bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design and evaluation of crowdsourcing platforms based on users’ confidence judgments
Authors: Ahmadabadi Samin Nili , Haghifam Maryam , Shah-Mansouri Vahid , Ershadmanesh Sara 
Published: August 2024

AbstractCrowdsourcing deals with solving problems by assigning them to a large number of non-experts called crowd using their spare time. In these systems, the final answer to the question is determined by summing up the votes obtained from the community. The popularity of these systems has increased by facilitating access for community members through mobile phones and the Internet. One of the issues raised in crowdsourcing is how to choose people and how to collect answers. Usually, users are separated based on their performance in a pre-test. Designing the pre-test for performance calculation is challenging; The pre-test questions should be selected to assess characteristics in individuals that are relevant to the main questions. One of the ways to increase the accuracy of crowdsourcing systems is by considering individuals’ cognitive characteristics and decision-making models to form a crowd and improve the estimation of their answer accuracy to questions. People can estimate the correctness of their responses while making a decision. The accuracy of this estimate is determined by a quantity called metacognition ability. Metacoginition is referred to the case where the confidence level is considered along with the answer to increase the accuracy of the solution. In this paper, by both mathematical and experimental analysis, we would answer the following question: Is it possible to improve the performance of a crowdsourcing system by understanding individuals’ metacognition and recording and utilizing users’ confidence in their answers?
High-throughput image processing software for the study of nuclear architecture and gene expression
Authors: Keikhosravi Adib , Almansour Faisal , Bohrer Christopher H. , Fursova Nadezda A. , Guin Krishnendu , Sood Varun , Misteli Tom , Larson Daniel R. , Pegoraro Gianluca 
Published: August 2024

AbstractHigh-throughput imaging (HTI) generates complex imaging datasets from a large number of experimental perturbations. Commercial HTI software programs for image analysis workflows typically do not allow full customization and adoption of new image processing algorithms in the analysis modules. While open-source HTI analysis platforms provide individual modules in the workflow, like nuclei segmentation, spot detection, or cell tracking, they are often limited in integrating novel analysis modules or algorithms. Here, we introduce the High-Throughput Image Processing Software (HiTIPS) to expand the range and customization of existing HTI analysis capabilities. HiTIPS incorporates advanced image processing and machine learning algorithms for automated cell and nuclei segmentation, spot signal detection, nucleus tracking, nucleus registration, spot tracking, and quantification of spot signal intensity. Furthermore, HiTIPS features a graphical user interface that is open to integration of new analysis modules for existing analysis pipelines and to adding new analysis modules. To demonstrate the utility of HiTIPS, we present three examples of image analysis workflows for high-throughput DNA FISH, immunofluorescence (IF), and live-cell imaging of transcription in single cells. Altogether, we demonstrate that HiTIPS is a user-friendly, flexible, and open-source HTI software platform for a variety of cell biology applications.
Predicting major clinical events among Canadian adults with laboratory-confirmed influenza infection using the influenza severity scale
Authors: Pott Henrique , LeBlanc Jason J. , ElSherif May , Hatchette Todd F. , McNeil Shelly A. , Andrew Melissa K. ,   the Serious Outcomes Surveillance (SOS) Network of the Canadian Immunization Research Network (CIRN), Boivin Guy , Trottier Sylvie , Diaz-Mitoma Francisco , Verschoor Chris , Stiver Grant , Bowie William , Green Karen , McGeer Allison , Johnstone Jennie , Loeb Mark , Katz Kevin , Lagacé-Wiens Phillipe , Light Bruce , McCarthy Anne , Poirier Andre , Powis Jeff , Richardson David , Semret Makeda , Smith Stephanie , Taylor Geoff , Smyth Daniel , Valiquette Louis , Webster Duncan 
Published: August 2024

