bluuebunny/crossref_metadata_2025_split huggingface dataset:
Revisiting ‘brain modes’ in a new computational era: approaches for the characterization of brain-behavioural associations
Authors: Toba Monica N , Godefroy Olivier , Rushmore R Jarrett , Zavaglia Melissa , Maatoug Redwan , Hilgetag Claus C , Valero-Cabré Antoni 
Published: October 2019

AbstractThe study of brain-function relationships is undergoing a conceptual and methodological transformation due to the emergence of network neuroscience and the development of multivariate methods for lesion-deficit inferences. Anticipating this process, in 1998 Godefroy and co-workers conceptualized the potential of four elementary typologies of brain-behaviour relationships named ‘brain modes’ (unicity, equivalence, association, summation) as building blocks able to describe the association between intact or lesioned brain regions and cognitive processes or neurological deficits. In the light of new multivariate lesion inference and network approaches, we critically revisit and update the original theoretical notion of brain modes, and provide real-life clinical examples that support their existence. To improve the characterization of elementary units of brain-behavioural relationships further, we extend such conceptualization with a fifth brain mode (mutual inhibition/masking summation). We critically assess the ability of these five brain modes to account for any type of brain-function relationship, and discuss past versus future contributions in redefining the anatomical basis of human cognition. We also address the potential of brain modes for predicting the behavioural consequences of lesions and their future role in the design of cognitive neurorehabilitation therapies.
Cortical Surfaces Mediate the Relationship Between Polygenic Scores for Intelligence and General Intelligence
Authors: Lett Tristram A , Vogel Bob O , Ripke Stephan , Wackerhagen Carolin , Erk Susanne , Awasthi Swapnil , Trubetskoy Vassily , Brandl Eva J , Mohnke Sebastian , Veer Ilya M , Nöthen Markus M , Rietschel Marcella , Degenhardt Franziska , Romanczuk-Seiferth Nina , Witt Stephanie H , Banaschewski Tobias , Bokde Arun L W , Büchel Christian , Quinlan Erin B , Desrivières Sylvane , Flor Herta , Frouin Vincent , Garavan Hugh , Gowland Penny , Ittermann Bernd , Martinot Jean-Luc , Martinot Marie-Laure Paillère , Nees Frauke , Papadopoulos-Orfanos Dimitri , Paus Tomáš , Poustka Luise , Fröhner Juliane H , Smolka Michael N , Whelan Robert , Schumann Gunter , Tost Heike , Meyer-Lindenberg Andreas , Heinz Andreas , Walter Henrik ,   IMAGEN consortium
Published: October 2019

Abstract
Recent large-scale, genome-wide association studies (GWAS) have identified hundreds of genetic loci associated with general intelligence. The cumulative influence of these loci on brain structure is unknown. We examined if cortical morphology mediates the relationship between GWAS-derived polygenic scores for intelligence (PSi) and g-factor. Using the effect sizes from one of the largest GWAS meta-analysis on general intelligence to date, PSi were calculated among 10 P value thresholds. PSi were assessed for the association with g-factor performance, cortical thickness (CT), and surface area (SA) in two large imaging-genetics samples (IMAGEN N = 1651; IntegraMooDS N = 742). PSi explained up to 5.1% of the variance of g-factor in IMAGEN (F1,1640 = 12.2–94.3; P &lt; 0.005), and up to 3.0% in IntegraMooDS (F1,725 = 10.0–21.0; P &lt; 0.005). The association between polygenic scores and g-factor was partially mediated by SA and CT in prefrontal, anterior cingulate, insula, and medial temporal cortices in both samples (PFWER-corrected &lt; 0.005). The variance explained by mediation was up to 0.75% in IMAGEN and 0.77% in IntegraMooDS. Our results provide evidence that cumulative genetic load influences g-factor via cortical structure. The consistency of our results across samples suggests that cortex morphology could be a novel potential biomarker for neurocognitive dysfunction that is among the most intractable psychiatric symptoms.
The contribution of sleep to social inequalities in cardiovascular disorders: a multi-cohort study
Authors: Petrovic Dusan , Haba-Rubio José , de Mestral Vargas Carlos , Kelly-Irving Michelle , Vineis Paolo , Kivimäki Mika , Nyberg Solja , Gandini Martina , Bochud Murielle , Vollenweider Peter , d’Errico Angelo , Barros Henrique , Fraga Silvia , Goldberg Marcel , Zins Marie , Steptoe Andrew , Delpierre Cyrille , Heinzer Raphael , Carmeli Cristian , Chadeau-Hyam Marc , Stringhini Silvia ,   for The Lifepath Consortium
Published: October 2019

