bluuebunny/crossref_metadata_2025_split huggingface dataset:
Research rigor and reproducibility in research education: A CTSA institutional survey
Authors: Axfors Cathrine , Malički Mario , Goodman Steven N. 
Published: February 2024

Abstract
We assessed the rigor and reproducibility (R&R) activities of institutions funded by the National Center for Advancing Translational Sciences (NCTSA) through a survey and website search (N = 61). Of 50 institutional responses, 84% reported incorporating some form of R&R training, 68% reported devoted R&R training, 30% monitored R&R practices, and 10% incentivized them. Website searches revealed 9 (15%) freely available training curricula, and 7 (11%) institutional programs specifically created to enhance R&R. NCATS should formally integrate R&R principles into its translational science models and institutional requirements.
Multiplicity of topological systems
Authors: BURGUET DAVID , SHI RUXI 
Published: February 2024

AbstractWe define the topological multiplicity of an invertible topological system
$(X,T)$
as the minimal number k of real continuous functions
$f_1,\ldots , f_k$
such that the functions
$f_i\circ T^n$
,
$n\in {\mathbb {Z}}$
,
$1\leq i\leq k,$
span a dense linear vector space in the space of real continuous functions on X endowed with the supremum norm. We study some properties of topological systems with finite multiplicity. After giving some examples, we investigate the multiplicity of subshifts with linear growth complexity.
Scaling up the task-sharing of psychological therapies: A formative study of the PEERS smartphone application for supervision and quality assurance in rural India
Authors: Singla Daisy R. , Fernandes Luanna , Savel Katarina , Shah Ankita , Agrawal Ravindra , Bhan Anant , Nadkarni Abhijit , Sharma Akshita , Khan Azaz , Lahiri Anuja , Tugnawat Deepak , Lesh Neal , Patel Vikram , Naslund John 
Published: February 2024

Abstract
Measurement-based peer supervision is one strategy to assure the quality of psychological treatments delivered by non-mental health specialist providers. In this formative study, we aimed to 1) describe the development and 2) examine the acceptability and feasibility of PEERS (Promoting Effective mental healthcare through peER Supervision)—a novel smartphone app that aims to facilitate registering and scheduling patients, collecting patient outcomes, rating therapy quality and assessing supervision quality—among frontline treatment providers delivering behavioral activation treatment for depression. The PEERS prototype was developed and tested in 2021, and version 1 was launched in 2022. To date, 215 treatment providers (98% female; ages 30–35) in Madhya Pradesh and Goa, India, have been trained to use PEERS and 65.58% have completed the supplemental, virtual PEERS course. Focus group discussions with 98 providers were examined according to four themes—training and education, app effectiveness, user experience and adherence and data privacy and safety. This yielded commonly endorsed facilitators (e.g., collaborative learning through group supervision, the convenience of consolidated patient data), barriers (e.g., difficulties with new technologies) and suggested changes (e.g., esthetic improvements, suicide risk assessment prompt). The PEERS app has the potential to scale measurement-based peer supervision to facilitate quality assurance of psychological treatments across contexts.
Validating ensemble historical simulations of Upernavik Isstrøm (1985–2019) using observations of surface velocity and elevation
Authors: Jager Eliot , Gillet-Chaulet Fabien , Mouginot Jérémie , Millan Romain 
Published: February 2024

Abstract
The future of tidewater glaciers in response to climate warming is one of the largest sources of uncertainty in the contribution of the Greenland ice sheet to global sea-level rise. In this study, we investigate the ability of an ice-sheet model to reproduce the past evolution of the velocity and surface elevation of a tidewater glacier, Upernavik Isstrøm, by prescribing front positions. To achieve this, we run two ensembles of simulations with a Weertman and a regularised-Coulomb friction law. We show that the ice-flow model has to include a reduction in friction in the first 15 km upstream of the ice front in fast-flowing regions to capture the trends observed during the 1985–2019 period. Without this process, the ensemble model overestimates the ice flow before the retreat of the front in 2005 and does not fully reproduce its acceleration during the retreat. This results in an overestimation of the total mass loss between 1985 and 2019 of 50% (300 vs 200 Gt). Using a variance-based sensitivity analysis, we show that uncertainties in the friction law and the ice-flow law have a greater impact on the model results than surface mass balance and initial surface elevation.
Against naïve induction from experimental data
Authors: Kellen David , Cox Gregory E. , Donkin Chris , Dunn John C. , Shiffrin Richard M. 
Published: February 2024

