bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-throughput protein characterization by complementation using DNA barcoded fragment libraries
Authors: Biggs Bradley W , Price Morgan N , Lai Dexter , Escobedo Jasmine , Fortanel Yuridia , Huang Yolanda Y , Kim Kyoungmin , Trotter Valentine V , Kuehl Jennifer V , Lui Lauren M , Chakraborty Romy , Deutschbauer Adam M , Arkin Adam P 
Published: October 2024

AbstractOur ability to predict, control, or design biological function is fundamentally limited by poorly annotated gene function. This can be particularly challenging in non-model systems. Accordingly, there is motivation for new high-throughput methods for accurate functional annotation. Here, we used complementation of auxotrophs and DNA barcode sequencing (Coaux-Seq) to enable high-throughput characterization of protein function. Fragment libraries from eleven genetically diverse bacteria were tested in twenty different auxotrophic strains of Escherichia coli to identify genes that complement missing biochemical activity. We recovered 41% of expected hits, with effectiveness ranging per source genome, and observed success even with distant E. coli relatives like Bacillus subtilis and Bacteroides thetaiotaomicron. Coaux-Seq provided the first experimental validation for 53 proteins, of which 11 are less than 40% identical to an experimentally characterized protein. Among the unexpected function identified was a sulfate uptake transporter, an O-succinylhomoserine sulfhydrylase for methionine synthesis, and an aminotransferase. We also identified instances of cross-feeding wherein protein overexpression and nearby non-auxotrophic strains enabled growth. Altogether, Coaux-Seq’s utility is demonstrated, with future applications in ecology, health, and engineering.
Parylene-MoOx crossbar memristors as a volatile reservoir and non-volatile readout: a homogeneous reservoir computing system
Authors: Ryabova Margarita A. , Matsukatova Anna N. , Emelyanov Andrey V. , Nesmelov Alexander A. , Patsaev Timofey D. , Demin Vyacheslav A. 
Published: October 2024

A transition between the volatile and non-volatile resistive switching regimes is demonstrated in nanocomposite parylene-MoOx crossbar memristors and used for the development of a homogeneous reservoir computing system.
A negative photoconductivity photodetector based on two-dimensional Nb3Cl8
Authors: Lee Bom , Zhang Xiaojie , Kang Jinsu , Jeong Byung Joo , Cho Sooheon , Choi Kyung Hwan , Jeon Jiho , Lee Sang Hoon , Kim Dahoon , Kim Yeong Hyeop , Kim Ji-Hee , Yu Hak Ki , Choi Jae-Young 
Published: October 2024

We developed a Nb3Cl8-based photodetector with negative photoconductivity from 400 to 1050 nm, featuring high electron mobility, a strong Ion/Ioff ratio, and high responsivity, making it ideal for energy-efficient optoelectronic applications.
Revisiting Student Stories: Understanding Microaggressions and Interpersonal Conflict Within Speech-Language and Hearing Sciences Training Programs
Authors: Abdelaziz Mariam M. , Rivera Pérez Jean F. 
Published: October 2024

Purpose:
The current study revisits our previous research, delving deeper into microaggressions (MAs) and interpersonal conflict (IC) in speech, language, and hearing sciences (SLHS) training programs. Participants came from both marginalized and nonmarginalized backgrounds.

Method:
A 39-item electronic survey based on our previous research was distributed online to 236 participants of current and former SLHS students through social media and e-mail listservs.

Results:
Students that identified as belonging to marginalized and nonmarginalized groups reported high levels of MAs and IC, respectively. Linear regression revealed that the more marginalized identities a participant reported, the more aggression they experienced. Analyses also suggest that specific cultural and linguistic identities more likely predicted experiencing specific types of MAs than others. MAs and IC were largely underreported.

Conclusions:
This study highlights the quantifiable prevalence of MAs and IC in SLHS training programs. It underscores the urgent need for targeted interventions to address systemic inequities. Overall, these findings emphasize the importance of fostering an inclusive and equitable environment in SLHS, promoting cultural competence, and social justice in the professions.

