bluuebunny/crossref_metadata_2025_split huggingface dataset:
Algorithmic bias and racial inequality: a critical review
Authors: Kasy Maximilian 
Published: November 2024

Abstract
Most definitions of algorithmic bias and fairness encode decision-maker interests, such as profits, rather than the interests of disadvantaged groups (e.g. racial minorities): bias is defined as a deviation from profit maximization. Future research should instead focus on the causal effect of automated decisions on the distribution of welfare, both across and within groups. The literature emphasizes some apparent contradictions between different notions of fairness, and between fairness and profits. These contradictions vanish, however, when profits are maximized. Existing work involves conceptual slippages between statistical notions of bias and misclassification errors, economic notions of profit, and normative notions of bias and fairness. Notions of bias nonetheless carry some interest within the welfare paradigm that I advocate for, if we understand bias and discrimination as mechanisms and potential points of intervention.
Do ethnic minorities have incentives to omit photographs from résumés? Experimental evidence from Germany and the Netherlands
Authors: Fernández-Reino Mariña , Rovira Martí 
Published: November 2024

Abstract
Ethnic minority job-seekers may have incentives to include or omit photographs from résumés depending on the social norms regarding this practice and the extent to which their outward appearances diverge from the majority group. To investigate minorities’ incentives to engage in a specific type of résumé whitening––omitting photographs to avoid discrimination based on phenotypical traits or religious attire––we draw on data from an audit field experiment conducted between 2016 and 2018 in the Netherlands and Germany. Our analysis highlights the challenges for anticipating discrimination (and, thus, deciding to engage in résumé whitening) since it is difficult to predict employers’ true preferences with respect to the inclusion of photographs. In the Netherlands, unveiled Turkish women were better off submitting their picture rather than omitting it, but the premium associated with the inclusion of photographs disappeared if they wore the Muslim headscarf. For unveiled Moroccan women, there was no discernible advantage or disadvantage associated with the inclusion of pictures in job applications. In contrast, in the German context, minority women with high prototypical appearance (brown phenotype or wearing the Muslim headscarf) would have incentives to omit their photographs from job applications, particularly if they wore the Muslim headscarf. For Moroccan and Turkish men in the two countries, the inclusion of pictures with different phenotypes does not affect employers’ responses. To conclude, we explore the advantages and disadvantages of blind recruitment policies (i.e. omitting all ethnic identifying cues from résumés, including photographs and names) in the European context.
Caste disparities and affirmative action in India
Authors: Deshpande Ashwini , Ramachandran Rajesh 
Published: November 2024

Abstract
This paper uses data from the National Family and Health Survey (NFHS) for India for 2019–21 to present estimates of contemporary caste gaps in education, occupational distribution, and wealth between three broad groups: Scheduled Castes–Scheduled Tribes (SC–ST), Other Backward Classes (OBCs), and Others, the latter being a proxy for higher-ranked castes and communities. We find the caste gaps continue to be significant, indicating the persistence of the traditional caste hierarchy. We then assess how these gaps have evolved since the previous round of NFHS (2015–16). We find convergence in asset ownership between OBCs and Others. Finally, using a difference-in-differences estimator, we identify the direct impact of the extension of reservations in the arena of tertiary education in 2006 to the OBCs. We find a positive impact on the probability of acquiring tertiary education in the treated cohorts of OBCs.
Rice Reference Genes: redefining reference genes in rice by mining RNA-seq datasets
Authors: Liu Xin , Tang Siyuan , Gao Yingbo , Zhang Xiaoxiang , Dong Guichun , Zhou Juan , Zhou Yong , Yang Zefeng , Huang Jianye , Yao Youli 
Published: November 2024

