bluuebunny/crossref_metadata_2025_split huggingface dataset:
The evolution of the internal structure of massive star-forming regions in the Milky Way as revealed by ALMA
Authors: Dib Sami 
Published: June 2023

ABSTRACT
We analyse the structure of 15 protocluster forming regions in the Milky Way using their 1.3 mm continuum emission maps from the ALMA-IMF large program. The analysis of the cloud structure is performed using the delta-variance spectrum technique. The calculated spectra display a self-similar regime on small scales as well as the presence of a prominent bump on larger scales and whose physical size, Lhub, falls in the range of ≈7000–60 000 au. These scales correspond to the sizes of the most compact clumps within the protocluster forming clouds. A significant correlation is found between Lhub and the surface density of the free–free emission estimated from the integrated flux of the H41α recombination line $\left(\Sigma _{\rm H41\alpha }^{\rm free \!-\! free}\right)$ as well as a significant anticorrelation between Lhub and the ratio of the 1.3–3 mm continuum emission fluxes $\left(S_{\rm 1.3 \, mm}^{\rm cloud}/S_{\rm 3 \, mm}^{\rm cloud}\right)$. Smaller values of $\left(S_{\rm 1.3 \, mm}^{\rm cloud}/S_{\rm 3 \, mm}^{\rm cloud}\right)$ and larger values of $\Sigma _{\rm H41\alpha }^{\rm free \!-\! free}$ correspond to more advanced evolutionary stages of the protocluster forming clumps. Hence, our results suggest that the sizes of the densest regions in the clouds are directly linked to their evolutionary stage and to their star formation activity with more evolved clouds having larger protocluster forming clumps. This is an indication that gravity plays a vital role in regulating the size, mass growth, and star formation activity of these clumps with ongoing gas accretion.
The tiered radio extragalactic continuum (T-RECS) simulation II: H i emission and continuum-H i cross-correlation
Authors: Bonaldi Anna , Hartley Philippa , Ronconi Tommaso , De Zotti Gianfranco , Bonato Matteo 
Published: June 2023

ABSTRACT
In this paper, we extend the Tiered Radio Extragalactic Continuum Simulation (T-RECS) to include H i emission. The H i T-RECS model is based on the most recent H i mass function estimates, combined with prescriptions to convert H i mass to total integrated H i flux. It further models source size, morphology, and kinematics, including rotational velocity and H i line width. The continuum T-RECS model is updated to improve the agreement with deeper number counts available at 150 MHz. The model for star-forming galaxies (SFGs) is also modified according to the most recent indications of a star formation rate (SFR)–radio luminosity relation, which depends primarily on stellar mass rather than redshift. We further introduce prescriptions to associate an H i mass with the T-RECS radio continuum SFG and active galactic nuclei (AGN) populations. This gives us a way to meaningfully associate counterparts between H i and continuum catalogues, thus building H i× continuum simulated observations. Clustering properties of the sources in both H i and the continuum are reproduced by associating the galaxies with dark matter haloes in a cosmological simulation. We deliver a set of mock catalogues as well as the code to produce them, which can be used for simulating observations and predicting results from radio surveys with existing and forthcoming radio facilities, such as the Square Kilometre Array (SKA).
Divergent directed evolution of a TetR-type repressor towards aromatic molecules
Authors: Nasr Mohamed A , Martin Vincent J J , Kwan David H 
Published: June 2023

AbstractReprogramming cellular behaviour is one of the hallmarks of synthetic biology. To this end, prokaryotic allosteric transcription factors (aTF) have been repurposed as versatile tools for processing small molecule signals into cellular responses. Expanding the toolbox of aTFs that recognize new inducer molecules is of considerable interest in many applications. Here, we first establish a resorcinol responsive aTF-based biosensor in Escherichia coli using the TetR-family repressor RolR from Corynebacterium glutamicum. We then perform an iterative walk along the fitness landscape of RolR to identify new inducer specificities, namely catechol, methyl catechol, caffeic acid, protocatechuate, L-DOPA, and the tumour biomarker homovanillic acid. Finally, we demonstrate the versatility of these engineered aTFs by transplanting them into the model eukaryote Saccharomyces cerevisiae. This work provides a framework for efficient aTF engineering to expand ligand specificity towards novel molecules on laboratory timescales, which, more broadly, is invaluable across a wide range of applications such as protein and metabolic engineering, as well as point-of-care diagnostics.
Replication DNA polymerases, genome instability and cancer therapies
Authors: Strauss Juliet D , Pursell Zachary F 
Published: June 2023

