bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gelatin expression from an engineered Saccharomyces cerevisiae CUP1 promoter in Pichia pastoris
Authors: Williams Kim E. , Olsen David R. 
Published: February 2021

AbstractThe methylotrophic yeast Pichia pastoris (reclassified as Komagataella phaffii) is a versatile protein expression system, yet many commonly used promoters have attributes undesirable for fermentation or its optimization. Hence, the copper‐inducible CUP1 gene promoter from the related yeast Saccharomyces cerevisiae was used to express human gelatin. Multimerization of a potential copper response element in the CUP1 promoter, a S. cerevisiae Ace1p binding site, significantly increased gelatin expression. Expression was induced by copper in a dose‐dependent fashion and was not dependent on cell density. Gelatin was additionally induced in standard copper‐containing fermentation basal salts media. Removal of a S. cerevisiae heat shock factor (Hsf1p) binding site reduced copper‐dependent gelatin induction suggesting that a similar protein may regulate this promoter in P. pastoris. This engineered copper inducible promoter expands the yeast recombinant protein production tool kit.
Evaluation einer SARS-CoV-2-Teststrategie zu Beginn der COVID-19-Pandemie in einem südwestdeutschen Universitätsklinikum
Authors: Trimborn Anna , Gerigk Marlis , Heininger Alexandra , Santhanam Nandhini , Walter Thomas , Lange Bettina 
Published: February 2021

Zusammenfassung
Hintergrund
Zu Beginn der COVID-19-Pandemie in Deutschland veröffentlichte das Robert Koch-Institut (RKI) Orientierungshilfen für eine bedarfsadaptierte und zielgerichtete Teststrategie auf SARS-CoV‑2. In der Universitätsmedizin Mannheim (UMM) wurde von Beginn an eine RKI-konforme Teststrategie, basierend auf den RKI-Orientierungshilfen angewendet. Ziel dieser Arbeit ist es, zu klären, ob sich diese RKI-konforme Teststrategie als lohnenswert erwiesen hat.

Material und Methoden
Es erfolgte eine retrospektive Auswertung aller SARS-CoV-2-Untersuchungen im Zeitraum 26.02.–06.04.2020. Mithilfe der Adressinformationen der getesteten Personen erfolgte zudem eine Geovisualisierung der SARS-CoV-2-Testhäufigkeiten und der positiven Testergebnisse im Stadtgebiet Mannheim.

Ergebnisse
Der Anteil SARS-CoV-2-positiver Befunde bei den diagnostischen Proben (n = 2808) lag durchschnittlich bei 7 %. Ein Mitarbeiterscreening (n = 448) blieb ohne positiven Befund. Es erfolgte lediglich ein nosokomialer SARS-CoV-2-Nachweis, Ausbruchsgeschehen gab es nicht. Die Geovisualisierung zeigte innerhalb des Untersuchungszeitraumes eine Verschiebung der Testhäufigkeiten und der lokalen Häufigkeit positiver SARS-CoV-2-Befunde im Stadtgebiet Mannheim.

Diskussion
Die festgelegte RKI-konforme Teststrategie führte sowohl zu einem stabilen Anteil positiver Ergebnisse als auch zu einer bedarfsadaptierten Anpassung der Testkapazitäten. Dadurch hat sich diese Strategie unter Praxisbedingungen aus infektionshygienischer und -präventiver Sicht als effektiv erwiesen. Geovisualisierungen können dabei helfen, innerhalb eines Stadtgebietes Verschiebungen von Infektionsherden deutlich zu machen, was im Sinne gezielter infektionspräventiver Maßnahmen (z. B. Impfkampagnen) sinnvoll eingesetzt werden kann.
Novel deep learning-based noise reduction technique for prostate magnetic resonance imaging
Authors: Wang Xinzeng , Ma Jingfei , Bhosale Priya , Ibarra Rovira Juan J. , Qayyum Aliya , Sun Jia , Bayram Ersin , Szklaruk Janio 
Published: February 2021

Abstract
Introduction
Magnetic resonance imaging (MRI) has played an increasingly major role in the evaluation of patients with prostate cancer, although prostate MRI presents several technical challenges. Newer techniques, such as deep learning (DL), have been applied to medical imaging, leading to improvements in image quality. Our goal is to evaluate the performance of a new deep learning-based reconstruction method, “DLR” in improving image quality and mitigating artifacts, which is now commercially available as AIRTM Recon DL (GE Healthcare, Waukesha, WI). We hypothesize that applying DLR to the T2WI images of the prostate provides improved image quality and reduced artifacts.

