bluuebunny/crossref_metadata_2025_split huggingface dataset:
GeneNetTools: tests for Gaussian graphical models with shrinkage
Authors: Bernal Victor , Soancatl-Aguilar Venustiano , Bulthuis Jonas , Guryev Victor , Horvatovich Peter , Grzegorczyk Marco 
Published: September 2022

AbstractMotivationGaussian graphical models (GGMs) are network representations of random variables (as nodes) and their partial correlations (as edges). GGMs overcome the challenges of high-dimensional data analysis by using shrinkage methodologies. Therefore, they have become useful to reconstruct gene regulatory networks from gene-expression profiles. However, it is often ignored that the partial correlations are ‘shrunk’ and that they cannot be compared/assessed directly. Therefore, accurate (differential) network analyses need to account for the number of variables, the sample size, and also the shrinkage value, otherwise, the analysis and its biological interpretation would turn biased. To date, there are no appropriate methods to account for these factors and address these issues.ResultsWe derive the statistical properties of the partial correlation obtained with the Ledoit–Wolf shrinkage. Our result provides a toolbox for (differential) network analyses as (i) confidence intervals, (ii) a test for zero partial correlation (null-effects) and (iii) a test to compare partial correlations. Our novel (parametric) methods account for the number of variables, the sample size and the shrinkage values. Additionally, they are computationally fast, simple to implement and require only basic statistical knowledge. Our simulations show that the novel tests perform better than DiffNetFDR—a recently published alternative—in terms of the trade-off between true and false positives. The methods are demonstrated on synthetic data and two gene-expression datasets from Escherichia coli and Mus musculus.Availability and implementationThe R package with the methods and the R script with the analysis are available in https://github.com/V-Bernal/GeneNetTools.Supplementary informationSupplementary data are available at Bioinformatics online.
The different brain areas occupied for integrating information of hierarchical linguistic units: a study based on EEG and TMS
Authors: Pei Changfu , Qiu Yuan , Li Fali , Huang Xunan , Si Yajing , Li Yuqin , Zhang Xiabing , Chen Chunli , Liu Qiang , Cao Zehong , Ding Nai , Gao Shan , Alho Kimmo , Yao Dezhong , Xu Peng 
Published: September 2022

AbstractHuman language units are hierarchical, and reading acquisition involves integrating multisensory information (typically from auditory and visual modalities) to access meaning. However, it is unclear how the brain processes and integrates language information at different linguistic units (words, phrases, and sentences) provided simultaneously in auditory and visual modalities. To address the issue, we presented participants with sequences of short Chinese sentences through auditory, visual, or combined audio-visual modalities while electroencephalographic responses were recorded. With a frequency tagging approach, we analyzed the neural representations of basic linguistic units (i.e. characters/monosyllabic words) and higher-level linguistic structures (i.e. phrases and sentences) across the 3 modalities separately. We found that audio-visual integration occurs in all linguistic units, and the brain areas involved in the integration varied across different linguistic levels. In particular, the integration of sentences activated the local left prefrontal area. Therefore, we used continuous theta-burst stimulation to verify that the left prefrontal cortex plays a vital role in the audio-visual integration of sentence information. Our findings suggest the advantage of bimodal language comprehension at hierarchical stages in language-related information processing and provide evidence for the causal role of the left prefrontal regions in processing information of audio-visual sentences.
The relevance of heterotopic callosal fibers to interhemispheric connectivity of the mammalian brain
Authors: Szczupak Diego , Iack Pamela Meneses , Rayêe Danielle , Liu Cirong , Lent Roberto , Tovar-Moll Fernanda , Silva Afonso C 
Published: September 2022

