bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combining MRI and clinical data to detect high relapse risk after the first episode of psychosis
Authors: Solanes Aleix , Mezquida Gisela , Janssen Joost , Amoretti Silvia , Lobo Antonio , González-Pinto Ana , Arango Celso , Vieta Eduard , Castro-Fornieles Josefina , Bergé Daniel , Albacete Auria , Giné Eloi , Parellada Mara , Bernardo Miguel ,   PEPs group (collaborators), Bioque Miquel , Morén Constanza , Pina-Camacho Laura , Díaz-Caneja Covadonga M. , Zorrilla Iñaki , Corres Edurne Garcia , De-la-Camara Concepción , Barcones Fe , Escarti María José , Aguilar Eduardo Jesus , Legido Teresa , Martin Marta , Verdolini Norma , Martinez-Aran Anabel , Baeza Immaculada , de la Serna Elena , Contreras Fernando , Bobes Julio , García-Portilla María Paz , Sanchez-Pastor Luis , Rodriguez-Jimenez Roberto , Usall Judith , Butjosa Anna , Salgado-Pineda Pilar , Salvador Raymond , Pomarol-Clotet Edith , Radua Joaquim 
Published: November 2022

AbstractDetecting patients at high relapse risk after the first episode of psychosis (HRR-FEP) could help the clinician adjust the preventive treatment. To develop a tool to detect patients at HRR using their baseline clinical and structural MRI, we followed 227 patients with FEP for 18–24 months and applied MRIPredict. We previously optimized the MRI-based machine-learning parameters (combining unmodulated and modulated gray and white matter and using voxel-based ensemble) in two independent datasets. Patients estimated to be at HRR-FEP showed a substantially increased risk of relapse (hazard ratio = 4.58, P < 0.05). Accuracy was poorer when we only used clinical or MRI data. We thus show the potential of combining clinical and MRI data to detect which individuals are more likely to relapse, who may benefit from increased frequency of visits, and which are unlikely, who may be currently receiving unnecessary prophylactic treatments. We also provide an updated version of the MRIPredict software.
COVID-19 in Switzerland real-time epidemiological analyses powered by EpiGraphHub
Authors: Coelho Flávio Codeço , Araújo Eduardo Corrêa , Keiser Olivia 
Published: November 2022

AbstractHere we present the design and results of an analytical pipeline for COVID-19 data for Switzerland. It is applied to openly available data from the beginning of the epidemic in 2020 to the present day (august 2022). We analyzed the spatio-temporal patterns of the spread of SARS-CoV2 throughout the country, applying Bayesian inference to estimate population prevalence and hospitalization ratio. We also developed forecasting models to characterize the transmission dynamics for all the country’s cantons taking into account their spatial correlations in COVID incidence. The two-week forecasts of new daily hospitalizations showed good accuracy, as reported herein. These analyses’ raw data and live results are available on the open-source EpiGraphHub platform to support further studies.
Health risk assessment and source apportionment of potentially toxic metal(loid)s in windowsill dust of a rapidly growing urban settlement, Iran
Authors: Madadi Reyhane , Mohamadi Sedigheh , Rastegari Mohammad , Karbassi Abdolreza , Rakib Md. Refat Jahan , Khandaker Mayeen Uddin , Faruque Mohammad Rashed Iqbal , Idris Abubakr M. 
Published: November 2022

AbstractRapid industrialization and urbanization have resulted in environmental pollution and unsustainable development of cities. The concentration of 12 potentially toxic metal(loid)s in windowsill dust samples (n = 50) were investigated from different functional areas of Qom city with the highest level of urbanization in Iran. Spatial analyses (ArcGIS 10.3) and multivariate statistics including Principal Component Analysis and Spearman correlation (using STATISTICA-V.12) were adopted to scrutinize the possible sources of pollution. The windowsill dust was very highly enriched with Sb (50 mg/kg) and Pb (1686 mg/kg). Modified degree of contamination (mCd) and the pollution load indices (PLIzone) indicate that windowsill dust in all functional areas was polluted in the order of industrial > commercial > residential > green space. Arsenic, Cd, Mo, Pb, Sb, Cu, and Zn were sourced from a mixture of traffic and industrial activities, while Mn in the dust mainly stemmed from mining activities. Non-carcinogenic health risk (HI) showed chronic exposure of Pb for children in the industrial zone (HI = 1.73). The estimations suggest the possible carcinogenic risk of As, Pb, and Cr in the dust. The findings of this study reveal poor environmental management of the city. Emergency plans should be developed to minimize the health risks of dust to residents.
Elemental, fatty acid, and protein composition of appendicoliths
Authors: Prieto James M. , Wang Andrew W. , Halbach Jonathan , Cauvi David M. , Day James M. D. , Gembicky Milan , Ghassemian Majid , Quehenberger Oswald , Kling Karen , Ignacio Romeo , DeMaio Antonio , Bickler Stephen W. 
Published: November 2022

