bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing potential coastal flood exposure along the Port-Bouët Bay in Côte d’Ivoire using the enhanced bathtub model
Authors: Kouakou Marcel , Tiémélé Jacques André , Djagoua Éric , Gnandi Kissao 
Published: September 2023

Abstract
Coastal flooding is a growing concern for many communities worldwide due to climate change. This study focuses on the Port-Bouët Bay, located in Abidjan, Côte d’Ivoire. A coastal flood model based on the enhanced bathtub model was used to map the present and future flood extent and assess exposure to quantify the likely affected populations, buildings, and land uses for different scenarios. The model incorporated a digital elevation model, surface roughness, flood water source, and the once a century extreme sea-level scenarios. Validation was conducted against GPS coordinates of recently flooded zones. The analysis revealed that, under current conditions, around 21.58 hectares are vulnerable to flooding, and approximately 2465 people and 544 buildings are exposed to flooding today. Based on future projections, the extent of flooding is anticipated to increase by different ranges depending on the time period and the climate change conditions. By the end of the century, the increase in flooding extent could reach a percentage of 27%, 37%, and 90% under SSP1-2.6, SSP2-4.5, and SSP5-8.5, respectively. The impacts would consequently be worsened with greater number of people and assets exposed to future coastal flood hazard. The land use analysis showed that informal settlements are the occupation most exposed, followed by residential settlements, commercial and industrial land, in that order. The spatial disaggregation of this exposure across neighborhoods indicates that Sogefiha is the most exposed, followed by Petit-Bassam and Vridi. However, a substantial increase in coastal flooding in Vridi by 2100 under the SSP5-8.5 scenario could lead to significant exposure level change for this scenario. This information is critical for evaluating and managing present and future coastal flood risks in the Port-Bouët Bay area and for informing decision-making processes.
Effect of loading/unloading rate on instrumented indentation measurements in alloy Cu-2%Be
Authors: Montecinos S , Tognana S , Salgueiro W 
Published: September 2023

Abstract
The influence of the loading/unloading rate on the indentation strain rate, hardness and elastic modulus in Cu-2wt%Be samples subjected to different aging treatments was analyzed. Homogenized samples were aged for 1 and 10 h at 400 °C to induce the formation of γ′ and γ precipitates, and instrumented indentation tests were performed at different loading rates between 0.15 and 1 mN s−1. The indentation curves of all the samples were influenced by the loading/unloading rate, but the behavior of the samples with precipitates was different from that of the homogenized samples. Strain rate levels during loading were also influenced by the loading rate. The strain rate increased almost linearly with the loading rate in the homogenized sample and the sample with γ′ nanoprecipitates, while it experienced a decelerated increase with the loading rate in the sample with γ phase. The hardness and reduced modulus were estimated from the indentation curves using the Oliver and Pharr method. Hardness remained almost constant at approximately 2.4 GPa as the rate was varied in the homogenized sample. On the other hand, the samples with γ′ and γ phase exhibited higher hardness values at 0.15 mN s−1, while it remained approximately constant for the other rates. The reduced modulus increased with the loading/unloading rate and this increase was more pronounced for the sample with γ precipitates, with a higher sensitivity of the reduced modulus increase.
Beyond Historicity: Aesthetic Authenticity in Cinematic Adaptations of Non-/Anti-Realist Fiction
Authors: Dridi Yosr 
Published: September 2023

