bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in renal function after nephroureterectomy for upper urinary tract carcinoma: analysis of a large multicenter cohort (Radical Nephroureterectomy Outcomes (RaNeO) Research Consortium)
Authors: Tafuri Alessandro , Marchioni Michele , Cerrato Clara , Mari Andrea , Tellini Riccardo , Odorizzi Katia , Veccia Alessandro , Amparore Daniele , Shakir Aliasger , Carbonara Umberto , Panunzio Andrea , Trovato Federica , Catellani Michele , Janello Letizia M. I. , Bianchi Lorenzo , Novara Giacomo , Dal Moro Fabrizio , Schiavina Riccardo , De Lorenzis Elisa , Parma Paolo , Cimino Sebastiano , De Cobelli Ottavio , Maiorino Francesco , Bove Pierluigi , Crocerossa Fabio , Cantiello Francesco , D’Andrea David , Di Cosmo Federica , Porpiglia Francesco , Ditonno Pasquale , Montanari Emanuele , Soria Francesco , Gontero Paolo , Liguori Giovanni , Trombetta Carlo , Mantica Guglielmo , Borghesi Marco , Terrone Carlo , Del Giudice Francesco , Sciarra Alessandro , Galosi Andrea , Moschini Marco , Shariat Shahrokh F. , Di Nicola Marta , Minervini Andrea , Ferro Matteo , Cerruto Maria Angela , Schips Luigi , Pagliarulo Vincenzo , Antonelli Alessandro 
Published: October 2022

AbstractPurposeTo investigate prevalence and predictors of renal function variation in a multicenter cohort treated with radical nephroureterectomy (RNU) for upper tract urothelial carcinoma (UTUC).MethodsPatients from 17 tertiary centers were included. Renal function variation was evaluated at postoperative day (POD)—1, 6 and 12 months. Timepoints differences were Δ1 = POD-1 eGFR − baseline eGFR; Δ2 = 6 months eGFR − POD-1 eGFR; Δ3 = 12 months eGFR − 6 months eGFR. We defined POD-1 acute kidney injury (AKI) as an increase in serum creatinine by ≥ 0.3 mg/dl or a 1.5 1.9-fold from baseline. Additionally, a cutoff of 60 ml/min in eGFR was considered to define renal function decline at 6 and 12 months. Logistic regression (LR) and linear mixed (LM) models were used to evaluate the association between clinical factors and eGFR decline and their interaction with follow-up.ResultsA total of 576 were included, of these 409(71.0%) and 403(70.0%) had an eGFR < 60 ml/min at 6 and 12 months, respectively, and 239(41.5%) developed POD-1 AKI. In multivariable LR analysis, age (Odds Ratio, OR 1.05,p < 0.001), male gender (OR 0.44,p = 0.003), POD-1 AKI (OR 2.88,p < 0.001) and preoperative eGFR < 60 ml/min (OR 7.58,p < 0.001) were predictors of renal function decline at 6 months. Age (OR 1.06,p < 0.001), coronary artery disease (OR 2.68,p = 0.007), POD-1 AKI (OR 1.83,p = 0.02), and preoperative eGFR < 60 ml/min (OR 7.80,p < 0.001) were predictors of renal function decline at 12 months. In LM models, age (p = 0.019), hydronephrosis (p < 0.001), POD-1 AKI (p < 0.001) and pT-stage (p = 0.001) influenced renal function variation (ß9.2 ± 0.7,p < 0.001) during follow-up.ConclusionAge, preoperative eGFR and POD-1 AKI are independent predictors of 6 and 12 months renal function decline after RNU for UTUC.
Serum metabolites associated with wholegrain consumption using nontargeted metabolic profiling: a discovery and reproducibility study
Authors: Noerman Stefania , Virtanen Jyrki K. , Lehtonen Marko , Brunius Carl , Hanhineva Kati 
Published: October 2022

Abstract
Purpose
To identify fasting serum metabolites associated with WG intake in a free-living population adjusted for potential confounders.