Methods
This study included 31 patients with a history of prostate cancer that had a multiparametric MRI of the prostate with an endorectal coil (ERC) at 1.5 T or 3.0 T. Four series of T2-weighted images were generated in total: one set with the ERC signal turned on (ERC) and another set with the ERC signal turned off (Non-ERC). Each of these sets then reconstructed using two different reconstruction methods: conventional reconstruction (Conv) and DL Recon (DLR): ERCDLR, ERCConv, Non-ERCDLR, and Non-ERCConv. Three radiologists independently reviewed and scored the four sets of images for (i) image quality, (ii) artifacts, and (iii) visualization of anatomical landmarks and tumor.

Results
The Non-ERCDLR scored as the best series for (i) overall image quality (p < 0.001), (ii) reduced artifacts (p < 0.001), and (iii) visualization of anatomical landmarks and tumor.

Conclusion
Prostate imaging without the use of an endorectal coil could benefit from deep learning reconstruction as demonstrated with T2-weighted imaging MRI evaluations of the prostate.
Which Socio-economic Conditions Drive the Selection of Agroforestry at the Forest Frontier?
Authors: Gosling Elizabeth , Knoke Thomas , Reith Esther , Reyes Cáceres Alyna , Paul Carola 
Published: February 2021

AbstractModels are essential to assess the socio-economic credentials of new agroforestry systems. In this study, we showcase robust optimisation as a tool to evaluate agroforestry’s potential to meet farmers’ multiple goals. Our modelling approach has three parts. First, we use a discrete land-use model to evaluate two agroforestry systems (alley cropping and silvopasture) and conventional land uses against five socio-economic objectives, focusing on the forest frontier in eastern Panama. Next, we couple the land-use model with robust optimisation, to determine the mix of land uses (farm portfolio) that minimises trade-offs between the five objectives. Here we consider uncertainty to simulate the land-use decisions of a risk-averse farmer. Finally, we assess how the type and amount of agroforestry included in the optimal land-use portfolio changes under different environmental, socio-economic and political scenarios, to explore the conditions that may make agroforestry more attractive for farmers. We identify silvopasture as a promising land use for meeting farmers’ goals, especially for farms with less productive soils. The additional labour demand compared to conventional pasture, however, may prove an important barrier to adoption for farms facing acute labour shortages. The selection of agroforestry responded strongly to changes in investment costs and timber prices, suggesting that cost-sharing arrangements and tax incentives could be effective strategies to enhance adoption. We found alley cropping to be less compatible with farmers’ risk aversion, but this agroforestry system may still be a desirable complement to the land-use portfolio, especially for farmers who are more profit-oriented and tolerant of risk.
A Quality Assessment of the Information Accessible to Patients on the Internet About the Whipple Procedure
Authors: Khachfe Hussein H. , Chahrour Mohamad A. , Habib Joseph R. , Yu Jun , Jamali Faek R. 
Published: February 2021

AbstractBackgroundThe Internet has become a central source of information on health‐related issues. The aim of this study is to assess the quality and readability of online information present on the Whipple surgical procedure by applying recognized scoring tools.MethodsA search using the top three online search engines (Google, Bing and Yahoo) was conducted in July 2020. Websites were classified as academic, physician, commercial or unspecified. The quality of information was assessed using the JAMA and DISCERN assessment instruments and presence of a HONcode seal. Readability was assessed using the Flesch Reading Ease Score (FRES).ResultsA total of 34 unique sources were included in our study. The average JAMA and DISCERN scores of all websites were 2.22 ± 0.48 and 47.28 ± 1.17, respectively, with a median of 1.9 (range 0–4) and 47 (range 18–71), respectively. Website classification distribution was 38% academic, 18% commercial, 9% unspecified, and 1% from physician‐based websites. Physician websites had the highest JAMA score with a mean of 3 ± 0.46. Unspecified websites had the highest DISCERN score with a mean of 54.60 ± 1.09. Only 3 websites had the HONcode seal. Physician websites had a significantly higher JAMA mean score than academic websites (p‐value = 0.004). Readability was difficult and is on the level of university students.ConclusionThe results of this study show a poor quality of online information present on the Whipple surgery. Academic and physician websites need to improve the quality of their websites on the procedure. More HONcode‐certified websites are needed as they are the best source for information on this operation.
Precision medicine in human heart modeling
Authors: Peirlinck M. , Costabal F. Sahli , Yao J. , Guccione J. M. , Tripathy S. , Wang Y. , Ozturk D. , Segars P. , Morrison T. M. , Levine S. , Kuhl E. 
Published: February 2021

