bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visualization of the composition of the urinary fluorescent metabolome. Why is it important to consider initial urine concentration?
Authors: Dubayová Katarína , Birková Anna , Lešo Martin , Žilková Jaroslava , Karabinoš Anton , Mareková Mária , Stupák Marek 
Published: July 2023

Abstract
Urine is a highly complex fluorescent system, the fluorescence of which can be affected by many factors, including the often-ignored initial urine concentration in comprehensive fluorescent urine analysis. In this study, a total urine fluorescent metabolome profile (uTFMP) was created as a three-dimensional fluorescence profile of serial synchronous spectra of urine diluted by geometric progression. uTFMP was generated using software designed for this purpose after recalculating the 3D data concerning the initial urine concentration. It can be presented as a contour map (top view) or as a more illustrative and straightforward simple curve, thus usable in various medicinal applications.
Could normalization improve robustness of abdominal MRI radiomic features?
Authors: Giannini Valentina , Panic Jovana , Regge Daniele , Balestra Gabriella , Rosati Samanta 
Published: July 2023

Abstract
Radiomics-based systems could improve the management of oncological patients by supporting cancer diagnosis, treatment planning, and response assessment. However, one of the main limitations of these systems is the generalizability and reproducibility of results when they are applied to images acquired in different hospitals by different scanners. Normalization has been introduced to mitigate this issue, and two main approaches have been proposed: one rescales the image intensities (image normalization), the other the feature distributions for each center (feature normalization). The aim of this study is to evaluate how different image and feature normalization methods impact the robustness of 93 radiomics features acquired using a multicenter and multi-scanner abdominal Magnetic Resonance Imaging (MRI) dataset. To this scope, 88 rectal MRIs were retrospectively collected from 3 different institutions (4 scanners), and for each patient, six 3D regions of interest on the obturator muscle were considered. The methods applied were min-max, 1st-99th percentiles and 3-Sigma normalization, z-score standardization, mean centering, histogram normalization, Nyul-Udupa and ComBat harmonization. The Mann-Whitney U-test was applied to assess features repeatability between scanners, by comparing the feature values obtained for each normalization method, including the case in which no normalization was applied. Most image normalization methods allowed to reduce the overall variability in terms of intensity distributions, while worsening or showing unpredictable results in terms of feature robustness, except for the z-score, which provided a slight improvement by increasing the number of statistically similar features from 9/93 to 10/93. Conversely, feature normalization methods positively reduced the overall variability across the scanners, in particular, 3sigma, z_score and ComBat that increased the number of similar features (79/93). According to our results, it emerged that none of the image normalization methods was able to strongly increase the number of statistically similar features.
Arctic warming in response to regional aerosol emissions reductions
Authors: Previdi Michael , Lamarque Jean-François , Fiore Arlene M , Westervelt Daniel M , Shindell Drew T , Correa Gustavo , Faluvegi Gregory 
Published: July 2023

Abstract
This study examines the Arctic surface air temperature response to regional aerosol emissions reductions using three fully coupled chemistry–climate models: National Center for Atmospheric Research-Community Earth System Model version 1, Geophysical Fluid Dynamics Laboratory-Coupled Climate Model version 3 (GFDL-CM3) and Goddard Institute for Space Studies-ModelE version 2. Each of these models was used to perform a series of aerosol perturbation experiments, in which emissions of different aerosol types (sulfate, black carbon (BC), and organic carbon) in different northern mid-latitude source regions, and of biomass burning aerosol over South America and Africa, were substantially reduced or eliminated. We find that the Arctic warms in nearly every experiment, the only exceptions being the U.S. and Europe BC experiments in GFDL-CM3 in which there is a weak and insignificant cooling. The Arctic warming is generally larger than the global mean warming (i.e. Arctic amplification occurs), particularly during non-summer months. The models agree that changes in the poleward atmospheric moisture transport are the most important factor explaining the spread in Arctic warming across experiments: the largest warming tends to coincide with the largest increases in moisture transport into the Arctic. In contrast, there is an inconsistent relationship (correlation) across experiments between the local radiative forcing over the Arctic and the simulated Arctic warming, with this relationship being positive in one model (GFDL-CM3) and negative in the other two. Our results thus highlight the prominent role of poleward energy transport in driving Arctic warming and amplification, and suggest that the relative importance of poleward energy transport and local forcing/feedbacks is likely to be model dependent.
Regional participation trends for community wildfire preparedness program Firewise USA
Authors: Kampfschulte Andrew R , Miller Rebecca K 
Published: July 2023