Abstract
Reverse transcription quantitative real-time PCR (RT-qPCR) is esteemed for its precision and reliability, positioning it as the standard for evaluating gene expression. Selecting suitable reference genes is crucial for acquiring accurate data on target gene expression. However, identifying appropriate reference genes for specific rice tissues or growth conditions has been a challenge. To overcome this, we introduce the Rice Reference Genes (RRG) tool ( https://www.rrgenes.com/ ), which assists researchers in selecting reference genes for diverse experimental conditions in rice. This tool utilizes 4404 rice-derived RNA-seq datasets, categorized by five tissue types—leaf, root, seedling, panicle, and seed—and seven stress conditions (cold, disease, drought, heat, hormone, metal, and salt), along with corresponding control groups (mock). In this research, we employed the RRG web-based tool to identify candidate reference genes in rice leaves, roots, and seedlings exposed to salt and drought stress. These candidates were rigorously tested against conventionally established reference genes, confirming their accuracy and reliability. The RRG tool is designed to be user-friendly, allowing even those with limited experience to efficiently select optimal reference genes in rice with ease.
The RALF1 peptide-FERONIA complex phosphorylates the endosomal sorting protein FREE1 to attenuate abscisic acid signaling
Authors: Fu Qiong , Li Hongbo , Wang Bingqian , Chen Weijun , Wu Dousheng , Gao Caiji , Yu Feng 
Published: November 2024

Abstract
The receptor-like kinase FERONIA (FER), together with its ligand rapid alkalinization factor 1 (RALF1) peptide, plays a crucial role in regulating stress responses, including its involvement in modulating abscisic acid (ABA) signaling. FER has been shown to activate ABA insensitive 2 in the cytoplasm, leading to the suppression of ABA signaling. However, its regulation of nucleus events in the ABA response remains unclear. FREE1, identified as a plant-specific component of the endosomal sorting complex required for transport in eukaryotes, serves as an important negative regulator in ABA signaling. In this study, we elucidate that upon RALF1 treatment, FER phosphorylates FREE1, promoting the accumulation of FREE1 protein in the nucleus in Arabidopsis (Arabidopsis thaliana). Consequently, FREE1 suppresses ABA sensitivity by inhibiting the expression of ABA-response genes. Mutating the 6 identified phosphorylation sites on FREE1, mediated by FER, to nonphosphorylable residues results in reduced nucleus localization of FREE1 and increased hypersensitivity to ABA. Our data also show that these 6 phosphorylation sites are likely involved in regulating plant survival under salt stress. Collectively, our study not only unveils an additional function of FER in attenuating ABA signaling in the nucleus but also provides a possible insight into the role of the RALF1-FER-FREE1 module in coordinating plant growth and salt stress tolerance.
The receptor MIK2 interacts with the kinase RKS1 to control quantitative disease resistance to Xanthomonas campestris
Authors: Delplace Florent , Huard-Chauveau Carine , Roux Fabrice , Roby Dominique 
Published: November 2024

Abstract
Molecular mechanisms underlying qualitative resistance have been intensively studied. In contrast, although quantitative disease resistance (QDR) is a common, durable, and broad-spectrum form of immune responses in plants, only a few related functional analyses have been reported. The atypical kinase Resistance related kinase 1 (RKS1) is a major regulator of QDR to the bacterial pathogen Xanthomonas campestris (Xcc) and is positioned in a robust protein–protein decentralized network in Arabidopsis (Arabidopsis thaliana). Among the putative interactors of RKS1 found by yeast two-hybrid screening, we identified the receptor-like kinase MDIS1-interacting receptor-like kinase 2 (MIK2). Here, using multiple complementary strategies including protein–protein interaction tests, mutant analysis, and network reconstruction, we report that MIK2 is a component of RKS1-mediated QDR to Xcc. First, by co-localization experiments, co-immunoprecipitation (Co-IP), and bimolecular fluorescence complementation, we validated the physical interaction between RKS1 and MIK2 at the plasma membrane. Using mik2 mutants, we showed that MIK2 is required for QDR and contributes to resistance to the same level as RKS1. Interestingly, a catalytic mutant of MIK2 interacted with RKS1 but was unable to fully complement the mik2-1 mutant phenotype in response to Xcc. Finally, we investigated the potential role of the MIK2–RKS1 complex as a scaffolding component for the coordination of perception events by constructing a RKS1–MIK2 centered protein–protein interaction network. Eight mutants corresponding to seven RKs in this network showed a strong alteration in QDR to Xcc. Our findings provide insights into the molecular mechanisms underlying the perception events involved in QDR to Xcc.
Seductive emails, dangerous consequences: how predatory journals, conferences, and publishers target early-career researchers
Authors: Rajakumar Hamrish Kumar 
Published: November 2024

Abstract

Background
In recent years, early-career researchers and medical students have become targets of predatory publishers and conference organizers. These groups exploit the pressure to publish and gain recognition. They often offer tempting opportunities, such as fast publication, free travel, and prestigious positions. However, these offers often hide a profit-driven agenda. They lack academic integrity. Many of these events have little or no peer review. The impact metrics they claim are often inflated, and event details are vague.