Methods
We selected fasting serum samples at baseline from a subset (n = 364) of the prospective population-based Kuopio Ischaemic Heart Disease Risk Factor Study (KIHD) cohort. The samples were analyzed using nontargeted metabolomics with liquid chromatography coupled with mass spectrometry (LC–MS). Association with WG intake was investigated using both random forest followed by linear regression adjusted for age, BMI, smoking, physical activity, energy and alcohol consumption, and partial Spearman correlation adjusted for the same covariates. Features selected by any of these models were shortlisted for annotation. We then checked if we could replicate the findings in an independent subset from the same cohort (n = 200).

Results
Direct associations were observed between WG intake and pipecolic acid betaine, tetradecanedioic acid, four glucuronidated alkylresorcinols (ARs), and an unknown metabolite both in discovery and replication cohorts. The associations remained significant (FDR<0.05) even after adjustment for the confounders in both cohorts. Sinapyl alcohol was positively correlated with WG intake in both cohorts after adjustment for the confounders but not in linear models in the replication cohort. Some microbial metabolites, such as indolepropionic acid, were positively correlated with WG intake in the discovery cohort, but the correlations were not replicated in the replication cohort.

Conclusions
The identified associations between WG intake and the seven metabolites after adjusting for confounders in both discovery and replication cohorts suggest the potential of these metabolites as robust biomarkers of WG consumption.
Neuropathology of central nervous system involvement in TTR amyloidosis
Authors: Taipa Ricardo , Sousa Luísa , Pinto Miguel , Reis Inês , Rodrigues Aurora , Oliveira Pedro , Melo-Pires Manuel , Coelho Teresa 
Published: October 2022

AbstractHereditary transthyretin amyloidosis (ATTRv) is a systemic disease caused by the accumulation of misfolded transthyretin (TTR). It usually presents with an adult-onset progressive axonal peripheral neuropathy and cardiomyopathy. In the central nervous system (CNS), variant TTR is produced by the choroid plexus and accumulates in the leptomeninges. CNS symptoms have been increasingly recognized in this population, including transient focal neurological episodes and stroke, particularly in patients with the V30M mutation and longstanding disease. The prevalence, pathophysiology, and progression of CNS involvement remain to be clarified. The present work explores if there is a recognizable sequence of CNS TTR deposition in ATTRv. We studied the topographical and severity distribution of TTR deposition in 16 patients with ATTRv, aged 27–69 years and with a mean disease duration of 10.9 years (range: 3–29). Our results suggest that CNS pathological involvement in V30M ATTRv occurs early in the disease course, probably starting in pre-symptomatic phases, and follows a distinct sequence. Leptomeninges and subarachnoid meningeal vessels are affected earlier, then followed by perforating cortical vessels and subpial deposition, and finally by deposition in the subependymal and basal ganglia vessels near the ependymal lining. Brainstem and spinal cord show early and severe involvement, with amyloid subpial deposition already seen in initial stages. Despite massive superficial amyloid deposition, no parenchymal deposition outside subpial or subependymal regions was found. Additionally, vascular lesions or superficial cortical siderosis were not frequent. Future studies with more patients from different populations and TTR mutations will be important to confirm these findings. Defining stages of TTR pathology in the CNS may be useful to better understand pathogenic mechanisms leading to symptoms and to interpret neuroimaging biomarkers.
Altered psychobiological reactivity but no impairment of emotion recognition following stress in adolescents with non-suicidal self-injury
Authors: Koenig Julian , Lischke Alexander , Bardtke Kay , Heinze Anna-Lena , Kröller Felix , Pahnke Rike , Kaess Michael 
Published: October 2022