Abstract
Community-wide wildfire mitigation can effectively protect homes from structure ignition. The Firewise USA program provides a framework for grassroots wildfire preparedness. Here, we examine the 500 Firewise USA sites in California to understand participation and demographic trends. We find important regional differences regarding the influence of underlying fire hazard, fire history, and other Firewise sites on new site formation. Sites in the Bay Area and Sierras respond strongly to fire history and proximity to other Firewise sites, while Northern and Southern California have few Firewise sites despite underlying hazardous conditions and large fire history. Firewise sites are often whiter, older, and more well-educated than California’s median population, potentially leaving out many communities that do not meet this demographic profile but face severe risks from wildfires. These findings offer important insights into the factors motivating communities to pursue wildfire protection, particularly important given recent severe and destructive wildfire seasons.
Earlier onset and slower heartwood investment in faster-growing trees of African tropical species
Authors: Kafuti Chadrack , Lehnebach Romain , Bourland Nils , Beeckman Hans , Van Acker Joris , Luambua Nestor K , Van den Bulcke Jan 
Published: July 2023

Abstract

Background and Aims
Heartwood plays an important role in maintaining the structural integrity of trees. Although its formation has long been thought to be driven solely by internal ageing processes, more recent hypotheses suggest that heartwood formation acts as a regulator of the tree water balance by modulating the quantity of sapwood. Testing both hypotheses would shed light on the potential ecophysiological nature of heartwood formation, a very common process in trees.

Methods
We measured quantities of heartwood and sapwood, xylem conduits and the width and number of growth rings on 406 stems of Pericopsis elata with ages ranging from 2 to 237 years. A subset of 17 trees with similar ages but varying growth rate were sampled in a shaded (slower-growth) site and a sun-exposed (faster-growth) site. We used regression analysis and structural equation modelling to investigate the dynamics and drivers of heartwood formation.

Key Results
We found a positive effect of growth rate on the probability of heartwood occurrence, suggesting an earlier heartwood onset in faster-growing stems. After this onset age, heartwood area increased with stem diameter and age. Despite the similar heartwood production per unit stem diameter increment, shaded trees produced heartwood faster than sun-exposed trees. Tree age and hydraulics showed similar direct effects on heartwood and sapwood area of sun-exposed trees, suggesting their mutual role in driving the heartwood dynamics of sun-exposed trees. However, for shaded trees, only tree hydraulics showed a direct effect, suggesting its prominent role over age in driving the heartwood dynamics in limited growing conditions. The positive relationship between growth rate and maximum stomatal conductance supported this conclusion.

Conclusions
Heartwood area increases as the tree ages, but at a slower rate in trees where water demand is balanced by a sufficient water supply. Our findings suggest that heartwood formation is not only a structural process but also functional.
Weak latitudinal trends in reproductive traits of Afromontane forest trees
Authors: Swart R C , Geerts S , Geldenhuys C J , Pauw J , Coetzee A 
Published: July 2023

Abstract

Background and Aims
Is the increase in species diversity patterns towards lower latitudes linked to reproductive traits? Plant reproductive organs influence reproductive isolation and hence species divergence. Abiotic differences between temperate and tropical regions can also directly impact on plant reproductive traits. Here we provide a novel overview of southern hemisphere, Afromontane forest tree taxonomical patterns and ask whether reproductive traits relate to latitude, while accounting for environmental (tree height) and evolutionary (biogeographical affinity) selective forces.

Methods
We compiled a novel dataset with (1) flower colour, size and pollination syndrome and (2) fruit colour, size and dispersal syndrome for 331 tree species found in six Afromontane forest regions. We categorized each species into latitudinal distribution using these six regions, spanning the southern Cape (34º S) to Mount Kenya (0º S). Additionally, we gathered maximum tree height (m) for each species and determined the global distribution of all 196 tree genera (Afrotropical, Palaeotropical or Pantropical).

