bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary model of protein secondary structure capable of revealing new biological relationships
Authors: Lai Jhih‐Siang , Rost Burkhard , Kobe Bostjan , Bodén Mikael 
Published: May 2020

AbstractAncestral sequence reconstruction has had recent success in decoding the origins and the determinants of complex protein functions. However, phylogenetic analyses of remote homologues must handle extreme amino acid sequence diversity resulting from extended periods of evolutionary change. We exploited the wealth of protein structures to develop an evolutionary model based on protein secondary structure. The approach follows the differences between discrete secondary structure states observed in modern proteins and those hypothesized in their immediate ancestors. We implemented maximum likelihood‐based phylogenetic inference to reconstruct ancestral secondary structure. The predictive accuracy from the use of the evolutionary model surpasses that of comparative modeling and sequence‐based prediction; the reconstruction extracts information not available from modern structures or the ancestral sequences alone. Based on a phylogenetic analysis of a sequence‐diverse protein family, we showed that the model can highlight relationships that are evolutionarily rooted in structure and not evident in amino acid‐based analysis.
Likelihood‐based inference for a frailty‐copula model based on competing risks failure time data
Authors: Wang Yin‐Chen , Emura Takeshi , Fan Tsai‐Hung , Lo Simon M.S. , Wilke Ralf Andreas 
Published: May 2020

AbstractA competing risks phenomenon arises in industrial life tests, where multiple types of failure determine the working duration of a unit. To model dependence among marginal failure times, copula models and frailty models have been developed for competing risks failure time data. In this paper, we propose a frailty‐copula model, which is a hybrid model including both a frailty term (for heterogeneity among units) and a copula function (for dependence between failure times). We focus on models that are useful to investigate the reliability of marginal failure times that are Weibull distributed. Furthermore, we develop likelihood‐based inference methods based on competing risks data, including accelerated failure time models. We also develop a model‐diagnostic procedure to assess the adequacy of the proposed model to a given dataset. Simulations are conducted to demonstrate the operational performance of the proposed methods, and a real dataset is analyzed for illustration. We make an R package “gammaGumbel” such that users can apply the suggested statistical methods to their data.
Using a lab wiki for longevity and knowledge transfer in undergraduate research
Authors: Nagan Maria C. 
Published: May 2020

AbstractContinuity in research group collective knowledge is critical for running a successful research program, but in an undergraduate research lab, this can be particularly challenging. A wiki site dedicated to the research laboratory, a lab wiki, can bridge gaps in student‐to‐student knowledge transfer and contribute to the longevity of a research program. A lab wiki is an organized, easily accessible, collaborative resource that can contain tutorials, group‐specific directions, links to resources, and guides to writing papers or proposals. The wiki language is easy for students to pick up and contributes to their participation in preserving group knowledge. This tutorial introduces the concept of a lab wiki, the advantages of it, example content, and practical implementation advice.
Diffuse large B‐cell lymphoma presenting with cavitary lung disease
Authors: Hibino Yukiko , Imai Ryosuke , Jinta Torahiko 
Published: May 2020

AbstractDiffuse large B‐cell lymphoma (DLBCL) with cavitary lung disease is rare and is often difficult to differentiate from primary lung cancer, granulomatous disease, or an infectious disease based on imaging findings alone. We herein report a case in which a patient with DLBCL presented with cavitary lung disease and splenic mass, which was diagnosed by transbronchial biopsy. DLBCL should be considered as a differential diagnosis in patients with cavitary lung diseases who have rare metastatic lesions for primary lung cancer, such as intra‐abdominal lymph nodes or spleen.
Input‐to‐state stability of impulsive switched nonlinear time‐delay systems with two asynchronous switching phenomena
Authors: Wang Zhichuang , Sun Jian , Chen Jie 
Published: May 2020