AbstractThe literature on authenticity in adaptation studies seems to be focused almost entirely on adaptations of either historical and (auto-)biographical literary texts or non-fiction narratives. The usual case studies are often generically limited to heritage and historical films, period dramas, documentaries, and biopics, to the exclusion of non-/anti-realist genres. However, there is more to adaptation than empirically and/or historically verifiable source texts, which warrants an examination of authenticity in adaptations of fantastical, science-fictional, and gothic fictions away from the fixation on historicity and veracity. This paper proposes an aesthetic (metadiscursive and experiential) outlook on authenticity in genre adaptations, namely George Miller’s adaptation of A. S. Byatt’s ‘The Djinn in the Nightingale’s Eye’, Three Thousand Years of Longing (2022); Denis Villeneuve’s adaptation of Ted Chiang’s ‘Story of Your Life’, Arrival (2016); and the different adaptations of Mary Shelley’s Frankenstein. Metadiscursively, authenticity depends on the self-consciousness of artistic representation, the extent to which the source text and its cinematic adaptation acknowledge their status as fictional narratives and their representational, medium-specific limits and potentials. Experientially, authenticity is judged by the degree of audience immersion in the storyworld, the feeling (generated by diegetic techniques) that what they are watching is experientially plausible despite the implausibility of the genre itself. Without lapsing in excessive realism and verbatim fidelity, an authentic adaptation is heedful of the paradoxes surrounding authenticity itself in any fictional narrative, attentive to their aesthetic and thematic treatment in the source text, aware of the representational affordances of the literary and cinematic media, and capable of offering the audience an immersive experience.
A cross-sectional study of sensory-motor neuropsychological function among sewage plant and sewage net workers exposed to hydrogen sulphide when handling wastewater
Authors: Goffeng Lars Ole , Austigard Åse Dalseth , Svendsen Kristin H , Skare Øivind , Einarsdottir Elin , Madsø Lene , Heldal Kari Kulvik 
Published: September 2023

Abstract

Objectives
Workers at sewage treatment plants are exposed to a complex mixture of toxins, including hydrogen sulphide (H2S). An issue of concern among sewage workers, is possible negative nervous system effects from low-level H2S exposure. Empirical neuropsychological evidence indicates both that low-dose exposure to H2S exposure affects the nervous system, and the contrary, that such exposure may facilitate nervous system function, since H2S is an endogenously produced central nervous system (CNS) gasotransmitter. The aim of this study is to describe a possible association between the H2S component of the total exposure and long-term effects on neuropsychological motor function among wastewater workers.

Methods
Workers (N = 138) treating wastewater in 6 sewage-treatment plants, or in the sewer net system participated in a cross-sectional study. H2S exposure was expressed in a dichotomous exposure variable defining currently H2S-exposed (N = 112) and unexposed referent workers (N = 26), and a variable defining a job-exposure matrix for long-term total typical workplace H2S exposure. The participants went through neuropsychological tests for hand coordination, reaction time (SRT), and balance, and completed questionnaires. Pearson chi-square test or independent samples t-test was used when comparing the currently H2S-exposed workers with the unexposed control group. Multiple linear regression was used to assess associations between the independent variables age, smoking and exposure variables, and the neuropsychological tests.

Results
The analyses indicate increased SRT in the currently H2S-exposed group compared to controls (mean [SD] = 225.8 [29.9] versus 210.7 [26.3] ms, P = 0.019), and an association between increased SRT and current H2S-exposure in the total study sample (β = 14.7, P = 0.026, R2 = 0.06, P = 0.050). Blindfolded balance testing indicates a nonsignificant trend in the total study sample, of reduced balance in the highest versus lowest H2S total long-term exposure-index group (Sway area [mean {SD}, mm2: 702 [410] versus 581 [278]), and a significant association between total long-term H2S exposure and reduced balance among smokers (Sway area, mm2 [β = 38.7, P = 0.039], mean sway, mm [β = 0.3, P = 0.015]).

Conclusion
The observed trends and associations may be due to exposure peaks in certain work operations and pinpoint the importance of minimizing and avoiding exposure peaks, also when H2S time-weighted average measurements do not exceed an occupational exposure limit of 5 ppm.
Prospects and perspectives: inferring physiological and regulatory targets for CAM from molecular and modelling approaches
Authors: Chomthong Methawi , Griffiths Howard 
Published: September 2023

Abstract

Background and Scope
This review summarizes recent advances in our understanding of Crassulacean Acid Metabolism (CAM) by integrating evolutionary, ecological, physiological, metabolic and molecular perspectives. A number of key control loops which moderate the expression of CAM phases, and their metabolic and molecular control, are explored. These include nocturnal stomatal opening, activation of phosphoenolpyruvate carboxylase by a specific protein kinase, interactions with circadian clock control, as well as daytime decarboxylation and activation of Rubisco. The vacuolar storage and release of malic acid and the interplay between the supply and demand for carbohydrate reserves are also key metabolic control points.