Abstract
This commentary argues against the indictment of current experimental practices such as piecemeal testing, and the proposed integrated experiment design (IED) approach, which we see as yet another attempt at automating scientific thinking. We identify a number of undesirable features of IED that lead us to believe that its broad application will hinder scientific progress.
Are language–cognition interactions bigger than a breadbox? Integrative modeling and design space thinking temper simplistic questions about causally dense phenomena
Authors: Titone Debra , Hernández-Rivera Esteban , Iniesta Antonio , Beatty-Martínez Anne L. , Gullifer Jason W. 
Published: February 2024

Abstract
We affirm the utility of integrative modeling, according to which it is advantageous to move beyond “one-at-a-time binary paradigms” through studies that position themselves within realistic multidimensional design spaces. We extend the integrative modeling approach to a target domain with which we are familiar, the consequences of bilingualism on mind and brain, often referred to as the “bilingual advantage.” In doing so, we highlight work from our group consistent with integrative modeling.
Consensus meetings will outperform integrative experiments
Authors: Primbs Maximilian A. , Dudda Leonie A. , Andresen Pia K. , Buchanan Erin M. , Peetz Hannah K. , Silan Miguel , Lakens Daniël 
Published: February 2024

Abstract
We expect that consensus meetings, where researchers come together to discuss their theoretical viewpoints, prioritize the factors they agree are important to study, standardize their measures, and determine a smallest effect size of interest, will prove to be a more efficient solution to the lack of coordination and integration of claims in science than integrative experiments.
Beyond integrative experiment design: Systematic experimentation guided by causal discovery AI
Authors: Kummerfeld Erich , Andrews Bryan 
Published: February 2024

Abstract
Integrative experiment design is a needed improvement over ad hoc experiments, but the specific proposed method has limitations. We urge a further break with tradition through the use of an enormous untapped resource: Decades of causal discovery artificial intelligence (AI) literature on optimizing the design of systematic experimentation.
Phenomena complexity, disciplinary consensus, and experimental versus correlational research in psychological science
Authors: Simonton Dean Keith 
Published: February 2024

Abstract
The target article ignores the crucial role of correlational methods in the behavioral and social sciences. Yet such methods are often mandated by the greater complexity of the phenomena investigated. This necessity is especially conspicuous in psychological research where its position in the hierarchy of the sciences implies the need for both experimental and correlational investigations, each featuring distinct assets.
Demography as a confounding factor to explain highly diverged loci between cultivated and wild rice
Authors: Xiang-Yu Jinggong , Gu Zhili , Li Haipeng , Lu Bao-Rong 
Published: February 2024

AbstractThe domestication of rice increases the divergence between cultivated rice and its wild progenitor because of artificial selection. However, it remains unknown whether highly diverged loci in rice can be explained by neutral demographic scenarios alone. In this study, we genotyped 45 InDels (insertion/deletion) in two subspecies of Asian cultivated rice (Oryza sativa ssp. japonica and Oryza sativa ssp. indica) and their wild progenitor (O. rufipogon/O. nivara). Among them, 17 loci are highly diverged (FST > 0.4) between rice cultivars and their ancestor. We performed coalescent-based simulations on neutral demographic scenarios and found that neutral demography alone could explain the polymorphic profiles on those highly diverged loci between cultivated and wild rice. Therefore, more signatures of selection should be considered when detecting artificial selection in rice.
Contextualising the absence of standardised approaches to transitional justice in the Philippines
Authors: Destrooper Tine 
Published: February 2024

AbstractThe professionalisation, institutionalisation and standardisation of transitional justice has often been critiqued for pushing more informal, vernacular or experimental approaches off the radar. While this concern is legitimate and needs to be addressed, this article explores the continued relevance of standardised approaches, and of a shared language of transitional justice more specifically. I develop this argument against the background of recent events in the Philippines where, in May 2022, Ferdinand Marcos Jr., son of the former dictator, won the presidential elections. In this article I show that there has been a multiplicity of context-sensitive, vernacular and experimental transitional justice initiatives to deal with intersecting and multilayered legacies of violence, but that what has been missing is an overarching framework as expressed through the discourse of transitional justice, and the potential to forge collaborations and coalitions on the basis thereof. The case of the Philippines hints at the potential of a more ecological understanding of transitional justice in which justice actors involved in standardised and vernacular, formal and informal, state and non-state, top-down and bottom-up approaches recognise each other and certain shared objectives through the shared language and normativity of transitional justice.
On clustering levels of a hierarchical categorical risk factor
Authors: Campo Bavo D.C. , Antonio Katrien 
Published: February 2024

