bluuebunny/crossref_metadata_2025_split huggingface dataset:
Applications and data analysis of next-generation sequencing
Authors: Vogl Ina , Benet-Pagès Anna , Eck Sebastian H. , Kuhn Marius , Vosberg Sebastian , Greif Philipp A. , Metzeler Klaus H. , Biskup Saskia , Müller-Reible Clemens , Klein Hanns-Georg 
Published: February 2015

Abstract:
Over the past 6 years, next-generation sequencing (NGS) has been established as a valuable high-throughput method for research in molecular genetics and has successfully been employed in the identification of rare and common genetic variations. Although the high expectations regarding the discovery of new diagnostic targets and an overall reduction of cost have been achieved, technological challenges in instrument handling, robustness of the chemistry, and data analysis need to be overcome. Each workflow and sequencing platform have their particular problems and caveats, which need to be addressed. Regarding NGS, there is a variety of different enrichment methods, sequencing devices, or technologies as well as a multitude of analyzing software products available. In this manuscript, the authors focus on challenges in data analysis when employing different target enrichment methods and the best applications for each of them.
Effective inhibition of glycolysis in venous whole blood and plasma samples1)
Authors: Yagmur Eray , van Helden Josef , Koch Alexander , Jadem Johny , Tacke Frank , Trautwein Christian 
Published: February 2015

Abstract

Background: To stabilize glucose immediately and to prevent preanalytical loss of glucose from blood samples after collection, additional acidification is needed.

Methods: In this study, we aimed to assess the value of citrate-buffered GlucoEXACT tubes (Sarstedt) compared to VenoSafe™ Glycaemia (Terumo) tubes. Conventional sodium fluoride (NaF) tubes were used as internal controls. First, stability of venous plasma glucose concentrations were compared in 10 healthy volunteers at nine definite time points (after 0, 0.5, 1, 1.5, 2, 3, 4, 8, and 12 h). Blood samples from VenoSafe™ Glycaemia and NaF tubes were immediately centrifuged and separated. Moreover, glucose concentrations in an additional five healthy volunteers were compared by collecting blood samples simultaneously in GlucoEXACT and VenoSafe™ Glycaemia tubes and storing for 0, 1, 2, 4, 12, 24, and 48 h until centrifugation. Dilution- and hematocrit-dependent bias of plasma glucose in GlucoEXACT tubes was assessed by serial dilution.

Results: Mean Terumo plasma glucose concentrations decreased within the first 4 h from 94.9 mg/dL to 92.5 mg/dL (–2.5%) and remained stable after 12 h. Mean conventional NaF plasma glucose concentrations decreased within the first 4 h from 90 mg/dL to 87 mg/dL (–3.3%, not significant) and decreased significantly after 12 h (82.6 mg/dL, –8.2%). There was no significant decrease or difference of plasma glucose levels in stored blood samples collected in GlucoEXACT and VenoSafe™ Glycaemia tubes [linear regression analysis: R2=0.9688; GlucoEXACT (y)=5.3871+0.9431× VenoSafe™ Glycaemia (x); Wilcoxon test, p=0.7125]. Citrate buffer in GlucoEXACT tubes does not impair glucose concentration.

Conclusions: Determination of plasma glucose concentration in GlucoEXACT tubes is a suitable diagnostic alternative compared with Terumo VenoSafe™ Glycaemia tubes.
Evaluation of computer-assisted digital microscopes for evaluation of blood films1)
Authors: Nebe Carl Thomas , Ossendorf Manfred , Stamminger Gudrun , Jansen Henk , Zerfaß Thorsten 
Published: February 2015

