohort confirmed concomitant upregulation of JUP (gamma‐catenin) & MYC (r = 0.71; p = 0.001) at mRNA and protein in sizeable number of tumors (45/96; 46.88%). Our study provides evidence for limited prevalence of ACS in the Indian ethnicity. Preventive colonoscopies for early identification and management of CRC may not be an effective strategy in this ethnicity.
Estimation of Ambulation and Survival in Neurodegeneration with Brain Iron Accumulation Disorders
Authors: Amini Elahe , Rohani Mohammad , Lang Anthony E. , Azad Zahra , Habibi Seyed Amir Hassan , Alavi Afagh , Shahidi Gholamali , Emamikhah Maziar , Chitsaz Ahmad 
Published: November 2023

AbstractBackgroundNeurodegeneration with Brain Iron Accumulation (NBIA) disorder is a group of ultra‐orphan hereditary diseases with very limited data on its course.ObjectivesTo estimate the probability of preserving ambulatory ability and survival in NBIA.MethodsIn this study, the electronic records of the demographic data and clinical assessments of NBIA patients from 2012 to 2023 were reviewed. The objectives of the study and factors impacting them were investigated by Kaplan–Meier and Cox regression methods.ResultsOne hundred and twenty‐two genetically‐confirmed NBIA patients consisting of nine subtypes were enrolled. Twenty‐four and twenty‐five cases were deceased and wheelchair‐bound, with a mean disease duration of 11 ± 6.65 and 9.32 ± 5 years. The probability of preserving ambulation and survival was 42.9% in 9 years and 28.2% in 15 years for classical Pantothenate Kinase‐Associated Neurodegeneration (PKAN, n = 18), 89.4% in 7 years and 84.7% in 9 years for atypical PKAN (n = 39), 23% in 18 years and 67.8% in 14 years for Mitochondrial Membrane Protein‐Associated Neurodegeneration (MPAN, n = 23), 75% in 20 years and 36.5% in 33 years for Kufor Rakeb Syndrome (KRS, n = 17), respectively. The frequencies of rigidity, spasticity, and female gender were significantly higher in deceased cases compared to surviving patients. Spasticity was the only factor associated with death (Pvalue = 0.03).ConclusionsKRS had the best survival with the most extended ambulation period. The classical PKAN and MPAN cases had similar progression patterns to loss of ambulation ability, while MPAN patients had a slower progression to death. Spasticity was revealed to be the most determining factor for death.
Independent component analysis (ICA) applied to dynamic oxygen‐enhanced MRI (OE‐MRI) for robust functional lung imaging at 3 T
Authors: Needleman Sarah H. , Kim Mina , McClelland Jamie R. , Naish Josephine H. , Tibiletti Marta , O'Connor James P. B. , Parker Geoff J. M. 
Published: November 2023

AbstractPurposeDynamic lung oxygen‐enhanced MRI (OE‐MRI) is challenging due to the presence of confounding signals and poor signal‐to‐noise ratio, particularly at 3 T. We have created a robust pipeline utilizing independent component analysis (ICA) to automatically extract the oxygen‐induced signal change from confounding factors to improve the accuracy and sensitivity of lung OE‐MRI.MethodsDynamic OE‐MRI was performed on healthy participants using a dual‐echo multi‐slice spoiled gradient echo sequence at 3 T and cyclical gas delivery. ICA was applied to each echo within a thoracic mask. The ICA component relating to the oxygen‐enhancement signal was automatically identified using correlation analysis. The oxygen‐enhancement component was reconstructed, and the percentage signal enhancement (PSE) was calculated. The lung PSE of current smokers was compared with nonsmokers; scan–rescan repeatability, ICA pipeline repeatability, and reproducibility between two vendors were assessed.ResultsICA successfully extracted a consistent oxygen‐enhancement component for all participants. Lung tissue and oxygenated blood displayed the opposite oxygen‐induced signal enhancements. A significant difference in PSE was observed between the lungs of current smokers and nonsmokers. The scan–rescan repeatability and the ICA pipeline repeatability were good.ConclusionThe developed pipeline demonstrated sensitivity to the signal enhancements of the lung tissue and oxygenated blood at 3 T. The difference in lung PSE between current smokers and nonsmokers indicates a likely sensitivity to lung function alterations that may be seen in mild pathology, supporting future use of our methods in patient studies.
Laboratory-bred Longfin Smelt produced offspring in the first year in captivity
Authors: Hung Tien-Chieh , Rahman Md. Moshiur , Lewis Levi S. , Yang Ya-Chi , Stevenson Troy A. , Menard Karl L. , Connon Richard E. , Bell Heather , Fangue Nann A. 
Published: November 2023