AbstractPrecision medicine is a new frontier in healthcare that uses scientific methods to customize medical treatment to the individual genes, anatomy, physiology, and lifestyle of each person. In cardiovascular health, precision medicine has emerged as a promising paradigm to enable cost-effective solutions that improve quality of life and reduce mortality rates. However, the exact role in precision medicine for human heart modeling has not yet been fully explored. Here, we discuss the challenges and opportunities for personalized human heart simulations, from diagnosis to device design, treatment planning, and prognosis. With a view toward personalization, we map out the history of anatomic, physical, and constitutive human heart models throughout the past three decades. We illustrate recent human heart modeling in electrophysiology, cardiac mechanics, and fluid dynamics and highlight clinically relevant applications of these models for drug development, pacing lead failure, heart failure, ventricular assist devices, edge-to-edge repair, and annuloplasty. With a view toward translational medicine, we provide a clinical perspective on virtual imaging trials and a regulatory perspective on medical device innovation. We show that precision medicine in human heart modeling does not necessarily require a fully personalized, high-resolution whole heart model with an entire personalized medical history. Instead, we advocate for creating personalized models out of population-based libraries with geometric, biological, physical, and clinical information by morphing between clinical data and medical histories from cohorts of patients using machine learning. We anticipate that this perspective will shape the path toward introducing human heart simulations into precision medicine with the ultimate goals to facilitate clinical decision making, guide treatment planning, and accelerate device design.
Protein in-cell NMR spectroscopy at 1.2 GHz
Authors: Luchinat Enrico , Barbieri Letizia , Cremonini Matteo , Banci Lucia 
Published: February 2021

AbstractIn-cell NMR spectroscopy provides precious structural and functional information on biological macromolecules in their native cellular environment at atomic resolution. However, the intrinsic low sensitivity of NMR imposes a big limitation in the applicability of the methodology. In this respect, the recently developed commercial 1.2 GHz NMR spectrometer is expected to introduce significant benefits. However, cell samples may suffer from detrimental effects at ultrahigh fields, that must be carefully evaluated. Here we show the first in-cell NMR spectra recorded at 1.2 GHz on human cells, and we compare resolution and sensitivity against those obtained at 900 and 950 MHz. To evaluate the effects of different spin relaxation rates, SOFAST-HMQC and BEST-TROSY spectra were recorded on intracellular α-synuclein and carbonic anhydrase. Major improvements are observed at 1.2 GHz when analyzing unfolded proteins, such as α-synuclein, while the TROSY scheme improves the resolution for both globular and unfolded proteins.
Cyclostratigraphy and paleoenvironmental inference from downhole logging of sediments in tropical Lake Towuti, Indonesia
Authors: Ulfers A. , Hesse K. , Zeeden C. , Russell J. M. , Vogel H. , Bijaksana S. , Wonik T. 
Published: February 2021