SummaryThis summary addresses the input‐to‐state stability (ISS) and integral ISS (iISS) problems of impulsive switched nonlinear time‐delay systems (ISNTDSs) under two asynchronous switching effects. In our investigated systems, impulsive instants and switching instants do not necessarily coincide with each other. Meanwhile, systems switching signals are not simultaneous with the corresponding controllers switching signals, which will induce instability seriously, and cause many difficulties and challenges. By utilizing methods of Lyapunov‐Krasovskii and Lyapunov‐Razumikhin, mode‐dependent average dwell time approach, and mode‐dependent average impulsive interval technique, some stability criteria are presented for ISNTDSs under two asynchronous switching effects. Our proposed results improve the related existing results on the same topic by removing some restrictive conditions and cover some existing results as special cases. Finally, some simulation examples are presented to illustrate the effectiveness and advantages of our results.
Link adaptation and SINR errors in practical multicast multibeam satellite systems with linear precoding
Authors: Tato Anxo , Andrenacci Stefano , Lagunas Eva , Chatzinotas Symeon , Mosquera Carlos 
Published: May 2020

SummaryThe application of linear precoding at the gateway side enables broadband multibeam satellite systems to use more aggressive frequency reuse patterns increasing the overall capacity of future high‐throughput satellites (HTS). In any practical precoded system, receivers can estimate only a few coefficients of the channel state information (CSI), while the others, in what is known as nullification, are set to zero. In this paper, the impact of the CSI nullification to the SINR estimation is analyzed statistically and geographically for a multicast multibeam satellite system. The errors in the SINR calculated by the gateway affect to the modulation and coding schemes (MCSs) selection, increasing the rate of erroneous frames or leading to an underutilization of the available resources. Therefore, as countermeasure, a link adaptation algorithm based on an adaptive margin per user is proposed, helping to achieve the error rate constraints of DVB‐S2X systems without compromising the throughput, even under severe CSI degradation due to nullification and Rician fading.
Probabilistic corrosion condition assessment of a tunnel structure
Authors: Keßler Sylvia 
Published: May 2020

AbstractReinforced concrete structures constitute the basis of our infrastructure. Their functionality and structural safety is essential to maintain our mobility and the industrial performance of our societies. Unexpected maintenance can lead to serious economic consequences. Most industrial countries are faced with the fact that the reliability of their infrastructure has decreased over the past decades due to ageing and associated durability issues. Most often reinforcement corrosion is the major problem with respect to ageing phenomena observed. Therefore, data from corrosion inspection and their implementation in probabilistic corrosion condition assessment are considered to be of major importance to assist engineers in the maintenance process. Reliable information about the corrosion condition state can be derived through half‐cell potential measurements. The half‐cell potential measurement method is an easy to apply nondestructive measurement method to detect ongoing corrosion. The procedure on how to update the service life based on a probabilistic treatment of measured half‐cell potentials is presented in a case study of a chloride‐contaminated reinforced concrete structure. Besides the chosen probabilistic model, major impact on the accuracy of the updated service life has the evaluation of the half‐cell potential measurements.
Decoding chemical information from vibrational spectroscopy data: Local vibrational mode theory
Authors: Kraka Elfi , Zou Wenli , Tao Yunwen 
Published: May 2020

AbstractModern vibrational spectroscopy is more than just an analytical tool. Information about the electronic structure of a molecule, the strength of its bonds, and its conformational flexibility is encoded in the normal vibrational modes. On the other hand, normal vibrational modes are generally delocalized, which hinders the direct access to this information, attainable only via local vibration modes and associated local properties. Konkoli and Cremer provided an ingenious solution to this problem by deriving local vibrational modes from the fundamental normal modes, obtained in the harmonic approximation of the potential, via mass‐decoupled Euler–Lagrange equations. This review gives a general introduction into the local vibrational mode theory of Konkoli and Cremer, elucidating how this theory unifies earlier attempts to obtain easy to interpret chemical information from vibrational spectroscopy: (a) the local mode theory furnishes bond strength descriptors derived from force constant matrices with a physical basis, (b) provides the highly sought after extension of the Badger rule to polyatomic molecules, (c) and offers a simpler way to derive localized vibrations compared to the complex route via overtone spectroscopy. Successful applications are presented, including a new measure of bond strength, a new detailed analysis of infrared/Raman spectra, and the recent extension to periodic systems, opening a new avenue for the characterization of bonding in crystals. At the end of this review the LMODEA software is introduced, which performs the local mode analysis (with minimal computational costs) after a harmonic vibrational frequency calculation optionally using measured frequencies as additional input.This article is categorized under:
Structure and Mechanism > Molecular Structures
Theoretical and Physical Chemistry > Spectroscopy
Software > Quantum Chemistry
Electronic Structure Theory > Ab Initio Electronic Structure Methods
Safety of 80 antidepressants, antipsychotics, anti‐attention‐deficit/hyperactivity medications and mood stabilizers in children and adolescents with psychiatric disorders: a large scale systematic meta‐review of 78 adverse effects
Authors: Solmi Marco , Fornaro Michele , Ostinelli Edoardo G. , Zangani Caroline , Croatto Giovanni , Monaco Francesco , Krinitski Damir , Fusar‐Poli Paolo , Correll Christoph U. 
Published: May 2020