Future Opportunities
We identify open questions and opportunities, with experimentation informed by top-down molecular modelling approaches allied with bottom-up mechanistic modelling systems. For example, mining transcriptomic datasets using high-speed systems approaches will help to identify targets for future genetic manipulation experiments to define the regulation of CAM (whether circadian or metabolic control). We emphasize that inferences arising from computational approaches or advanced nuclear sequencing techniques can identify potential genes and transcription factors as regulatory targets. However, these outputs then require systematic evaluation, using genetic manipulation in key model organisms over a developmental progression, combining gene silencing and metabolic flux analysis and modelling to define functionality across the CAM day–night cycle. From an evolutionary perspective, the origins and function of CAM succulents and responses to water deficits are set against the mesophyll and hydraulic limitations imposed by cell and tissue succulence in contrasting morphological lineages. We highlight the interplay between traits across shoots (3D vein density, mesophyll conductance and cell shrinkage) and roots (xylem embolism and segmentation). Thus, molecular, biophysical and biochemical processes help to curtail water losses and exploit rapid rehydration during restorative rain events. In the face of a changing climate, we hope such approaches will stimulate opportunities for future research.
Cessation of berry growth coincides with leaf complete stomatal closure at pre-veraison for grapevine (Vitis vinifera) subjected to progressive drought stress
Authors: Knipfer T , Wilson N , Jorgensen-Bambach N E , McElrone A J , Bartlett M K , Castellarin S D 
Published: September 2023

Abstract

Background and Aims
Drought events have devasting impacts on grape berry production. The aim of this study was to investigate berry growth in the context of leaf stomatal closure under progressive drought stress.

Methods
Potted grapevine plants (varieties ‘Syrah’ and ‘Cabernet Sauvignon’) were evaluated at pre-verasion (30–45 d after anthesis, DAA) and post-veraison (90–107 DAA). Berry diameter, berry absolute growth rate (AGR), leaf stomatal conductance (Gs) at midday, plant water potential at predawn and midday (ΨPD and ΨMD, respectively), and soil relative water content were measured repeatedly. The ΨPD-threshold of 90 % loss in stomatal conductance (Gs10, i.e. complete stomatal closure) was determined. Data were related to plant dehydration phases I, II and III with corresponding boundaries Θ1 and Θ2, using the water potential curve method.

Key Results
At pre-veraison, berry AGR declined together with leaf Gs in response to soil drying in both varieties. Berry AGR transitioned from positive to negative (shrinkage) values when leaf Gs approached zero. The Gs10-threshold was −0.81 MPa in ‘Syrah’ and −0.74 MPa in ‘Cabernet Sauvignon’ and was linked to boundary Θ1. At post-veraison, berry AGR was negligible and negative AGR values were not intensified by increasing drought stress in either variety.

Conclusion
Leaf complete stomatal closure under progressive drought stress coincides with cessation of berry growth followed by shrinkage at pre-veraison (growth stage 1).
Synthesis of isomaltooligosaccharides using 4-O-α-d-isomaltooligosaccharylmaltooligosaccharide 1,4-α-isomaltooligosaccharohydrolase
Authors: Kitagawa Noriaki , Watanabe Hikaru , Mori Tetsuya , Kawauchi Yuki , Aga Hajime , Ushio Shimpei , Yamamoto Koryu 
Published: September 2023

ABSTRACT
Isomaltooligosaccharides (IMOs), including isomaltose, are valuable oligosaccharides, and the development of methods to synthesize high-purity IMOs has long been underway. We recently discovered a novel enzyme, 4-O-α-d-isomaltooligosaccharylmaltooligosaccharide 1,4-α-isomaltooligosaccharohydrolase (IMM-4IH), that showed promise for improving the synthesis process. In this study, we establish methods for synthesizing isomaltose and IMOs consisting of a variety of degrees of polymerization from starch using IMM-4IH. With 5% substrate, by combining IMM-4IH with 1,4-α-glucan 6-α-glucosyltransferase from Bacillus globisporus N75, the yield of isomaltose was 63.0%; incorporating isoamylase and cyclomaltodextrin glucanotransferase increased the yield to 75.3%. On the other hand, by combining IMM-4IH with 1,4-α-glucan 6-α-glucosyltransferase from Paenibacillus sp. PP710, IMOs were synthesized. The inclusion of isoamylase and α-amylase led to the 136 mM IMOs, consisting of oligosaccharides from isomaltose to isomaltodecaose, from 10% starch. The development of these efficient methods will be an important contribution to the industrial production of IMOs.
The impact of food availability on risk-induced trait responses in prey
Authors: Sheriff Michael J , Mancini Isabella , Aguiar Olivia K , DiNuzzo Eleanor R , Maloney-Buckley Sophia , Sonnega Sam , Donelan Sarah C 
Published: September 2023