Abstract
Currently, automated microscopes are increasingly entering clinical and private labs, making necessary a critical review of their performance. Within two trials, the two most advanced systems were compared with a hematology analyzer, a manual whole blood differential and an immunophenotypic approach. The diverse handling of nuclear shadows leads to the largest differences, followed by different classification schemes for lymphocytes and judgement of red cells and platelets. The implementation of these instruments into hematological step by step diagnostic schemes will be discussed. Because of poor low count statistics, an automated hematology analyzer differential and an immunological differential were included for comparison.
Kardiovaskuläre Verkalkungen im Rahmen des chronischen kardiorenalen Syndroms: welche Bedeutung haben Biomarker für Diagnostik und Risikostratifizierung?
Authors: Brandenburg Vincent , Krüger Thilo 
Published: February 2015

Zusammenfassung
Die frühzeitig auftretende Gefäßverkalkung ist nach wie vor wesentliche mortalitätsbestimmende Begleiterkrankung von Patienten mit schwerer oder terminaler Niereninsuffizienz. Sie ist pathoanatomisches Leitbild der kardiovaskulären Morbidität und Mortalität von Patienten mit chronischem kardiorenalem Syndrom. Die Untersuchung der Pathogenese sowie daraus erwachsende Therapiekonzepte der urämischen Vaskulopathie stehen nach wie vor im Fokus der nephrologischen Forschung. Die Entstehung der Gefäßverkalkung ist ein aktiv regulierter und regulierbarer Prozess. Die Identifikation von beteiligten Faktoren hat dazu geführt, Biomarker bzw. laborchemische Risikofaktoren für die Inzidenz bzw. Prävalenz von kardiovaskulären Verkalkungen definieren zu können. Solche Parameter können sich dann zur Diagnostik, zur Risikostratifizierung und/oder zum Therapiemonitoring eignen. Kein bekannter biochemischer Faktor des kardiorenalen Syndroms erfüllt allerdings alle diese Eigenschaften zur vollen Zufriedenheit. Wir möchten im Folgenden eine praxisorientierte Übersicht geben, welche Erkenntnisse zur vaskulären Kalzifikation in der chronischen Niereninsuffizienz in den letzten Jahren gewonnen wurden und welche Parameter in der aktuellen Kardionephrologie als Biomarker und/oder Risikofaktoren bezüglich der kardiovaskulären Verkalkung eine Bedeutung haben. Interessanterweise kann man für fast alle an der kardiovaskulären Verkalkung beteiligten Laborparameter auch einen direkten Zusammenhang zum Knochenstoffwechsel nachweisen, was ein deutlicher Hinweis für die Existenz der sogenannten „Knochen-Gefäß-Achsen“ Theorie ist.
Molecular karyotyping in routine diagnostics – a view back and forth1)
Authors: Heinrich Uwe , Gabert Meike , Rost Imma 
Published: February 2015

Abstract
Since its introduction in the routine diagnostics of patients with mental retardation/developmental delay, array-comparative genomic hybridization (aCGH) has become an indispensable tool for the detection of clinically relevant copy number variants (CNVs). Despite the current tendency for higher resolution arrays, the growing number of public internet databases as well as better calling algorithms allow save reporting and a better classification of CNVs. The application of combined aCGH plus single nucleotide polymorphism (SNP) arrays will increase detection rates by revealing copy number neutral changes, such as uniparental disomy. In the future, next generation sequencing techniques will lead to a further increase in resolution with the simultaneous detection of unbalanced and even balanced chromosomal aberrations.
Neue Entwicklungen in der Laboranalytik für Klinische Studien zur Zulassung von Arzneimitteln– Good Clinical Laboratory Practice (GCLP)
Authors: Wieland Eberhard , Klühe Cornelia , Shipkova Maria 
Published: February 2015

