bluuebunny/crossref_metadata_2025_split huggingface dataset:
The graded multidimensional geometry of phenotypic variation and progression in neurodegenerative syndromes
Authors: Ramanan Siddharth , Akarca Danyal , Henderson Shalom K , Rouse Matthew A , Allinson Kieren , Patterson Karalyn , Rowe James B , Lambon Ralph Matthew A 
Published: July 2024

Abstract
Clinical variants of Alzheimer’s disease and frontotemporal lobar degeneration display a spectrum of cognitive-behavioural changes varying between individuals and over time. Understanding the landscape of these graded individual/group level longitudinal variations is critical for precise phenotyping; however, this remains challenging to model.
Addressing this challenge, we leverage the National Alzheimer’s Coordinating Center database to derive a unified geometric framework of graded longitudinal phenotypic variation in Alzheimer’s disease and frontotemporal lobar degeneration. We included three time point, cognitive-behavioural and clinical data from 390 typical, atypical and intermediate Alzheimer’s disease and frontotemporal lobar degeneration variants (114 typical Alzheimer’s disease; 107 behavioural variant frontotemporal dementia; 42 motor variants of frontotemporal lobar degeneration; and 103 primary progressive aphasia patients). On these data, we applied advanced data-science approaches to derive low-dimensional geometric spaces capturing core features underpinning clinical progression of Alzheimer’s disease and frontotemporal lobar degeneration syndromes.
To do so, we first used principal component analysis to derive six axes of graded longitudinal phenotypic variation capturing patient-specific movement along and across these axes. Then, we distilled these axes into a visualizable 2D manifold of longitudinal phenotypic variation using Uniform Manifold Approximation and Projection. Both geometries together enabled the assimilation and interrelation of paradigmatic and mixed cases, capturing dynamic individual trajectories and linking syndromic variability to neuropathology and key clinical end points, such as survival.
Through these low-dimensional geometries, we show that (i) specific syndromes (Alzheimer’s disease and primary progressive aphasia) converge over time into a de-differentiated pooled phenotype, while others (frontotemporal dementia variants) diverge to look different from this generic phenotype; (ii) phenotypic diversification is predicted by simultaneous progression along multiple axes, varying in a graded manner between individuals and syndromes; and (iii) movement along specific principal axes predicts survival at 36 months in a syndrome-specific manner and in individual pathological groupings. The resultant mapping of dynamics underlying cognitive-behavioural evolution potentially holds paradigm-changing implications to predicting phenotypic diversification and phenotype-neurobiological mapping in Alzheimer’s disease and frontotemporal lobar degeneration.
Modulation of the intermolecular interactions of cucurbit[7]uril with phenylalanine derivatives by the functional groups
Authors: Ueno-Noto Kaori , Toyama Seina , Kono Yuki , Takano Keiko 
Published: July 2024

Abstract
Intermolecular interactions in 1:1 inclusion complexes of cucurbit[7]uril (CB[7]) with phenylalanine derivatives were investigated by density functional theory (B97-D) calculations. For each complex, 2 optimized geometries were found: conformer C in which a guest molecule resided in the center of CB[7], and conformer E where a guest molecule was present at the edge of CB[7]. The order of energy differences between these conformers agreed well with previously reported differences in the affinity of guest molecules for CB[7]. Molecular dynamics simulations of the complexes showed that the guest molecules in CB[7] had different stabilities, and the calculated binding free energies between them also qualitatively agreed with the experimental results. Pair-interaction energy decomposition analyses of the complexes at FMO-MP2/6-31G(d) and aug-cc-pVDZ level of theory were performed using snapshot structures at 500 ns of simulations. The dispersion interaction characterized the interaction, and the order of total interaction energies between the guest molecules and CB[7] was also associated with the experimental results. A significant difference in electrostatic interaction energies was observed in conformer E, which was correlated with the stability of the guest molecules at the edge of CB[7]. The balance between the stabilities of these conformers was correlated with the affinity of guest molecules for CB[7].
Restorative justice in Brazil: does it provide a place for community involvement and a path to penal abolition?
Authors: Achutti Daniel , Pallamolla Raffaella , Giamberardino André 
Published: July 2024