Abstract
Prey respond to predation risk by altering their morphology, physiology, and behavior, responses that may come at a cost to prey foraging and growth. However, their perception of risk may depend upon the environmental context in which the interaction occurs. Here, we examined how food availability influenced prey’s responses to a nonlethal but free-ranging predator. We used an experimental mesocosm set-up of an intertidal system of green crab (Carcinus maenas) predators and dogwhelk snail (Nucella lapillus) prey, with blue mussels as the basal resource. We measured individual Nucella risk-aversion behavior (summed value of their habitat use) and their growth throughout the 28-day experiment. We found that when Nucella were exposed to predation risk, they had greater risk-aversion behavior when food was available as compared to when food was not. We also found that risk-aversion behavior increased over time in all treatments but that individuals exposed to predation risk with food always had greater risk-aversion behavior. Nucella had significantly more growth when provided with food as compared to without. In treatments with food, snails exposed to predation risk had significantly reduced growth compared to those not exposed to risk. In treatments without food, predation risk had no effect on growth. Our results support the hypothesis that greater resource availability significantly increases individual risk responses and the costs of risk avoidance, thus food magnifies risk-induced non-consumptive effects. They provide insights into context-based predation risk effects and how individuals may prioritize safety versus foraging depending upon perceived risk, food availability, and the costs of responding.
Competition for acoustic space in a temperate-forest bird community
Authors: Staniewicz Agata , Sokołowska Emilia , Muszyńska Adrianna , Budka Michał 
Published: September 2023

Abstract
Animals that communicate by acoustic signaling share a common acoustic environment. Birds are particularly vocal examples, using a wide repertoire of broadcast signals for mate attraction and territorial defense. However, interference caused by sounds that overlap in frequency and time can disrupt signal detection and reduce reproductive success. Here, we investigated competition avoidance mechanisms used by the bird community inhabiting a primeval lowland temperate forest in Białowieża, Eastern Poland. We recorded the dawn chorus at 84 locations in early and late spring and calculated dissimilarity indices of the broadcast signals to examine how species with greater song similarities use spatial and temporal partitioning to avoid competition for acoustic space throughout the breeding season. The bird community changed its use of acoustic space throughout the day and season. Birds did not use spatial partitioning of signal space when we looked at recording locations over the whole study period, but they did in a seasonal context, with species more acoustically different than expected by chance recorded at the same point in the same part of the season. Our results also indicate that daily temporal niche partitioning may only occur at certain times before sunrise, with no evidence of large-scale temporal partitioning between species vocalizing during the same 1-min recordings in daytime. These results contribute toward our understanding of the evolution of bird communication and highlight the strategies employed by different species to improve their signal transmission.
PTBGRP: predicting phage–bacteria interactions with graph representation learning on microbial heterogeneous information network
Authors: Pan Jie , You Zhuhong , You Wencai , Zhao Tian , Feng Chenlu , Zhang Xuexia , Ren Fengzhi , Ma Sanxing , Wu Fan , Wang Shiwei , Sun Yanmei 
Published: September 2023

Abstract
Identifying the potential bacteriophages (phage) candidate to treat bacterial infections plays an essential role in the research of human pathogens. Computational approaches are recognized as a valid way to predict bacteria and target phages. However, most of the current methods only utilize lower-order biological information without considering the higher-order connectivity patterns, which helps to improve the predictive accuracy. Therefore, we developed a novel microbial heterogeneous interaction network (MHIN)–based model called PTBGRP to predict new phages for bacterial hosts. Specifically, PTBGRP first constructs an MHIN by integrating phage–bacteria interaction (PBI) and six bacteria–bacteria interaction networks with their biological attributes. Then, different representation learning methods are deployed to extract higher-level biological features and lower-level topological features from MHIN. Finally, PTBGRP employs a deep neural network as the classifier to predict unknown PBI pairs based on the fused biological information. Experiment results demonstrated that PTBGRP achieves the best performance on the corresponding ESKAPE pathogens and PBI dataset when compared with state-of-art methods. In addition, case studies of Klebsiella pneumoniae and Staphylococcus aureus further indicate that the consideration of rich heterogeneous information enables PTBGRP to accurately predict PBI from a more comprehensive perspective. The webserver of the PTBGRP predictor is freely available at http://120.77.11.78/PTBGRP/.
EXPANSION: a webserver to explore the functional consequences of protein-coding alternative splice variants in cancer genomics
Authors: Arora Chakit , De Oliveira Rosa Natalia , Matic Marin , Cascone Mariastella , Miglionico Pasquale , Raimondi Francesco 
Published: September 2023