Supplemental Material:

https://doi.org/10.23641/asha.27105613
The Flu-ID: A New Evidence-Based Method of Assessing Fluency in Aphasia
Authors: Gordon Jean K. , Clough Sharice 
Published: October 2024

Purpose:
Assessing fluency in aphasia is diagnostically important for determining aphasia type and severity and therapeutically important for determining appropriate treatment targets. However, wide variability in the measures and criteria used to assess fluency, as revealed by a recent survey of clinicians (Gordon & Clough, 2022), results in poor reliability. Furthermore, poor specificity in many fluency measures makes it difficult to identify the underlying impairments. Here, we introduce the Flu-ID Aphasia, an evidence-based tool that provides a more informative method of assessing fluency by capturing the range of behaviors that can affect the flow of speech in aphasia.

Method:
The development of the Flu-ID was based on prior evidence about factors underlying fluency (Clough & Gordon, 2020; Gordon & Clough, 2020) and clinical perceptions about the measurement of fluency (Gordon & Clough, 2022). Clinical utility is maximized by automated counting of fluency behaviors in an Excel template. Reliability is maximized by outlining thorough guidelines for transcription and coding. Eighteen narrative samples representing a range of fluency were coded independently by the authors to examine the Flu-ID's utility, reliability, and validity.

Results:
Overall reliability was very good, with point-to-point agreement of 86% between coders. Ten of the 12 dimensions showed good to excellent reliability. Validity analyses indicated that Flu-ID scores were similar to clinician ratings on some dimensions, but differed on others. Possible reasons and implications of the discrepancies are discussed, along with opportunities for improvement.

Conclusions:
The Flu-ID assesses fluency in aphasia using a consistent and comprehensive set of measures and semi-automated procedures to generate individual fluency profiles. The profiles generated in the current study illustrate how similar ratings of fluency can arise from different underlying impairments. Supplemental materials include an analysis template, extensive guidelines for transcription and coding, a completed sample, and a quick reference guide.

Supplemental Material:

https://doi.org/10.23641/asha.27078199
What Impacts What: Clinicians' Perspectives of Causality in Aphasia Rehabilitation
Authors: Castro Nichol , Ashaie Sameer A. 
Published: October 2024

Purpose:
Determining the prognosis of aphasia recovery is an important task for clinicians in the rehabilitation of persons with aphasia. Although there are many variables identified as impactful to aphasia recovery, it is less clear (a) how clinicians perceive causality in aphasia rehabilitation and (b) how prognostic variables interact with each other. This study aimed to understand causal relations between prognostic variables from the clinician perspective.

Method:

Ratings of perceived causality were obtained from 11 clinicians serving people with aphasia. Participants were presented with 255 directed causal relations (e.g., depression → aphasia severity), representing a total of 18 demographic, diagnostic, and psychosocial variables. Participants rated the perceived causality on a Likert scale from 0 (
no causal effect
) to 10 (
strong causal effect
). We also obtained ratings about frequency of access to information about each of the 18 variables.

Results:
A perceived causal network showed differences among variables in their perceived causality. There were many causal relations identified, particularly between diagnostic and psychosocial variables. The variables with the strongest perceived causality were predominantly psychosocial variables, including depression, social support, and participation. However, these psychosocial variables were also the variables that clinicians had the least frequent access to information about. There were also notable differences between participants in their perceived causal networks.

Conclusions:
Clinicians hold valuable information about aphasia rehabilitation, including what variables are important to aphasia recovery. Understanding the complexity of interaction among prognostic variables and obtaining data from clinicians about prognostic variables and causality will advance the rehabilitation of aphasia.

Supplemental Material:

https://doi.org/10.23641/asha.27105865
Recognizing and Resisting Ableist Language in Schools: Suggestions for School-Based Speech-Language Pathologists and Related Professionals
Authors: Bottema-Beutel Kristen , Sasson Noah J. , McKinnon Rachael , Braun Caroline , Guo Ruoxi , Hand Brittany N. , Kapp Steven K. , Espinas Daniel R. , Bailin Aiyana , Lester Jessica Nina , Yu Betty 
Published: October 2024

Purpose:
The language that school professionals use to describe disabled students can reveal and perpetuate ableist assumptions. Professionals' language choices can also challenge ableist attitudes to help create more inclusive, equitable learning environments. This tutorial seeks to guide speech-language pathologists (SLPs) and other school professionals to identify ableist language, understand the ableist ideologies that such language reveals, and develop strategies to implement ways of communicating with and about disabled students that align with an anti-ableist stance. We offer a brief description of ableism in schools, describe models of disability and their varying alignments toward ableist ideologies, and identify ways in which language can reflect and perpetuate ableism. Using Individualized Education Program goals as an example, we examine the ways in which ableist language can manifest in school practices. Finally, we provide suggestions to guide SLPs and other school professionals to examine and change their language to better align with an anti-ableist stance.

