bluuebunny/crossref_metadata_2025 huggingface dataset:
Late Holocene lagoon succession and its response to environmental variations at Yongle atoll, Xisha Islands, South China Sea
Authors: Chen Wanli , Liu Gang , Wu Shiguo , Ma Benjun , Gao Jinwei , Zhang Hanyu
Published: February 2021

Tropical coral reef lagoons that are characterized by high deposition rates are potentially useful for high‐resolution palaeoenvironmental reconstructions. We present the geochemical and accelerator mass spectrometry (AMS) 14C‐dating data of a 113‐cm gravity core obtained from the Yongle atoll lagoon in the South China Sea. The core record preserves a continuous 1,500‐year depositional history of the back‐reef lagoon environment, with sedimentation rates varying from 0.55 to 1.55 mm yr−1 (mean of 0.74 mm yr−1). Calcium carbonate (CaCO3) production was calculated based on the sediment accumulation rates and sediment density to be 807 g m−2 yr−1. The geochemical records of the studied core displayed a progressively increasing trend of storms over the past 1,500 years. The stable carbon and oxygen isotopes of the lagoon sediment have the potential to record monsoon intensity. The lagoon system of the Yongle atoll appears to have been influenced by minor terrestrial input from 1,500 calendar years before present (cal yr BP) to 500 cal yr BP, and by a strong anthropogenic influence over the past 200 years.
Zircon U–Pb ages, geochemistry, and Sr–Nd–Pb–Hf isotopes of the Mugagangri monzogranite in the southern Qiangtang of Tibet, western China: Implications for the evolution of the Bangong Co‐Nujiang Meso‐Tethyan Ocean
Authors: Huang Han‐Xiao , Dai Zuo‐Wen , Liu Hong , Li Guang‐Ming , Huizenga Jan Marten , Zhang Lin‐Kui , Huang Yong , Cao Hua‐Wen , Fu Jian‐Gang
Published: February 2021

We present in‐situ zircon laser ablation‐inductively coupled plasma‐mass spectrometry (LA‐ICP‐MS) U–Pb ages, whole‐rock geochemistry, and Sr–Nd–Pb–Hf isotopes of the Mugagangri monzogranite in the southern margin of the Qiangtang Block, Tibet, western China. The zircons yield a U–Pb age of ca. 123 Ma. The hornblende‐bearing monzogranite shows metaluminous to weak peraluminous and high‐K calc‐alkaline characteristics exemplified by high silica (SiO2 = 67.57–70.57 wt%), high aluminium (Al2O3 = 14.68–15.78 wt%), high potassium (K2O = 4.00–5.14 wt%), high alkali (K2O + Na2O = 7.88–8.62 wt%), and low calcium contents (CaO = 1.72–2.17 wt%), with the aluminium saturation index (A/CNK) ranging from 0.98 to 1.09, suggesting that the Mugagangri monzogranite is a metaluminous to weak peraluminous I‐type high‐K calc‐alkaline granite. Geochemically, similar to the arc magmas, the monzogranite is enriched in large‐ion lithophile elements, and relatively depleted in high‐field‐strength elements. The monzogranite displays relatively high (87Sr/86Sr)i values (0.70972–0.71240), uniform εNd(t) values (−2.24 to −3.40), variable zircon εHf(t) values (−14.1 to +8.0), and high radiogenic Pb isotopic values (206Pb/204Pb = 18.588–18.790, 207Pb/204Pb = 15.616–15.642, and 208Pb/204Pb = 38.838–39.053). These geochemical characteristics indicate that the monzogranite was derived from a mixed source comprising ancient crustal and mantle materials, and experienced fractional crystallization during emplacement. We propose that the parental magma of the Mugagangri monzogranite was most likely generated during northward subduction of the Bangong Co‐Nujiang Meso‐Tethys Ocean.
Midkine is neuroprotective and influences glial reactivity and the formation of Müller glia‐derived progenitor cells in chick and mouse retinas
Authors: Campbell Warren A. , Fritsch‐Kelleher Amanda , Palazzo Isabella , Hoang Thanh , Blackshaw Seth , Fischer Andy J.
Published: February 2021