AbstractWe developed and validated the Influenza Severity Scale (ISS), a standardized risk assessment for influenza, to estimate and predict the probability of major clinical events in patients with laboratory-confirmed infection. Data from the Canadian Immunization Research Network’s Serious Outcomes Surveillance Network (2011/2012–2018/2019 influenza seasons) enabled the selecting of all laboratory-confirmed influenza patients. A machine learning-based approach then identified variables, generated weighted scores, and evaluated model performance. This study included 12,954 patients with laboratory-confirmed influenza infections. The optimal scale encompassed ten variables: demographic (age and sex), health history (smoking status, chronic pulmonary disease, diabetes mellitus, and influenza vaccination status), clinical presentation (cough, sputum production, and shortness of breath), and function (need for regular support for activities of daily living). As a continuous variable, the scale had an AU-ROC of 0.73 (95% CI, 0.71–0.74). Aggregated scores classified participants into three risk categories: low (ISS < 30; 79.9% sensitivity, 51% specificity), moderate (ISS ≥ 30 but < 50; 54.5% sensitivity, 55.9% specificity), and high (ISS ≥ 50; 51.4% sensitivity, 80.5% specificity). ISS demonstrated a solid ability to identify patients with hospitalized laboratory-confirmed influenza at increased risk for Major Clinical Events, potentially impacting clinical practice and research.
Biogas potential of organosolv pretreated wheat straw as mono and co-substrate: substrate synergy and microbial dynamics
Authors: Sarkar Omprakash , Rova Ulrika , Christakopoulos Paul , Matsakas Leonidas 
Published: August 2024

AbstractAnaerobic digestion (AD) technology can potentially address the gap between energy demand and supply playing a crucial role in the production of sustainable energy from utilization of biogenic waste materials as feedstock. The biogas production from anaerobic digestion is primarily influenced by the chemical compositions and biodegradability of the feedstock. Organosolv-steam explosion offers a constructive approach as a promising pretreatment method for the fractionation of lignocellulosic biomasses delivering high cellulose content.This study showed how synergetic co-digestion serves to overcome the challenges of mono-digestion's low efficiency. Particularly, the study evaluated the digestibility of organosolv-steam pretreated wheat straw (WSOSOL) in mono as well as co-digesting substrate with cheese whey (CW) and brewery spent grains (BSG). The highest methane yield was attained with co-digestion of WSOSOL + CW (338 mL/gVS) representing an enhanced biogas output of 1–1.15 times greater than its mono digestion. An ammonium production was favored under co-digestion strategy accounting for 921 mg/L from WSOSOL + BSG. Metagenomic study was conducted to determine the predominant bacteria and archaea, as well as its variations in their populations and their functional contributions during the AD process. The Firmicutes have been identified as playing a significant role in the hydrolysis process and the initial stages of AD. An enrichment of the most prevalent archaea genera enriched were Methanobacterium, Methanothrix, and Methanosarsina. Reactors digesting simpler substrate CW followed the acetoclastic, while digesting more complex substrates like BSG and WSOSOL followed the hydrogenotrophic pathway for biomethane production. To regulate the process for an enhanced AD process to maximize CH4, a comprehensive understanding of microbial communities is beneficial.
Assessing the impact of glazing and window shade systems on view clarity
Authors: Ko Won Hee , Burgess Isabel , Schiavon Stefano , Chung Susana T. L. , MacNaughton Piers , Um Chai Yoon 
Published: August 2024

AbstractWindows provide access to daylight and outdoor views, influencing building design. Various glazing and window shade materials are used to mitigate glare, overheating and privacy issues, and they affect view clarity. Among them, we evaluated the effect of window films, electrochromic (EC) glass, and fabric shades on view clarity. We conducted an experiment with 50 participants using visual tests adapted from clinical vision tests (visual acuity, contrast sensitivity, color sensitivity) and images displayed on a computer monitor in a controlled laboratory. Window films and EC glass tints outperformed fabric shades in visual acuity, contrast sensitivity and view satisfaction with the exception of the darkest EC tint state and dark grey VLT 3% shade for color sensitivity and view satisfaction. The EC tints pose internal reflection issues and fabric shades are preferred for visual privacy. Window films and EC glass hinder participants’ blue–green color discrimination while fabric shades also decrease red–yellow color discrimination. Visual acuity predicts view satisfaction and contrast sensitivity is the strongest predictor for visual privacy. Generally, higher visible light transmittance and lower solar reflectance (darker color) enhance human visual performance. The proposed workflow provides an experimental procedure, identifies the primary variables and establishes a predictive framework for assessing view clarity of fenestration.
Morphology analysis of PEEK 450G using scanning electron microscopy directly on fast scanning calorimetry chips
Authors: Comelli Cleiton André , Yi Nan , van der Pol HenkJan , Ghita Oana 
Published: August 2024