Abstract
It has been over a decade since the initial identification of exonuclease domain mutations in the genes encoding the catalytic subunits of replication DNA polymerases ϵ and δ (POLE and POLD1) in tumors from highly mutated endometrial and colorectal cancers. Interest in studying POLE and POLD1 has increased significantly since then. Prior to those landmark cancer genome sequencing studies, it was well documented that mutations in replication DNA polymerases that reduced their DNA synthesis accuracy, their exonuclease activity or their interactions with other factors could lead to increased mutagenesis, DNA damage and even tumorigenesis in mice. There are several recent, well-written reviews of replication DNA polymerases. The aim of this review is to gather and review in some detail recent studies of DNA polymerases ϵ and δ as they pertain to genome instability, cancer and potential therapeutic treatments. The focus here is primarily on recent informative studies on the significance of mutations in genes encoding their catalytic subunits (POLE and POLD1), mutational signatures, mutations in associated genes, model organisms, and the utility of chemotherapy and immune checkpoint inhibition in polymerase mutant tumors.
Hypertension in chronic kidney disease—treatment standard 2023
Authors: Georgianos Panagiotis I , Agarwal Rajiv 
Published: June 2023

ABSTRACT
Hypertension is very common and remains often poorly controlled in patients with chronic kidney disease (CKD). Accurate blood pressure (BP) measurement is the essential first step in the diagnosis and management of hypertension. Dietary sodium restriction is often overlooked, but can improve BP control, especially among patients treated with an agent to block the renin–angiotensin system. In the presence of very high albuminuria, international guidelines consistently and strongly recommend the use of an angiotensin-converting enzyme inhibitor or an angiotensin receptor blocker as the antihypertensive agent of first choice. Long-acting dihydropyridine calcium channel blockers and diuretics are reasonable second- and third-line therapeutic options. For patients with treatment-resistant hypertension, guidelines recommend the addition of spironolactone to the baseline antihypertensive regimen. However, the associated risk of hyperkalemia restricts the broad utilization of spironolactone in patients with moderate-to-advanced CKD. Evidence from the CLICK (Chlorthalidone in Chronic Kidney Disease) trial indicates that the thiazide-like diuretic chlorthalidone is effective and serves as an alternative therapeutic opportunity for patients with stage 4 CKD and uncontrolled hypertension, including those with treatment-resistant hypertension. Chlorthalidone can also mitigate the risk of hyperkalemia to enable the concomitant use of spironolactone, but this combination requires careful monitoring of BP and kidney function for the prevention of adverse events. Emerging agents, such as the non-steroidal mineralocorticoid receptor antagonist ocedurenone, dual endothelin receptor antagonist aprocitentan and the aldosterone synthase inhibitor baxdrostat offer novel targets and strategies to control BP better. Larger and longer term clinical trials are needed to demonstrate the safety and efficacy of these novel therapies in the future. In this article, we review the current standards of treatment and discuss novel developments in pathophysiology, diagnosis, outcome prediction and management of hypertension in patients with CKD.
Warming-induced phenological mismatch between trees and shrubs explains high-elevation forest expansion
Authors: Li Xiaoxia , Liang Eryuan , Camarero J Julio , Rossi Sergio , Zhang Jingtian , Zhu Haifeng , Fu Yongshuo H , Sun Jian , Wang Tao , Piao Shilong , Peñuelas Josep 
Published: June 2023