Conclusions:
School professionals' language use is not neutral and may reveal and maintain ableist assumptions about disability and disabled students. While dismantling ableism requires systemic change, we suggest that individual professionals can use language in ways that resist ableism and powerfully impact their students' educational experiences.
Grey‐box modelling for estimation of optimum cut point temperature of crude distillation column
Authors: Shahzad Junaid , Ahmad Iftikhar , Ahsan Muhammad , Ahmad Farooq , Saghir Husnain , Kano Manabu , Caliskan Hakan , Hong Hiki 
Published: October 2024

AbstractA grey‐box modelling framework was developed for the estimation of cut point temperature of a crude distillation unit (CDU) under uncertainty in crude composition and process conditions. First principle (FP) model of CDU was developed for Pakistani crudes from Zamzama and Kunnar fields. A hybrid methodology based on the integration of Taguchi method and genetic algorithm (GA) was employed to estimate the optimal cut point temperature for various sets of process variables. Optimised datasets were utilised to develop an artificial neural networks (ANN) model for the prediction of optimum values of cut points. The ANN model was then used to replace the hybrid framework of the Taguchi method and the GA. The integration of the ANN and FP model makes it a grey‐box (GB) model. For the case of Zamama crude, the GB model helped in the decrease of up to 38.93% in energy required per kilo barrel of diesel and an 8.2% increase in diesel production compared to the stand‐alone FP model under uncertainty. Similarly, for Kunnar crude, up to 18.87% decrease in energy required per kilo barrel of diesel and a 33.96% increase in diesel production was observed in comparison to the stand‐alone FP model.
A fused score computation approach to reflect the overlap between the predicted box and the ground truth in pedestrian detection
Authors: Chen Zefei , Lin Yongjie , Xu Jianmin , Lu Kai , Huang Zihao 
Published: October 2024

AbstractIn pedestrian detection task, numerous predicted boxes and their corresponding scores are generated and these scores are used to filter these predicted boxes by non‐maximum suppression. This paper analysed the training process of the popular anchor‐based pedestrian detection models (e.g. YOLO and Faster RCNN), and found that the score of the predicted box reflects the overlap between the corresponding anchor and the ground truth, rather than the predicted box itself. Due to the many‐to‐one strategy adopted by anchor‐based methods, multiple predicted boxes could be generated around one predicted box. This study refers to the number of other predicted boxes around the target predicted box as its local density. When a predicted box has a higher local density, it should have a greater overlap with the ground truth. Therefore, this study proposed the fused score by introducing local density into the score. The experiments showed that replacing the score with the fused score can effectively improve the model's detection accuracy. The code and experiments will soon be open‐sourced at https://github.com/zefeichen/FusedScore.
Optical and near-infrared photometry of 94 type II supernovae from the Carnegie Supernova Project
Authors: Anderson J. P. , Contreras C. , Stritzinger M. D. , Hamuy M. , Phillips M. M. , Suntzeff N. B. , Morrell N. , González-Gaitán S. , Gutiérrez C. P. , Burns C. R. , Hsiao E. Y. , Anais J. , Ashall C. , Baltay C. , Baron E. , Bersten M. , Busta L. , Castellón S. , de Jaeger T. , DePoy D. , Filippenko A. V. , Folatelli G. , Förster F. , Galbany L. , Gall C. , Goobar A. , Gonzalez C. , Hadjiyska E. , Hoeflich P. , Krisciunas K. , Krzemiński W. , Li W. , Madore B. , Marshall J. , Martinez L. , Nugent P. , Pessi P. J. , Piro A. L. , Rheault J.-P. , Ryder S. , Serón J. , Shappee B. J. , Taddia F. , Torres S. , Thomas-Osip J. , Uddin S. 
Published: October 2024