AbstractTo explore the morphology of polyetheretherketone (PEEK), this study employed fast scanning calorimetry (FSC) and scanning electron microscopy (SEM). The objective was to observe the PEEK microstructure under various thermal profiles replicating the additive manufacturing material extrusion process. Samples were observed using SEM directly from the FSC chips, allowing high-accuracy evaluation of the microstructure relative to the thermal profiles. This approach allowed for the evaluation of the microstructure with high accuracy concerning the thermal profiles to which the samples were previously exposed. Each sample was coated with a 10 nm layer of gold–palladium (20–80% ratio), and no etching was necessary to observe the micro features of the microstructure. The approach enabled successful observation and quantification of PEEK microstructure, linking substrate temperature and temperature peaks to microstructural outcomes. Notably, temperature peaks during the process enhanced the formation of well-developed, thick lamellae due to increased chain mobility. Additionally, embryos formed post-remelting of the substrate structure were observed.
Cotton-quality fibers from complexation between anionic and cationic cellulose nanoparticles
Authors: Jaekel Esther E. , Torres Guillermo Reyes , Antonietti Markus , Rojas Orlando J. , Filonenko Svitlana 
Published: August 2024

AbstractNatural polymers are attractive sustainable materials for production of fibers and composite materials. Cotton and flux are traditional plants used to produce textiles with comforting properties while technologies like Viscose, Lyocell and Ioncell-F allowed to extent fiber use into regenerated cellulose from wood. Neither natural nor man-made fibers completely satisfy the needs for cellulose based fabrics boosting development of new approaches to bring more sustainability into the fashion. Technologies like Spinnova are arising based on the spinning of mechanically pretreated cellulose materials with a lower environmental impact though challenged by the fiber quality and strength related to the inconsistency of the mechanical fibers. Nanoscaled cellulose is an excellent solution to improve the consistency of spin fibers, but charges introduced by traditional chemical treatments prevent rebuilding native hydrogen bonding and compromise the mechanical properties especially in wet conditions. We used nanocellulose with low surface charge isolated using reactive eutectic media to spin fibers able to restore the native hydrogen bonding and enable constitutional mechanical strength of cellulose. We performed un-optimized spinning to reveal the intrinsic properties of the fibers and confirmed the preserved strength of wet fibers compliant with the low surface charge enabling further engineering towards cotton-like fabric from wood.
Polarizing and equalizing trends in international trade and Sustainable Development Goals
Authors: Malik Arunima , Lenzen Manfred , Li Mengyu , Mora Camille , Carter Sarah , Giljum Stefan , Lutter Stephan , Gómez-Paredes Jorge 
Published: August 2024

AbstractThe influence of international trade on the United Nations Sustainable Development Goals is multi-faceted. International trade can either promote or hinder progress, thus directly impacting people, economies and livelihoods. Here we explore the relevance of consumption-based proxies, which capture global demand for goods and services, to assess progress towards Sustainable Development Goals. We link these proxies to environmental and social issues for understanding trends in international outsourcing of resource and pollution-intensive production. We undertake a temporal assessment from 1990 to 2018 for the Global North and South to highlight polarizing trends that are affecting progress on achieving Sustainable Development Goals. We conclude that global trade can lead to both polarizing and equalizing trends that can influence a country’s ability to meet the 2030 Agenda for Sustainable Development.
An integrative structural study of the human full-length RAD52 at 2.2 Å resolution
Authors: Balboni Beatrice , Marotta Roberto , Rinaldi Francesco , Milordini Giulia , Varignani Giulia , Girotto Stefania , Cavalli Andrea 
Published: August 2024