Recent studies suggest midkine (MDK) is involved in the development and regeneration of the zebrafish retina. We investigate the expression patterns of MDK and related factors, roles in neuronal survival, and influence upon the formation of Müller glia‐derived progenitor cells (MGPCs) in chick and mouse model systems. By using single‐cell RNA‐sequencing, we find that MDK and pleiotrophin (PTN), a MDK‐related cytokine, are upregulated by Müller glia (MG) during later stages of development in chick. While PTN is downregulated, MDK is dramatically upregulated in mature MG after retinal damage or FGF2 and insulin treatment. By comparison, MDK and PTN are downregulated by MG in damaged mouse retinas. In both chick and mouse retinas, exogenous MDK induces expression of cFos and pS6 in MG. In the chick, MDK significantly decreases numbers dying neurons, reactive microglia, and proliferating MGPCs, whereas PTN has no effect. Inhibition of MDK‐signaling with Na3VO4 blocks neuroprotective effects with an increase in the number of dying cells and negates the pro‐proliferative effects on MGPCs in damaged retinas. Inhibitors of PP2A and Pak1, which are associated with MDK‐signaling through integrin β1, suppressed the formation of MGPCs in damaged chick retinas. In mice, MDK promotes a small but significant increase in proliferating MGPCs in damaged retinas and potently decreases the number of dying cells. We conclude that MDK expression is dynamically regulated in Müller glia during embryonic maturation, following retinal injury, and during reprogramming into MGPCs. MDK mediates glial activity, neuronal survival, and the re‐programming of Müller glia into proliferating MGPCs.
Effects of in vitro exposure of perfluorooctanoic acid and monocrotophos on astroglia SVG p12 cells
Authors: Osemwegie Odia , Butler Landon , Subbiah Seenivasan , Smith Ernest
Published: February 2021

Glia cells provide supportive functions to the central nervous system and can be compromised by environmental contaminants. The primary objective of this study was to characterize the effects of in vitro exposure to perfluorooctanoic acid, a persistent environmental contaminant and/or monocrotophos (MCP), a neurotoxic organophosphate that is rapidly metabolized, to astroglia SVG p12 cells. The endpoints evaluated include cell viability, intracellular glutamate levels as a marker of astrocyte homeostasis function, differential gene expression for selected proteins, which include inflammatory markers (tachykinin), astrocytosis (nestin), S100B, and metabolism enzymes (CYP1A1). The results from cell viability revealed significant differences from the controls at some of the concentrations tested. Also, intracellular glutamate levels were elevated at the 10‐μM concentration for perfluorooctanoic acid (PFOA) as well as the 10‐μM PFOA/5‐μM MCP concentration. Gene expression results at 80‐μM PFOA concentration revealed a significant increase in the expression of S100B, tachykinin and CYP1A1. A combination of 10‐μM PFOA/20‐μM MCP caused a significant decrease in the expression of tachykinin. Gene expression for MCP exposures produced a decrease at the 20‐μM MCP concentration. Immunofluorescence results indicated an increase in nestin protein expression for the 20‐μM concentration of MCP, which contradicted the gene expression at the same concentration tested. The results indicate that toxicity to glia cells can compromise critical glia functions and could be implicated in neurodegenerative diseases.
Exploring the Relationship Between Colorectal Cancer and Allopurinol: A Taiwanese Population‐Based Propensity‐Matched Case‐Control Study
Authors: Hsu Fan‐Gen , Lai Jung‐Nien , Huang Ching‐Ya , Lin Mei‐Chen , Hsieh Yow‐Wen
Published: February 2021

The role of allopurinol usage in colorectal cancer (CRC) has no definite conclusion. The aim of this study was to explore the correlation between allopurinol usage and CRC risk in Taiwan. Using the National Health Insurance Database, we conducted a case‐control study of cases who were ≥20 years old and had newly diagnosed CRC for the period from 2000 to 2013. The controls were matched to cases by age, sex, index year, comorbidities, and socioeconomic status using propensity scores. Odds ratios (ORs) and 95% confidence intervals (95%CIs) were measured by the conditional logistic regression model. We examined 4372 cases and 4372 matched controls. A statistically significant correlation was noted between allopurinol usage and CRC risk (OR, 0.79; 95%CI, 0.69‐0.90). We used the cumulative‐defined daily doses (cDDDs) in a further subgroup analysis, the ORs decreased from tertile 1 (T1; low dose, <12 cDDDs), T2 (medium dose, 12 to 88.5 cDDDs), to T3 (high dose, >88.5 cDDDs). These values were 0.85 (95%CI, 0.69‐1.06), 0.77 (95%CI, 0.62‐0.95), to 0.76 (95%CI, 0.61‐0.94). The results indicated a dose‐response relationship between allopurinol usage and CRC risk (P for trend < .001). We thus inferred that patients with medium and high doses of allopurinol (≥12 cDDDs) had a statistically significantly decreased CRC risk.
Conformational analysis of 2,5‐diaryl‐4‐methyl‐2,4‐dihydro‐3H‐1,2,4‐triazol‐3‐ones: Multinuclear NMR and DFT calculations
Authors: Sánchez‐Andrada Pilar , Marín‐Luna Marta , Alkorta Ibon , Elguero José , Percho Gema , Santa María Dolores , Claramunt Rosa M.
Published: February 2021