Mental disorders frequently begin in childhood or adolescence. Psychotropic medications have various indications for the treatment of mental dis­orders in this age group and are used not infrequently off‐label. However, the adverse effects of these medications require special attention during developmentally sensitive periods of life. For this meta‐review, we systematically searched network meta‐analyses and meta‐analyses of randomized controlled trials (RCTs), individual RCTs, and cohort studies reporting on 78 a priori selected adverse events across 19 categories of 80 psychotropic medications – including antidepressants, antipsychotics, anti‐attention‐deficit/hyperactivity disorder (ADHD) medications and mood stabilizers – in children and adolescents with mental disorders. We included data from nine network meta‐analyses, 39 meta‐analyses, 90 individual RCTs, and eight cohort studies, including 337,686 children and adolescents. Data on ≥20% of the 78 adverse events were available for six antidepressants (sertraline, escitalopram, paroxetine, fluoxetine, venlafaxine and vilazodone), eight antipsychotics (risperidone, quetiapine, aripiprazole, lurasidone, paliperidone, ziprasidone, olanzapine and asenapine), three anti‐ADHD medications (methylphenidate, atomoxetine and guanfacine), and two mood stabilizers (valproate and lithium). Among these medications with data on ≥20% of the 78 adverse events, a safer profile emerged for escitalopram and fluoxetine among antidepressants, lurasidone for antipsychotics, methylphenidate among anti‐ADHD medications, and lithium among mood stabilizers. The available literature raised most concerns about the safety of venlafaxine, olanzapine, atomoxetine, guanfacine and valproate. Nausea/vomiting and discontinuation due to adverse event were most frequently associated with antidepressants; sedation, extrapyramidal side effects, and weight gain with antipsychotics; anorexia and insomnia with anti‐ADHD medications; sedation and weight gain with mood stabilizers. The results of this comprehensive and updated quantitative systematic meta‐review of top‐tier evidence regarding the safety of antidepressants, antipsychotics, anti‐ADHD medications and mood stabilizers in children and adolescents can inform clinical practice, research and treatment guidelines.
Efficacy of repeated PSMA PET-directed radiotherapy for oligorecurrent prostate cancer after initial curative therapy
Authors: Henkenberens Christoph , Oehus Ann-Kathrin , Derlin Thorsten , Bengel Frank , Ross Tobias L. , Kuczyk Markus A. , Janssen Stefan , Christiansen Hans , von Klot Christoph A. J. 
Published: May 2020

Abstract
Purpose
To assess the outcome of prostate cancer (PCa) patients diagnosed with oligorecurrent disease and treated with a first and a second PSMA (prostate-specific membrane antigen ligand) PET(positron-emission tomography)-directed radiotherapy (RT).

Patients and methods
Thirty-two patients with oligorecurrent relapse after curative therapy received a first PSMA PET-directed RT of all metastases. After biochemical progression, all patients received a second PSMA PET-directed RT of all metastases. The main outcome parameters were biochemical progression-free survival (bPFS) and androgen deprivation therapy-free survival (ADT-FS). The intervals of BPFS were analyzed separately as follows: the interval from the last day of PSMA PET-directed RT to the first biochemical progression was defined as bPFS_1 and the interval from second PSMA PET-directed RT to further biochemical progression was defined as bPFS_2.