Zusammenfassung
Klinische Studien zur Zulassung von Arzneimitteln beim Menschen müssen in Europa unter Berücksichtigung der Deklaration von Helsinki und nach der Leitlinie der International Conference of Harmonisation – Good Clinical Practice (ICH-GCP) durchgeführt werden. Die klinische Prüfung von Arzneimitteln ist seit 2001 durch die Richtlinie 2001/20/EC über die Anwendung der guten klinischen Praxis (GCP-Richtlinie) EU-weit geregelt. In Deutschland hat dies im Arzneimittelgesetz (AMG) Berücksichtigung gefunden. Für die Labormedizin in klinischen Studien gelten damit auch die international gültigen ethischen Anforderungen an den Schutz der Studienpatienten und Probanden. Für die Qualität der Laboranalytik in klinischen Studien fehlten bisher Vorgaben. Die Anforderungen der Guten Laborpraxis (GLP) gelten nur für präklinische Untersuchungen und nicht für klinische Studien der Phasen I-IV beim Menschen. Die Lücke zwischen der ICH-GCP-Leitlinie und den GLP-Prinzipien ist letztes Jahr durch die Publikation einer Laborleitlinie der Europäischen Zulassungsbehörde für Arzneimittel EMA (European Medicines Agency) in der Form des „Reflection paper for laboratories that perform the analysis or evaluation of clinical trial samples“ geschlossen worden. Kernpunkte der Leitlinie sind die Prinzipien der Good Clinical Laboratory Practice (GCLP), die ursprünglich 1999 in Frankreich und dann später in Großbritannien formuliert wurden. Die Abkürzung GCLP spiegelt die Synthese von GCP- und GLP-Prinzipien wider. Das Ziel der Publikation ist es, medizinische Laboratorien, die an klinischen Studien mitwirken, darüber zu informieren, was europäische Gesetze fordern und Inspektoren der internationalen und nationalen Behörden erwarten, wenn sie Einrichtungen inspizieren, die an der Erhebung von Daten für klinische Studien mitgewirkt haben. Die Leitlinie richtet sich vor allem an Laboratorien, die zulassungsrelevante Daten zur Sicherheit und Wirksamkeit bei Arzneimittelprüfungen erheben und weniger an solche, die klinisch chemische Routinediagnostik durchführen. Da aber auch in Krankenhauslaboratorien Proben von Studienpatienten gemessen werden und manche dieser Laboratorien gezielt Industriekooperationen suchen, ist die Leitlinie besonders auch für Laboratorien in Krankenhäusern der Maximalversorgung von Interesse. Diesen Laboratorien wird grundsätzlich empfohlen, für den Umgang mit Studienproben Regeln unter GCP-Gesichtspunkten einzuführen.
Der Über-Code der DNA: epigenetische Mechanismen und deren Bedeutung für die Entstehung von Krankheiten
Authors: Ammerpohl Ole , Bens Susanne , Siebert Reiner 
Published: February 2015

Zusammenfassung:
Die Beschreibung epigenetischer Veränderungen gewinnt zunehmend an Bedeutung für das Verständnis der Entstehung von Phänotypen und Krankheiten. Dabei bezeichnet der Begriff der Epigenetik meiotisch und/oder mitotisch vererbbare Veränderungen der Genexpression, die nicht in der DNA-Sequenz selbst kodiert sind. Epigenetische Mechanismen umfassen die Modifikation von DNA sowie von Histon- bzw. Chromatin-Proteinen, die Expression nicht-kodierender RNAs sowie die Positionierung von Genen im Zellkern. Es stehen eine Reihe von Lokus-spezifischen und Genom-weiten Methoden zur Verfügung, um epigenetische Muster und Veränderungen zu charakterisieren. Diese reichen von der methylierungs-spezifischen PCR bis zur Gesamt-Genom-Bisulfitsequenzierung und von der Chromatin-Immunpräzipitation bis zur Konformations-Analyse mittels HiC. Veränderungen von epigenetischen Modifikationen und Mechanismen finden sich bei seltenen monogenen Erkrankungen und Störungen des Imprinting aber auch bei häufigen Volkskrankheiten. Momentan diskutierten Hypothesen folgend, werden letztere möglicherweise bereits vorgeburtlich durch epigenetische Prägung determiniert. Insbesondere bei Krebserkrankungen finden sich umfangreiche epigenetische Veränderungen. Diese betreffen sowohl die DNA-Methylierung als auch Mutationen von Genen, deren Produkte epigenetische Mechanismen vermitteln. Die prinzipielle Reversibilität epigenetischer Veränderungen hat zur Entwicklung von Medikamenten wie HDAC-Inhibitoren und demethylierenden Agentien geführt, die heute schon im klinischen Einsatz sind. Dieser Artikel gibt eine Übersicht über epigenetische Mechanismen, deren Veränderungen bei Erkrankungen sowie deren Nachweis.
12. Jahrestagung der Sektion Molekulare Diagnostik der DGKL am 6. und 7. Juni 2013 in der Evangelischen Akademie Tutzing / Report on the 12th Annual Meeting of the Section of Molecular Diagnostics of the DGKL on 6th/7th June 2013 in Tutzing
Authors: Pfeufer Arne , Dockhorn-Dworniczak Barbara , Findeisen Peter , Hoffmann Georg , Kiehntopf Michael , Klein Hanns-Georg , Teupser Daniel 
Published: February 2015