Objective
This paper aims to highlight the rise of predatory journals and conferences. It focuses on the harmful effects these organizations have on young researchers. We will identify the tactics they use. We will also point out key red flags. The goal is to help researchers, particularly medical students, understand how to navigate academic publishing and protect their careers.

Conclusion
Predatory publishers and conferences pose a growing threat to academic integrity. Young researchers are especially vulnerable to these deceptive practices. It is important for academics to recognize warning signs. They should focus on quality over quantity when publishing. Educating the next generation of researchers is essential for preserving academic credibility.
Scattering of Transverse Electric and Transverse Magnetic Waves and Quantum Dynamics Generated by non-Hermitian Hamiltonians
Authors: Loran Farhang , Mostafazadeh Ali 
Published: November 2024

Abstract
The study of the scattering of electromagnetic waves by a linear isotropic medium with planar symmetry can be reduced to that of their transverse electric (TE) and transverse magnetic (TM) modes. For situations where the medium consists of parallel homogeneous slabs, one may use the standard transfer matrix technique to address the scattering problem for these modes. We extend the utility of this technique to inhomogeneous permittivity and permeability profiles by proposing a dynamical formulation of the scattering of TE and TM waves in which the transfer matrix for the medium is given in terms of the evolution operator for an effective nonunitary quantum system. This leads to a system of dynamical equations for the reflection and transmission amplitudes. Decoupling these equations, we reduce the solution of the scattering problem for TE and TM modes to that of an initial-value problem for a Riccati equation. We discuss the application of this observation in identifying media that do not reflect TE or TM waves with a given wavenumber and incidence angle.
Understanding the social and political dimensions of research(er) assessment: evaluative flexibility and hidden criteria in promotion processes at research institutes
Authors: Ross-Hellauer Tony , Aubert Bonn Noémie , Horbach Serge P J M 
Published: November 2024

Abstract
Debates about appropriate, fair and effective ways of assessing research and researchers have raged through the scientific community for decades, recently mostly concerned with discussing the merits and limitations of metric-based, quantitative assessments versus peer review-based, qualitative alternatives. Ample attention has been paid to formal assessment criteria, building to a consensus that less emphasis should be placed on quantification, while supporting open and diverse sets of criteria. Yet the theory and evidence upon which such policy reform depends is still surprisingly sparse. Based on qualitative free-text responses from 121 respondents gathered during an international survey of active researchers, this study examines researchers’ perspectives on how criteria are applied in practice and how those being assessed perceive informal criteria to determine the outcomes of assessments. While confirming the general critique on over-emphasizing quantification, respondents particularly identify a mismatch between formal criteria and actual evaluation practices. Hidden criteria, including social, political, and demographic factors, are perceived important, especially in intransparent assessment procedures, opening up for assessors’ evaluative flexibility. This adds to ongoing discussions on the performativity of assessment criteria and lays bare a tension between the rigidity and flexibility of criteria and the extent to which these can be transparently communicated.
Tired and out of control? Effects of total and partial sleep deprivation on response inhibition under threat and no-threat conditions
Authors: Nieuwenhuys Arne , Wadsley Corey G , Sullivan Robyn , Cirillo John , Byblow Winston D 
Published: November 2024

Abstract

Study Objectives
Sleep deprivation may impair top-down inhibitory control over emotional responses (e.g. under threat). The current study examined the behavioral consequences of this phenomenon and manipulated the magnitude of individuals’ sleep deficit to determine effect thresholds.

Methods
Twenty-four healthy human participants were provided with 0, 2, 4, and 8 hours of sleep opportunity and, subsequently, performed a bimanual anticipatory response inhibition task under threat and no-threat conditions. Behavioral responses (button presses) and surface electromyography (EMG) from task effectors were collected to examine going and stopping processes.

Results
Bayesian analyses revealed that compared to 8 hours of sleep, go-trial accuracy was reduced with 0 hours of sleep. Stopping speed was reduced with 0 and 2 hours of sleep, as evidenced by longer stop-signal delays, but only in a selective stopping context. None of the outcome measures were impacted by 4 hours of sleep. Under threat, go-trial accuracy was maintained, while responses were slightly delayed and characterized by amplified EMG bursts. Stopping speed was increased under threat across both stop-all and selective stopping contexts. No evidence was observed for interactions between sleep and threat.