AbstractImpairments in both stress regulation and emotion recognition have been associated with borderline personality disorder (BPD) and non-suicidal self-injury (NSSI). Although it has been proposed that emotion recognition deficits particularly emerge during stress, this hypothesis has not been fully investigated. Adolescents with and without NSSI performed emotion recognition tasks before and after the employment of the Trier Social Stress Test (TSST). The psychobiological stress response was captured with psychological self-reports (affect, stress and dissociation), physiological recordings (heart rate, HR, and heart rate variability, HRV) and endocrinological sampling of saliva (cortisol and alpha-amylase). Mixed-linear models were applied to analyze stress-induced changes in emotion recognition performance and respective stress response measures. The TSST elicited altered psychobiological stress responses in adolescents with NSSI: A more pronounced decrease in positive affect, a more pronounced increase in negative affect, a less pronounced increase in HR, a less pronounced decrease in HRV and a more pronounced increase in alpha-amylase throughout the stress induction than adolescents without NSSI. Stress responses (dissociation, negative affect, cortisol and HR) differed as a function of BPD severity on a continuum, illustrating greater reactivity on self-reports but decreased biological responsiveness in those with greater BPD severity. Stress induction had similar effects on emotion recognition in adolescents with and without NSSI. Recognition sensitivity and recognition speed equally increased, in the absence of any differences in recognition accuracy. In contrast to prominent propositions, psychosocial stress does not appear to account for impaired emotion recognition across the BPD spectrum.
Procedure to implement shear evolution in fast rolling models with online capability on the example of an aluminum flat rolling process
Authors: Rabindran R. , Karhausen K. , Hirt G. , Teller M. , Hojda S. 
Published: October 2022

AbstractThe rolling process induces a heterogeneous deformation over the rolling stock height. The causes are the frictional shear stress between the contacting surfaces and the roll gap geometry. They induce a complex material flow within the rolling stock describable by the shear evolution. The shear evolution has a significant impact on rolling values like grain size and crystallographic texture and therefore on the final material properties of the rolled product. Industry and academia use fast rolling models for flat rolling processes to predict the material properties due to their short computation time. The time advantage enables online applicability to adapt processes in real time or to evaluate the influence of different process conditions several times within seconds. However, these models have a limitation regarding the shear evolution. They do not consider all relevant influences or apply simplifying assumptions, valid only for specific rolling cases. This work presents a general approach to extend fast rolling models to consider the shear evolution without any restrictions to specific rolling cases. The approach derives the shear evolution as shear angle $$\alpha$$
α
evolution based on FE simulations. The shear angle $$\alpha$$
α
is a geometrical description and not influenced by rotations, which occur during the rolling process. This enables an enhanced and simple analysis of the material flow. The outcome is an extended model that completely describes the deformation along a deformation path and enables the calculation of each desired deformation value (strain, deformation gradient, velocity gradient, etc.).
Genetic variation and structural diversity in major seed proteins among and within Camelina species
Authors: Hegedus Dwayne , Coutu Cathy , Gjetvaj Branimir , Hannoufa Abdelali , Harrington Myrtle , Martin Sara , Parkin Isobel A. P. , Perera Suneru , Wanasundara Janitha 
Published: October 2022

Abstract
Main conclusion
Genetic variation in seed protein composition, seed protein gene expression and predictions of seed protein physiochemical properties were documented in C. sativa and other Camelina species.

Abstract
Seed protein diversity was examined in six Camelina species (C. hispida, C. laxa, C. microcarpa, C. neglecta, C. rumelica and C. sativa). Differences were observed in seed protein electrophoretic profiles, total seed protein content and amino acid composition between the species. Genes encoding major seed proteins (cruciferins, napins, oleosins and vicilins) were catalogued for C. sativa and RNA-Seq analysis established the expression patterns of these and other genes in developing seed from anthesis through to maturation. Examination of 187 C. sativa accessions revealed limited variation in seed protein electrophoretic profiles, though sufficient to group the majority into classes based on high MW protein profiles corresponding to the cruciferin region. C. sativa possessed four distinct types of cruciferins, named CsCRA, CsCRB, CsCRC and CsCRD, which corresponded to orthologues in Arabidopsis thaliana with members of each type encoded by homeologous genes on the three C. sativa sub-genomes. Total protein content and amino acid composition varied only slightly; however, RNA-Seq analysis revealed that CsCRA and CsCRB genes contributed > 95% of the cruciferin transcripts in most lines, whereas CsCRC genes were the most highly expressed cruciferin genes in others, including the type cultivar DH55. This was confirmed by proteomics analyses. Cruciferin is the most abundant seed protein and contributes the most to functionality. Modelling of the C. sativa cruciferins indicated that each type possesses different physiochemical attributes that were predicted to impart unique functional properties. As such, opportunities exist to create C. sativa cultivars with seed protein profiles tailored to specific technical applications.
Emergence of CWD strains
Authors: Otero Alicia , Duque Velasquez Camilo , McKenzie Debbie , Aiken Judd 
Published: October 2022