Context. Type II supernovae (SNe II) mark the endpoint in the lives of hydrogen-rich massive stars. Their large explosion energies and luminosities allow us to measure distances, metallicities, and star formation rates into the distant Universe. To fully exploit their use in answering different astrophysical problems, high-quality low-redshift data sets are required. Such samples are vital to understand the physics of SNe II, but also to serve as calibrators for distinct – and often lower-quality – samples.
Aims. We present uBgVri optical and YJH near-infrared (NIR) photometry for 94 low-redshift SNe II observed by the Carnegie Supernova Project (CSP). A total of 9817 optical and 1872 NIR photometric data points are released, leading to a sample of high-quality SN II light curves during the first ∼150 days post explosion on a well-calibrated photometric system.
Methods. The sample is presented and its properties are analysed and discussed through comparison to literature events. We also focus on individual SNe II as examples of classically defined subtypes and outlier objects. Making a cut in the plateau decline rate of our sample (s2), a new subsample of fast-declining SNe II is presented.
Results. The sample has a median redshift of 0.015, with the nearest event at 0.001 and the most distant at 0.07. At optical wavelengths (V), the sample has a median cadence of 4.7 days over the course of a median coverage of 80 days. In the NIR (J), the median cadence is 7.2 days over the course of 59 days. The fast-declining subsample is more luminous than the full sample and shows shorter plateau phases. Of the non-standard SNe II highlighted, SN 2009A particularly stands out with a steeply declining then rising light curve, together with what appears to be two superimposed P-Cygni profiles of Hα in its spectra. We outline the significant utility of these data, and finally provide an outlook of future SN II science.
High-resolution spectroscopy of detached eclipsing binaries during total eclipses
Authors: Hełminiak K. G. , Olszewska J. M. , Puciata-Mroczynska M. , Pawar T. 
Published: October 2024

Context. We present results of high-resolution spectroscopic observations of detached eclipsing binaries (DEBs) with total eclipses, for which UVES spectra were obtained during the phase of totality. These observations serve as a key way to determine the age and initial metallicity of the systems and to verify evolutionary phases of their components and distances.
Aims. With the additional, independent information concerning the effective temperature and metallicity of one of the components, we aim to estimate the precise ages of the studied binaries and show the usefulness of totality spectra. The second goal was to provide precise orbital and physical stellar parameters of the components of systems in question.
Methods. Using the VLT/UVES, we obtained high-resolution spectra of 11 DEBs during their total-eclipse phase. Atmospheric parameters of then-visible (larger) components were obtained with iSpec. With additional spectroscopy from the Comprehensive Research with Échelles on the Most interesting Eclipsing binaries (CRÉME) project, public archives, and literature, we obtained radial-velocity (RV) measurements, from which orbital parameters were calculated. Photometric time-series observations from TESS and ASAS were modelled with the JKTEBOP code, and, combined with RV-based results, they allowed us to obtain physical parameters for nine double-lined systems from our sample. All the available data were used to constrain the ages with our own approach, utilising MESA isochrones. Reddening-free, isochrone-based distances were also estimated and confronted with Gaia Data Release 3 (GDR3) results.
Results. We show that single spectroscopic observations taken during a total eclipse can break the age-metallicity degeneracy and allow for the precise determination of the age of a DEB. With high-quality spectroscopic and photometric data, we are able to reach a 5−10% level of uncertainty (e.g. 724−24+52 Myr). Even for single-lined DEBs, where absolute masses are not possible to obtain, the spectroscopic analysis of one of the components allows one to put strong constraints on the properties of both stars. For some cases, we noted inconsistencies between isochrone-based and GDR3 distances. For one binary, which could not be fitted with a single isochrone (RZ Eri), we suggest a new explanation.
Compact and high excitation molecular clumps in the extended ultraviolet disk of M83
Authors: Koda Jin , Combes Françoise , Rubio Monica , Andersen Morten , Bigiel Frank , Gil de Paz Armando , Junais  , Lee Amanda M , Meyer Jennifer Donovan , Morokuma-Matsui Kana , Yagi Masafumi , Zavagno Annie 
Published: October 2024