Key Results
Species, genera and families showed a general decrease in richness away from tropical and subtropical forests towards warm temperate forests. Southern Afrotemperate forests (the furthest south) had the highest tree endemism. There was no relationship between latitude and the reproductive traits tested here. Biogeographical affinity related to fruit colour and dispersal syndrome, with palaeotropical genera showing relative increases in black-purple fruit colour compared with pantropical genera, and palaeotropical genera showing relative increases in biotic seed dispersal compared with Afrotropical genera, which showed higher relative abiotic seed dispersal. Taller trees had a higher chance to be wind or insect pollinated (compared with bird pollinated) and had larger fruits.

Conclusions
Latitude explained patterns in Afromontane tree taxonomic diversity; however, tree reproductive traits did not relate to latitude. We suggest that phylogenetic conservatism or convergence, or both, explain the reported patterns.
Integrating stay-green and PIN-FORMED genes: PIN-FORMED genes as potential targets for designing climate-resilient cereal ideotypes
Authors: Wong Albert Chern Sun , van Oosterom Erik J , Godwin Ian D , Borrell Andrew K 
Published: July 2023

Abstract
Plant architecture modification (e.g. short-stature crops) is one of the key outcomes of modern crop breeding for high-yielding crop varieties. In cereals, delayed senescence, or stay-green, is an important trait that enables post-anthesis drought stress adaptation. Stay-green crops can prolong photosynthetic capacity during grain-filling period under post-anthesis drought stress, which is essential to ensure grain yield is not impacted under drought stress conditions. Although various stay-green quantitative trait loci have been identified in cereals, the underlying molecular mechanisms regulating stay-green remain elusive. Recent advances in various gene-editing technologies have provided avenues to fast-track crop improvement, such as the breeding of climate-resilient crops in the face of climate change. We present in this viewpoint the focus on using sorghum as the model cereal crop, to study PIN-FORMED (PIN) auxin efflux carriers as means to modulate plant architecture, and the potential to employ it as an adaptive strategy to address the environmental challenges posed by climate uncertainties.
Brain MRI detects early-stage alterations and disease progression in Friedreich ataxia
Authors: Adanyeguh Isaac M , Joers James M , Deelchand Dinesh K , Hutter Diane H , Eberly Lynn E , Guo Bin , Iltis Isabelle , Bushara Khalaf O , Henry Pierre-Gilles , Lenglet Christophe 
Published: July 2023

Abstract
Friedreich ataxia is a progressive neurodegenerative disorder characterized by cerebellar and spinal atrophy. However, studies to elucidate the longitudinal progression of the pathology in the brain are somewhat inconsistent and limited, especially for early-stage Friedreich ataxia. Using a multimodal neuroimaging protocol, combined with advanced analysis methods, we sought to identify macrostructural and microstructural alterations in the brain of patients with early-stage Friedreich ataxia to better understand its distribution patterns and progression. We enrolled 28 patients with Friedreich ataxia and 20 age- and gender-matched controls. Longitudinal clinical and imaging data were collected in the patients at baseline, 12, 24 and 36 months. Macrostructural differences were observed in patients with Friedreich ataxia, compared to controls, including lower volume of the cerebellar white matter (but not cerebellar grey matter), superior cerebellar peduncle, thalamus and brainstem structures, and higher volume of the fourth ventricle. Diffusion tensor imaging and fixel-based analysis metrics also showed microstructural differences in several brain regions, especially in the cerebellum and corticospinal tract. Over time, many of these macrostructural and microstructural alterations progressed, especially cerebellar grey and white matter volumes, and microstructure of the superior cerebellar peduncle, posterior limb of the internal capsule and superior corona radiata. In addition, linear regressions showed significant associations between many of those imaging metrics and clinical scales. This study provides evidence of early-stage macrostructural and microstructural alterations and of progression over time in the brain in Friedreich ataxia. Moreover, it allows to non-invasively map such brain alterations over a longer period (3 years) than any previous study, and identifies several brain regions with significant involvement in the disease progression besides the cerebellum. We show that fixel-based analysis of diffusion MRI data is particularly sensitive to longitudinal change in the cerebellar peduncles, as well as motor and sensory white matter tracts. In combination with other morphometric measures, they may therefore provide sensitive imaging biomarkers of disease progression for clinical trials.
Differentiating between activation via the lectin or the classical complement pathway in patients with systemic lupus erythematosus
Authors: Larsen Mads Lamm , Troldborg Anne , Toonen Erik J M , Hurler Lisa , Prohaszka Zoltan , Cervenak László , Gudmann Hansen Annette , Thiel Steffen 
Published: July 2023