AbstractThe corpus callosum (CC) is the largest white matter structure and the primary pathway for interhemispheric brain communication. Investigating callosal connectivity is crucial to unraveling the brain’s anatomical and functional organization in health and disease. Classical anatomical studies have characterized the bulk of callosal axonal fibers as connecting primarily homotopic cortical areas. Whenever detected, heterotopic callosal fibers were ascribed to altered sprouting and pruning mechanisms in neurodevelopmental diseases such as CC dysgenesis (CCD). We hypothesized that these heterotopic connections had been grossly underestimated due to their complex nature and methodological limitations. We used the Allen Mouse Brain Connectivity Atlas and high-resolution diffusion-weighted imaging to identify and quantify homotopic and heterotopic callosal connections in mice, marmosets, and humans. In all 3 species, we show that ~75% of interhemispheric callosal connections are heterotopic and comprise the central core of the CC, whereas the homotopic fibers lay along its periphery. We also demonstrate that heterotopic connections have an essential role in determining the global properties of brain networks. These findings reshape our view of the corpus callosum’s role as the primary hub for interhemispheric brain communication, directly impacting multiple neuroscience fields investigating cortical connectivity, neurodevelopment, and neurodevelopmental disorders.
Parallel Analysis of Pre- and Postoperative Circulating Tumor DNA and Matched Tumor Tissues in Resectable Pancreatic Ductal Adenocarcinoma: A Prospective Cohort Study
Authors: Lee Jee-Soo , Han Youngmin , Yun Won-Gun , Kwon Wooil , Kim Hongbeom , Jeong Hyeonju , Seo Myoung-Seock , Park Yongsook , Cho Sung Im , Kim Haeryoung , Kim Ji Yeon , Seong Moon-Woo , Jang Jin-Young , Park Sung Sup 
Published: September 2022

Abstract

Background
Circulating tumor DNA (ctDNA) is a promising biomarker for early tumor detection and minimal residual disease (MRD) assessment in early-stage cancer, but quantifying minute amounts of ctDNA is challenging and well-designed studies on ctDNA in early-stage cancer are still lacking. Here, we adapted a sensitive next-generation sequencing (NGS) technology and performed parallel analysis of pre- and postoperative ctDNA and matched tumor tissues in a prospective cohort of patients with resectable pancreatic ductal adenocarcinoma (PDAC).

Methods
In total, 70 consecutive patients undergoing curative resection for resectable PDAC were enrolled. We performed integrated digital error suppression-enhanced cancer personalized profiling by deep sequencing NGS of triple-matched samples (pre/postoperative plasma cell-free DNA [cfDNA], tumor tissue, and genomic DNA) targeting 77 genes.

Results
Preoperative ctDNA was detected in 37.7% of the evaluable patients, with a median variant allele frequency of 0.09%. Twelve additional oncogenic mutations were detected exclusively in preoperative ctDNA but not in tissue. When quantitative concentrations of ctDNA were estimated in haploid genome equivalents per milliliter (hGE/mL), the risk of early recurrence was high in patients with postoperative ctDNA &gt;1 hGE/mL. cfDNA variants from 24.5% of patients had features compatible with clonal hematopoiesis.

Conclusions
An optimized NGS approach might add value beyond tissue analysis through the highly sensitive detection of minute amounts of ctDNA in resectable PDAC. Postoperative ctDNA concentration could be a tool for MRD assessment. Moreover, parallel analyses of matched tissues and leukocytes might be required to accurately detect clinically relevant ctDNA.
Resistance of Grapevine Genotypes (Vitisspp.) toDaktulosphaira vitifoliae(Hemiptera: Phylloxeridae) in Brazil: Implications for Pest Management
Authors: Andzeiewski S , Oliveira D C , Bernardi D , Botton M 
Published: September 2022

AbstractThe phylloxera Daktulosphaira vitifoliae (Fitch) is considered the main pest in vine crops in the world. One of the alternatives for pest management is the use of resistant rootstocks. In the present study, 14 vine genotypes comprised of 6 canopy cultivars (Bordô, Isabel, BRS Lorena, Cabernet Sauvignon, Magnólia, and Chardonnay), 4 commercial rootstocks (Paulsen 1103, SO4, IAC 766, and IAC 572), and 4 promising rootstocks for pest management (1111-21, 548-44, 548-15, and IBCA-125) were evaluated for resistance to infestation the of root form of pest. For each genotype, the number of eggs, nymphs, and adults present in the roots were evaluated at 15, 20, 25, 30, and 35 d after egg infestation. In addition, the feeding place (lignified or nonlignified root), the presence or absence of tuberosities and nodosities, and the total fecundity of females were evaluated. The highest survival rates of nymphs and adults were observed in Cabernet Sauvignon, BRS Lorena, Chardonnay, and IBCA-25 in lignified roots, with the formation of tuberosities characterizing the materials as susceptible. In contrast, SO4, Paulsen 1103, IAC 572, IAC 766, 548-44, 548-15, Magnólia, and 1111-21 provided the least nymph and adult survival over time in nonlignified roots present in the nodosities, characterizing the materials as resistant. In addition, the lowest fecundity was observed in the roots of Magnólia (16 eggs). According to the results, it was verified that the cultivar Magnolia and the selections 548-15 and 1111-21 present reduced infestation and survival of nymphs of D. vitifoliae in the roots. This fact demonstrates the potential of the materials to be used as new resistant rootstocks or sources of insect resistance.
What drives performance in machine learning models for predicting heart failure outcome?
Authors: Gutman Rom , Aronson Doron , Caspi Oren , Shalit Uri 
Published: September 2022