Abstract

Aims
Sleep disturbances exhibit a strong social patterning, and inadequate sleep has been associated with adverse health outcomes, including cardiovascular disorders (CVD). However, the contribution of sleep to socioeconomic inequalities in CVD is unclear. This study pools data from eight European cohorts to investigate the role of sleep duration in the association between life-course socioeconomic status (SES) and CVD.

Methods and results
We used cross-sectional data from eight European cohorts, totalling 111 205 participants. Life-course SES was assessed using father’s and adult occupational position. Self-reported sleep duration was categorized into recommended (6–8.5 h/night), long (&gt;8.5 h/night), and short (&lt;6 h/night). We examined two cardiovascular outcomes: coronary heart disease (CHD) and stroke. Main analyses were conducted using pooled data and examined the association between life-course SES and CVD, and the contribution of sleep duration to this gradient using counterfactual mediation. Low father’s occupational position was associated with an increased risk of CHD (men: OR = 1.19, 95% CI [1.04; 1.37]; women: OR = 1.25, 95% CI [1.02; 1.54]), with marginal decrease of the gradient after accounting for adult occupational position (men: OR = 1.17, 95% CI [1.02; 1.35]; women: OR = 1.22, 95% CI [0.99; 1.52]), and no mediating effect by short sleep duration. Low adult occupational position was associated with an increased risk of CHD in both men and women (men: OR = 1.48, 95% CI [1.14; 1.92]; women: OR = 1.53, 95% CI [1.04; 2.21]). Short sleep duration meaningfully contributed to the association between adult occupational position and CHD in men, with 13.4% mediation. Stroke did not exhibit a social patterning with any of the variables examined.

Conclusion
This study suggests that inadequate sleep accounts to a meaningful proportion of the association between adult occupational position and CHD, at least in men. With sleep increasingly being considered an important cardiovascular risk factor in its own terms, our study additionally points to its potential role in social inequalities in cardiovascular disease.
Diagnostic criteria and symptom grading for delayed gastric conduit emptying after esophagectomy for cancer: international expert consensus based on a modified Delphi process
Authors: Konradsson M , van Berge Henegouwen M I , Bruns C , Chaudry M A , Cheong E , Cuesta M A , Darling G E , Gisbertz S S , Griffin S M , Gutschow C A , van Hillegersberg R , Hofstetter W , Hölscher A H , Kitagawa Y , van Lanschot J J B , Lindblad M , Ferri L E , Low D E , Luyer M D P , Ndegwa N , Mercer S , Moorthy K , Morse C R , Nafteux P , Nieuwehuijzen G A P , Pattyn P , Rosman C , Ruurda J P , Räsänen J , Schneider P M , Schröder W , Sgromo B , Van Veer H , Wijnhoven B P L , Nilsson M 
Published: October 2019