Conformational exploration of five 2,5‐diaryl‐4‐methyl‐2,4‐dihydro‐3H‐1,2,4‐triazol‐3‐ones has been carried out based on a combination of their NMR chemical shifts determined in CDCl3 and the scrutiny of their computed relative energies and absolute shieldings calculated at the DFT/GIAO/B3LYP/6–311++G(d,p) level. The very flat potential energy curves corresponding to the three relevant single bond rotations were explored by calculating the energy of the rotational barriers and comparing the experimental chemical shifts with those theoretically calculated in each rotamer by statistical analysis.
Technical Note: Validation of an automatic ACR phantom quality assurance tool for an MR‐guided radiotherapy system
Authors: Gao Yu , Lotey Rajiv , Low Daniel A. , Hu Peng , Yang Yingli
Published: February 2021

Purpose

To modify and evaluate an automatic American College of Radiology (ACR) phantom analysis toolbox for ACR quality assurance (QA) on a low‐field MR‐guided radiotherapy system (ViewRay).

Methods

An open‐source toolbox was modified for ACR QA of a 0.35T MRI system (ViewRay MRIdian). A total of 17 ACR datasets were evaluated, including 10 datasets acquired from different systems across the world, and seven datasets acquired at our center between 2014 and 2020. All required ACR tests, geometric accuracy (GA), high‐contrast spatial resolution (HCSR), slice thickness accuracy (ST), slice position accuracy (SP), percent integral uniformity (PIU), percentage signal ghosting (PSG), and low‐contrast object detectability (LCOD), were assessed manually and using the toolbox automatically. Measurements between manual and automatic analysis were compared. Precision, recall, and accuracy were calculated, where the manual results were used as the ground truth.

Results

The software took less than 2 min to complete all seven tests, which usually requires 40 min or more if analyzed manually. Overall, the automatic measurement was consistent with the manual result. The absolute differences between the two measurements were 0.72 ± 0.66 (mm), 0.01 ± 0.03, 0.50 ± 0.60 (mm), 0.39 ± 0.41 (mm), 1.01 ± 1.00 (%), 0.0016 ± 0.0019, and 2.79 ± 2.29 for the seven tests. The precision of the automatic toolbox was 100% for all tests, indicating that a test would 100% pass a manual analysis if it had passed the automatic analysis. Recall and accuracy were ≥ 96% for GA, HCSR, SP, PIU, PSG, and LCOD tests, and 91% for the ST test.

Conclusion

An automatic ACR QA tool was adopted and evaluated for the low‐field MR‐guided radiotherapy (MRgRT) system. Overall, the toolbox provided comparable results as manual analysis, and reduced the processing time from over 40 min to <2 min. This toolbox holds the potential to be widely adopted either as a second check tool or partially replace human measurement for MRgRT programs using the same system.
T2 mapping of the median nerve in patients with carpal tunnel syndrome and healthy volunteers
Authors: Maeda Atsushi , Suzuki Taku , Hayakawa Katsuhiko , Funahashi Takuya , Kuroiwa Takashi , Fujita Nobuyuki
Published: February 2021

Introduction

We investigated the changes in MRI T2 mapping values in subjects with carpal tunnel syndrome (CTS) compared to healthy controls.

Methods

We enrolled 71 patients with CTS and 26 healthy controls. Median nerve T2 values were measured at the distal carpal tunnel, hamate bone, proximal carpal tunnel, and forearm levels. These were compared between patients and controls and correlated with median nerve cross‐sectional area (CSA) and nerve conduction measurements.