AbstractAimsThe development of acute heart failure (AHF) is a critical decision point in the natural history of the disease and carries a dismal prognosis. The lack of appropriate risk-stratification tools at hospital discharge of AHF patients significantly limits clinical ability to precisely tailor patient-specific therapeutic regimen at this pivotal juncture. Machine learning-based strategies may improve risk stratification by incorporating analysis of high-dimensional patient data with multiple covariates and novel prediction methodologies. In the current study, we aimed at evaluating the drivers for success in prediction models and establishing an institute-tailored artificial Intelligence-based prediction model for real-time decision support.Methods and resultsWe used a cohort of all 10 868 patients AHF patients admitted to a tertiary hospital during a 12 years period. A total of 372 covariates were collected from admission to the end of the hospitalization. We assessed model performance across two axes: (i) type of prediction method and (ii) type and number of covariates. The primary outcome was 1-year survival from hospital discharge. For the model-type axis, we experimented with seven different methods: logistic regression (LR) with either L1 or L2 regularization, random forest (RF), Cox proportional hazards model (Cox), extreme gradient boosting (XGBoost), a deep neural-net (NeuralNet) and an ensemble classifier of all the above methods. We were able to achieve an area under receiver operator curve (AUROC) prediction accuracy of more than 80% with most prediction models including L1/L2-LR (80.4%/80.3%), Cox (80.2%), XGBoost (80.5%), NeuralNet (80.4%). RF was inferior to other methods (78.8%), and the ensemble model was slightly superior (81.2%). The number of covariates was a significant modifier (P &lt; 0.001) of prediction success, the use of multiplex-covariates preformed significantly better (AUROC 80.4% for L1-LR) compared with a set of known clinical covariates (AUROC 77.8%). Demographics followed by lab-tests and administrative data resulted in the largest gain in model performance.ConclusionsThe choice of the predictive modelling method is secondary to the multiplicity and type of covariates for predicting AHF prognosis. The application of a structured data pre-processing combined with the use of multiple-covariates results in an accurate, institute-tailored risk prediction in AHF
Empirical shaking scenarios for Europe: a feasibility study
Authors: Bindi D , Zaccarelli R , Razafindrakoto H N T , Yen M-H , Cotton F 
Published: September 2022

SUMMARY
We process a large number of seismic recordings in Europe (i.e. about half a million recordings from about 19 500 earthquakes) with the aim of decomposing the Fourier amplitude spectra into source, propagation and site effects. To account for first-order, large-scale regional differences in propagation effects, the spectral decomposition simultaneously solves six different models describing the spectral attenuation within different subregions. Since the decomposition approach is affected by trade-offs that make the solution non-unique, we assume a station installed on rock in Switzerland as reference station and we invert for relative site amplifications. To propagate the reference site condition to the entire data set, we develop a procedure based on a sequence of decompositions considering increasing and overlapping data sets. The applied procedure allows for a consistent evaluation of relative site effects for about 3200 station channels using a single reference station for the whole data set. Comparisons with site amplifications obtained in previous studies at common stations in Italy and Switzerland confirm the site amplification results. The target of this work is to show that the spectral models obtained for attenuation and site effects can be used to generate empirical shaking scenarios in the Fourier domain. Therefore, we conclude our feasibility study by presenting shaking maps generated at different frequencies for hypothetical magnitude 6.5 earthquakes with a Brune-type stress drop of 10 MPa located at different positions across Europe.
Concordance and Discordance Between Patient-reported Remission, Patient-reported Outcomes, and Physician Global Assessment
Authors: Kamp Kendra J , Hawes Stephen E , Tse Chung Sang , Singh Siddharth , Dang Nhu , Oberai Ridhima , Weaver S Alandra , Melmed Gil Y , Siegel Corey A , van Deen Welmoed K ,   IBD Qorus, Younes Ziad , Mattar Mark C , Metwally Mark , Scott Frank , Ostrov Arthur , Rubin David T , Gerich Mark , Gerner Donna , Heagy Erica , Nelson Eugene , Holthoff Megan , Hudesman David , Oberai Ridhima , Almario Christopher , Bray Harry , Crate Damara , Hou Jason K , Singh Siddharth , Arrieta Rose , Banty Andrea , Betteridge John , Carron Jessica , Charabaty Aline , Danielewicz Michael , Deitch Josh , Farraye Francis , Fasanya Helen , Flynn Ann , Ha Christina , Kaufman Lia , Kaur Nirmal , Kearney Kristi , Kennedy Alice M , Kim Betty , Kwon Michelle , Le Helen , Mize Carrie , Morgan Emily , Morris-McCoy Linda , Oonk Alexis , Pashby Teresa , Rai Victoria , Reddy Swapna , Roake Kami , Shukla Richa , Syal Gaurav , Traboulsi Cindy , Turner Quin , Valentine John , Vrabie Raluca , Walker Trisha , Weatherly Julie , Williams Emmanuelle , Yun Laura , Zisman Tim 
Published: September 2022