Zusammenfassung:
Die diesjährige 12. Jahrestagung der Sektion Molekulare Diagnostik der Deutschen Vereinten Gesellschaft für Klinische Chemie und Laboratoriumsmedizin (DGKL) stand unter dem Leitthema „Molekulare Signaturen“ und fand vom 06.–07.06.2013 in Tutzing statt. Molekulare Signaturen ergeben sich aus der Bewertung mehrerer gleichzeitig bestimmter Biomarker mit dem Ziel einer verbesserten Prävention und gezielteren Therapie von Erkrankungen. Mit diesem zentralen Aspekt der personalisierten Medizin befassten sich die vier Arbeitsgruppen der Sektion Molekulare Diagnostik aus ihren jeweiligen Blickwinkeln: Der Fokus der einführenden Sitzung der Arbeitsgruppe Genomics aus der Sichtweise der Pathologie und Laboratoriumsmedizin lag auf onkologischen Fragestellungen. In der darauf folgenden Sitzung widmet sich die Arbeitsgruppe Biobanken der Erhebung molekularer Signaturen aus archivierten Geweben und Körperflüssigkeiten. Die Arbeitsgruppe Bioinformatik ging der Frage nach, wie viele Biomarker man konkret für eine aussagekräftige Signatur benötigt. In der abschließenden Sitzung der Arbeitsgruppe Proteomics/Metabolomics wurden diese Erkenntnisse auf der Metabolitenebene am Beispiel endokrinologischer und maligner Erkrankungen in die Praxis übersetzt.
Im Rahmen der Jahrestagung fand eine Übergabe des Vorsitzes von Michael Neumeier (Heidelberg-Mannheim), der die Sektion seit ihrer Gründung geleitet hatte, an Daniel Teupser (München) statt. An dieser Stelle möchten die Autoren Herrn Professor Neumeier ihren tiefempfundenen Dank für den Aufbau und die sehr erfolgreiche Leitung der Sektion in den zurückliegenden Jahren aussprechen. Ihm ist es gelungen, die Molekulare Diagnostik als Zukunftsgebiet weit über die Grenzen der Fachgesellschaft hinaus bekannt zu machen. Dies wird auch aus dem fachübergreifenden Rednerspektrum der diesjährigen Tagung evident.
Biomarkers for neurological disorders – call for standardization
Authors: Torzewski Michael 
Published: February 2015