Abstract
This article addresses the major criticisms of Brazilian restorative practices, which mainly focus on the offender and are shaped by the idea of punitivism. In this scenario, it is crucial to understand the centrality of Judicial Power in the implementation of restorative justice. That this approach risks refreshing old practices of criminal justice, under the cover of innovative discourses, is widely ignored. Such consequences have become reality, with recent research highlighting the absence of the victim, the individualization of the conflict and the lack of debate on the context of structural injustices prior to the conflict. We argue that the exclusion of the community and limited involvement by civil society might be the biggest obstacles for the inclusion of restorative justice in the development of a Brazilian transformative justice towards an abolitionist future.
Insular environment-dependent introgression from an arid-grassland orchid to a wetland orchid on an oceanic island
Authors: Suetsugu Kenji , Hirota Shun K , Ishibashi Masayuki , Ishida Kenya , Hayakawa Hiroshi , Suyama Yoshihisa 
Published: July 2024

Abstract
Adaptive introgression plays a vital role in allowing recipient species to adapt and colonize new environments. However, our understanding of such environment-dependent introgressions is primarily limited to specific plant taxa in particular settings. In Japan, two related orchid species, the autonomously self-pollinating Pogonia minor and the outcrossing Pogonia japonica, typically inhabit dry grasslands and wetlands, respectively. Intriguingly, an island ecotype of P. japonica exists in arid, wind-swept, open sites on volcanic mountain slopes on Kozu Island, in the oceanic Izu Islands. To investigate potential introgression and its implications between P. japonica and P. minor on Kozu Island, we applied a comprehensive approach that included examining morphological traits, genome-wide SNP data, and plastid DNA sequences. We also examined the breeding systems of these species on Kozu Island through artificial pollination experiments to determine if introgression from P. minor has endowed the P. japonica ecotype with selfing capabilities. Extensive sampling on Kozu Island revealed that all P. japonica specimens exhibit signs of introgression from P. minor, suggesting the absence of pure P. japonica populations on the island. Furthermore, the chloroplast haplotypes of the insular P. japonica ecotype consistently match those of P. minor, indicating a predominantly asymmetrical initial hybridization with P. minor acting mainly as the maternal parent in the formation of F1 hybrids. Despite the advantages of self-fertilization in isolated environments, the insular P. japonica does not exhibit autogamy. Consequently, the scarcity of moist habitats, rather than selection pressure for selfing, likely contributes to the observed widespread introgression. Our study strongly suggests that the arid-environment-adapted P. minor has introgressed into the insular ecotype of P. japonica, enabling its successful colonization of arid volcanic mountain slopes of the oceanic island.
Chk2 homolog Mek1 limits exonuclease 1–dependent DNA end resection during meiotic recombination in Saccharomyces cerevisiae
Authors: Krystosek Jennifer T , Bishop Douglas K 
Published: July 2024

Abstract
The conserved Rad2/XPG family 5′–3′ exonuclease, exonuclease 1 (Exo1), plays many roles in DNA metabolism including during resolution of DNA double-strand breaks via homologous recombination. Prior studies provided evidence that the end resection activity of Exo1 is downregulated in yeast and mammals by Cdk1/2 family cyclin-dependent and checkpoint kinases, including budding yeast kinase Rad53 which functions in mitotic cells. Here, we provide evidence that the master meiotic kinase Mek1, a paralog of Rad53, limits 5′–3′ single-strand resection at the sites of programmed meiotic DNA breaks. Mutational analysis suggests that the mechanism of Exo1 suppression by Mek1 differs from that of Rad53.
Restorer of fertility like 30, encoding a mitochondrion-localized pentatricopeptide repeat protein, regulates wood formation in poplar
Authors: Fu Xiaokang , Yang Ziwei , Guo Li , Luo Lianjia , Tao Yuanxun , Lan Ting , Hu Jian , Li Zeyu , Luo Keming , Xu Changzheng 
Published: July 2024