AbstractChronic wasting disease (CWD) strains present a novel challenge to defining and mitigating this contagious prion disease of deer, elk, moose, and reindeer. Similar to strains of other prion diseases (bovine spongiform encephalopathy, sheep scrapie), CWD strains can affect biochemical and neuropathological properties of the infectious agent, and importantly interspecies transmission. To date, ten CWD strains have been characterized. The expanding range of CWD in North America and its presence in South Korea as well as Scandinavian countries will potentially result in millions of cervids infected with CWD; thus, novel strains will continue to emerge. In this review, we will summarize the characteristics of known CWD strains and describe the impact of prion protein gene polymorphisms on the generation of strains. We will also discuss the evidence that individual cervids can harbor more than one CWD strain, complicating strain analysis, and affecting selection and adaptation of strains in new hosts.
AbcApp: incidence of intra-abdominal ABsCesses following laparoscopic vs. open APPendectomy in complicated appendicitis
Authors: Zamaray Bobby , de Boer M. F. J. , Popal Z. , Rijbroek A. , Bloemers F. W. , Oosterling S. J. 
Published: October 2022

Abstract
Background
Patients with complicated appendicitis are more at risk for the occurrence of postoperative intra-abdominal abscesses than patients with uncomplicated appendicitis. Studies comparing laparoscopic and open appendectomy showed limitations and contradictory findings on the incidence of intra-abdominal abscesses after appendicitis, as most of these studies analysed both uncomplicated and complicated appendicitis as one group. The aim of the present study is to investigate the incidence of intra-abdominal abscesses after laparoscopic versus open appendectomy for complicated appendicitis.

Methods
A retrospective cohort study was performed over the period January 2009 till May 2020. All patients who had an intra-operative diagnosis of complicated appendicitis (e.g. perforation, necrosis) were included. The outcome measure was the occurrence of intra-abdominal abscesses with a postoperative follow-up of 30 days. Multivariate logistic regression analysis was performed including adjustments for significant confounders.

Results
A total of 900 patients had undergone appendectomy for complicated appendicitis. The majority was operated laparoscopically (78%, n = 705). The incidence of postoperative intra-abdominal abscess was 12.3% in both laparoscopic and open appendectomy groups. On univariable analysis, the postoperative rates of intra-abdominal abscesses between laparoscopic and open appendectomy were not significantly different (odds ratio 1.11, 95% CI [0.67–1.84], p = 0.681).

Conclusion
The present study provides evidence that, in current daily practice, intra-abdominal abscess formation remains a common postoperative complication for complicated appendicitis. Nonetheless, no significant difference was found with regard to intra-abdominal abscess formation when comparing laparoscopy with open surgery.
Carrier-Domain Method for high-resolution computation of time-periodic long-wake flows
Authors: Liu Yang , Takizawa Kenji , Tezduyar Tayfun E. , Kuraishi Takashi , Zhang Yufei 
Published: October 2022