AbstractAppendicoliths are commonly found obstructing the lumen of the appendix at the time of appendectomy. To identify factors that might contribute to their formation we investigated the composition of appendicoliths using laser ablation inductively coupled plasma mass spectroscopy, gas chromatography, polarized light microscopy, X-ray crystallography and protein mass spectroscopy. Forty-eight elements, 32 fatty acids and 109 human proteins were identified within the appendicoliths. The most common elements found in appendicoliths are calcium and phosphorus, 11.0 ± 6.0 and 8.2 ± 4.2% weight, respectively. Palmitic acid (29.7%) and stearate (21.3%) are the most common fatty acids. Some stearate is found in crystalline form—identifiable by polarized light microscopy and confirmable by X-ray crystallography. Appendicoliths have an increased ratio of omega-6 to omega-3 fatty acids (ratio 22:1). Analysis of 16 proteins common to the appendicoliths analyzed showed antioxidant activity and neutrophil functions (e.g. activation and degranulation) to be the most highly enriched pathways. Considered together, these preliminary findings suggest oxidative stress may have a role in appendicolith formation. Further research is needed to determine how dietary factors such as omega-6 fatty acids and food additives, redox-active metals and the intestinal microbiome interact with genetic factors to predispose to appendicolith formation.
CA125 as a predictor of endometrial cancer lymphovascular space invasion and lymph node metastasis for risk stratification in the preoperative setting
Authors: Shawn LyBarger K. , Miller Hunter A. , Frieboes Hermann B. 
Published: November 2022

AbstractEndometrial cancer (EC) is the most common malignancy of the female reproductive system. Cancer antigen 125 (CA125) is a serum tumor marker widely reported in EC patients, particularly those with poor prognostic factors such as grade 3 tumors, deep myometrial invasion, lymph node metastasis (LNM), and extra-uterine disease. This retrospective study stratifies pre-operative CA125 levels to evaluate odds ratios (OR) and relative risk (RR) between CA125 levels and the likelihood of +LNM, lymphovascular space invasion (LVSI), grade, and stage. Patient charts for women 18 years or older with a diagnosis of EC and pre-operative or within one week CA125 measurement from January 2000 to January 2015 at a regional hospital were reviewed. OR and RR were determined by unconditional maximum likelihood estimation for CA125 levels as the predictor with staging, grade, +LVSI and +LNM as outcomes. The largest increase in risk for patients having stage I/II/III disease was 52% greater (1.52-fold risk) while largest increase in risk for patients having stage III/IV disease was 67% greater (1.67-fold risk), both at CA125 ≥ 222U/ml. Patients with CA125 ≥ 122U/ml had significantly increased risk of +LNM, with maximum increase in risk of 98% (1.98-fold risk) at 222U/ml. Patients with CA125 ≥ 175U/ml had significantly increased risk of +LVSI, with maximum increase in risk of 39% (1.39-fold risk) at 222U/ml. This study shows that elevated CA125 levels correspond to increased stage, +LVSI, and +LNM in patients with EC.
Environmental impact of diets for dogs and cats
Authors: Pedrinelli Vivian , Teixeira Fabio A. , Queiroz Mariana R. , Brunetto Marcio A. 
Published: November 2022

AbstractFood production is responsible for almost one-quarter of the environmental impact and, therefore, its importance regarding sustainability should not be overlooked. The companion animal population is increasing, and an important part of pet food is composed of ingredients that have a high environmental impact. This study aimed to evaluate the impact of dry, wet, and homemade pet diets on greenhouse gas emission, land use, acidifying emission, eutrophying emissions, freshwater withdrawals, and stress-weighted water use. The wet diets were responsible for the highest impact, and dry diets were the type of diet that least impacted the environment, with a positive correlation between the metabolizable energy provided by animal ingredients and the environmental impact. It is necessary to consider the environmental impact of pet food since it is significant, and the population of pets tends to increase.
PIV and CFD investigation of paddle flocculation hydrodynamics at low rotational speeds
Authors: Chatila Jean George , Danageuzian Hrair Razmig 
Published: November 2022