Abstract
Delayed gastric conduit emptying (DGCE) after esophagectomy for cancer is associated with adverse outcomes and troubling symptoms. Widely accepted diagnostic criteria and a symptom grading tool for DGCE are missing. This hampers the interpretation and comparison of studies. A modified Delphi process, using repeated web-based questionnaires, combined with live interim group discussions was conducted by 33 experts within the field, from Europe, North America, and Asia. DGCE was divided into early DGCE if present within 14 days of surgery and late if present later than 14 days after surgery. The final criteria for early DGCE, accepted by 25 of 27 (93%) experts, were as follows: &gt;500 mL diurnal nasogastric tube output measured on the morning of postoperative day 5 or later or &gt;100% increased gastric tube width on frontal chest x-ray projection together with the presence of an air–fluid level. The final criteria for late DGCE accepted by 89% of the experts were as follows: the patient should have ‘quite a bit’ or ‘very much’ of at least two of the following symptoms; early satiety/fullness, vomiting, nausea, regurgitation or inability to meet caloric need by oral intake and delayed contrast passage on upper gastrointestinal water-soluble contrast radiogram or on timed barium swallow. A symptom grading tool for late DGCE was constructed grading each symptom as: ‘not at all’, ‘a little’, ‘quite a bit’, or ‘very much’, generating 0, 1, 2, or 3 points, respectively. For the five symptoms retained in the diagnostic criteria for late DGCE, the minimum score would be 0, and the maximum score would be 15. The final symptom grading tool for late DGCE was accepted by 27 of 31 (87%) experts. For the first time, diagnostic criteria for early and late DGCE and a symptom grading tool for late DGCE are available, based on an international expert consensus process.
Short- and mid-term outcomes of robotic versus thoraco-laparoscopic McKeown esophagectomy for squamous cell esophageal cancer: a propensity score-matched study
Authors: Yang Y , Zhang X , Li B , Hua R , Yang Y , He Y , Ye B , Guo X , Sun Y , Li Z 
Published: October 2019

SUMMARY
Controversy exists on the advantages of robotic McKeown esophagectomy (RME) versus thoraco-laparoscopic McKeown esophagectomy (TLME). The aim was to evaluate the short- and mid-term outcomes of RME and TLME in the treatment of patients with esophageal squamous cell carcinoma (ESCC). A consecutive series of 652 patients, 280 in RME and 372 in TLME, who underwent minimally invasive McKeown esophagectomy for ESCC at our department from November 2015 to June 2018 was analyzed. A propensity score-matched comparison with clinicopathological covariates was performed between the two groups. Complications were categorized based on the Esophagectomy Complications Consensus Group (ECCG) recommendation. To identify the recurrence, all patients with R0 resection were followed with a median follow-up period of 20.2 months (range 1–33 months). After propensity score matching, 271 patients were identified for each cohort. In the matched cohorts, two patients died within 90 days in TLME, whereas no patients died in RME. RME was associated with similar intraoperative blood loss (P = 0.895), but with shorter surgical duration (244.5 vs. 276.0 min, P &lt; 0.001), shorter thoracic duration (85.0 vs. 102.9 min, P &lt; 0.001) and lower thoracic conversions (0.7% vs. 5.9%, P = 0.001). In spite of the similar results on total and thoracic lymph nodes dissection, RME yielded more lymph nodes along recurrent laryngeal nerve (4.8 vs. 4.1, P = 0.012), as well as the higher incidence of recurrent nerve injury (29.2% vs. 15.1%, P &lt; 0.001) when compared to TLME. Tumor recurrence occurred in 30 patients and was locoregional only in 9 (3.5%) patients, systemic only in 17 (6.7%) patients, and combined in 4 (1.6%) patients in RME, while in 26 patients and was locoregional only in 10 (10.6%) patients, systemic only in 7 (2.8%) patients, and combined in 9 (3.6%) patients in TLME. RME was associated with a lower rate of mediastinal lymph nodes recurrence (2.0% vs. 5.3%, P = 0.044). Overall and disease-free survival was not different between the two cohorts (P = 0.097 and P = 0.248, respectively). RME was shown to be a safe and oncologically effective approach with favorable short- and mid-term outcomes in the treatment of patients with ESCC.
Simultaneous deblending and data reconstruction to supply proper time-lapse data sets throughout the field life in a cost-effective and efficient manner
Authors: Nakayama Shotaro , Blacquière Gerrit 
Published: October 2019