Abstract
Nuclear–mitochondrial communication is crucial for plant growth, particularly in the context of cytoplasmic male sterility (CMS) repair mechanisms linked to mitochondrial genome mutations. The restorer of fertility-like (RFL) genes, known for their role in CMS restoration, remain largely unexplored in plant development. In this study, we focused on the evolutionary relationship of RFL family genes in poplar specifically within the dioecious Salicaceae plants. PtoRFL30 was identified to be preferentially expressed in stem vasculature, suggesting a distinct correlation with vascular cambium development. Transgenic poplar plants overexpressing PtoRFL30 exhibited a profound inhibition of vascular cambial activity and xylem development. Conversely, RNA interference-mediated knockdown of PtoRFL30 led to increased wood formation. Importantly, we revealed that PtoRFL30 plays a crucial role in maintaining mitochondrial functional homeostasis. Treatment with mitochondrial activity inhibitors delayed wood development in PtoRFL30-RNAi transgenic plants. Further investigations unveiled significant variations in auxin accumulation levels within vascular tissues of PtoRFL30-transgenic plants. Wood development anomalies resulting from PtoRFL30 overexpression and knockdown were rectified by NAA and NPA treatments, respectively. Our findings underscore the essential role of the PtoRFL30-mediated mitochondrion-auxin signaling module in wood formation, shedding light on the intricate nucleus–organelle communication during secondary vascular development.
Prospective evaluation of the relevance of Epstein–Barr virus antibodies for early detection of nasopharyngeal carcinoma in Chinese adults
Authors: Yang Ling , Kartsonaki Christiana , Simon Julia , Yao Pang , Guo Yu , Lv Jun , Walters Robin G , Chen Yiping , Fry Hannah , Avery Daniel , Yu Canqing , Jin Jianrong , Mentzer Alexander J , Allen Naomi , Butt Julia , Hill Michael , Li Liming , Millwood Iona Y , Waterboer Tim , Chen Zhengming 
Published: July 2024

Abstract

Background
Epstein–Barr virus (EBV) is a major cause of nasopharyngeal carcinoma (NPC) and measurement of different EBV antibodies in blood may improve early detection of NPC. Prospective studies can help assess the roles of different EBV antibodies in predicting NPC risk over time.

Methods
A case-cohort study within the prospective China Kadoorie Biobank of 512 715 adults from 10 (including two NPC endemic) areas included 295 incident NPC cases and 745 subcohort participants. A multiplex serology assay was used to quantify IgA and IgG antibodies against 16 EBV antigens in stored baseline plasma samples. Cox regression was used to estimate adjusted hazard ratios (HRs) for NPC and C-statistics to assess the discriminatory ability of EBV-markers, including two previously identified EBV-marker combinations, for predicting NPC.

Results
Sero-positivity for 15 out of 16 EBV-markers was significantly associated with higher NPC risk. Both IgA and IgG antibodies against the same three EBV-markers showed the most extreme HRs, i.e. BGLF2 (IgA: 124.2 (95% CI: 63.3–243.9); IgG: 8.6 (5.5–13.5); LF2: [67.8 (30.0–153.1), 10.9 (7.2–16.4)]); and BFRF1: 26.1 (10.1–67.5), 6.1 (2.7–13.6). Use of a two-marker (i.e. LF2/BGLF2 IgG) and a four-marker (i.e. LF2/BGLF2 IgG and LF2/EA-D IgA) combinations yielded C-statistics of 0.85 and 0.84, respectively, which persisted for at least 5 years after sample collection in both endemic and non-endemic areas.

Conclusions
In Chinese adults, plasma EBV markers strongly predict NPC occurrence many years before clinical diagnosis. LF2 and BGLF2 IgG could identify NPC high-risk individuals to improve NPC early detection in community and clinical settings.
Generative early architectural visualizations: incorporating architect’s style-trained models
Authors: Lee Jin-Kook , Yoo Youngjin , Cha Seung Hyun 
Published: July 2024

Abstract
This study introduces a novel approach to architectural visualization using generative artificial intelligence (AI), particularly emphasizing text-to-image technology, to remarkably improve the visualization process right from the initial design phase within the architecture, engineering, and construction industry. By creating more than 10 000 images incorporating an architect’s personal style and characteristics into a residential house model, the effectiveness of base AI models. Furthermore, various architectural styles were integrated to enhance the visualization process. This method involved additional training for styles with low similarity rates, which required extensive data preparation and their integration into the base AI model. Demonstrated to be effective across multiple scenarios, this technique markedly enhances the efficiency and speed of production of architectural visualization images. Highlighting the vast potential of AI in design visualization, our study emphasizes the technology’s shift toward facilitating more user-centered and personalized design applications.
A genome assembly of the American black bear, Ursus americanus, from California
Authors: Supple Megan A , Escalona Merly , Adkins Jillian , Buchalski Michael R , Alexandre Nicolas , Sahasrabudhe Ruta M , Nguyen Oanh , Sacco Samuel , Fairbairn Colin , Beraut Eric , Seligmann William , Green Richard E , Meredith Erin , Shapiro Beth 
Published: July 2024