ABSTRACT
Despite the importance of species interaction in modulating the range shifts of plants, little is known about the responses of coexisting life forms to a warmer climate. Here, we combine long-term monitoring of cambial phenology in sympatric trees and shrubs at two treelines of the Tibetan Plateau, with a meta-analysis of ring-width series from 344 shrubs and 575 trees paired across 11 alpine treelines in the Northern Hemisphere. Under a spring warming of +1°C, xylem resumption advances by 2–4 days in trees, but delays by 3–8 days in shrubs. The divergent phenological response to warming was due to shrubs being 3.2 times more sensitive than trees to chilling accumulation. Warmer winters increased the thermal requirement for cambial reactivation in shrubs, leading to a delayed response to warmer springs. Our meta-analysis confirmed such a mechanism across continental scales. The warming-induced phenological mismatch may give a competitive advantage to trees over shrubs, which would provide a new explanation for increasing alpine treeline shifts under the context of climate change.
Response to “Plant-based diets and postprandial hyperkalemia”
Authors: St-Jules David E , Fouque Denis 
Published: June 2023

AbstractDiet therapy for hyperkalemia in people with chronic kidney disease (CKD) has shifted considerably in recent years with the observations that reported potassium intake is weakly, or not at all, associated with plasma potassium levels in this population. One of the lingering debates is whether dietary potassium presents a risk of hyperkalemia in the postprandial state. Although there is general agreement about the need for additional research, the commentary by Varshney et al contends that the available research sufficiently demonstrates that high-potassium plant foods do not pose a risk of postprandial hyperkalemia. Others argue that this remains unsettled science. Although the traditional approach of providing people with CKD lists of high-potassium foods to limit or avoid may be unnecessary, those at high risk of hyperkalemia should be encouraged to consume balanced meals and control portions, at least until some of the key research gaps in this area are resolved. This editorial critiques the analyses offered by Varshney et al and explains the rationale for a more cautious approach to care.
The predictors of paradoxical reactions, especially psoriasis, to biologic therapy—findings from the TReasure database: a 5-year follow-up study
Authors: Yagiz Burcu , Lermi Nihal , Coskun Belkis N , Dalkilic Ediz , Kiraz Sedat , Erden Abdulsamet , Ertenli Ihsan , Duran Emine , Bilgin Emre , Yılmaz Recep , Ateş Aşkın , Tufan Abdurrahman , Küçük Hamit , Mercan Ridvan , Cinaklı Haluk , Akar Servet , Yaşar Bilge Nazife Ş , Kaşifoglu Timucin , Türk Sümeyye M , Gonullu Emel Orge , Bes Cemal , Alpay Kanitez Nilufer , Emmungil Hakan , Kalyoncu Umut , Pehlivan Yavuz 
Published: June 2023

Abstract

Objectives
The objectives of this study were to assess the clinical characteristics, predictive factors, and practical algorithms of paradoxical reactions (PRs), specifically paradoxical psoriasis (PP).

Methods
The TReasure database is a web-based prospective observational cohort comprised of patients with RA and SpA from 17 centres around Turkey since 2017. A cohort study and a case–control study nestled within the cohort were identified.

Results
In total, 2867 RA and 5316 SpA patients were evaluated. The first biologic agent was found to have caused PRs in 60% of the 136 patients (1.66%) who developed the PRs. The median time interval between the PRs and biological onset was 12 months (range 1–132 months, mean 21 months). The most common types of PP, constituting 92.6% of PRs, were pustular (60.3%) and palmoplantar (30.9%). Adalimumab (30.9%), infliximab (19%) and etanercept (17.4%) were the most common agents causing the PP. In the treatment of most PP patients (73.2%), switching biologic agents was favoured, with TNF inhibitor (TNFi) chosen in 46.03% and non-TNFi in 26.9% of cases. The three most frequently selected drugs were etanercept (24.6%), secukinumab (9.5%) and adalimumab (8.7%). Only 5.17% of patients who switched to another TNFi showed progression. The odds ratios (s) for SSZ, HCQ, and LEF use were significantly higher in RA controls than in PP patients (P = 0.033, OR = 0.15; P = 0.012, OR = 0.15; and P = 0.015, OR = 0.13, respectively). In the PP group with SpA, the number of smokers was significantly higher (P = 0.003, OR: 2.0, 95% CI: 1.05, 3.81).