SUMMARYAcquisition of multiple seismic data sets at different moments in time is capable of satisfying the continuously increasing demand for high-quality subsurface images to reveal both static and dynamic elements during the field development. However, in practice, challenges of pursuing this strategy lie in different perspectives related to budgetary, operational and regulatory constraints. Seismic surveys performed in a compressed manner in time and/or space can provide high-quality seismic data sets in a cost-effective and productive manner. This way of acquisition normally accompanies decompression of recorded data such as deblending and/or data reconstruction. The performance of the recovery process is of fundamental importance in determining the technical success of compressed measurements. Our proposed approach aims at realizing the benefits from compression in data acquisition, contributing to cost and efficiency, while recovering deblended and reconstructed data of sufficient quality. The approach deals jointly with deblending and data reconstruction via a sparse inversion in the frequency–wavenumber domain, coupled with constraints on causality and coherency. Additionally, we formulate a single objective function aimed at sharing static information among vintages and, at the same time, at extracting dynamic changes in the reservoir of interest according to prior subsurface information. We apply the proposed approach to both synthetic and real data. A comparison with a strategy that independently recovers compressed data sets demonstrates the viability of the proposed simultaneous method to effectively enhance the quality of recovered data and extract reliable time-lapse signatures.
Follow-up Care for Breast Cancer Survivors
Authors: Ruddy Kathryn J , Herrin Jeph , Sangaralingham Lindsey , Freedman Rachel A , Jemal Ahmedin , Haddad Tufia C , Allen Summer V , Hieken Tina , Boughey Judy C , Ganz Patricia A , Havyer Rachel D , Shah Nilay D 
Published: October 2019

Abstract
Breast cancer survivorship guidelines recommend at least annual follow-up visits, yet the degree to which this occurs in clinical practice is uncertain. Claims data from a US commercial insurance database (OptumLabs) were used to identify women treated with curative intent surgery for newly diagnosed breast cancer between 2006 and 2014. In 25 035 women, median follow-up was 3 years. In the second year after surgery, 9.6% of the patients did not visit a primary care provider, an oncologist, or a surgeon (guideline-nonadherent). The guideline-nonadherent proportion increased from 7.8% in women diagnosed in 2006 to 12.2% in those diagnosed in 2014 (two-sided Wald P &lt; .001). During years 2–6, guideline-nonadherence was also associated with older age, nonwhite race, no radiation, no chemotherapy, no endocrine therapy, and increasing time after surgery. There is a substantial and increasing rate of inadequate follow-up among breast cancer survivors. This has the potential to impair outcomes.
Large-scale analysis of the cassava transcriptome reveals the impact of cold stress on alternative splicing
Authors: Li Shuxia , Yu Xiang , Cheng Zhihao , Zeng Changying , Li Wenbin , Zhang Liangsheng , Peng Ming 
Published: October 2019

Abstract
Alternative splicing is an essential post-transcriptional regulatory mechanism that can impact mRNA stability and protein diversity of eukaryotic genomes. Although numerous forms of stress-responsive alternative splicing have been identified in model plants, a large-scale study of alternative splicing dynamics under abiotic stress conditions in cassava has not been conducted. Here, we report the parallel employment of isoform-Seq, ssRNA-Seq, and Degradome-Seq to investigate the diversity, abundance, and fate of alternatively spliced isoforms in response to cold and drought stress. We identified 38 164 alternative splicing events, among which 3292 and 1025 events were significantly regulated by cold and drought stress, respectively. Intron retention was the most abundant subtype of alternative splicing. Global analysis of splicing regulators revealed that the number of their alternatively spliced isoforms and the corresponding abundance were specifically modulated by cold stress. We found that 58.5% of cold-regulated alternative splicing events introduced a premature termination codon into the transcripts, and 77.6% of differential alternative splicing events were detected by Degradome-Seq. Our data reveal that cold intensely affects both quantitative and qualitative aspects of gene expression via alternative splicing pathways, and advances our understanding of the high complexity and specificity of gene regulation in response to abiotic stresses.
Alternative splicing is responsible for reprogramming of the transcriptome and the sensitivity of cassava plants to cold.
Hsp70 plays a role in programmed cell death during the remodelling of leaves of the lace plant (Aponogeton madagascariensis)
Authors: Rowarth Nathan M , Dauphinee Adrian N , Denbigh Georgia L , Gunawardena Arunika Hlan 
Published: October 2019