Abstract
Complement activation is a hallmark of systemic lupus erythematosus (SLE) and can proceed through the classical (CP), lectin (LP), or alternative pathway (AP). When managing SLE patients, pathway-specific complement activation is rarely monitored as clinical assays are unavailable. In this study, we aim to differentiate between CP- or LP-mediated complement activation in SLE patients by quantifying pathway-specific protein complexes, namely C1s/C1-inhibitor (C1-INH) (CP-specific activation) and MASP-1/C1-INH (LP-specific activation). Levels for both complexes were assessed in 156 SLE patients and 50 controls using two newly developed ELISAs. We investigated whether pathway-specific complement activation was associated with disease activity and lupus nephritis (LN). Disease activity stratification was performed using SLEDAI scores assessed at inclusion. C1s/C1-INH concentrations were significantly increased in active SLE patients (SLEDAI ≥6) when compared with SLE patients with low disease activity (SLEDAI &lt;6, P &lt; 0.01) and correlated with SLEDAI score (r = .29, P &lt; 0.01). In active LN, MASP-1/C1-INH plasma concentrations were significantly increased compared with nonactive LN (P = 0.02). No differences in MASP-1/C1-INH plasma concentrations were observed between active SLE patients and patients with low disease activity (P = 0.11) nor did we observe a significant correlation with disease activity (r = 0.12, P = 0.15). Our data suggest that the CP and the LP are activated in SLE. The CP is activated in active SLE disease, whereas activation of the LP might be more specific to disease manifestations like LN. Our results warrant further research into specific complement pathway activation in SLE patients to potentially improve specific-targeted and tailored-treatment approaches.
Neural underpinnings of preferential pain learning and the modulatory role of fear
Authors: Forkmann Katarina , Wiech Katja , Schmidt Katharina , Schmid-Köhler Julia , Bingel Ulrike 
Published: July 2023

Abstract
Due to its unique biological relevance, pain-related learning might differ from learning from other aversive experiences. This functional magnetic resonance imaging study compared neural mechanisms underlying the acquisition and extinction of different threats in healthy humans. We investigated whether cue-pain associations are acquired faster and extinguished slower than cue associations with an equally unpleasant tone. Additionally, we studied the modulatory role of stimulus-related fear. Therefore, we used a differential conditioning paradigm, in which somatic heat pain stimuli and unpleasantness-matched auditory stimuli served as US. Our results show stronger acquisition learning for pain- than tone-predicting cues, which was augmented in participants with relatively higher levels of fear of pain. These behavioral findings were paralleled by activation of brain regions implicated in threat processing (insula, amygdala) and personal significance (ventromedial prefrontal cortex). By contrast, extinction learning seemed to be less dependent on the threat value of the US, both on the behavioral and neural levels. Amygdala activity, however, scaled with pain-related fear during extinction learning. Our findings on faster and stronger (i.e. “preferential”) pain learning and the role of fear of pain are consistent with the biological relevance of pain and may be relevant to the development or maintenance of chronic pain.
The coexistence of diabetic retinopathy and diabetic nephropathy is associated with worse kidney outcomes
Authors: Bermejo Sheila , González Ester , López-Revuelta Katia , Ibernon Meritxell , López Diana , Martín-Gómez Adoración , Garcia-Osuna Rosa , Linares Tania , Díaz Montserrat , Martín Nàdia , Barros Xoana , Marco Helena , Navarro Maruja Isabel , Esparza Noemí , Elias Sandra , Coloma Ana , Robles Nicolás Roberto , Agraz Irene , Poch Esteban , Rodas Lida , Lozano Víctor , Fernández-Fernández Beatriz , Hernández Eduardo , Martínez Maria Isabel , Stanescu Ramona Ionela , Moirón José Pelayo , García-Fernández Núria , Goicoechea Marian , Calero Francesca , Bonet Josep , Liaño Fernando , Pascual Julio , Bestard Oriol , Praga Manuel , Fulladosa Xavier , Soler María José 
Published: July 2023

