bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitochondrial genome amplification of avian haemosporidian parasites from single-infected wildlife samples using a novel nested PCR approach
Authors: Musa Sandrine 
Published: October 2023

AbstractHaemosporidian parasites that infect birds (Apicomplexa: Haemosporida) are blood parasites that require an invertebrate host (vector) and a vertebrate host for their lifecycle and cause malaria-like diseases. This group of parasites has provided valuable insights into host specificity, virulence, and parasite dispersal. Additionally, they have played a significant role in reshaping our understanding of the evolutionary history of apicomplexans. In order to accurately identify species and to address phylogenetic questions such as the timing of the haemosporidian radiation, the use of a sufficiently large genetic data set is crucial. However, acquiring this genetic data poses significant challenges. In this research, a sensitive nested PCR assay was developed. This assay allows for the easy amplification of complete mitochondrial genomes of haemosporidian parasites in birds, even during the chronic stage of infection. The effectiveness of this new nested PCR assay was evaluated using blood and tissue samples of birds with verified single parasite infections from previous studies. The approach involves amplifying four overlapping fragments of the mitochondrial genome and requires DNA extracts from single-infected samples. This method successfully amplified the complete mitochondrial genomes of 24 distinct haemosporidian parasite lineages found in various bird species. This data is invaluable for conducting phylogenetic analyses and accurately defining species. Furthermore, this study proposes the existence of at least 15 new haemosporidian parasite species based on the genetic information obtained. Data regarding pGRW04, previously categorized as Plasmodium relictum like pSGS1 and pGRW11, indicates that the pGRW04 lineage is actually a separate, hidden Plasmodium species.
Lateral edifice collapse and volcanic debris avalanches: a post-1980 Mount St. Helens perspective
Authors: Siebert Lee , Reid Mark E. 
Published: October 2023

AbstractThe 1980 eruption of Mount St. Helens was instrumental in advancing understanding of how volcanoes work. Lateral edifice collapses and the generation of volcanic debris avalanches were not widely recognized prior to that eruption, making assessment of their hazards and risks challenging. The proliferation of studies since 1980 on resulting deposits and evaluation of processes leading to their generation has built on the insights from the 1980 eruption. Volcano-related destabilizing phenomena, such as strength reduction by hydrothermal alteration, deformation and structural modifications from shallow magma intrusion, and thermal pressurization of pore fluids supplement those factors also affecting nonvolcanic slopes and can lead to larger failures. Remote and ground-based monitoring techniques can aid in detecting potentially destabilizing dynamic processes and in forecasting the size and location of future large lateral collapses, although forecasting remains a topic of investigation. More than a thousand large lateral collapse events likely ≥ 0.01 km3in volume have now been identified from deposits or inferred from source area morphology, leading to a recognition of their importance in the evolution of volcanoes and the hazards they pose. Criteria for recognition of debris-avalanche deposits include morphological factors and textural characteristics from outcrop to microscopic scale, allowing discrimination from other volcaniclastic deposits. Lateral edifice failure impacts a broad spectrum of volcanic structures in diverse tectonic settings and can occur multiple times during the evolution of individual volcanoes. Globally, collapses ≥ 0.1 km3in volume have been documented 5–6 times per century since 1500 CE, with about one per century having a volume ≥ 1 km3. Smaller events < 0.1 km3are underrepresented in the earlier record but also have high hazard impact.
Bayesian Convolutional Neural Networks in Medical Imaging Classification: A Promising Solution for Deep Learning Limits in Data Scarcity Scenarios
Authors: Bargagna Filippo , De Santi Lisa Anita , Martini Nicola , Genovesi Dario , Favilli Brunella , Vergaro Giuseppe , Emdin Michele , Giorgetti Assuero , Positano Vincenzo , Santarelli Maria Filomena 
Published: October 2023