AbstractLake Towuti is located on central Sulawesi/Indonesia, within the Indo Pacific Warm Pool, a globally important region for atmospheric heat and moisture budgets. In 2015 the Towuti Drilling Project recovered more than 1000 m of drill core from the lake, along with downhole geophysical logging data from two drilling sites. The cores constitute the longest continuous lacustrine sediment succession from the Indo Pacific Warm Pool. We combined lithological descriptions with borehole logging data and used multivariate statistics to better understand the cyclic sequence, paleoenvironments, and geochronology of these sediments. Accurate chronologies are crucial to analyze and interpret paleoclimate records. Astronomical tuning can help build age-depth models and fill gaps between age control points. Cyclostratigraphic investigations were conducted on a downhole magnetic susceptibility log from the lacustrine facies (10–98 m below lake floor) from a continuous record of sediments in Lake Towuti. This study provides insights into the sedimentary history of the basin between radiometric ages derived from dating a tephra layer (~ 797 ka) and C14-ages (~ 45 ka) in the cores. We derived an age model that spans from late marine isotope stage (MIS) 23 to late MIS 6 (903 ± 11 to 131 ± 67 ka). Although uncertainties caused by the relatively short record and the small differences in the physical properties of sediments limited the efficacy of our approach, we suggest that eccentricity cycles and/or global glacial-interglacial climate variability were the main drivers of local variations in hydroclimate in central Indonesia. We generated the first nearly complete age-depth model for the lacustrine facies of Lake Towuti and examined the potential of geophysical downhole logging for time estimation and lithological description. Future lake drilling projects will benefit from this approach, since logging data are available just after the drilling campaign, whereas core descriptions, though more resolved, only become available months to years later.
Convolutional Neural Network for the Semantic Segmentation of Remote Sensing Images
Authors: Alam Muhammad , Wang Jian-Feng , Guangpei Cong , Yunrong LV , Chen Yuanfang 
Published: February 2021

AbstractIn recent years, the success of deep learning in natural scene image processing boosted its application in the analysis of remote sensing images. In this paper, we applied Convolutional Neural Networks (CNN) on the semantic segmentation of remote sensing images. We improve the Encoder- Decoder CNN structure SegNet with index pooling and U-net to make them suitable for multi-targets semantic segmentation of remote sensing images. The results show that these two models have their own advantages and disadvantages on the segmentation of different objects. In addition, we propose an integrated algorithm that integrates these two models. Experimental results show that the presented integrated algorithm can exploite the advantages of both the models for multi-target segmentation and achieve a better segmentation compared to these two models.
The relationships between selected soil properties and caesium-137 identify organic carbon, nitrogen and water soluble phenols as indicators of soil erosion processes in different forest stands
Authors: Romeo Federico , Porto Paolo , Mallamaci Carmelo , Muscolo Adele 
Published: February 2021

AbstractIn the last few decades, the use of environmental radionuclides, particularly caesium-137 (137Cs), represented one of the most valid methods for estimating soil erosion. However, the cost associated with the use of the equipment needed for radiometric analyses is still high and, for this reason, finding more easily measurable indicators can be useful. There is a strong correlation between 137Cs, organic carbon (OC), nitrogen (N) and water soluble phenols (WSP) exists, indicating the latter parameters as possible early indicators of soil erosion. Based on the above assumptions, the main purpose of this work is to identify specific soil chemical parameters able to indicate early triggering of soil erosion. Specifically, several soil parameters such as pH, electric conductivity (EC), WSP, OC, N and C/N have been evaluated against 137Cs and on a comparative basis. In addition, since the rate of soil erosion depends on the degree of coverage and canopy structure, two different tree species (Pinus nigra laricio Poir. and Fagus sylvatica L.) have been considered in this contribution in which ten different scenarios of forest management have been analysed. The results show that the reduction in tree cover of managed sites triggers erosion and nutrient loss processes. It has been observed that the loss of 137Cs, compared to the control areas, is closely correlated with those of WSP, OC and N. These parameters (WSP, OC and N), more easily assessable, can be a valid tool to understand easily, triggering of erosive phenomena.
Neue Klasse von Methyltransferasen mit Zyklisierungsaktivität
Authors: Piechulla Birgit , Magnus Nancy , Lemfack Marie Chantal , Von Reuss Stephan 
Published: February 2021

AbstractMicroorganisms release small volatile metabolites with unique structures, e. g. the polymethylated homosesquiterpene sodorifen from Serratia plymuthica. Two unusual enzymes with novel features are involved in its biosynthesis, a C-methyltransferase with cyclization activity and a terpene synthase that accepts a non-canonical monocyclic C16 substrate. The novel class of methyltransferases represents an alternative route that enlarges terpene diversity.
Molekulare Grundlagen des Vogelzugs
Authors: Langebrake Corinna , Meyer Britta S. , Liedvogel Miriam 
Published: February 2021