Context. The extended ultraviolet (XUV) disks of nearby galaxies show ongoing massive-star formation, but their parental molecular clouds remain mostly undetected despite searches in CO(1–0) and CO(2–1). The recent detection of 23 clouds in the higher excitation transition CO(3–2) within the XUV disk of M83 thus requires an explanation.
Aims. We test the hypothesis introduced to explain the non-detections and recent detection simultaneously: The clouds in XUV disks have a clump-envelope structure similar to those in Galactic star-forming clouds, having dense star-forming clumps (or concentrations of multiple clumps) at their centers, which predominantly contribute to the CO(3–2) emission and are surrounded by less dense envelopes, where CO molecules are photo-dissociated due to the low-metallicity environment there.
Methods. We utilize new high-resolution ALMA CO(3–2) observations of a subset (11) of the 23 clouds in the XUV disk of M83.
Results. We confirm the compactness of the CO(3–2)-emitting dense clumps (or their concentrations), finding clump diameters below the spatial resolution of 6–9 pc. This is similar to the size of the dense gas region in the Orion A molecular cloud, a local star-forming cloud with massive-star formation.
Conclusions. The dense star-forming clumps are common between normal and XUV disks. This may also indicate that once the cloud structure is set, the process of star formation is governed by the cloud’s internal physics rather than by external triggers. This simple model explains the current observations of clouds with ongoing massive-star formation, although it may require some adjustment, for example including the effect of cloud evolution, to describe star formation in molecular clouds more generally.
On thermal conduction in the solar atmosphere: An analytical solution for nonlinear diffusivity without compact support
Authors: Furuseth S. V. , Cherry G. , Martínez-Sykora J. 
Published: October 2024

Context. The scientific community employs complicated multiphysics simulations to understand the physics in solar, stellar, and interstellar media. These must be tested against known solutions to ensure their validity. Several well-known tests exist, such as the Sod shock tube test. However, a test for nonlinear diffusivity is missing. This problem is highly relevant in the solar atmosphere, where various events release energy that subsequently diffuses by Spitzer thermal conductivity.
Aims. The aim is to derive an analytical solution for nonlinear diffusivity in 1D, 2D, and 3D, which allows for a nonzero background value. The solution is used to design a test for numerical solvers and study Spitzer conductivity in the solar atmosphere.
Methods. There exists an ideal solution assuming zero background value. We performed an analytical first-order perturbation of this solution. The first-order solution was first tested against a dedicated nonlinear diffusion solver, whereupon it was used to benchmark the single- and multifluid radiative magnetohydrodynamics code Ebysus, used to study the Sun. The theory and numerical modeling were used to investigate the role of Spitzer conductivity in the transport of energy released in a nanoflare.
Results. The derived analytical solution models nonlinear diffusivity accurately within its region of validity and approximately beyond. Various numerical schemes implemented in the Ebysus code is found to model Spitzer conductivity correctly. The energy from a representative nanoflare is found to diffuse 9 Mm within the first second of its lifetime due to Spitzer conductivity alone, strongly dependent on the electron density.
Conclusions. The analytical first-order solution is a step forward in ensuring the physical validity of intricate simulations of the Sun. Additionally, since the derivation and argumentation are general, they can easily be followed to treat other nonlinear diffusion problems.
Training in der Hämatoonkologie
Authors: Kühl Rea , Pahl Antonia , Limbach Matthias , Wegener Annika , Bertz Hartmut , Wiskemann Joachim , Otto Stephanie 
Published: October 2024

ZusammenfassungSport- und Bewegungstherapie stellt bei onkologischen Erkrankungen mittlerweile
ein etabliertes supportivmedizinisches Angebot dar. Die Evidenz zu positiven
Effekten hinsichtlich der Reduktion von Therapienebenwirkungen entwickelt sich
rasant und internationale, allgemeine Trainingsempfehlungen wurden definiert.
Aufgrund oft langwieriger und sehr intensiver Therapieprotokolle, sind
hämatoonkologische Patient*innen eine Gruppe von Patient*innen mit besonderem
und herausforderndem bewegungstherapeutischen Unterstützungsbedarf. Die
Arbeitsgruppe „Hämatoonkologie“ der NEBKO (Nationale Expertengruppe für
Bewegungstherapie in der Onkologie) hat daher wissenschaftliche Evidenz und
praktische Erfahrung zusammengetragen. Empfohlen wird ein Prozess, bestehend aus
Anamnese, Trainingsplanung, Monitoring und Aufrechterhaltung. Besprochen werden
u.a. typische Nebenwirkungen wie starke Dekonditionierung oder veränderte
Blutwerte und Komplikationen wie Graft-versus Host Disease nach allogener
Stammzelltransplantation. Ziel dieser Arbeit ist es Sport- und
Bewegungstherapeuten zu unterstützen ein individualisiertes, möglichst
evidenzbasiertes und vor allem sicheres und effektives Trainingsprogramm für
hämatoonkologische Patient*innen zusammen zu stellen.