AbstractHandling nominal covariates with a large number of categories is challenging for both statistical and machine learning techniques. This problem is further exacerbated when the nominal variable has a hierarchical structure. We commonly rely on methods such as the random effects approach to incorporate these covariates in a predictive model. Nonetheless, in certain situations, even the random effects approach may encounter estimation problems. We propose the data-driven Partitioning Hierarchical Risk-factors Adaptive Top-down algorithm to reduce the hierarchically structured risk factor to its essence, by grouping similar categories at each level of the hierarchy. We work top-down and engineer several features to characterize the profile of the categories at a specific level in the hierarchy. In our workers’ compensation case study, we characterize the risk profile of an industry via its observed damage rates and claim frequencies. In addition, we use embeddings to encode the textual description of the economic activity of the insured company. These features are then used as input in a clustering algorithm to group similar categories. Our method substantially reduces the number of categories and results in a grouping that is generalizable to out-of-sample data. Moreover, we obtain a better differentiation between high-risk and low-risk companies.
Entre guerra, política e “uma visão positiva lá de casa”: Descortinando as primeiras experiências moçambicanas na senda da “World Music” (1987-1994)
Authors: FREITAS MARCO ROQUE DE 
Published: February 2024

AbstractEste artigo analisa a internacionalização de música moçambicana no âmbito da categoria de mercado “World Music”, durante o período de transição de um sistema de partido único e socialista, para um sistema multipartidário e liberal (1987-1994), enquadrado no processo de “construção da nação”. A análise comparativa de três casos – Orquestra Marrabenta Star de Moçambique, a canção “Baila Maria” do Grupo RM (Amoya), e os discos de Eyuphuro e Ghorwane (Real World Records) – confirma o recurso à World Music enquanto alternativa à letargia da indústria fonográfica do país e como veículo para promover internacionalmente a política musical de Moçambique durante a guerra civil.
Balancing Non‐CO2 GHG Emissions and Soil Carbon Change in U.S. Rice Paddies: A Retrospective Meta‐Analysis and Agricultural Modeling Study
Authors: Zhang Jingting , Tian Hanqin , You Yongfa , Liang Xin‐Zhong , Ouyang Zutao , Pan Naiqing , Pan Shufen 
Published: February 2024

AbstractU.S. rice paddies, critical for food security, are increasingly contributing to non‐CO2 greenhouse gas (GHG) emissions like methane (CH4) and nitrous oxide (N2O). Yet, the full assessment of GHG balance, considering trade‐offs between soil organic carbon (SOC) change and non‐CO2 GHG emissions, is lacking. Integrating an improved agroecosystem model with a meta‐analysis of multiple field studies, we found that U.S. rice paddies were the rapidly growing net GHG emission sources, increased 138% from 3.7 ± 1.2 Tg CO2eq yr−1 in the 1960s to 8.9 ± 2.7 Tg CO2eq yr−1 in the 2010s. CH4, as the primary contributor, accounted for 10.1 ± 2.3 Tg CO2eq yr−1 in the 2010s, alongside a notable rise in N2O emissions by 0.21 ± 0.03 Tg CO2eq yr−1. SOC change could offset 14.0% (1.45 ± 0.46 Tg CO2eq yr−1) of the climate‐warming effects of soil non‐CO2 GHG emissions in the 2010s. This escalation in net GHG emissions is linked to intensified land use, increased atmospheric CO2, higher synthetic nitrogen fertilizer and manure application, and climate change. However, no/reduced tillage and non‐continuous irrigation could reduce net soil GHG emissions by approximately 10% and non‐CO2 GHG emissions by about 39%, respectively. Despite the rise in net GHG emissions, the cost of achieving higher rice yields has decreased over time, with an average of 0.84 ± 0.18 kg CO2eq ha−1 emitted per kilogram of rice produced in the 2010s. The study suggests the potential for significant GHG emission reductions to achieve climate‐friendly rice production in the U.S. through optimizing the ratio of synthetic N to manure fertilizer, reducing tillage, and implementing intermittent irrigation.
Understanding the Diversity of CMIP6 Models in the Projection of Precipitation Over Tibetan Plateau
Authors: Qiu Hui , Zhou Tianjun , Chen Xiaolong , Wu Bo , Jiang Jie 
Published: February 2024