Conclusions
Sleep deprivation negatively affected response inhibition in a selective stopping context, with stopping speed reduced following a single night of ≤2 hours of sleep. Performance-contingent threat improved response inhibition, possibly due to a prioritizing of stopping. No evidence was observed for increased threat-related responses after sleep deprivation, suggesting that sleep deprivation and threat may impact inhibitory control via independent mechanisms.
Pregnancy-onset obstructive sleep apnea and ambulatory blood pressure
Authors: Sanapo Laura , Raker Christina , Merhi Basma , Guillen Melissa , Avalos Ashanti , Aldana Annaly , Bublitz Margaret , Bai Alice , Bourjeily Ghada 
Published: November 2024

Abstract

Study Objective
Elevated nocturnal blood pressure (BP) increases the risk for hypertensive disorders of pregnancy (HDP). Though obstructive sleep apnea (OSA) increases the risk for HDP, data on OSA, and 24-hour ambulatory blood pressure monitoring (ABPM) in pregnancy are scarce. We aim to examine the BP profile of women with pregnancy-onset OSA.

Methods
Pregnant women with overweight/obesity and snoring were recruited at &lt;13 weeks gestation and underwent level III home sleep apnea testing and 24-hour ABPM at enrollment and at 31–34 weeks’ gestation. Women with OSA at enrollment were excluded. Mean differences in nocturnal BP and 24-hour BP measurements, between women with pregnancy-onset OSA and women without OSA, were computed by multivariable linear regression.

Results
Participants (40/101) had pregnancy-onset OSA (respiratory event index (REI) ≥5 events per hour) in the third trimester. Despite no significant differences in baseline BP, nocturnal systolic and diastolic BP were significantly higher in women with pregnancy-onset OSA compared to women without OSA, after adjusting for multiple covariates (mean difference 5.49 (1.45–9.52) and 3.89 (0.19–7.60), respectively). Differences in systolic BP persisted into the daytime in the OSA group. Lack of nocturnal dipping was highly prevalent in both groups, but the difference was not significant in the adjusted model.

Conclusions
Pregnancy-onset OSA in the 3rd trimester is associated with elevated nocturnal BP and daytime systolic BP. The lack of nocturnal dipping irrespective of REI cut-off in pregnant women at risk for SDB further demonstrates the limitations of REI in defining pathology in pregnancy.
Lead exposure at the feto-maternal interface: a cause for concern for fetal membrane trophoblasts
Authors: Flores-Espinosa Pilar , Menon Ramkumar , Kammala Ananth , Richardson Lauren S 
Published: November 2024

Abstract
The integrity of fetal membranes enables biological functions that protect the fetus and maintain the pregnancy. Any compromise in fetal membrane function can predispose a pregnant woman to prelabor rupture of the membranes (pPROMs) and subsequently to preterm birth (PTB). Epidemiologic data suggest that lead exposure during pregnancy is one of several risk factors associated with PTB and pPROM. This heavy metal can cross placental and fetal membrane barriers, disrupting homeostasis in these tissues. Autophagy contributes to the maintenance of fetal membrane homeostasis during gestation, and dysfunctional autophagy is associated with pPROM. In this study, we determined the mechanistic impact of lead-induced cellular changes, autophagy, senescence, and inflammation in chorion trophoblast cells (CTCs) and amnion epithelial cells (AECs) of the fetal membranes. Lead exposure in CTCs induced autophagy dysfunction (increase in LC3B-II), augmented senescence (increased SA-β-galactosidase activity), and increased the release of inflammation. In AECs, lead exposure did effect autophagy, senescence, nor inflammation. The differential changes observed in CTCs and AECs after exposure to high lead concentrations may promote the weakening of fetal membranes and contribute to preterm rupture.
Deep Trade Agreements and FDI in Partial and General Equilibrium: A Structural Estimation Framework
Authors: Larch Mario , Yotov Yoto V 
Published: November 2024