AbstractHuman RAD52 (RAD52) is a DNA-binding protein involved in many DNA repair mechanisms and genomic stability maintenance. In the last few years, this protein was discovered to be a promising novel pharmacological target for anticancer strategies. Although the interest in RAD52 has exponentially grown in the previous decade, most information about its structure and mechanism still needs to be elucidated. Here, we report the 2.2 Å resolution cryo-EM reconstruction of the full-length RAD52 (FL-RAD52) protein. This allows us to describe the hydration shell of the N-terminal region of FL-RAD52, which is structured in an undecamer ring. Water molecules coordinate with protein residues to promote stabilization inside and among the protomers and within the inner DNA binding cleft to drive protein-DNA recognition. Additionally, through a multidisciplinary approach involving SEC-SAXS and computational methods, we comprehensively describe the highly flexible and dynamic organization of the C-terminal portion of FL-RAD52. This work discloses unprecedented structural details on the FL-RAD52, which will be critical for characterizing its mechanism of action and inhibitor development, particularly in the context of novel approaches to synthetic lethality and anticancer drug discovery.
Nuclear spin polarization of lactic acid via exchange of parahydrogen-polarized protons
Authors: Them Kolja , Kuhn Jule , Pravdivtsev Andrey N. , Hövener Jan-Bernd 
Published: August 2024

AbstractHyperpolarization has become a powerful tool to enhance the sensitivity of magnetic resonance. A universal tool to hyperpolarize small molecules in solution, however, has not yet emerged. Transferring hyperpolarized, labile protons between molecules is a promising approach towards this end. Therefore, hydrogenative parahydrogen-induced polarization (PHIP) was recently proposed as a source to polarize exchanging protons (PHIP-X). Here, we identified four key components that govern PHIP-X: adding the spin order, polarizing the labile proton, proton exchange, and polarization of the target nucleus. We investigated the last two steps experimentally and using simulations. We found optimal exchange rates and field cycling methods to polarize the target molecules. We also investigated the influence of spin relaxation of exchanging protons on the target polarization. It was found experimentally that transferring the polarization from protons directly bound to the target X-nucleus (here 13C) of lactate and methanol using a pulse sequence was more efficient than applying a corresponding sequence to the labile proton. Furthermore, varying the concentrations of the transfer and target molecules yielded a distinct maximum 13C polarization. We believe this work will further help to understand and optimize PHIP-X towards a broadly applicable hyperpolarization method.
Hydrogen bonding to the electron accepting group controls the absorption spectrum of a push–pull stilbene adsorbed on amorphous silica
Authors: Vörös Dóra , Proché Felix , González Leticia , Mai Sebastian 
Published: August 2024

AbstractThe photophysical and photochemical properties of push–pull photoswitches, such as stilbene derivatives, are very sensitive to their surroundings, allowing, e.g., for the control of the spectral properties or alternatively for probing the molecular environment. Here, we investigate how various adsorption motifs of 4-(N, N-Dimethylamino)-4’-nitrostilbene (DANS) on an amorphous glass surface influence its absorption spectra. Particular attention is given to the prominent first bright charge transfer state and the factors governing these modifications. The absorption spectra is simulated using time-dependent density functional theory on a large set of adsorption geometries that exhibit different kinds of molecule–surface interactions. We find that C–H⋯O interactions of the methyl or phenyl moieties with the glass affect the spectrum only marginally, whereas the dispersion interaction of the π system with the surface tends to diminish the intensity of the first absorption band. Moreover, an enhancement of the push–pull properties of DANS and a significant redshift occur whenever O–H⋯O hydrogen bonds with the NO2 group are present, whereas a hydrogen bond O–H⋯N to the NMe2 group results in a blueshift.
Structural characterization of DNA-binding domain of essential mammalian protein TTF 1
Authors: Singh Gajender , Bhopale Abhinetra Jagdish , Khatri Saloni , Prakash Prashant , Kumar Rajnish , Singh Sukh Mahendra , Singh Samarendra Kumar 
Published: August 2024