AbstractIn this study, flocculation hydrodynamics were evaluated by investigating the velocity field of turbulent flow experimentally and numerically, in a laboratory scale paddle flocculator. Turbulence that either promotes the particle aggregation or the breakage of flocs is complicated and has been considered and compared in this work using two turbulence models; namely, the SST k–ω and the IDDES. Results showed that IDDES provided very slight improvement as compared to SST k–ω, yielding the latter sufficient in accurately simulating the flow inside the paddle flocculator. A Goodness-of-Fit evaluation was adopted to study the convergence between PIV and CFD results, and to compare the results of the used CFD turbulence models. The study focused, as well, on the quantification of the slippage factor k, as 0.18 at low rotational speeds of 3 rpm and 4 rpm, and compared to conventional typical value of 0.25. This reduction of k from 0.25 to 0.18 yields around 27–30% increase in the power imparted to the fluid, and about 14% increase in velocity gradient (G). This implies that more mixing is provided than expected, and therefore, less energy is input and thus the electric consumption for the flocculation unit at a drinking water treatment plant could be potentially decreased.
Relationship between red blood cell aggregation and dextran molecular mass
Authors: Bosek Maciej , Ziomkowska Blanka , Pyskir Jerzy , Wybranowski Tomasz , Pyskir Małgorzata , Cyrankiewicz Michał , Napiórkowska Marta , Durmowicz Maciej , Kruszewski Stefan 
Published: November 2022

AbstractThe aim of this study was to investigate the aggregation of red blood cells (RBCs) suspended in dextran solution at various levels of molecular mass. Dextran solutions at molecular mass 40, 70, 100 and 500 kDa at concentration from 2 to 5 g/dL were used to suspend the RBCs. The radius and velocity of sedimenting RBC aggregates were investigated using image analysis. The radius and sedimentation velocity of aggregates increased initially, then decreased after achieving maxima. The maximal velocity of RBC aggregates showed a bell-shaped dependence on dextran molecular mass and concentration, whereas maximal radius showed monotonic increase with both factors. Difference between aggregate and solution density was estimated using aggregate radius and sedimentation velocity and dextran solution viscosity, and was consistent across most molecular mass and concentration levels. This allowed to calculate the porosity of aggregates and to show that it monotonically decreased with the increase in the solution density, caused by the increase in the dextran concentration. The results provide insight into the RBC aggregation process in solutions of proteins of different size, reflecting various pathological conditions. The currently reported data can be potentially applied to specific pathophysiological conditions giving an interpretation that is not yet fully discussed in the literature.
Health-related quality of life and clinical outcome after radiotherapy of patients with intracranial meningioma
Authors: Lisowski Dominik , Trömel Jannik , Lutyj Paul , Lewitzki Victor , Hartrampf Philipp E. , Polat Bülent , Flentje Michael , Tamihardja Jörg 
Published: November 2022

AbstractThis retrospective, single-institutional study investigated long-term outcome, toxicity and health-related quality of life (HRQoL) in meningioma patients after radiotherapy. We analyzed the data of 119 patients who received radiotherapy at our department from 1997 to 2014 for intracranial WHO grade I-III meningioma. Fractionated stereotactic radiotherapy (FSRT), intensity modulated radiotherapy (IMRT) or radiosurgery radiation was applied. The EORTC QLQ-C30 and QLQ-BN20 questionnaires were completed for assessment of HRQoL. Overall survival (OS) for the entire study group was 89.6% at 5 years and 75.9% at 10 years. Local control (LC) at 5 and 10 years was 82.4% and 73.4%, respectively. Local recurrence was observed in 22 patients (18.5%). Higher grade acute and chronic toxicities were observed in seven patients (5.9%) and five patients (4.2%), respectively. Global health status was rated with a mean of 59.9 points (SD 22.3) on QLQ-C30. In conclusion, radiotherapy resulted in very good long-term survival and tumor control rates with low rates of severe toxicities but with a deterioration of long-term HRQoL.
Hydrogen diffusion and its electrical properties variation as a function of the IGZO stacking structure
Authors: Noh Hee Yeon , Lee Woo-Geun , G. R. Haripriya , Cha Jung-Hwa , Kim June-Seo , Yun Won Seok , Lee Myoung-Jae , Lee Hyeon-Jun 
Published: November 2022