AbstractWe are introducing the Carrier-Domain Method (CDM) for high-resolution computation of time-periodic long-wake flows, with cost-effectives that makes the computations practical. The CDM is closely related to the Multidomain Method, which was introduced 24 years ago, originally intended also for cost-effective computation of long-wake flows and later extended in scope to cover additional classes of flow problems. In the CDM, the computational domain moves in the free-stream direction, with a velocity that preserves the outflow nature of the downstream computational boundary. As the computational domain is moving, the velocity at the inflow plane is extracted from the velocity computed earlier when the plane’s current position was covered by the moving domain. The inflow data needed at an instant is extracted from one or more instants going back in time as many periods. Computing the long-wake flow with a high-resolution moving mesh that has a reasonable length would certainly be far more cost-effective than computing it with a fixed mesh that covers the entire length of the wake. We are also introducing a CDM version where the computational domain moves in a discrete fashion rather than a continuous fashion. To demonstrate how the CDM works, we compute, with the version where the computational domain moves in a continuous fashion, the 2D flow past a circular cylinder at Reynolds number 100. At this Reynolds number, the flow has an easily discernible vortex shedding frequency and widely published lift and drag coefficients and Strouhal number. The wake flow is computed up to 350 diameters downstream of the cylinder, far enough to see the secondary vortex street. The computations are performed with the Space–Time Variational Multiscale method and isogeometric discretization; the basis functions are quadratic NURBS in space and linear in time. The results show the power of the CDM in high-resolution computation of time-periodic long-wake flows.
Teaching and Research in the Digital World
Authors: Lagoudakis Michail G. , Gkizeli Maria , Fotiou Afroditi , Fragkedaki Dina , Kollnig Sarah 
Published: October 2022

AbstractAcademia has entered a new teaching, learning, and researching era: an era in which more and more services turn to digital and online forms, distances are eliminated, geographical borders disappear, and telepresence becomes common. Though accelerated by the pandemic of the last two years, this transition has been in progress for some time. The importance of creatively nurturing students, academic, and scientific staff in the realms of education, practical knowledge, skills, and competence growth has only increased. Investing in best practices in this digital world, both in teaching and in research, supports a connection between the academic world and society at large, raises societal, environmental awareness, and promotes innovation and excellence at all levels. Each of these considerations plays an important role for the EURECA-PRO European University Alliance, a group of eight partner universities from different European countries working together to establish a modern, diverse European institution. This article focuses on how EURECA-PRO partners collaborate to create a digital campus that supports education, research, and innovation. These efforts rely on the Work Package 4 (WP4) and are led by the Technical University of Crete (TUC).
Solving TSP by using combinatorial Bees algorithm with nearest neighbor method
Authors: Sahin Murat 
Published: October 2022

AbstractBees Algorithm (BA) is a popular meta-heuristic method that has been used in many different optimization areas for years. In this study, a new version of combinatorial BA is proposed and explained in detail to solve Traveling Salesman Problems (TSPs). The nearest neighbor method was used in the population generation section of BA, and the Multi-Insert function was added to the local search section instead of the Swap function. To see the efficiency of the proposed method, 24 different TSPs were used in experimentation and the obtained results were compared with both classical combinatorial BA and other successful meta-heuristic methods. After detailed analyses and experimental studies on different problems, it has been observed that the proposed method performs well for TSPs and competes well with other methods.
Toward reliable machine learning with Congruity: a quality measure based on formal concept analysis
Authors: De Maio Carmen , Fenza Giuseppe , Gallo Mariacristina , Loia Vincenzo , Stanzione Claudio 
Published: October 2022

AbstractThe spreading of machine learning (ML) and deep learning (DL) methods in different and critical application domains, like medicine and healthcare, introduces many opportunities but raises risks and opens ethical issues, mainly attaining to the lack of transparency. This contribution deals with the lack of transparency of ML and DL models focusing on the lack of trust in predictions and decisions generated. In this sense, this paper establishes a measure, namely Congruity, to provide information about the reliability of ML/DL model results. Congruity is defined by the lattice extracted through the formal concept analysis built on the training data. It measures how much the incoming data items are close to the ones used at the training stage of the ML and DL models. The general idea is that the reliability of trained model results is highly correlated with the similarity of input data and the training set. The objective of the paper is to demonstrate the correlation between the Congruity and the well-known Accuracy of the whole ML/DL model. Experimental results reveal that the value of correlation between Congruity and Accuracy of ML model is greater than 80% by varying ML models.