AbstractBackgroundAlthough validated patient-reported outcome (PRO) measurements can categorize patients with inflammatory bowel disease (IBD) into clinical remission or active disease, patients may have different definitions of remission. The purpose of this study was to compare patient-defined remission to remission based on PRO measures and physician global assessment (PGA) and to understand the clinical and demographic factors associated with disagreements.MethodsWe retrospectively analyzed 3257 de-identified surveys from 2004 IBD patients who consented to participate in the Crohn’s and Colitis Foundation’s IBD Qorus Learning Health System between September 2019 and February 2021. We used logistic regression models with generalized estimating equations to analyze the clinical and demographic factors (eg, age, disease duration, health confidence) associated with discordance between patient-defined remission (yes/no) and PRO-defined remission for ulcerative colitis (UC; PRO2: stool frequency, rectal bleeding) and Crohn’s disease (CD; PRO-3: average number of liquid stools, abdominal pain, well-being).ResultsAmong patients with UC, overall concordance was 79% between patient self-report and PRO2-defined remission and 49% between patient self-report and PGA-defined remission. Among patients with CD, overall concordance was 69% between patient self-report and PRO3-defined remission and 54% between patient self-report and PGA-defined remission. Patients in PRO-defined remission were more likely to report active disease if they had IBD &lt;5 years and low health confidence. Patients with PRO-defined active disease were more likely to report remission if they were not using prednisone and had high health confidence.ConclusionDiscordance exists between how remission is defined by patients, PRO measures, and PGA.
A retrospective study of Enterococcus faecalis infective endocarditis: comparison of clinical characteristics and outcomes associated with treatment
Authors: Vigneswaran N , McKew G 
Published: September 2022

Abstract

Introduction
A synergistic antibiotic combination of a penicillin and gentamicin (AG) or ceftriaxone (AC) is used in the management of Enterococcus faecalis infective endocarditis (EFIE). We compare the treatment outcomes between AG and AC, including low and high dose ceftriaxone (1 and 2 g 12 hourly).

Methods
A retrospective cohort study of patients treated for EFIE at single tertiary centre (2012–2019). Outcome measures examined were 90- and 180-day mortality, treatment associated adverse events and relapse of bacteraemia (within 1 year).

Results
39 patients were enrolled [61.6% given (AC) (n = 24), 24% received ACL (n = 10) and 34% received ACN (n = 14)], 38.4% received AG (n = 15). We noted a difference in the mortality outcomes at 90 and 180 days between those treated with AG and AC overall (6.7% and 33.3%, respectively) although this did not reach statistical significance (P = 0.114, P = 0.061). No significant difference was noted between these groups in incidence of relapsed bacteraemia with two cases noted in the AC cohort (8.3%, 2/24) and none observed (0/15) in the AG cohort (P = 0.662, P = 0.414). A greater number of adverse events was observed in the AG group (11/15, 73.3%) compared to the overall AC group (6/24, 25.0%) (P = 0.009), with no difference between the high and low dose ceftriaxone groups (P = 0.05).