Abstract
The American black bear, Ursus americanus, is a widespread and ecologically important species in North America. In California, the black bear plays an important role in a variety of ecosystems and serves as an important species for recreational hunting. While research suggests that the populations in California are currently healthy, continued monitoring is critical, with genomic analyses providing an important surveillance tool. Here we report a high-quality, near chromosome-level genome assembly from a U. americanus sample from California. The primary assembly has a total length of 2.5 Gb contained in 316 scaffolds, a contig N50 of 58.9 Mb, a scaffold N50 of 67.6 Mb, and a BUSCO completeness score of 96%. This U. americanus genome assembly will provide an important resource for the targeted management of black bear populations in California, with the goal of achieving an appropriate balance between the recreational value of black bears and the maintenance of viable populations. The high quality of this genome assembly will also make it a valuable resource for comparative genomic analyses among black bear populations and among bear species.
The diagnostic value of pleural effusion/serum ratio of carcinoembryonic antigen and pleural effusion/serum ratio of interferon-γ in classification of pleural effusion
Authors: Liang Shu-hui , Li Cui , Xie Si 
Published: July 2024

Abstract

Background
Distinguishing between different types of pleural effusions (PEs) is crucial for clinical diagnosis and treatment. This study evaluates the diagnostic value of carcinoembryonic antigen (CEA) and interferon-gamma (IFN-γ) levels in PE and serum, as well as the PE/serum ratios of these markers, in classifying PE.

Methods
We retrospectively analyzed 99 patients with PE, categorizing them into malignant pleural effusion (MPE), tuberculous pleural effusion (TPE), and benign PE groups. Levels of CEA and IFN-γ in PE and serum were quantified and their ratios were calculated. Diagnostic performance was assessed using receiver operating characteristic analysis, focusing on the area under the curve (AUC) to determine the efficacy of these biomarkers.

Results
Significantly elevated levels of CEA in PE and serum were observed in the MPE group compared to the benign and TPE groups, with the PE/serum CEA ratio offering substantial diagnostic value (AUCs: PE = 0.843, serum = 0.744). Conversely, IFN-γ levels in PE and serum were markedly higher in the TPE group, demonstrating notable diagnostic accuracy (AUCs: PE = 0.970, serum = 0.917).

Conclusion
Both CEA and IFN-γ demonstrate high clinical utility in differentiating between MPE and TPE. The PE/serum ratio of these biomarkers enhances diagnostic accuracy, potentially facilitating earlier and more accurate therapeutic interventions.
Investigating the antimicrobial potential of bovine lactoferrin against the neonatal pathogen, Staphylococcus capitis
Authors: Desmond Anna , Cotter Lesley , Field Des , O'Halloran Fiona 
Published: July 2024

Abstract
Lactoferrin is an antimicrobial glycoprotein that demonstrates a broad-spectrum of activity against a wide variety of clinical pathogens. This study investigated the potential of bovine lactoferrin (bLf) against multidrug resistant Staphylococcus capitis (S. capitis) strains. Growth curve analysis and time-kill curves demonstrated that at 750 µg ml−1 lactoferrin significantly inhibited (50.6%, P &lt; 0.05) the growth of most isolates tested (90%), and this effect was based on a bacteriostatic mechanism. At the same concentration, bLf also significantly inhibited (30%, P &lt; 0.05) biofilm formation in 40% of strains tested. Combinations of bLf with selected antibiotics were assessed for enhanced antimicrobial activity using growth curves. BLf combined with β-lactam antibiotics reduced the growth of S. capitis strains, however, the effects were not significant. BLf displays antimicrobial effects against multidrug resistant S. capitis isolates, but with strain-specific effects.
Inferring the iron K emissivity profiles of accretion discs irradiated by extended coronae
Authors: Zhang Wenda , Dovčiak Michal , Bursa Michal , Svoboda Jiří , Karas Vladimír 
Published: July 2024