Abstract

Objective
This study aims to develop the culture methods for Longfin Smelt Spirinchus thaleichthys in a laboratory setting, achieving the first production of a fully captive second generation (F2). The objective includes understanding the critical factors influencing the breeding and maturation of this species in captivity, contributing to conservation efforts and potential revival of this threatened species.

Methods
Longfin Smelt broodstock were collected from the San Francisco Estuary and reared in controlled conditions at the University of California Davis Fish Conservation and Culture Laboratory (FCCL). The study involved spawning of wild broodstock, rearing of first generation (F1) progeny to adulthood, and subsequent spawning to produce F2 offspring. Key variables such as salinity, temperature, and diet were carefully managed throughout the process. Fertilization and hatching rates were calculated, and the larvae were reared using the same methods to closely monitor and understand their growth and development.

Result
First generation Longfin Smelt successfully matured and spawned at age 1, earlier than commonly observed in the wild. From five crosses, four produced viable offspring. The study recorded a range of fertilization rates (10–40%) and high hatching rates (75–97%). Salinity was identified as a critical factor in both larval development and adult maturation. While initial larval survival was challenging, the larval rearing system used in this study proved effective.

Conclusion
The study represents a major breakthrough in the cultivation of Longfin Smelt, showing that it is possible to complete their life cycle under controlled conditions. It has provided valuable understanding of the maturation and breeding processes in these fish, with an emphasis on the influence of salinity. These outcomes are crucial for conservation strategies, offering the potential to help establish a refuge population and laying the groundwork for further research aimed at refining captive breeding methods for this species.
Patterns in distribution and density of larval lampreys in the main-stem Columbia River, Washington–Oregon
Authors: Blanchard Monica R. , Harris Julianne E. , Skalicky Joseph J. , Silver Gregory S. , Jolley Jeffrey C. 
Published: November 2023

Abstract

Objective
This study compiled data sets from multiple research efforts from 2010 to 2018 to describe patterns in the presence and density of larval lampreys in deep water habitats across 430 river kilometers of the lower and middle main-stem Columbia River.

Methods
We used logistic regression to evaluate the influence of landscape-level factors on Pacific Lamprey Enthosphenus tridentatus and Lampetra spp. presence. Additionally, we used N-mixture models to estimate larval lamprey densities in six river mouths in the spring and fall of multiple years.

Result
At the landscape-level, the models suggested that the probability of presence for both Pacific Lampreys and Lampetra spp. decreased with increasing distance from the ocean, distance from the closest upstream tributary river mouth, and distance from the nearest main-stem riverbank. The probability of presence also varied by upstream tributary river mouth. The probability of larval presence in river mouths was an order of magnitude greater than in reservoir pools. Evaluating river mouth habitats, larval lamprey densities varied seasonally, annually, and among river mouths, ranging from 0.04 to 9.63 larvae/m2. Results generally suggested broader distributions and higher densities within river mouths during spring when flows were high compared to the fall when flows were lower, although not in all river mouths or across all years. Larval densities increased in the Wind and Klickitat rivers (the most consistently examined tributary river mouths) over the study period.