Results

The mean T2 values at the proximal carpal tunnel levels were higher in the CTS group (56.7 ms) than in the control group (51.2 ms, P = .02) and also were higher than at the distal carpal tunnel (51.0 ms, P < .001) and forearm levels (47.6 ms, P < .001). T2 values were not significantly associated with CSA or nerve conduction measurements.

Discussion

T2 mapping of the carpal tunnel provides qualitative information on median nerve pathology but does not reflect CTS severity.
Explaining Channel Catfish Population Characteristics in Ohio Reservoirs
Authors: Tyszko Stephen M. , Pritt Jeremy J. , Conroy Joseph D.
Published: February 2021

North American fisheries management agencies commit considerable resources to managing reservoir fisheries for Channel Catfish Ictalurus punctatus, which often includes stocking. However, Channel Catfish population characteristics often vary greatly among reservoirs, resulting in variable and unpredictable fishery quality. We sampled Channel Catfish populations in 44 Ohio reservoirs with tandem, baited hoop nets to understand relationships among population characteristics (density, as CPUE from hoop nets; growth, as mean length at age 7; mortality, as total annual mortality from catch-curve analysis; and size structure, as proportional size distribution), stocking, and the relationships between these characteristics and reservoir size (as surface area), predator density (as Largemouth Bass Micropterus salmoides electrofishing CPUE), and productivity (as chlorophyll-a concentration). We used multiple linear regression and an information theoretic approach to select the most parsimonious models for explaining observed variation in Channel Catfish density, growth, mortality, and size structure. We found that population density varied greatly among our study reservoirs, and none of our models sufficiently explained variation in density. Reservoir size and the interaction between reservoir size and population density explained the most variation in Channel Catfish growth, but productivity was also important. Small reservoirs (≤101 ha) had low to moderate densities and growth was uniformly slow; however, in larger reservoirs, lower densities resulted in faster growth. Growth increased as productivity increased. Total annual mortality was uniformly low (<0.26) but increased with density. Faster growth led to populations with larger size structures. These outcomes show that the largest Ohio reservoirs (≥406 ha) are the most suitable for supporting populations with fast growth and large size structures. Dense populations (CPUE > 50 Channel Catfish/net set) resulted in slower growth, greater mortality, and poor size structure. Future research to understand natural recruitment in reservoir Channel Catfish populations could be important for explaining variation in density.
Historical Data Provide Important Context for Understanding Declines in Cutthroat Trout
Authors: Nordberg Brittany J. , Mandeville Elizabeth G. , Walters Annika W. , Burckhardt Jason C. , Wagner Catherine E.
Published: February 2021

We used historical stocking and population survey records of Yellowstone Cutthroat Trout Oncorhynchus clarkii bouvieri and other salmonids in the North Fork Shoshone River drainage, Wyoming to summarize fish stocking history and population trends. Based on 98 years of historical records, we found that despite extensive stocking of Yellowstone Cutthroat Trout and minimal stocking of nonnative salmonids after about 1950, populations of wild Yellowstone Cutthroat Trout declined relative to those of nonnative salmonid species. The timing of increases in nonnative salmonids (1970s) did not coincide with their period of most intensive stocking (1935–1950). It is plausible that Yellowstone Cutthroat Trout populations persisted because of high levels of supplemental stocking from 1935 to 1965 and declined with reduced stocking efforts in the 1970s, thereby allowing the increase of introduced nonnative salmonids. The establishment of nonnative salmonids likely further reduced stocking success of Yellowstone Cutthroat Trout due to competition and hybridization. This study demonstrates that an understanding of long-term stocking records and population survey data can be useful for developing and implementing successful management frameworks for the conservation of imperiled fish populations across the United States.
Validation of an International Classification of Disease, 10th revision coding adaptation for the Charlson Comorbidity Index in United States healthcare claims data
Authors: Beyrer Julie , Manjelievskaia Janna , Bonafede Machaon , Lenhart Gregory , Nolot Sandra , Haldane Diane , Johnston Joseph
Published: February 2021

Purpose

An International Classification of Disease (ICD‐10) Charlson Comorbidity Index (CCI) adaptation had not been previously developed and validated for United States (US) healthcare claims data. Many researchers use the Canadian adaption by Quan et al (2005), not validated in US data. We sought to evaluate the predictive validity of a US ICD‐10 CCI adaptation in US claims and compare it with the Canadian standard.