Abstract

Summary
EXPANSION (https://expansion.bioinfolab.sns.it/) is an integrated web-server to explore the functional consequences of protein-coding alternative splice variants. We combined information from Differentially Expressed (DE) protein-coding transcripts from cancer genomics, together with domain architecture, protein interaction network, and gene enrichment analysis to provide an easy-to-interpret view of the effects of protein-coding splice variants. We retrieved all the protein-coding Ensembl transcripts and mapped Interpro domains and post-translational modifications on canonical sequences to identify functionally relevant splicing events. We also retrieved isoform-specific protein–protein interactions and binding regions from IntAct to uncover isoform-specific functions via gene-set over-representation analysis. Through EXPANSION, users can analyze precalculated or user-inputted DE transcript datasets, to easily gain functional insights on any protein spliceform of interest.

Availability and Implementation
EXPANSION is freely available at http://expansion.bioinfolab.sns.it/. The code of the scripts used for EXPASION is available at: https://github.com/raimondilab/expansion. Datasets associated to this resource are available at the following URL: https://doi.org/10.5281/zenodo.8229120. The web-server was developed using Apache2 (https://https.apache.org/) and Flask (v2.0.2) (http://flask.pocoo.org/) for the web frontend and for the internal pipeline to handle back-end processes. We additionally used the following Python and JavaScript libraries at both back- and front-ends: D3 (v4), jQuery (v3.2.1), DataTables (v2.3.2), biopython (v1.79), gprofiler-officia l(v1.0.0), Mysql-connector-python (v8.0.31). To construct the API, Fast API library (v0.95.1) was used.
ScribbleDom: using scribble-annotated histology images to identify domains in spatial transcriptomics data
Authors: Rahman Mohammad Nuwaisir , Noman Abdullah Al , Turza Abir Mohammad , Abrar Mohammed Abid , Samee Md Abul Hassan , Rahman M Saifur 
Published: September 2023

Abstract

Motivation
Spatial domain identification is a very important problem in the field of spatial transcriptomics. The state-of-the-art solutions to this problem focus on unsupervised methods, as there is lack of data for a supervised learning formulation. The results obtained from these methods highlight significant opportunities for improvement.

Results
In this article, we propose a potential avenue for enhancement through the development of a semi-supervised convolutional neural network based approach. Named “ScribbleDom”, our method leverages human expert’s input as a form of semi-supervision, thereby seamlessly combines the cognitive abilities of human experts with the computational power of machines. ScribbleDom incorporates a loss function that integrates two crucial components: similarity in gene expression profiles and adherence to the valuable input of a human annotator through scribbles on histology images, providing prior knowledge about spot labels. The spatial continuity of the tissue domains is taken into account by extracting information on the spot microenvironment through convolution filters of varying sizes, in the form of “Inception” blocks. By leveraging this semi-supervised approach, ScribbleDom significantly improves the quality of spatial domains, yielding superior results both quantitatively and qualitatively. Our experiments on several benchmark datasets demonstrate the clear edge of ScribbleDom over state-of-the-art methods—between 1.82% to 169.38% improvements in adjusted Rand index for 9 of the 12 human dorsolateral prefrontal cortex samples, and 15.54% improvement in the melanoma cancer dataset. Notably, when the expert input is absent, ScribbleDom can still operate, in a fully unsupervised manner like the state-of-the-art methods, and produces results that remain competitive.

Availability and implementation
Source code is available at Github (https://github.com/1alnoman/ScribbleDom) and Zenodo (https://zenodo.org/badge/latestdoi/681572669).