AbstractDeep neural networks (DNNs) have already impacted the field of medicine in data analysis, classification, and image processing. Unfortunately, their performance is drastically reduced when datasets are scarce in nature (e.g., rare diseases or early-research data). In such scenarios, DNNs display poor capacity for generalization and often lead to highly biased estimates and silent failures. Moreover, deterministic systems cannot provide epistemic uncertainty, a key component to asserting the model’s reliability. In this work, we developed a probabilistic system for classification as a framework for addressing the aforementioned criticalities. Specifically, we implemented a Bayesian convolutional neural network (BCNN) for the classification of cardiac amyloidosis (CA) subtypes. We prepared four different CNNs: base-deterministic, dropout-deterministic, dropout-Bayesian, and Bayesian. We then trained them on a dataset of 1107 PET images from 47 CA and control patients (data scarcity scenario). The Bayesian model achieved performances (78.28 (1.99) % test accuracy) comparable to the base-deterministic, dropout-deterministic, and dropout-Bayesian ones, while showing strongly increased “Out of Distribution” input detection (validation-test accuracy mismatch reduction). Additionally, both the dropout-Bayesian and the Bayesian models enriched the classification through confidence estimates, while reducing the criticalities of the dropout-deterministic and base-deterministic approaches. This in turn increased the model’s reliability, also providing much needed insights into the network’s estimates. The obtained results suggest that a Bayesian CNN can be a promising solution for addressing the challenges posed by data scarcity in medical imaging classification tasks.
Polymorphisms in genes of melatonin biosynthesis and signaling support the light-at-night hypothesis for breast cancer
Authors: Wichert Katharina , Hoppe Reiner , Ickstadt Katja , Behrens Thomas , Winter Stefan , Herold Robert , Terschüren Claudia , Lo Wing-Yee , Guénel Pascal , Truong Thérèse , Bolla Manjeet K. , Wang Qin , Dennis Joe , Michailidou Kyriaki , Lush Michael , Andrulis Irene L. , Brenner Hermann , Chang-Claude Jenny , Cox Angela , Cross Simon S. , Czene Kamila , Eriksson Mikael , Figueroa Jonine D. , García-Closas Montserrat , Goldberg Mark S. , Hamann Ute , He Wei , Holleczek Bernd , Hopper John L. , Jakubowska Anna , Ko Yon-Dschun , Lubiński Jan , Mulligan Anna Marie , Obi Nadia , Rhenius Valerie , Shah Mitul , Shu Xiao-Ou , Simard Jacques , Southey Melissa C. , Zheng Wei , Dunning Alison M. , Pharoah Paul D. P. , Hall Per , Easton Douglas F. , Brüning Thomas , Brauch Hiltrud , Harth Volker , Rabstein Sylvia 
Published: October 2023

AbstractLight-at-night triggers the decline of pineal gland melatonin biosynthesis and secretion and is an IARC-classified probable breast-cancer risk factor. We applied a large-scale molecular epidemiology approach to shed light on the putative role of melatonin in breast cancer. We investigated associations between breast-cancer risk and polymorphisms at genes of melatonin biosynthesis/signaling using a study population of 44,405 women from the Breast Cancer Association Consortium (22,992 cases, 21,413 population-based controls). Genotype data of 97 candidate single nucleotide polymorphisms (SNPs) at 18 defined gene regions were investigated for breast-cancer risk effects. We calculated adjusted odds ratios (ORs) and 95% confidence intervals (CI) by logistic regression for the main-effect analysis as well as stratified analyses by estrogen- and progesterone-receptor (ER, PR) status. SNP-SNP interactions were analyzed via a two-step procedure based on logic regression. The Bayesian false-discovery probability (BFDP) was used for all analyses to account for multiple testing. Noteworthy associations (BFDP < 0.8) included 10 linked SNPs in tryptophan hydroxylase 2 (TPH2) (e.g. rs1386492: OR = 1.07, 95% CI 1.02–1.12), and a SNP in the mitogen-activated protein kinase 8 (MAPK8) (rs10857561: OR = 1.11, 95% CI 1.04–1.18). The SNP-SNP interaction analysis revealed noteworthy interaction terms with TPH2- and MAPK-related SNPs (e.g. rs1386483R ∧ rs1473473D ∧ rs3729931D: OR = 1.20, 95% CI 1.09–1.32). In line with the light-at-night hypothesis that links shift work with elevated breast-cancer risks our results point to SNPs in TPH2 and MAPK-genes that may impact the intricate network of circadian regulation.
Slow data public health
Authors: Chiolero Arnaud , Tancredi Stefano , Ioannidis John P. A. 
Published: October 2023

AbstractSurveillance and research data, despite their massive production, often fail to inform evidence-based and rigorous data-driven health decision-making. In the age of infodemic, as revealed by the COVID-19 pandemic, providing useful information for decision-making requires more than getting more data. Data of dubious quality and reliability waste resources and create data-genic public health damages. We call therefore for a slow data public health, which means focusing, first, on the identification of specific information needs and, second, on the dissemination of information in a way that informs decision-making, rather than devoting massive resources to data collection and analysis. A slow data public health prioritizes better data, ideally population-based, over more data and aims to be timely rather than deceptively fast. Applied by independent institutions with expertise in epidemiology and surveillance methods, it allows a thoughtful and timely public health response, based on high-quality data fostering trustworthiness.
The growth performance of pond-reared common carp (Cyprinus carpio) larvae propagated using cryopreserved sperm
Authors: Bokor Zoltán , Láng Zete Levente , Várkonyi Levente , Fodor Ferenc , Nagy Borbála , Csókás Endre , Molnár József , Csorbai Balázs , Csenki-Bakos Zsolt , Ivánovics Bence , Griffitts Jeffrey Daniel , Urbányi Béla , Bernáth Gergely 
Published: October 2023