Conclusion
Combination treatment of EFIE with AC is associated with a reduced number of adverse events in comparison to AG groups. Although increased mortality was observed in the AC group, this did not reach statistical significance, and reflects the greater comorbidities and reduced capacity for surgical source control in this cohort.
Sediment processing by two estuarine crabs in Bangladesh: small efficient consumers alongside big inefficient ones
Authors: Kumari Gayatri , Phillott Andrea D , Cruz-Rivera Edwin 
Published: September 2022

Abstract
Due to their foraging and burrowing behaviors, many crabs in the brachyuran superfamily Ocypodoidea are considered important bioturbators that enhance sediment turnover, energy and matter flow, and nutrient cycling in sandy beaches, mangrove forests, and estuaries. There is surprisingly little comparative work assessing the relative effects of sympatric species, even though many co-occur over broad ranges. We compared uptake of sediment water, organic matter, and carbonate by two sympatric deposit-feeding crabs from Chittagong, Bangladesh, the small sand-bubbler Dotilla intermedia De Man, 1888 and the much larger ghost crab Ocypode macrocera H. Milne Edwards, 1837. Comparisons between feeding pellets and surrounding surface sediments showed that D. intermedia reduced sediment water content by 66% and organic matter content by 67%. In contrast, feeding by O. macrocera had no significant effects on these two parameters. Although sediments excavated by O. macrocera were twice as rich in organic matter compared to surface sediments, variance was high, rendering the difference not statistically significant. Inorganic carbonate distribution was affected by both crabs in different ways. Dotilla feeding pellets had significantly less carbonate than unprocessed surface sediments. In contrast, Ocypode feeding pellets had similar carbonate concentrations to surface sediments, but sediments excavated by those crabs were significantly lower in carbonates (~28%) than those at the surface. While both crab species have the potential to affect sediment properties, they do so through different mechanisms.
Prostate-Specific Membrane Antigen Expression in Meningioma: A Promising Theranostic Target
Authors: Tubre Teddi , Hacking Sean , Alexander Abigail , Brickman Arlen , Delalle Ivana , Elinzano Heinrich , Donahue John E 
Published: September 2022

AbstractMeningioma is the most common intracranial neoplasm, yet there is no effective therapy for recurrent/refractory meningiomas after surgery and radiation. Prostate-specific membrane antigen (PSMA) is an enzyme upregulated on endothelial cells of multiple neoplasms and is being investigated as a theranostic target. Until now, PSMA has not been studied in meningiomas. We aimed to verify PSMA endothelial expression in meningiomas, detect tumor grade variability, and investigate the relationship of PSMA signal with tumor recurrence. We analyzed 96 archival meningiomas including 58 de novo and 38 recurrent specimens. All specimens were stained routinely and immunostained for CD31 and PSMA. Slides were scanned and analyzed producing raw data for images of PSMA, CD31, PSMA/CD31, and PSMA/vasculature. PSMA expression was seen within 98.9% of meningioma samples. In the total cohort, higher-grade tumors had increased expression of raw PSMA and PSMA/CD31, and PSMA/vasculature ratios compared to grade 1 tumors. PSMA expression and PSMA/vasculature ratios (p = 0.0015) were higher in recurrent versus de novo tumors among paired samples. ROC curves demonstrated PSMA/CD31, PSMA/vasculature, and raw CD31 as indicators of tumor recurrence. Thus, PSMA is expressed within endothelial cells of meningiomas, is increased with tumor grade and recurrence, and persists with prior irradiation.
A non-detection of red supergiant convection in Gaia
Authors: Kochanek C S 
Published: September 2022

ABSTRACT
Large-scale surface convection on red supergiants (RSGs) can lead to shifts in the photocentre of the star that might be measured by Gaia and used as a new probe of the surface dynamics of these rare but important stars. Unlike brightness variations, photocentre motions would provide information on the physical scale of the convective cells. The signal would be that RSGs show an excess astrometric noise at the level of a few per cent of the stellar radius. Unfortunately, we find that the excess astrometric noise level of Gaia EDR3 is roughly an order of magnitude too large to detect the predicted motions and that RSGs have excess astrometric noise indistinguishable from other stars of similar magnitude, colour, or parallax. The typical excess astrometric noise steadily decreases with G magnitude (for G &lt; 11 mag), so it is crucial to compare stars of similar brightness.