ABSTRACT
One of the most promising methods to measure the spin of an accreting black hole is fitting the broad iron K$\alpha$ line in the X-ray spectrum. The line profile also depends on the geometry of the hard X-ray emitting corona. To put constraints on the black hole spin and corona geometry, it is essential to understand how do they affect the iron K$\alpha$ line emissivity profile. In this work, we present calculations of the illumination and the iron K$\alpha$ emissivity profiles performed with the Monte Carlo GR radiative transfer code monk. We focus on distinction between the illumination and emissivity profiles, which is in most previous studies neglected. We show that especially for the case of black hole X-ray binaries (BHXRBs), the difference is very large. For active galactic nuclei (AGNs), the emissivity profile has a more similar shape as the illumination profile, but it is notably steeper in the innermost region within a few gravitational radii. We find out that the different behaviour between AGN and BHXRB discs is due to the different energy spectra of the illuminating radiation. This suggests that the emissivity profile of the iron K$\alpha$ line cannot be determined by black hole spin and corona geometry alone and the energy spectrum of the illuminating radiation has to be taken into account. We also examined the effect of including the self-irradiation, and find it to be more important than the corona emission in BHXRBs.
Content–state dimensions characterize different types of neuronal markers of consciousness
Authors: Pérez Pauline , Manasova Dragana , Hermann Bertrand , Raimondo Federico , Rohaut Benjamin , Bekinschtein Tristán A , Naccache Lionel , Arzi Anat , Sitt Jacobo D 
Published: July 2024

Abstract
Identifying the neuronal markers of consciousness is key to supporting the different scientific theories of consciousness. Neuronal markers of consciousness can be defined to reflect either the brain signatures underlying specific conscious content or those supporting different states of consciousness, two aspects traditionally studied separately. In this paper, we introduce a framework to characterize markers according to their dynamics in both the “state” and “content” dimensions. The 2D space is defined by the marker’s capacity to distinguish the conscious states from non-conscious states (on the x-axis) and the content (e.g. perceived versus unperceived or different levels of cognitive processing on the y-axis). According to the sign of the x- and y-axis, markers are separated into four quadrants in terms of how they distinguish the state and content dimensions. We implement the framework using three types of electroencephalography markers: markers of connectivity, markers of complexity, and spectral summaries. The neuronal markers of state are represented by the level of consciousness in (i) healthy participants during a nap and (ii) patients with disorders of consciousness. On the other hand, the neuronal markers of content are represented by (i) the conscious content in healthy participants’ perception task using a visual awareness paradigm and (ii) conscious processing of hierarchical regularities using an auditory local–global paradigm. In both cases, we see separate clusters of markers with correlated and anticorrelated dynamics, shedding light on the complex relationship between the state and content of consciousness and emphasizing the importance of considering them simultaneously. This work presents an innovative framework for studying consciousness by examining neuronal markers in a 2D space, providing a valuable resource for future research, with potential applications using diverse experimental paradigms, neural recording techniques, and modeling investigations.
Rehabilitation utilization in malignant primary brain tumors compared to stroke and traumatic brain injury: Analysis using a large claim database
Authors: Giovanazzi Samantha , Ugiliweneza Beatrice , Alvarez Elsa , Boakye Maxwell , Kaelin Darryl , Nelson Megan B 
Published: July 2024

Abstract

Background
There is concern regarding the underutilization of rehabilitation services for the malignant primary brain tumor (MPBT) population following hospitalization. Our aim is to assess physical therapy (PT), occupational therapy (OT), and speech-language pathology (SLP) use after an MPBT diagnosis, evaluate the trend from 2001 to 2018, and compare to traumatic brain injury (TBI) and stroke.

Methods
Adult cases of MPBT, TBI, and stroke were extracted from MarketScan database. Inpatient and outpatient data were screened for inpatient rehabilitation use at the time of diagnosis and postdischarge outpatient PT, OT, and SLP over 12 months. Generalized linear regressions were used for analysis.

Results
The cohort was composed of 3381 MPBT, 205 366 stroke, and 24 825 TBI patients. After diagnosis, 1% of MPBTs were discharged to skilled nursing facilities (SNF) and 3% to inpatient rehabilitation facilities (IRF). Rehabilitation use at 12 months was 19% PT, 8% OT, and 6% SLP. These percentages were lower than stroke and TBI; stroke: 8% SNF, 8% IRF, 22% PT, 10% OT, and 8% SLP; TBI: 7% SNF, 7% IRF, 22% PT, 8% OT, and 6% SLP. Outpatient therapies increased from 2001 to 2018, with PT use consistently higher than OT and SLP. MPBT had the greatest increases in OT (7.95 times) and PT (3.89 times) compared to stroke and TBI, while stroke had the greatest increase in SLP (0.98 times).

Conclusions
MPBT patients had the highest increase in OT and PT utilization when compared to stroke and TBI. However, there remains a utilization gap which demonstrates the need for improvement.