ABSTRACT

Background
Up to 50–60% of patients with diabetes have non-diabetic kidney disease (NDKD) on kidney biopsy. Diabetic retinopathy (DR) is a microvascular complication of diabetes frequently associated with diabetic nephropathy (DN). The objective of the current study was to investigate the kidney outcomes and survival in patients with biopsy diagnoses of DN and NDKD according to the presence of DR.

Methods
We conducted an observational, multicentre and retrospective study of the pathological findings of renal biopsies from 832 consecutive patients with diabetes from 2002 to 2014 from 18 nephrology departments. The association of DR with kidney replacement therapy (KRT) or survival was assessed by Kaplan–Meier and Cox regression analyses.

Results
Of 832 patients with diabetes and renal biopsy, 768 had a retinal examination and 221/768 (22.6%) had DR. During a follow-up of 10 years, 288/760 (37.9%) patients with follow-up data needed KRT and 157/760 (20.7%) died. The incidence of KRT was higher among patients with DN (alone or with NDKD) and DR [103/175 (58.9%)] than among patients without DR [88/216 (40.7%), P &lt; .0001]. The incidence of KRT was also higher among patients with only NDKD and DR than among those without DR [18/46 (39.1%) versus 79/331 (23.9%), P &lt; .0001]. In multivariate analysis, DR or DN were independent risk factors for KRT {hazard ratio [HR] 2.48 [confidence interval (CI) 1.85–3.31], P &lt; .001}. DN (with or without DR) was also identified as an independent risk factor for mortality [HR 1.81 (CI 1.26–2.62), P = .001].

Conclusions
DR is associated with a higher risk of progression to kidney failure in patients with histological DN and in patients with NDKD.
Political Aspects of Full Employment in Retrospect
Authors: Toporowski Jan 
Published: July 2023

Abstract
Kalecki’s ‘Political Aspects of Full Employment’ is a classic work of political economy, showing how full employment may be obtained by fiscal policy. However, full employment challenges key institution of capitalism, in the labour market evoking resistance from business and finance and the possibility of a political business cycle. The paper compares Kalecki’s vision of full employment with that of Keynes and the contribution of mass unemployment to fascism. The paper argues that Kalecki saw full employment as a transition to socialism.
CropGF: a comprehensive visual platform for crop gene family mining and analysis
Authors: Xu Jingtian , Zhu Can , Su Minzeng , Li Sida , Chao Haoyu , Chen Ming 
Published: July 2023

Abstract
A gene family refers to a group of genes that share a common ancestry and encode proteins or RNA molecules with similar functions or structural features. Gene families play a crucial role in determining the traits of plants and can be utilized to develop new crop varieties. Therefore, a comprehensive database of gene family is significant for gaining deep insight into crops. To address this need, we have developed CropGF (https://bis.zju.edu.cn/cropgf), a comprehensive visual platform that encompasses six important crops (rice, wheat, maize, barley, sorghum and foxtail millet) and one model plant (Arabidopsis), as well as genomics, transcriptomics and proteomics data for gene family mining and analysis, covering a total of 314 611 genes and 4399 types of domains. CropGF provides a versatile search system that allows for the identification of gene families and their members in a single crop or multiple crops. Users can customize their search based on gene family domains and/or homology using keywords or BLAST. To enhance usability, we have collected the corresponding ID information from various public databases for both genes and domains. Furthermore, CropGF comprises numerous downstream analysis modules, such as ka/ks analysis, phylogenetic tree construction, subcellular localization analysis and more. These visually-displayed modules provide intuitive insights into gene expression patterns, gene family expansion and functional relationships across different molecular levels and different species. We believe that CropGF will be a valuable resource for deep mining and analysis in future studies of crop gene families.
Database URL https://bis.zju.edu.cn/cropgf