Results
The median follow-up duration was 39.5 months (18–60). One out of 32 (3.1%) patients died after 47 months of progressive metastatic prostate cancer (mPCa). All patients showed biochemical responses after the first PSMA PET-directed RT and the median prostate-specific antigen (PSA) level before RT was 1.70 ng/mL (0.2–3.8), which decreased significantly to a median PSA nadir level of 0.39 ng/mL (range <0.07–3.8; p = 0.004). The median PSA level at biochemical progression after the first PSMA PET-directed RT was 2.9 ng/mL (range 0.12–12.80; p = 0.24). Furthermore, the PSA level after the second PSMA PET-directed RT at the last follow-up (0.52 ng/mL, range <0.07–154.0) was not significantly different (p = 0.36) from the median PSA level (1.70 ng/mL, range 0.2–3.8) before the first PSMA PET-directed RT. The median bPFS_1 was 16.0 months after the first PSMA PET-directed RT (95% CI 11.9–19.2) and the median bPFS_2 was significantly shorter at 8.0 months (95% CI 6.3–17.7) after the second PSMA PET-directed RT (p = 0.03; 95% CI 1.9–8.3). Multivariate analysis revealed no significant parameter for bPFS_1, whereas extrapelvic disease was the only significant parameter (p = 0.02, OR 2.3; 95% CI 0.81-4.19) in multivariate analysis for bPFS_2. The median ADT-FS was 31.0 months (95% CI 20.1–41.8) and multivariate analysis showed that patients with bone metastases, compared to patients with only lymph node metastases at first PSMA PET-directed RT, had a significantly higher chance (p = 0.007, OR 4.51; 95% CI 1.8–13.47) of needing ADT at the last follow-up visit.

Conclusion
If patients are followed up closely, including PSMA PET scans, a second PSMA PET-directed RT represents a viable treatment option for well-informed and well-selected patients.
Magnetresonanzelastographie der Leber
Authors: Plaikner Michaela , Kremser Christian , Viveiros André , Zoller Heinz , Henninger Benjamin 
Published: May 2020

ZusammenfassungHintergrundDie Magnetresonanzelastographie (MRE) ist ein nichtinvasives, quantitatives, Magnetresonanz(MRT)-basiertes Verfahren zur Bestimmung derGewebesteifigkeit. Aufgrund der guten Reproduzierbarkeit, der möglichen Analyse großer Organflächen, der Durchführbarkeit bei Adipositas, Aszites und Darmgasüberlagerungen nimmt diese bildgebende Methode neben der Ultraschall(US)-Elastographie sowie der Biopsie vielerorts einen wichtigen Stellenwert in der Detektion und additiven Charakterisierung von Lebererkrankungen ein.Ziel der ArbeitBasierend auf der Literatur wird ein Überblick über die zugrundeliegende MRE-Methodik gegeben und die Technik des kommerziell erhältlichen Produktes vorgestellt. Es wird die praktische Durchführung, Analyse und Interpretation bei klinisch relevanten Fragestellungen veranschaulicht sowie ein Vergleich zur US-Elastographie angeführt.ErgebnisseDiese insgesamt noch relativjungeMRT-Methode ermöglicht eine umfassende Evaluierung mechanischer Eigenschaften der Leber und spielt insbesondere im Rahmen von Verlaufsuntersuchungen eine wichtige Rolle. Die MRE der Leber ist bei einer technischen Versagerrate von maximal 5,8 % eine robuste Technik mit hoher Treffsicherheit und exzellenter Retest-Reliabilität sowie Intra- und Interobserver-Reproduzierbarkeit. Es zeigt sich eine gute diagnostische Sicherheit im Rahmen der wichtigsten klinischen Indikation, der Fibrosequantifizierung, mit hoher Korrelation zu der noch alsGoldstandarddefinierten Biopsie.DiskussionAufgrund der zunehmenden klinischen Bedeutung sowie des immer breiter werdenden Einsatzgebiets wird die MRE der Leber bereits in vielen Zentren ins Routineprotokoll miteingebunden, sodass zumindest Grundkenntnisse dieser Methode für jeden Radiologen/In unverzichtbar sind.
Challenges in the analytical determination of ultra-short-chain perfluoroalkyl acids and implications for environmental and human health
Authors: Björnsdotter Maria K. , Yeung Leo W. Y. , Kärrman Anna , Ericson Jogsten Ingrid 
Published: May 2020