AbstractThe aim of our study was to determine the efficacy of utilizing cryopreserved common carp sperm (in comparison to fresh sperm) for propagation at a Hungarian aquaculture facility. The sperm was frozen in 5 mL straws using an extender method that was previously tested in common carp. Sperm motility was monitored using a computer-assisted sperm analysis system. The hatching and malformation rates among the specimens were recorded before the stocking of larvae in both groups. The growth (body weight, total length) and survival rates of the fish were measured during the pre-nursing (from May to June: between 1 and 26 days post hatching) and grow-out periods (from June to October: between 26 and 105 days post hatching) of the same year. The fresh sperm, which was collected and pooled prior to fertilization, showed high MOT (97%), pMOT (92%), VCL (106 µm s−1), LIN (75%), and ALH (1.84 µm). Prior to the fertilization trial of the cryopreserved sperm, low MOT (34%), pMOT (14%), and VCL (61 µm s−1) values were observed in frozen-thawed sperm. A significantly higher hatching rate was measured in the fresh sperm group (87%) when compared to the cryopreserved sperm group (42%). No significant difference in the overall malformation rate was observed in larvae originating from either the fresh or frozen sperm. A significant difference between the two test groups was observed in the incidence of deformed tails (fresh: 20%, cryopreserved: 55%). Except for one sampling period, no significant difference in the body weight and total length of the fish larvae was found between the two groups throughout the pre-nursing and grow-out periods. A significantly higher larvae survival rate was noted in the fresh sperm (72%) as compared to the cryopreserved group (43%) by the end of the pre-nursing stage. However, no significant difference in survival rate was observed for the cryopreserved sperm (96%) in comparison to the fresh sperm (95%) by the end of the grow-out stage. The results of this study showed, for the first time in large-scale pond culturing, an equal growth and viability in larvae propagated from cryopreserved sperm when compared to fresh sperm (despite the limited available rearing ponds provided by the commercial company).
Know When You Are Too Many: Density-Dependent Release of Pheromones During Host Colonisation by the European Spruce Bark Beetle, Ips typographus (L.)
Authors: Frühbrodt Tobias , Du Baoguo , Delb Horst , Burzlaff Tim , Kreuzwieser Jürgen , Biedermann Peter H. W. 
Published: October 2023

AbstractIndividuals across various animal species communicate their presence to conspecifics. Especially phytophagous and parasitoid insects with their brood developing on limited resources rely on chemical cues, such as host-marking pheromones, to reduce intraspecific competition. Bark beetles are phytophagous insects with some species being economically and ecologically relevant forest pests. Several of them use the volatile compound verbenone to inhibit attraction and reduce intraspecific competition. However, in the Eurasian spruce bark beetle, Ips typographus (L.), temporal emission patterns did so far not quite support the putative function of verbenone as an indicator of densely colonised host trees. More importantly, it is currently unclear how well verbenone emission is actually related to colonisation density and thus intraspecific competition. Here, we inoculated Norway spruce logs with I. typographus at two defined colonisation densities in the greenhouse and measured the emission of verbenone and its precursors α-pinene and verbenol over time. Verbenone emission was 3–7 times greater from colonised logs compared to decaying logs without beetles during the major part of larval development. Furthermore, our data supports the quantitative hypothesis, that the termination of attack on a tree is mediated by a cessation of the release of verbenol and continuous emission of verbenone. The latter is most likely a passively produced host-marking cue reflecting the actual density of conspecifics since per-beetle emission was unaffected by colonisation density. These findings shed new light on the regulation of bark beetle mass aggregations, which are currently causing previously unseen economic damages in temperate forests.
Psychometric Validation of the Robotics Interest Questionnaire (RIQ) Scale with Italian Teachers
Authors: Agus Mirian , Bonaiuti Giovanni , Marras Arianna 
Published: October 2023

AbstractIn recent years, numerous research studies have highlighted how teachers’ perceptions of educational robotics (ER) and their sense of self-efficacy can influence the learning process. Although different instruments exist to investigate teachers’ perspectives on ER, the Robotics Interest Questionnaire (RIQ) scale, developed within the Portuguese K–12 education framework to analyse the impact of domain knowledge (i.e. coding and robotics), interest in robotics, and confidence in one’s self-efficacy as a robotics teacher, was used in the present work. This instrument has been validated in Portugal, meeting rigorous statistical and reliability measures that our work intends to verify in its Italian version. To test the validity of the instrument, the Teacher Self-Efficacy (QAI) Questionnaire, already validated in Italian and accredited in the literature, was administered jointly. The instruments were administered to a non-probabilistic sample of 823 teachers working in different school orders. Exploratory and confirmatory factor analyses were carried out, confirming a four-factor model. The results suggest the applicability of the RIQ instrument in the Italian school context to test teachers’ levels of interest, knowledge, problem-solving, collaborative work, and sense of self-efficacy, successfully discriminating between experienced and inexperienced ER teachers. These constructs, as suggested in multiple works, are relevant factors in promoting the use of robotics for educational purposes.
Investigations of indoor radon levels and its mapping in the Greater Accra region, Ghana
Authors: Akuo-ko Esther Osei , Adelikhah Mohammademad , Amponsem Eunice , Csordás Anita , Kovács Tibor 
Published: October 2023