Conclusion
Our findings suggest that the main-stem Columbia River supports larval lamprey rearing year-round. Probability of presence was highest and variable among river mouths, suggesting the importance of some river mouths as rearing habitats. Understanding shifts (seasonal, annual, and those as result of changes in environmental conditions) in lamprey presence and density could inform how specific management actions (e.g., dewatering for in-river work) and their timing could affect larval lampreys in rivers.
Downwind and upwind approximations for mesh and model adaptivity of elasto‐plastic composites
Authors: Simeu Arnold Tchomgue , Mahnken Rolf 
Published: November 2023

AbstractThe use of heterogeneous materials, such as composites with Prandtl‐Reuss‐type material laws, has increased in industrial praxis, making finite element modeling with homogenization techniques a well‐accepted tool. These methods are particularly advantageous to account for microstructural mechanisms which can be related to nonlinearities and time‐dependency due to elasto‐plasticity behavior. However, their advantages are diminished by increasing computational demand. The present contribution deals with the balance of accuracy and numerical efficiency of nonlinear homogenization associated with a framework of goal‐oriented adaptivity, which takes into account error accumulation over time. To this end, model adaptivity of homogenization methods is coupled to mesh adaptivity on the macro scale. Our new proposed adaptive procedure is driven by a goal‐oriented a posteriori error estimator based on duality techniques using downwind and upwind approximations. Due to nonlinearities and time‐dependency of the plasticity, the estimation of error transport and error generation is obtained with a backward‐in‐time dual method despite a high demand on memory capacity. In this contribution, the dual problem is solved with a forward‐in‐time dual method that allows estimating the full error during the resolution of the primal problem without the need for extra memory capacity. Finally, a numerical example illustrates the effectiveness of the proposed adaptive approach.
Evaluation of ChatGPT's performance in providing treatment recommendations for pediatric diseases
Authors: Wei Qiuhong , Wang Yanqin , Yao Zhengxiong , Cui Ying , Wei Bo , Li Tingyu , Xu Ximing 
Published: November 2023

AbstractWith the advance of artificial intelligence technology, large language models such as ChatGPT are drawing substantial interest in the healthcare field. A growing body of research has evaluated ChatGPT's performance in various medical departments, yet its potential in pediatrics remains under‐studied. In this study, we presented ChatGPT with a total of 4160 clinical consultation questions in both English and Chinese, covering 104 pediatric conditions, and repeated each question independently 10 times to assess the accuracy of its responses in pediatric disease treatment recommendations. ChatGPT achieved an overall accuracy of 82.2% (95% CI: 81.0%–83.4%), with superior performance in addressing common diseases (84.4%, 95% CI: 83.2%–85.7%), offering general treatment advice (83.5%, 95% CI: 81.9%–85.1%), and responding in English (93.0%, 95% CI: 91.9%–94.1%). However, it was prone to errors in disease definitions, medications, and surgical treatment. In conclusion, while ChatGPT shows promise in pediatric treatment recommendations with notable accuracy, cautious optimism is warranted regarding the potential application of large language models in enhancing patient care.
The PB1 and the ZZ domain of the autophagy receptor p62/SQSTM1 regulate the interaction of p62/SQSTM1 with the autophagosome protein LC3B
Authors: Alcober‐Boquet Lucia , Zang Tabea , Pietsch Larissa , Suess Evelyn , Hartmann Markus , Proschak Ewgenij , Gross Lissy Z. F. , Sacerdoti Mariana , Zeuzem Stefan , Rogov Vladimir V. , Leroux Alejandro E. , Piiper Albrecht , Biondi Ricardo M. 
Published: November 2023

AbstractAutophagy is a highly conserved cellular process that allows degradation of large macromolecules. p62/SQSTM1 is a key adaptor protein that interacts both with material to be degraded and with LC3 at the autophagosome, enabling degradation of cargos such as protein aggregates, lipid droplets and damaged organelles by selective autophagy. Dysregulation of autophagy contributes to the pathogenesis of many diseases. In this study, we investigated if the interaction of p62/SQSTM1 with LC3B could be regulated. We purified full‐length p62/SQSTM1 and established an in vitro assay that measures the interaction with LC3B. We used the assay to determine the role of the different domains of p62/SQSTM1 in the interaction with LC3B. We identified a mechanism of regulation of p62/SQSTM1 where the ZZ and the PB1 domains regulate the exposure of the LIR‐sequence to enable or inhibit the interaction with LC3B. A mutation to mimic the phosphorylation of a site on the ZZ domain leads to increased interaction with LC3B. Also, a small compound that binds to the ZZ domain enhances interaction with LC3B. Dysregulation of these mechanisms in p62/SQSTM1 could have implications for diseases where autophagy is affected. In conclusion, our study highlights the regulated nature of p62/SQSTM1 and its ability to modulate the interaction with LC3B through a LIR‐sequence Accessibility Mechanism (LAM). Furthermore, our findings suggest the potential for pharmacological modulation of the exposure of LIR, paving the way for future therapeutic strategies.
Entomopathogens in the integrated management of forest insects: from science to practice
Authors: Skrzecz Iwona , Sierpińska Alicja , Tumialis Dorota 
Published: November 2023