AbstractThe oxygen vacancies and hydrogen in oxide semiconductors are regarded as the primary sources of charge carriers and various studies have investigated the effect of hydrogen on the properties of oxide semiconductors. However, the carrier generation mechanism between hydrogen and oxygen vacancies in an a-IGZO semiconductor has not yet been clearly examined. In this study we investigated the effect of hydrogen and the variation mechanisms of electrical properties of a thin film supplied with hydrogen from the passivation layer. SiOx and SiNx, which are used as passivation or gate insulator layers in the semiconductor process, respectively, were placed on the top or bottom of an a-IGZO semiconductor to determine the amount of hydrogen penetrating the a-IGZO active layer. The hydrogen diffusion depth was sufficiently deep to affect the entire thin semiconductor layer. A large amount of hydrogen in SiNx directly affects the electrical resistivity of a-IGZO semiconductor, whereas in SiOx, it induces a different behavior from that in SiNx, such as inducing an oxygen reaction and O–H bond behavior change at the interface of an a-IGZO semiconductor. Moreover, the change in electrical resistivity owing to the contribution of free electrons could be varied based on the bonding method of hydrogen and oxygen.
Novel pruning and truncating of the mixture of vine copula clustering models
Authors: Alanazi Fadhah Amer 
Published: November 2022

AbstractThe mixture of the vine copula densities allows selecting the vine structure, the most appropriate type of parametric marginal distributions, and the pair-copulas individually for each cluster. Therefore, complex hidden dependence structures can be fully uncovered and captured by the mixture of vine copula models without restriction to the parametric shape of margins or dependency patterns. However, this flexibility comes with the cost of dramatic increases in the number of model parameters as the dimension increases. Pruning and truncating each cluster of the mixture model will dramatically reduce the number of model parameters. This paper, therefore, introduced the first pruning and truncating techniques for the model-based clustering algorithm using the vine copula model, providing a significant contribution to the state-of-the-art. We apply the proposed methods to a number of well-known data sets with different dimensions. The results show that the performance of the individual pruning and truncation for each model cluster is superior to an existing vine copula clustering model.
Self-rated health and chronic inflammation are related and independently associated with hospitalization and long-term mortality in the general population
Authors: Tavenier Juliette , Rasmussen Line Jee Hartmann , Tolstrup Janne , Petersen Janne , Sobocki Jakob , Pisinger Charlotta , Eugen-Olsen Jesper , Gamst-Jensen Hejdi 
Published: November 2022

AbstractThe subjective indicator of health self-rated health (SRH) and the chronic inflammation biomarker soluble urokinase plasminogen activator receptor (suPAR) are both robust predictors of healthcare use and mortality. However, the possible relationship between SRH and suPAR in the assessment of hospitalization and mortality risk is unknown. We used data from the Danish population-based Inter99 cohort to examine the association between SRH and suPAR and test their individual and combined associations with 2-year risk of acute hospitalization and 5- and 15-year mortality. SRH and serum suPAR levels were measured in 5490 participants (median age 45.1 years, 48.7% men). Poorer SRH was associated with elevated suPAR. In unadjusted analyses, SRH and suPAR were individually associated with higher risks of acute hospitalization and mortality, and both measures remained independently associated with higher risks of hospitalization and 15-year mortality after mutual adjustments. The association of suPAR with mortality was stronger in poorer SRH categories, and when combined, SRH and suPAR could identify different groups of individuals with increased risk of acute hospitalization and mortality. Both SRH and suPAR were independently associated with risk of acute hospitalization and mortality, and different combinations of the two measures could identify different groups of individuals at increased risk.
Both abundant and rare fungi colonizing Fagus sylvatica ectomycorrhizal root-tips shape associated bacterial communities
Authors: Dietrich Marlies , Montesinos-Navarro Alicia , Gabriel Raphael , Strasser Florian , Meier Dimitri V. , Mayerhofer Werner , Gorka Stefan , Wiesenbauer Julia , Martin Victoria , Weidinger Marieluise , Richter Andreas , Kaiser Christina , Woebken Dagmar 
Published: November 2022