Conclusion
Contrary to expectations based on earlier research suggesting that paradoxical reactions develop with the class effect of biological agents, the response of patients who were shifted to another TNFi was favourable.
Linking Polygenic Risk of Schizophrenia to Variation in Magnetic Resonance Imaging Brain Measures: A Comprehensive Systematic Review
Authors: Jameei Hadis , Rakesh Divyangana , Zalesky Andrew , Cairns Murray J , Reay William R , Wray Naomi R , Di Biase Maria A 
Published: June 2023

Abstract

Background and hypothesis
Schizophrenia is highly heritable, with a polygenic effect of many genes conferring risk. Evidence on whether cumulative risk also predicts alterations in brain morphology and function is inconsistent. This systematic review examined evidence for schizophrenia polygenic risk score (sczPRS) associations with commonly used magnetic resonance imaging (MRI) measures. We expected consistent evidence to emerge for significant sczPRS associations with variation in structure and function, specifically in frontal, temporal, and insula cortices that are commonly implicated in schizophrenia pathophysiology.

Study Design
In accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we searched MEDLINE, Embase, and PsycINFO for peer-reviewed studies published between January 2013 and March 2022. Studies were screened against predetermined criteria and National Institutes of Health (NIH) quality assessment tools.

Study Results
In total, 57 studies of T1-weighted structural, diffusion, and functional MRI were included (age range = 9–80 years, Nrange = 64–76 644). We observed moderate, albeit preliminary, evidence for higher sczPRS predicting global reductions in cortical thickness and widespread variation in functional connectivity, and to a lesser extent, region-specific reductions in frontal and temporal volume and thickness. Conversely, sczPRS does not predict whole-brain surface area or gray/white matter volume. Limited evidence emerged for sczPRS associations with diffusion tensor measures of white matter microstructure in a large community sample and smaller cohorts of children and young adults. These findings were broadly consistent across community and clinical populations.

Conclusions
Our review supports the hypothesis that schizophrenia is a disorder of disrupted within and between-region brain connectivity, and points to specific whole-brain and regional MRI metrics that may provide useful intermediate phenotypes.
Beyond crony capitalism: financialization, flexible actors and private power in transition economies—the case of Agrokor
Authors: Stubbs Paul , Žitko Mislav 
Published: June 2023

Abstract
In this article, we provide a critique of the concept of crony capitalism as the dominant explanation of change in economies in transition-based as it is on an idealized technocratic representation of ‘free markets’. We do this through an analysis of the fall of the Croatian company Agrokor, one of the most important companies in post-socialist Southeast Europe. The Agrokor case allows for an understanding of state-economy restructurings in times of crisis, and the competing temporalities and rhythms of corporate practices, political interventions and public perceptions. Agrokor can be considered as a symbol of many of the unfolding contradictions of transnational capitalism in the semi-periphery. The nature of Agrokor’s demise is understood as a result of the hyper-financialization of the firm and the rise of transnational predatory finance. The translation of liquidity and debt crises into a fundamental restructuring of the conglomerate, ushering in a shift in power and control, is the product of active work by a range of agents and an attempted resolution, partial and unfinished, of a struggle for dominance between fractions of capital.
Segregation and Group Threat: Specifying Hispanic-White Punishment Disparity
Authors: Zvonkovich Jordan , Ulmer Jeffery T 
Published: June 2023

AbstractEvidence of racial disparity in punishment has been pervasive in the U.S. criminal justice system. Furthermore, a growing body of literature suggests that racial and ethnic disparities in criminal punishment, typically motivated by group threat perspectives, vary in relation to social and contextual conditions of court jurisdictions. One important factor relevant to minority threat and intergroup contact is segregation, yet research on social contexts and criminal sentencing has largely ignored this feature of local social structure. However, segregation might condition the effects of minority population size on dominant group threat responses in social control. Focusing on Hispanic-White segregation, we assess competing hypotheses regarding segregation’s role in conditioning Hispanic-White punishment disadvantage. Pennsylvania, which has recently undergone significant population change related to these processes, presents a unique and valuable context for study. Analyses of statewide sentencing data from 2013–2017 along with Census and American Community Survey data, reveal that Hispanic-White residential segregation seems to foster greater Hispanic punishment disadvantage. Moreover, segregation specifies the association between local Hispanic population size and Hispanic-White incarceration disparity. In counties with both greater than average Hispanic population share and greater segregation, Hispanic defendants faced even greater incarceration disparities.
Artificial Intelligence Supports Automated Characterization of Differentiated Human Pluripotent Stem Cells
Authors: Marzec-Schmidt Katarzyna , Ghosheh Nidal , Stahlschmidt Sören Richard , Küppers-Munther Barbara , Synnergren Jane , Ulfenborg Benjamin 
Published: June 2023