Abstract
Transcription Termination Factor 1 (TTF1) is a multifunctional mammalian protein with vital roles in various cellular processes, including Pol I-mediated transcription initiation and termination, pre-rRNA processing, chromatin remodelling, DNA damage repair, and polar replication fork arrest. It comprises two distinct functional regions; the N-terminal regulatory region (1-445 aa), and the C-terminal catalytic region (445-859 aa). The Myb domain located at the C-terminal region is a conserved DNA binding domain spanning from 550 to 732 aa (183 residues). Despite its critical role in various cellular processes, the physical structure of TTF1 remains unsolved. Attempts to purify the functional TTF1 protein have been unsuccessful till date. Therefore, we focused on characterizing the Myb domain of this essential protein. We started with predicting a 3-D model of the Myb domain using homology modelling, and ab-initio method. We then determined its stability through MD simulation in an explicit solvent. The model predicted is highly stable, which stabilizes at 200ns. To experimentally validate the computational model, we cloned and expressed the codon optimized Myb domain into a bacterial expression vector and purified the protein to homogeneity. Further, characterization of the protein shows that, Myb domain is predominantly helical (65%) and is alone sufficient to bind the Sal Box DNA. This is the first-ever study to report a complete in silico model of the Myb domain, which is physically characterized. The above study will pave the way towards solving the atomic structure of this essential mammalian protein.
The structural biology and dynamics of malate dehydrogenases
Authors: Berndsen Christopher E. , Bell Jessica K. 
Published: August 2024

Abstract
Malate dehydrogenase (MDH) enzymes catalyze the reversible oxidoreduction of malate to oxaloacetate using NAD(P) as a cofactor. This reaction is vital for metabolism and the exchange of reducing equivalents between cellular compartments. There are more than 100 structures of MDH in the Protein Data Bank, representing species from archaea, bacteria, and eukaryotes. This conserved family of enzymes shares a common nucleotide-binding domain, substrate-binding domain, and subunits associate to form a dimeric or a tetrameric enzyme. Despite the variety of crystallization conditions and ligands in the experimental structures, the conformation and configuration of MDH are similar. The quaternary structure and active site dynamics account for most conformational differences in the experimental MDH structures. Oligomerization appears essential for activity despite each subunit having a structurally independent active site. There are two dynamic regions within the active site that influence substrate binding and possibly catalysis, with one of these regions adjoining the subunit interface. In this review, we introduce the reader to the general structural framework of MDH highlighting the conservation of certain features and pointing out unique differences that regulate MDH enzyme activity.
Relations Among Multiple Dimensions of Self-Reported Listening Effort in Response to an Auditory Psychomotor Vigilance Task
Authors: Golob Edward J. , Olayo Ricardo C. , Brown Denver M. Y. , Mock Jeffrey R. 
Published: August 2024

Purpose:
Listening effort is a broad construct, and there is no consensus on how to subdivide listening effort into dimensions. This project focuses on the subjective experience of effortful listening and tests if cognitive workload, mental fatigue, and mood are interrelated dimensions.

Method:

Two online studies tested young adults (
n
= 74 and
n
= 195) and measured subjective workload, fatigue (subscales of fatigue and energy), and mood (subscales of positive and negative mood) before and after a challenging listening task. In the listening effort task, participants responded to intermittent 1-kHz target tones in continuous white noise for approximately 12 min.

Results:
Correlations and principal component analysis showed that fatigue and mood were distinct but interrelated constructs that weakly correlated with workload. Effortful listening provoked increased fatigue and decreased energy and positive mood yet did not influence negative mood or workload.

Conclusions:
The findings suggest that self-reported listening effort has multiple dimensions that can have different responses to the same effortful listening episode. The results can help guide evidence-based development of clinical listening effort tests and may reveal mechanisms for how listening effort relates to quality of life in those with hearing impairment.

Supplemental Material:

https://doi.org/10.23641/asha.26418976