Abstract
With increasing life expectancy, neurodegenerative diseases such as Alzheimer’s disease (AD) and Parkinson’s disease (PD), as well as neurovascular diseases such as cerebral ischemia, are becoming a rapidly growing worldwide problem causing an increased burden on society. The development of biomarkers is aimed to enable the identification of at-risk individuals, enable early diagnosis, and reflect the progression of disease. Future challenges refer to the need for standardization of known biomarkers on the one hand and the identification of new biomarkers on the other hand. The former is impressively exemplified by a recent study addressing the impact of various types of cerebrospinal fluid collection tubes for detection of total tau, phosphorylated tau, and β-amyloid 1–42 on the diagnosis of AD. This issue was identified as a key issue by the Alzheimer’s Biomarkers Standardization Initiative (ABSI) and recommendations were listed which should be used to enable better standardization between laboratories and enable results for the AD biomarkers to be comparable between different sites. The latter challenge in particular concerns PD and is addressed by the Parkinson Progression Marker Initiative (PPMI), a comprehensive observational, international, multi-center study designed to identify PD progression biomarkers both to improve understanding of disease etiology and course and to provide crucial tools to enhance the likelihood of success of PD modifying therapeutic trials. With regard to cerebral ischemia, at present there are no clinically validated biomarkers. Nevertheless, the development of a clinically validated biomarker of acute cerebral ischemia would have the potential to facilitate the use of time-sensitive reperfusion strategies, allow for individualization of patient care by predicting relative risk of hemorrhage and volume of penumbral tissue, and add valuable prognostic information for patients presenting with acute stroke. Thereby, it is expected that a panel of biomarkers rather than one single marker will meet these criteria in the future. Unlike cerebral ischemia, cerebral hemorrhage biomarkers will probably be limited to the assessment of prognosis in the course of the disease.
A routine-qualified flow cytometric method for the identification of multiple sclerosis patients with a reduced therapeutic effectiveness of natalizumab
Authors: Oppermann Katrin , Harrer Andrea , Pilz Georg , Wipfler Peter , Afazel Shahrzad , Haschke-Becher Elisabeth , Sellner Johann , Deisenhammer Florian , Trinka Eugen , Kraus Jörg 
Published: February 2015

Abstract

Background: Natalizumab-neutralizing antibodies (NABs) occur in 9% of natalizumab-treated multiple sclerosis (MS) patients. Loss of clinical and biological efficacy in patients with persisting NABs requires termination of natalizumab treatment. Because high-titer NABs are strongly associated with persistence of NABs, we investigated if determination of natalizumab saturation levels of α-4 integrins by flow cytometry has the potential to identify patients early with NABs.

Methods: Cell-bound natalizumab and natalizumab saturation of α-4 integrins on T cells were detected by flow cytometry using a monoclonal anti-human IgG4 antibody. Peripheral blood mononuclear cells were enriched from venous blood collected at the start (baseline) and every 4 weeks immediately before subsequent infusions until up to 9 months from natalizumab-treated patients with NABs (n=4) and at the start and after 1 (n=15), 2 (n=14), 3 (n=9), 6 (n=7), and 9 months (n=3) from natalizumab-treated patients without NABs. Natalizumab saturation levels (in %) of T cells were determined by relating median fluorescence intensities (MFIs) of in vivo bound natalizumab to MFIs after in vitro incubation with saturating amounts of natalizumab. Determination of serum NABs was performed by ELISA.

Results: In patients without NABs, the median natalizumab saturation level of T cells over 9 months was 75% (confidence interval of 95%: 72–78%). In two of the four patients with NABs, the natalizumab saturation level of T cells only reached approximately 50% after the first infusion and further declined to baseline levels with the second infusion. Low-titer NABs were measured after the first infusion and development of persistent high-titer NABs led to termination of natalizumab treatment after 6 months. In another two patients, the natalizumab saturation level of T cells was 74% and 68% after the first infusion, temporarily decreased to approximately baseline levels and re-increased after approximately 6 months. Transient NABs were detected after 2 and 3 months, which resolved after 5 and 6 months.