AbstractThe most important aim of the integrated management of forest insect pests remains the prevention of insect outbreaks, which are a consequence of the interaction of many factors in forest ecosystems, including species composition, age and health of the forest, soil type, the presence of natural enemies, and climatic factors. Integrated pest management until now has been achieved using measures aimed at shaping the functioning of stands in a changing environment. The aim of this review is to summarize research on the use of entomopathogens (microorganisms and nematodes) in the management of forest insect pests and to identify the principal knowledge gaps. We briefly describe the main research directions on the use of pathogens and nematodes to control insect pests and discuss limitations affecting their implementation. Research on entomopathogens for the biocontrol of forest insects has provided a wealth of knowledge that can be used effectively to reduce insect populations. Despite this, few entomopathogens are currently used in integrated pest management in forestry. They are applied in inoculation or inundation biocontrol strategies. While the use of entomopathogens in forest pest management shows great promise, practical implementation remains a distant goal. Consequently, sustainable reduction of forest pests, mainly native species, will be largely based on conservation biological control, which aims to modify the environment to favor the activity of natural enemies that regulate pest populations. This type of biocontrol can be supported by a range of silvicultural measures to increase the resilience of stands to insect infestations. © 2023 Society of Chemical Industry.
Functional analysis of a down‐regulated transcription factor‐SoxNeuroA gene involved in the acaricidal mechanism of scopoletin against spider mites
Authors: Zhou Hong , Ning Yeshuang , Jian Yufan , Zhang Miao , Klakong Matthana , Guo Fuyou , Shao Qingyi , Li Yanhong , Yang Pinglong , Li Zongquan , Yang Liang , Li Shili , Ding Wei 
Published: November 2023

AbstractBACKGROUNDInsight into the mode of action of plant‐derived acaricides will help in the development of sustainable control strategies for mite pests. Scopoletin, a promising plant‐derived bioactive compound, displays prominent acaricidal activity against Tetranychus cinnabarinus. The transcription factor SoxNeuroA plays a vital role in maintaining calcium ion (Ca2+) homeostasis. Down‐regulation of SoxNeuroA gene expression occurs in scopoletin‐exposed mites, but the functional role of this gene remains unknown.RESULTSA SoxNeuroA gene from T. cinnabarinus (TcSoxNeuroA) was first cloned and identified. Reverse transcription polymerase chain reaction (RT‐PCR), quantitative real‐time polymerase chain reaction (qPCR), and Western blotting assays all confirmed that the gene expression and protein levels of TcSoxNeuroA were significantly reduced under scopoletin exposure. Furthermore, RNA interference silencing of the weakly expressed SoxNeuroA gene significantly enhanced the susceptibility of mites to scopoletin, suggesting that the acaricidal mechanism of scopoletin was mediated by the weakly expressed SoxNeuroA gene. Additionally, yeast one‐hybrid (Y1H) and dual‐luciferase reporter assays revealed that TcSoxNeuroA was a repressor of Orai1 Ca2+ channel gene transcription, and the key binding sequence was ATCAAAG (positions −361 to −368 of the Orai1 promoter). Importantly, site‐directed mutagenesis and microscale thermophoresis assays further indicated that ASP185, ARG189, and LYS217, which were key predicted hydrogen‐bonding sites in the molecular docking model, may be the vital binding sites for scopoletin in TcSoxNeuroA.CONCLUSIONThese results demonstrate that the acaricidal mechanism of scopoletin involves inhibition of the transcription factor SoxNeuroA, thus inducing the activation of the Orai1 Ca2+ channel, eventually leading to Ca2+ overload and lethality. Elucidation of the transcription factor‐targeted mechanism for this potent plant‐derived acaricide has vital implications for the design of next‐generation green acaricides with novel targets. © 2023 Society of Chemical Industry.