AbstractA reliable projection of precipitation over the Tibetan Plateau (TP) is crucial for climate adaptation activities in this climate‐sensitive region, but existing studies show a large spread in magnitude. Based on Coupled Model Intercomparison Project Phase 6 models, we investigate the TP summer precipitation projection and understand the sources of uncertainty. The results show that the TP exhibits a profound wetting trend throughout the 21st century, with precipitation increasing by 0.64 ± 0.06 mm day−1 during 2050–2099 under the SSP5–8.5 scenario. The moisture budget analysis indicates that the thermodynamical response to global warming determines the precipitation increase. However, both the thermodynamical and dynamical components contribute to the uncertainty of precipitation projection. The inter‐model spread of the thermodynamic term arises from divergent global mean warming, which is closely related to model climate sensitivity. The uncertainty of the dynamic component is driven by model‐dependent circulation changes induced by different equatorial Pacific warming rates.
Crafting chirality in three dimensions via a novel fabrication technique for bound states in the continuum metasurfaces
Authors: Haddadin Zaid , Nguyen Anna My , Poulikakos Lisa V. 
Published: February 2024

AbstractAn additional deposition step was added to a multi-step electron beam lithographic fabrication process to unlock the height dimension as an accessible parameter for resonators comprising unit cells of quasi-bound states in the continuum metasurfaces, which is essential for the geometric design of intrinsically chiral structures.
Continuous-wave operation of 1550 nm low-threshold triple-lattice photonic-crystal surface-emitting lasers
Authors: Wang Ziye , Liu Xia , Wang Pinyao , Lu Huanyu , Meng Bo , Zhang Wei , Wang Lijie , Wang Yanjing , Tong Cunzhu 
Published: February 2024

AbstractBenefitting from narrow beam divergence, photonic crystal surface-emitting lasers are expected to play an essential role in the ever-growing fields of optical communication and light detection and ranging. Lasers operating with 1.55 μm wavelengths have attracted particular attention due to their minimum fiber loss and high eye-safe threshold. However, high interband absorption significantly decreases their performance at this 1.55 μm wavelength. Therefore, stronger optical feedback is needed to reduce their threshold and thus improve the output power. Toward this goal, photonic-crystal resonators with deep holes and high dielectric contrast are often used. Nevertheless, the relevant techniques for high-contrast photonic crystals inevitably complicate fabrication and reduce the final yield. In this paper, we demonstrate the first continuous-wave operation of 1.55 μm photonic-crystal surface-emitting lasers by using a ‘triple-lattice photonic-crystal resonator’, which superimposes three lattice point groups to increase the strength of in-plane optical feedback. Using this geometry, the in-plane 180° coupling can be enhanced threefold compared to the normal single-lattice structure. Detailed theoretical and experimental investigations demonstrate the much lower threshold current density of this structure compared to ‘single-lattice’ and ‘double-lattice’ photonic-crystal resonators, verifying our design principles. Our findings provide a new strategy for photonic crystal laser miniaturization, which is crucial for realizing their use in future high-speed applications.
DNA methylation patterns of FKBP5 regulatory regions in brain and blood of humanized mice and humans
Authors: Yusupov Natan , Roeh Simone , Sotillos Elliott Laura , Chang Simon , Loganathan Srivaishnavi , Urbina-Treviño Lidia , Fröhlich Anna S. , Sauer Susann , Ködel Maik , Matosin Natalie , Czamara Darina , Deussing Jan M. , Binder Elisabeth B. 
Published: February 2024