Conclusions: Monitoring the natalizumab saturation level on T cells is a fast and reliable method to identify patients with a reduced treatment effect due to NABs. Both high- and low-titer NABs were equally effective in reducing cellular natalizumab saturation levels. We were able to show that monitoring the natalizumab saturation levels by flow cytometry, is a sensitive method for detecting a prolonged NAB-mediated reduced treatment effect because NABs are apparently effective longer than suggested by the detection limit of ELISA.
Prediction, modeling and characterization of surface texturing by sulfuric etchant on non-toxic titanium bio-material using artificial neural networks and fuzzy logic systems
Authors: Khanlou Hossein Mohammad , Ang Bee Chin , Barzani Mohsen Marani 
Published: February 2015

AbstractMultilayer feed forward network, radial biased function network, generalized regression neural network and adaptive network-based fuzzy inference system (ANFIS) were used to predict the surface roughness of Ti-13Zr-13Nb alloy in etching sulfuric acid. Subsequent processes – polishing, sandblasting and acid etching or SLA – were employed to modify the surface. Alumina particles for surface blasting and concentrated sulfuric acid for acid etching were utilized in this experiment. This was performed for three different periods of time (10, 20 and 30 s) and temperature (25, 45 and 60°C). Correspondingly, the Ti-13Zr-13Nb surfaces were evaluated using a field emission scanning electron microscope for roughening and a contact mode profilometer for the average surface roughness (Ra) (nm). Different configurations of neural networks and ANFIS approaches are examined in order to minimize the root mean square error. Consequently, the ANFIS model is selected by dividing the time and temperature into one and three spaces, respectively, using the Gaussian-shaped membership function. A mathematical model is attained from the best approach in terms of root mean square error to realize the relation of the surface roughness of Ti-13Zr-13Nb alloy in etching sulfuric acid and time and temperature as the effective parameters.
Nanoindentation Characterization of Moisture Damage in Different Phases of Asphalt Concrete
Authors: Faisal Hasan , Tarefder Rafiqul , Weldegiorgis Mekdim 
Published: February 2015

Abstract
Traditional microscale testing cannot be performed on asphalt binder, mastic, or aggregate, while they are an integral part of asphalt concrete (AC). Recently, nanoindentation has created an opportunity to characterize mastic and asphalt binder while they reside in an AC sample. In the study, laboratory nanoindentation testing is carried out to characterize moisture-induced damage in different phases of AC. A moisture-induced sensitivity testing (MIST) device is used for moisture conditioning of AC. In the MIST device, an AC sample is fully submerged under water and all-around cyclic pressure is applied through the pores inside an AC sample to cause damage. Damaged AC samples are indented for an extended dwell time of 200 s using an unloading rate of 0.02 mN/s to minimize viscous effects of asphalt on test results. The indentation load-displacement curve is analyzed by the Oliver–Pharr method to obtain elastic modulus and hardness. When comparing wet and dry sample indentation test results, it is observed that the modulus of the wet mastic reduces to 60 % of dry mastic modulus. Overall moisture conditioning reduces the modulus of AC by 70 %. In addition, the creep response of the mastic phase is modeled by a viscoelastic Burger model. The creep compliance value of wet mastic is 42 % higher than that of dry mastic.
Effect of Overconsolidation on K in Centrifuge Models Using CPT and Tactile Pressure Sensor
Authors: El-Sekelly Waleed , Abdoun Tarek , Dobry Ricardo 
Published: February 2015

Abstract
Assessing the state of stress in soil in the free field, as defined by the vertical and lateral earth pressures, is important in some geotechnical problems such as the design of underground structures and estimation of soil liquefaction potential. Unlike the vertical earth pressure, several factors can influence the lateral earth pressure, particularly overconsolidation. This is typically accounted for by relating the coefficient of lateral earth pressure at rest, K0, with the estimated overconsolidation ratio (OCR). The corresponding relations available in the literature are related to the K0 occurring for a given OCR during unloading, and do not take into account the unloading–reloading effect that may be present in centrifuge tests. In this paper, the relationship between the coefficient of lateral earth pressure at rest, K0, and overconsolidation ratio, OCR, is investigated for the whole loading–unloading–reloading condition. Four centrifuge model experiments were conducted on Ottawa F#55 sand. Two of the models were tested using a tactile pressure sensor to measure K0 and the other two models were tested using a miniature cone penetration test (CPT) system. The paper concludes with recommendations for centrifuge operation when testing overconsolidated sand in the centrifuge.