AbstractMigration is a complex behavior of which a significant proportion is genetic. Which genes and epigenetic changes underpin migratory behavior remains largely unknown, but a revolution of sequencing technology, analytical approaches, and functional genomic tools promises rapid advances. We summarize our current understanding of the (epi)genetic architecture of seasonal traits and outline our vision of how technical developments and integrative approaches could be employed to identify and functionally validate candidate genes and regulatory elements in migratory species.
Archaea in der Biotechnologie
Authors: Rittmann Simon K.-M. R. , Pfeifer Kevin , Palabikyan Hayk , Ergal İpek , Schuster Bernhard 
Published: February 2021

AbstractArchaea are prokaryotic organisms with highly interesting physiological features. They have also shown potential for the production of biotechnological compounds. Today, the commercially available products of archaea are bacterioruberin, squalene, bacteriorhodopsin, and lipids — all of which are produced by utilizing halophilic archaea. Other products include carotenoids, bioplastics, molecular hydrogen, and methane. Here we give a brief an overview of the current state of Archaea biotechnology.
Coronavirus-Replikation: Mechanismus und Inhibition durch Remdesivir
Authors: Cramer Patrick , Kokic Goran , Dienemann Christian , Höbartner Claudia , Hillen Hauke S. 
Published: February 2021

AbstractCoronaviruses use an RNA-dependent RNA polymerase to replicate and transcribe their RNA genome. The structure of the SARS-CoV-2 polymerase was determined by cryo-electron microscopy within a short time in spring 2020. The structure explains how the viral enzyme synthesizes RNA and how it replicates the exceptionally large genome in a processive manner. The most recent structure-function studies further reveal the mechanism of polymerase inhibition by remdesivir, an approved drug for the treatment of COVID-19.
Methanothermobacter — bedeutungsvoll für Wasser, Energie, Klima
Authors: Engelhardt Harald 
Published: February 2021

AbstractMethanogenic microbes live secretly in a kind of “parallel universe”, without light and oxygen. We can approach these microbes only by scientific means, but they are already of practical value for us and could — if we do not take care of efficient climate protection — even be of noticeable impact for our future world.
Von der Stöchiometrie zur Kontrolle metabolischer Netzwerke
Authors: Schramm Thorben , Link Hannes 
Published: February 2021

AbstractCellular metabolism is very complex and extensively regulated. For many organisms we know almost the complete set of biochemical reactions in their metabolic network. However, it is not well understood how these reactions are regulated and how they interact in order to enable cellular functions. In this review, we describe recent methodological advances to study metabolic networks with a focus on bacterial metabolism.
Slope Stability Analysis Based on Rock Mass Rating, Geological Strength Index and Kinematic Analysis in Vindhyan Rock Formation
Authors: Kumar Saurabh , Pandey Hemant Kumar 
Published: February 2021

Abstract
The Rock Mass Rating (RMR), Geological Strength Index (GSI) and kinematic analysis are widely employed in geotechnical engineering practice. The RMR and GSI both are used for rock mass characterization while the kinematic analysis is applied to identify the mode of failure of slope based on rock discontinuities and slope face characteristics of rock.
An attempt has been made to analyze the RMR, GSI and Kinematic Analysis using in-situ data corresponding to Vindhyan sandstone. The data has been collected from outcrops at seven different locations in and around Markundi hill along SH-5, Chopan, Sonbhadra. The relationship between RMR and GSI for Vindhyan sandstone in the study area has been attempted using generalize equation proposed by Hoek (2013) while the kinematic analysis has been applied to decipher the weak zone of failure using RocScience Dips software.
The lowest RMR value estimated is 35 for location S-4 and the highest RMR value is 58 for location S-1. Other locations viz, S-2, S-3, S-5, S-6 and S-7 have the RMR value from 42 to 49 which infers that the Vindhyan sandstone existing at Markundi is characterized by both poor as well as fair rock mass.
The GSI value of the location S-1 is estimated as 34 (minimum) and 46 (maximum) of location S-4. GSI value of the same rock formation also corroborates that the rock mass belongs to poor as well as fair rock mass.
The wedge failure is inferred due to intersection of two sets of joints oriented in north-west and north-east direction. The line of intersections of these two discontinuities are observed in wedge shaped block. It is concluded that the locations under investigations have tendency of wedge failure.