AbstractEctomycorrhizal fungi live in close association with their host plants and form complex interactions with bacterial/archaeal communities in soil. We investigated whether abundant or rare ectomycorrhizal fungi on root-tips of young beech trees (Fagus sylvatica) shape bacterial/archaeal communities. We sequenced 16S rRNA genes and fungal internal transcribed spacer regions of individual root-tips and used ecological networks to detect the tendency of certain assemblies of fungal and bacterial/archaeal taxa to inhabit the same root-tip (i.e. modularity). Individual ectomycorrhizal root-tips hosted distinct fungal communities associated with unique bacterial/archaeal communities. The structure of the fungal-bacterial/archaeal association was determined by both, dominant and rare fungi. Integrating our data in a conceptual framework suggests that the effect of rare fungi on the bacterial/archaeal communities of ectomycorrhizal root-tips contributes to assemblages of bacteria/archaea on root-tips. This highlights the potential impact of complex fine-scale interactions between root-tip associated fungi and other soil microorganisms for the ectomycorrhizal symbiosis.
A lineage tree-based hidden Markov model quantifies cellular heterogeneity and plasticity
Authors: Mohammadi Farnaz , Visagan Shakthi , Gross Sean M. , Karginov Luka , Lagarde J. C. , Heiser Laura M. , Meyer Aaron S. 
Published: November 2022

AbstractIndividual cells can assume a variety of molecular and phenotypic states and recent studies indicate that cells can rapidly adapt in response to therapeutic stress. Such phenotypic plasticity may confer resistance, but also presents opportunities to identify molecular programs that could be targeted for therapeutic benefit. Approaches to quantify tumor-drug responses typically focus on snapshot, population-level measurements. While informative, these methods lack lineage and temporal information, which are particularly critical for understanding dynamic processes such as cell state switching. As new technologies have become available to measure lineage relationships, modeling approaches will be needed to identify the forms of cell-to-cell heterogeneity present in these data. Here we apply a lineage tree-based adaptation of a hidden Markov model that employs single cell lineages as input to learn the characteristic patterns of phenotypic heterogeneity and state transitions. In benchmarking studies, we demonstrated that the model successfully classifies cells within experimentally-tractable dataset sizes. As an application, we analyzed experimental measurements in cancer and non-cancer cell populations under various treatments. We find evidence of multiple phenotypically distinct states, with considerable heterogeneity and unique drug responses. In total, this framework allows for the flexible modeling of single cell heterogeneity across lineages to quantify, understand, and control cell state switching.
Megashears and hydrothermalism at the Martian crustal dichotomy in Valles Marineris
Authors: Gurgurewicz Joanna , Mège Daniel , Schmidt Frédéric , Douté Sylvain , Langlais Benoit 
Published: November 2022

AbstractObservations of ancient deep deformation systems on Mars are important for constraining planetary dynamics, as well as to identify potential mineral resources. However, such systems were thought to be unexposed and inaccessible to analysis. Here, we apply structural and hyperspectral analyses, and correlate results with magnetic anomaly patterns, to investigate two large right-lateral brittle-ductile shear zones and fault megabreccia exposed in the deepest parts of Valles Marineris. The shear zones follow the trace of the edge of the Borealis impact basin, thought to represent the planetary dichotomy boundary. We identify hydrothermally altered mafic igneous rocks in the sheared basement. We suggest that the shear system was initiated as basin ring fault system in the pre-Noachian, with further reactivation up until the Hesperian, and may still be a potential source of marsquakes. Hydrothermal circulation through the shear zones may have initiated primary mineralizations which are promising for base and rare metal exploration.
Toward an improved definition of a healthy microbiome for healthy aging
Authors: Ghosh Tarini Shankar , Shanahan Fergus , O’Toole Paul W. 
Published: November 2022

AbstractThe gut microbiome is a modifier of disease risk because it interacts with nutrition, metabolism, immunity and infection. Aging-related health loss has been correlated with transition to different microbiome states. Microbiome summary indices including alpha diversity are apparently useful to describe these states but belie taxonomic differences that determine biological importance. We analyzed 21,000 fecal microbiomes from seven data repositories, across five continents spanning participant ages 18–107 years, revealing that microbiome diversity and uniqueness correlate with aging, but not healthy aging. Among summary statistics tested, only Kendall uniqueness accurately reflects loss of the core microbiome and the abundance and ranking of disease-associated and health-associated taxa. Increased abundance of these disease-associated taxa and depletion of a coabundant subset of health-associated taxa are a generic feature of aging. These alterations are stronger correlates of unhealthy aging than most microbiome summary statistics and thus help identify better targets for therapeutic modulation of the microbiome.