AbstractLace plant leaves utilize programmed cell death (PCD) to form perforations during development. The role of heat shock proteins (Hsps) in PCD during lace plant leaf development is currently unknown. Hsp70 amounts were measured throughout lace plant leaf development, and the results indicate that it is highest before and during PCD. Increased Hsp70 amounts correlate with raised anthocyanin content and caspase-like protease (CLP) activity. To investigate the effects of Hsp70 on leaf development, whole plants were treated with either of the known regulators of PCD [reactive oxygen species (ROS) or antioxidants] or an Hsp70 inhibitor, chlorophenylethynylsulfonamide (PES-Cl). ROS treatment significantly increased Hsp70 2-fold and CLP activity in early developing leaves, but no change in anthocyanin and the number of perforations formed was observed. Antioxidant treatment significantly decreased Hsp70, anthocyanin, and CLP activity in early leaves, resulting in the fewest perforations. PES-Cl (25 μM) treatment significantly increased Hsp70 4-fold in early leaves, while anthocyanin, superoxide, and CLP activity significantly declined, leading to fewer perforations. Results show that significantly increased (4-fold) or decreased Hsp70 amounts lead to lower anthocyanin and CLP activity, inhibiting PCD induction. Our data support the hypothesis that Hsp70 plays a role in regulating PCD at a threshold in lace plant leaf development.Hsp70 affects anthocyanin content and caspase-like protease activity, and helps regulate PCD during the remodelling of leaves of lace plant, Aponogeton madagascariensis.
Exosomal microRNAs and other non-coding RNAs as colorectal cancer biomarkers: a review
Authors: Francavilla Antonio , Turoczi Szimonetta , Tarallo Sonia , Vodicka Pavel , Pardini Barbara , Naccarati Alessio 
Published: October 2019

Abstract
The circulating human transcriptome, which includes both coding and non-coding RNA (ncRNA) molecules, represents a rich source of potential biomarkers for colorectal cancer (CRC) that has only recently been explored. In particular, the release of RNA-containing extracellular vesicles (EVs), in a multitude of different in vitro cell systems and in a variety of body fluids, has attracted wide interest. The role of RNA species in EVs is still not fully understood, but their capacity to act as a form of distant communication between cells and their higher abundance in association with cancer demonstrated their relevance. In this review, we report the evidence from both in vitro and human studies on microRNAs (miRNAs) and other ncRNA profiles analysed in EVs in relation to CRC as diagnostic, prognostic and predictive markers. The studies so far highlighted that, in exosomes, the most studied category of EVs, several miRNAs are able to accurately discriminate CRC cases from controls as well as to describe the progression of the disease and its prognosis. Most of the time, the in vitro findings support the miRNA profiles detected in human exosomes. The expression profiles measured in exosomes and other EVs differ and, interestingly, there is a variability of expression also among different subsets of exosomes according to their proteic profile. On the other hand, evidence is still limited for what concerns exosome miRNAs as early diagnostic and predictive markers of treatment. Several other ncRNAs that are carried by exosomes, mostly long ncRNAs and circular RNAs, seem also to be dysregulated in CRC. Besides various technical challenges, such as the standardisation of EVs isolation methods and the optimisation of methodologies to characterise the whole spectrum of RNA molecules in exosomes, further studies are needed in order to elucidate their relevance as CRC markers.
The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics
Authors: Deutsch Eric W , Bandeira Nuno , Sharma Vagisha , Perez-Riverol Yasset , Carver Jeremy J , Kundu Deepti J , García-Seisdedos David , Jarnuczak Andrew F , Hewapathirana Suresh , Pullman Benjamin S , Wertz Julie , Sun Zhi , Kawano Shin , Okuda Shujiro , Watanabe Yu , Hermjakob Henning , MacLean Brendan , MacCoss Michael J , Zhu Yunping , Ishihama Yasushi , Vizcaíno Juan A 
Published: October 2019

AbstractThe ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) has standardized data submission and dissemination of mass spectrometry proteomics data worldwide since 2012. In this paper, we describe the main developments since the previous update manuscript was published in Nucleic Acids Research in 2017. Since then, in addition to the four PX existing members at the time (PRIDE, PeptideAtlas including the PASSEL resource, MassIVE and jPOST), two new resources have joined PX: iProX (China) and Panorama Public (USA). We first describe the updated submission guidelines, now expanded to include six members. Next, with current data submission statistics, we demonstrate that the proteomics field is now actively embracing public open data policies. At the end of June 2019, more than 14 100 datasets had been submitted to PX resources since 2012, and from those, more than 9 500 in just the last three years. In parallel, an unprecedented increase of data re-use activities in the field, including ‘big data’ approaches, is enabling novel research and new data resources. At last, we also outline some of our future plans for the coming years.