AbstractHumanized mouse models can be used to explore human gene regulatory elements (REs), which frequently lie in non-coding and less conserved genomic regions. Epigenetic modifications of gene REs, also in the context of gene x environment interactions, have not yet been explored in humanized mouse models. We applied high-accuracy measurement of DNA methylation (DNAm) via targeted bisulfite sequencing (HAM-TBS) to investigate DNAm in three tissues/brain regions (blood, prefrontal cortex and hippocampus) of mice carrying the human FK506-binding protein 5 (FKBP5) gene, an important candidate gene associated with stress-related psychiatric disorders. We explored DNAm in three functional intronic glucocorticoid-responsive elements (at introns 2, 5, and 7) of FKBP5 at baseline, in cases of differing genotype (rs1360780 single nucleotide polymorphism), and following application of the synthetic glucocorticoid dexamethasone. We compared DNAm patterns in the humanized mouse (N = 58) to those in human peripheral blood (N = 447 and N = 89) and human postmortem brain prefrontal cortex (N = 86). Overall, DNAm patterns in the humanized mouse model seem to recapitulate DNAm patterns observed in human tissue. At baseline, this was to a higher extent in brain tissue. The animal model also recapitulated effects of dexamethasone on DNAm, especially in peripheral blood and to a lesser extent effects of genotype on DNAm. The humanized mouse model could thus assist in reverse translation of human findings in psychiatry that involve genetic and epigenetic regulation in non-coding elements.
Efficacy of novel agents against cellular models of familial platelet disorder with myeloid malignancy (FPD-MM)
Authors: Mill Christopher P. , Fiskus Warren C. , DiNardo Courtney D. , Reville Patrick , Davis John A. , Birdwell Christine E. , Das Kaberi , Hou Hanxi , Takahashi Koichi , Flores Lauren , Ruan Xinjia , Su Xiaoping , Loghavi Sanam , Khoury Joseph D. , Bhalla Kapil N. 
Published: February 2024

AbstractGermline, mono-allelic mutations in RUNX1 cause familial platelet disorder (RUNX1-FPD) that evolves into myeloid malignancy (FPD-MM): MDS or AML. FPD-MM commonly harbors co-mutations in the second RUNX1 allele and/or other epigenetic regulators. Here we utilized patient-derived (PD) FPD-MM cells and established the first FPD-MM AML cell line (GMR-AML1). GMR-AML1 cells exhibited active super-enhancers of MYB, MYC, BCL2 and CDK6, augmented expressions of c-Myc, c-Myb, EVI1 and PLK1 and surface markers of AML stem cells. In longitudinally studied bone marrow cells from a patient at FPD-MM vs RUNX1-FPD state, we confirmed increased chromatin accessibility and mRNA expressions of MYB, MECOM and BCL2 in FPD-MM cells. GMR-AML1 and PD FPD-MM cells were sensitive to homoharringtonine (HHT or omacetaxine) or mebendazole-induced lethality, associated with repression of c-Myc, EVI1, PLK1, CDK6 and MCL1. Co-treatment with MB and the PLK1 inhibitor volasertib exerted synergistic in vitro lethality in GMR-AML1 cells. In luciferase-expressing GMR-AML1 xenograft model, MB, omacetaxine or volasertib monotherapy, or co-treatment with MB and volasertib, significantly reduced AML burden and improved survival in the immune-depleted mice. These findings highlight the molecular features of FPD-MM progression and demonstrate HHT, MB and/or volasertib as effective agents against cellular models of FPD-MM.
Emerging roles of circular RNAs in regulating the hallmarks of thyroid cancer
Authors: Zhou Tianjiao , Li Zheng , Jiang Yumeng , Su Kaiming , Xu Chuan , Yi Hongliang 
Published: February 2024

AbstractThyroid cancer is a prevalent endocrine malignancy with increasing incidence in recent years. Although most thyroid cancers grow slowly, they can become refractory, leading to a high mortality rate once they exhibit recurrence, metastasis, resistance to radioiodine therapy, or a lack of differentiation. However, the mechanisms underlying these malignant characteristics remain unclear. Circular RNAs, a type of closed-loop non-coding RNAs, play multiple roles in cancer. Several studies have demonstrated that circular RNAs significantly influence the development of thyroid cancers. In this review, we summarize the circular RNAs identified in thyroid cancers over the past decade according to the hallmarks of cancer. We found that eight of the 14 hallmarks of thyroid cancers are regulated by circular RNAs, whereas the other six have not been reported to be correlated with circular RNAs. This review is expected to help us better understand the roles of circular RNAs in thyroid cancers and accelerate research on the mechanisms and cure strategies for thyroid cancers.