AbstractUltra-short-chain perfluoroalkyl acids have recently gained attention due to increasing environmental concentrations being observed. The most well-known ultra-short-chain perfluoroalkyl acid is trifluoroacetic acid (TFA) which has been studied since the 1990s. Potential sources and the fate of ultra-short-chain perfluoroalkyl acids other than TFA are not well studied and data reporting their environmental occurrence is scarce. The analytical determination of ultra-short-chain perfluoroalkyl acids is challenging due to their high polarity resulting in low retention using reversed-phase liquid chromatography. Furthermore, recent studies have reported varying extraction recoveries in water samples depending on the water matrix and different methods have been suggested to increase the extraction recovery. The present review gives an overview of the currently used analytical methods and summarizes the findings regarding potential analytical challenges. In addition, the current state of knowledge regarding TFA and other ultra-short-chain perfluoroalkyl acids, namely perfluoropropanoic acid, trifluoromethane sulfonic acid, perfluoroethane sulfonic acid, and perfluoropropane sulfonic acid‚ are reviewed. Both known and potential sources as well as environmental concentrations are summarized and discussed together with their fate and the environmental and human implications.
Transcription Profile of Potato (Solanum tuberosum L.) Growing In Vitro
Authors: Dobránszki Judit , Hidvégi Norbert , Gulyás Andrea , Tóth Bianka , Teixeira da Silva Jaime A. 
Published: May 2020

AbstractDespite countless papers on plant tissue culture, few have assessed the transcriptional changes that occur in a developing explant from the moment it is cut and plated, and during early stages of development. In this study, the mRNA profile of in vitro potato (Solanum tuberosumL.) plantlets derived from internode stems was assessed via four comparisons during five time intervals (0 h, 24 h, 48 h, 1 week, and 4 weeks) using the Kyoto Encyclopedia of Genes and Genomes (KEGG) classification. After screening KEGG metabolic groups, 35 processes were shown to be either up- or down-regulated. The vast majority (28 processes) were related to growth or development. The expression intensity of 40,430 genes was assessed and 158, 107, 163, and 142 sequences were either significantly up- or down-regulated at 0 h vs 24 h, 24 h vs 48 h, 48 h vs 1 week, and 1 week vs 4 weeks, respectively. A total of 10 DEGs coding for transcription factors were significantly down-regulated, including five ethylene-responsive transcription factors, and two probable WRKY transcription factors. RT-qPCR was used to validate RNA-seq data: Spearman and Pearson correlation coefficients between SeqMonk LFC and RT-qPCR LFC were 0.748 and 0.879, respectively. To the best of our knowledge, this is the first transcriptomic assessment of the changes taking place in the mRNA profile of a developing potato stem explant.
Predictors for low TAVI-prosthesis position assessed by fusion imaging of pre- and post-procedural CT angiography
Authors: Breitbart Philipp , Pache Gregor , Minners Jan , Hein Manuel , Schröfel Holger , Neumann Franz-Josef , Ruile Philipp 
Published: May 2020

Abstract
Background
Low prosthesis position after transcatheter aortic valve implantation (TAVI) is associated with higher rates of new onset conduction disturbances and permanent pacemaker implantations. Purpose of this study was to investigate possible predictors of a low prosthesis position of the SAPIEN 3 (Edwards Lifesciences, Irvine, California, USA) valve type using fusion imaging of pre- and post-procedural computed tomography angiography (CTA).

Methods
CTA fusion imaging was performed in 120 TAVI-patients with 3D-reconstruction of the transcatheter heart valve (THV) position within the device landing zone. A low implantation position was defined according to the manufacturer’s recommendations as > 30% of the prosthesis below the native annulus plane.

Results
A low THV position was found in 17 patients (14%). Patients with low THV position had less calcification of the annulus region and a smaller annulus size compared to patients with a normal or high THV position (P = 0.003 and 0.041, respectively). The only independent predictor of a low THV position in multivariate logistic regression analysis was the extent of calcification of the cusp region (odds ratio [CI] 0.842 [0.727–0.976], P = 0.022).

Conclusions
Fusion imaging of pre-and post-procedural CTA identified reduced calcification of the cusp region as an independent predictor of a low THV position of the SAPIEN 3. This should be considered when planning the TAVI procedure.

Graphic abstract
Correlation of cusp region calcification and prosthesis position after TAVI