AbstractIn this work, the indoor radon concentration and radiation dose risks were studied in dwellings within the Greater Accra region, using CR-39 detectors. The indoor radon concentrations ranged from 36.1 ± 2.7 to 92.0 ± 5.2 Bq m−3 with an annual average of 50.8 ± 3.4 Bq m−3. The annual mean effective dose was estimated as 1.3 mSv year−1. Excess lifetime cancer risk and lung cancer cases were assessed with 5% annual lung cancer deaths due to radon was realized. Indoor radon maps created with ArcGIS software over a 5 × 5 km2 grid showed radon prone areas in the region.
Patchy range retractions in response to climate change and implications for terrestrial species conservation
Authors: Jones Rachel , Wilson Robert J. , Bourn Nigel A. D. , Maclean Ilya M. D. 
Published: October 2023

Abstract
Context
Efforts to adapt conservation to climate change often focus on facilitating range shifts to higher latitudes, by enhancing landscape capacity for poleward expansion. The need to protect populations at trailing edges of species distributions, and how and where to do so, has received less attention.

Objectives
We assess how population declines caused by variation over space and time in exposure to climate change can necessitate conservation adaptation to climate change throughout species’ geographic ranges. We propose approaches for conservation in landscapes where species are vulnerable.

Methods
We synthesize primary literature relating to recent landscape-scale changes to species distributions to identify evidence for patchy patterns of climate-driven decline. We use this evidence to propose a framework to adapt terrestrial species conservation.

Results
Patchy retractions occur throughout species ranges as environmental heterogeneity results in spatial variation in climate and rates of climate change, whereas equatorward range margins are often not the first place to exceed climatic limits. Furthermore, climate effects on fitness, survival and reproduction interact with habitat quality, creating both localized extinction hotspots and climatically resilient microrefugial landscapes across species ranges. Conservation can benefit from the identification of vulnerable versus microrefugial landscapes, and implementation of targeted interventions.

Conclusions
A focus on expansions and retractions at broad latitudinal range margins risks overlooking declines throughout species’ distributions. Understanding fine-resolution ecological responses to the climate can help to identify resilient microrefugial landscapes, and targeted management to promote cooler or more stable conditions can complement facilitation of broader-scale range shifts.
Current status of the analytical validation of next generation sequencing applications for pharmacogenetic profiling
Authors: Huebner Tatjana , Steffens Michael , Scholl Catharina 
Published: October 2023

Abstract
Background
Analytical validity is a prerequisite to use a next generation sequencing (NGS)-based application as an in vitro diagnostic test or a companion diagnostic in clinical practice. Currently, in the United States and the European Union, the intended use of such NGS-based tests does not refer to guided drug therapy on the basis of pharmacogenetic profiling of drug metabolizing enzymes, although the value of pharmacogenetic testing has been reported. However, in research, a large variety of NGS-based tests are used and have been confirmed to be at least comparable to array-based testing.

Methods and Results
A systematic evaluation was performed screening and assessing published literature on analytical validation of NGS applications for pharmacogenetic profiling of CYP2C9, CYP2C19, CYP2D6, VKORC1 and/or UGT1A1. Although NGS applications are also increasingly used for implementation assessments in clinical practice, we show in the present systematic literature evaluation that published information on the current status of analytical validation of NGS applications targeting drug metabolizing enzymes is scarce. Furthermore, a comprehensive performance evaluation of whole exome and whole genome sequencing with the intended use for pharmacogenetic profiling has not been published so far.

Conclusions
A standard in reporting on analytical validation of NGS-based tests is not in place yet. Therefore, many relevant performance criteria are not addressed in published literature. For an appropriate analytical validation of an NGS-based qualitative test for pharmacogenetic profiling at least accuracy, precision, limit of detection and specificity should be addressed to facilitate the implementation of such tests in clinical use.
Two forms of transfer matrix for one-dimensional optical structures
Authors: Morozov Gregory V. 
Published: October 2023

AbstractTwo forms of the transfer matrix applied for treatment of light propagation through one-dimensional optical structures are discussed. A detailed comparison between those forms is presented. A case of structures with absorption (gain) is included. The relation between the transfer matrix method and the Floquet-Bloch theory is highlighted for the case of a periodic structure.