Abstract
This paper quantifies the relationships between deep trade agreements and foreign direct investment (FDI). The analysis relies on a structural framework that simultaneously enables (a) estimating the direct impact of deep trade agreements on FDI, (b) translating the partial deep trade agreement estimates into general equilibrium effects on FDI, and (c) obtaining partial deep trade agreement effects on trade and quantifying the impact of deep trade agreements on FDI through trade. The effects of deep trade agreements on both trade and FDI are sizeable, positive, and statistically significant. A counterfactual analysis suggests that together with direct and indirect channels deep trade agreements have contributed to a large but asymmetric increase in inward versus outward FDI.
Generation of Inheritable A-to-G Transitions Using Adenine Base Editing and NG-PAM Cas9 in Arabidopsis thaliana
Authors: Tan Yi Yun , Liew Yin Yin , Lee Rachelle R. Q. , Castel Baptiste , Chan Nga Man , Wan Wei-Lin , Zhang Yizhong , Hu Donghui , Chan Persis , Kim Sang-Tae , Chae Eunyoung 
Published: November 2024

Towards precise genome editing, base editors have been developed by fusing catalytically compromised Cas9 with deaminase components, mediating C-to-T (cytosine base editors) or A-to-G (adenine base editors) transition. We developed a set of vectors consisting of a 5′-NG-3′ PAM-recognizing variant of SpCas9 with adenosine deaminases TadA7.10 or TadA8e. Using a phenotype-based screen in Arabidopsis thaliana targeting multiple PDS3 intron splice sites, we achieved up to 81% somatic A-to-G editing in primary transformants at a splice acceptor site with NGG PAM, while 35% was achieved for the same target adenine with NGA PAM. Among tested vectors, pECNUS4 (Addgene #184887), carrying TadA8e, showed the highest adenine base editor (ABE) efficiency. With pECNUS4, we recreated a naturally occurring allele of DANGEROUS MIX3 ( DM3) in two generations, transgene-free, for NGC PAM. We also simultaneously base-edited four redundant DM1/SSI4 homologs, encoding nucleotide-binding leucine-rich repeat (NLR) proteins, using a single gRNA with NGA PAM targeting the conserved yet functionally crucial P-loop motif of NLR proteins. We found fixation of A-to-G in three NLR genes for all three possible adenine sites within base-editing window 3-9, as the edited genes segregate in T2. Multigene targeting succeeded in rescuing the previously reported autoimmune phenotype in two generations. Mediating desired ABE on seven NLR genes simultaneously was successful as well; above 77% editing was achieved in six of the seven possible targets in a T1 plant, with the remaining having a moderately high (32%) editing. ABE application to specifically inactivate functional motifs is anticipated to expedite the discovery of novel roles for proteins. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Overexpression of enhanced yellow fluorescent protein fused with Channelrhodopsin‐2 causes contractile dysfunction in skeletal muscle
Authors: Lamia Syeda N. , Davis Carol S. , Macpherson Peter C. D. , Willingham T. Brad , Zhang Yingfan , Liu Chengyu , Iannucci Leanne , Ganji Elahe , Harden Desmond , Bhattacharya Iman , Abraham Adam C. , Brooks Susan V. , Glancy Brian , Killian Megan L. 
Published: November 2024

AbstractSkeletal muscle activation using optogenetics has emerged as a promising technique for inducing noninvasive muscle contraction and assessing muscle function both in vivo and in vitro. Transgenic mice overexpressing the optogenetic fusion protein, Channelrhodopsin 2‐EYFP (ChR2‐EYFP) in skeletal muscle are widely used; however, overexpression of fluorescent proteins can negatively impact the functionality of activable tissues. In this study, we characterized the contractile properties of ChR2‐EYFP skeletal muscle and introduced the ChR2‐only mouse model that expresses light‐responsive ChR2 without the fluorescent EYFP in their skeletal muscles. We found a significant reduction in the contractile ability of ChR2‐EYFP muscles compared with ChR2‐only and WT mice, observed under both electrical and optogenetic stimulation paradigms. Bulk RNAseq identified the downregulation of genes associated with transmembrane transport and metabolism in ChR2‐EYFP muscle, while the ChR2‐only muscle did not demonstrate any notable deviations from WT muscle. The RNAseq results were further corroborated by a reduced protein‐level expression of ion channel‐related HCN2 in ChR2‐EYFP muscles and gluconeogenesis‐modulating FBP2 in both ChR2‐EYFP and ChR2‐only muscles. Overall, this study reveals an intrinsic skeletal dysfunction in the widely used ChR2‐EYFP mice model and underscores the importance of considering alternative optogenetic models, such as the ChR2‐only, for future research in skeletal muscle optogenetics.