Abstract
Revolutionary advances in AI and deep learning in recent years have resulted in an upsurge of papers exploring applications within the biomedical field. Within stem cell research, promising results have been reported from analyses of microscopy images to, that is, distinguish between pluripotent stem cells and differentiated cell types derived from stem cells. In this work, we investigated the possibility of using a deep learning model to predict the differentiation stage of pluripotent stem cells undergoing differentiation toward hepatocytes, based on morphological features of cell cultures. We were able to achieve close to perfect classification of images from early and late time points during differentiation, and this aligned very well with the experimental validation of cell identity and function. Our results suggest that deep learning models can distinguish between different cell morphologies, and provide alternative means of semi-automated functional characterization of stem cell cultures.
Advancing the science of policy implementation: a call to action for the implementation science field
Authors: Chriqui Jamie F , Asada Yuka , Smith Natalie Riva , Kroll-Desrosiers Aimee , Lemon Stephenie C 
Published: June 2023

Abstract
Public policies have been essential in addressing many of the most pressing public health problems in the USA and around the world. A large and convincing body of multidisciplinary research has established the impacts or effectiveness of public policies, such as smoke-free air laws and nutrition standards, on improving health outcomes and behaviors. Most of this research assumes that because an evidence-based policy is adopted or takes effect, it is implemented as intended. This assumption, however, is often incorrect. Like with clinical guidelines and other interventions, implementation science has an important role to play in promoting the uptake and implementation of evidence-based public policies that promote public health. To realize this potential, there remains a critical need to first establish a common understanding of what public policy is, the role of specific policies in the context of implementation (i.e., is it the evidence-based intervention or the implementation strategy?), and to establish an appropriate methodological foundation for the field of policy implementation science. We recommend that the field must evolve to (i) include policy experts and actors on policy implementation science study teams; (ii) identify theories, models, and frameworks that are suitable for policy implementation science; (iii) identify policy implementation strategies; (iv) adapt and/or identify study designs best suited for policy implementation science research; and (v) identify appropriate policy implementation outcome measures.
Local adaptation to aridity in a widely distributed angiosperm tree species is mediated by seasonal increase of sugars and reduced growth
Authors: Piper Frida I , Fajardo Alex 
Published: June 2023

Abstract
Trees in dry climates often have higher concentrations of total non-structural carbohydrates (NSC = starch + soluble sugars [SS]) and grow less than conspecifics in more humid climates. This pattern might result from the growth being more constrained by aridity than the carbon (C) gain, or reflect local adaptation to aridity, since NSC fuel metabolism and ensure adequate osmoregulation through the supply of SS, while low growth reduces water and C demands. It has been further proposed that C allocation to storage could come at the expense of growth (i.e., a growth–storage trade-off). We examined whether NSC and growth reflect the local adaptation to aridity in Embothrium coccineum J. R. Forst & G. Forst. (Proteaceae), a species with an exceptionally wide niche. To control for any influence of phenotypic plasticity on NSC and growth, we collected seeds from dry (46° 16′S, 71° 55′W, 500 mm year−1) and moist (45° 24′S, 72° 40′W, &gt;2500 mm year−1) climates and grew seedlings in a common garden experiment for 3 years. We then compared the NSC and SS concentrations and pools (i.e., total contents) and the biomass of seedlings at spring, summer and fall. Seedlings from the dry climate had significantly lower biomass and similar NSC concentrations and pools as seedlings from moist climate, suggesting that reduced growth in arid environments does not result from a prioritization of C allocation to storage but that it confers advantages under aridity (e.g., lower transpiration area). Across organs, starch and NSC decreased similarly in seedlings from both climates from spring onward. However, root and stem SS concentrations increased during the growing season, and these increases were significantly higher in seedlings from the dry climate. The greater SS accumulation in seedlings from the dry climate compared with those from the moist climate demonstrates ecotypic differentiation in the seasonal dynamics of SS, suggesting that SS underlie local adaptation to aridity.