Methods

Diverse patient cohorts (rheumatoid arthritis, hip/knee replacement, lumbar spine surgery, acute myocardial infarction [AMI], stroke, pneumonia) in the IBM® MarketScan® Research Databases were linked with the IBM MarketScan Mortality file. Predictive performance was measured using c‐statistics for binary outcomes (1‐year and postoperative mortality, in‐hospital complications) and root mean square prediction error (RMSE) for continuous outcomes (1‐year all‐cause medical costs, index hospitalization costs, length of stay [LOS]), after adjusting for age and sex. C‐statistics were compared by the method of DeLong and colleagues (1988); RMSEs, by resampling.

Results

C‐statistics were generally high (≥ ~ 0.8) for mortality but lower for in‐hospital complications (~0.6–0.7). RMSEs for costs and hospitalization LOS were relatively large and comparable to standard deviations. Results were similar overall between the US and Canadian adaptations, with relative differences typically <1%.

Conclusions

This US‐based coding adaptation and a previously published Canadian adaptation resulted in similar predictive ability for all outcomes evaluated but may have different construct validity (not evaluated in our study). We recommend using adaptations specific to the country of data origin based on good research practice.
Evaluation of Mechanical Properties of Composite Solid Propellant by Genetic Engineering of Materials: Part B: Modeling of Minimum Representative Unit for Multi‐Modal Particle Packing Structure Based on Formulation of Composite Solid Propellant
Authors: Dong Ge , Zhang Wei , Zhou Xing , Bao Tong , Deng Lei
Published: February 2021

To show the actual particle packing structure of AP/Al/HTPB propellant with multi‐modal fillers, a minimum representative unit of particle packing structure is established. In the minimum representative unit, the particle size of fillers in each mode is identical to the value in the propellant formulation. Meanwhile, on the basis of the amount series of fillers in the per unit propellant, the amount of fillers in each mode is respectively divided by that of the fewest filler, thus the amount series of fillers in the minimum representative unit is obtained. Further, with the condition that the average density of the unit is the same as that of the propellant, the side length of the minimum representative unit could be uniquely determined. In order to generate the particle packing structure with particles evenly distributed in the unit, a two‐step algorithm is put forward. In the first step, the genetic algorithm is adopted to search for an evenly and non‐overlapping distribution for the few and coarser particles. In the second step, the residual finer particles are randomly placed in the voids among the coarser particles by a modified L−S algorithm. Results showed that the particles are distributed more evenly in the packs generated by the two‐step algorithm than in packs generated by the classic L−S algorithm.
Structural Energetic Properties of Al/PVDF Composite Materials Prepared Using Fused Filament Fabrication
Authors: Fleck Trevor J. , Manship Timothy D. , Son Steven F. , Rhoads Jeffrey F.
Published: February 2021

The constituents of an aluminum/polyvinylidene fluoride multifunctional energetic structural material (MESM) were varied in order to determine the effect of solids loading and particle size on the structural energetic properties of the material. More specifically, seven different material formulations were paired with additive manufacturing to quantify key performance metrics relevant to the MESM use case. Determined via the quasi‐static tensile testing of 3D printed dogbone samples, both the modulus of elasticity and the ultimate strength was found to be heavily dependent on the solids loading; respectively increasing from 71 MPa to 208 MPa and decreasing from 34.5 MPa to 21.6 MPa, when transitioning from a 10 % Al loading to a 50 % Al loading. To characterize the combustion properties, a thermochemical code was used to predict the heat of combustion and the adiabatic flame temperature for the formulations considered, showing a maximum predicted temperature near 20 % Al. Also, burning rate measurements were conducted on the 3D printed formulations in order to quantify their combustion performance. When burning in air, a maximum burning rate was found to occur at the slightly fuel‐rich condition of 30 % Al. Upon completion of the characterization, the trade‐off between mechanical performance and combustion performance was visualized by plotting critical MESM design parameters against one another.
Influence of Strain Rate on Mechanical Properties of HTPE/PCL Propellant Applying to Wide Temperature Range
Authors: Yuan Shen , Zhang Bowen , Wen Xiaomu , Chen Keke , Jiang Shengkun , Luo Yunjun
Published: February 2021

The mechanical properties of hydroxyl‐terminated polyether/poly(ϵ‐caprolactone) (HTPE/PCL) propellant applying to the wide temperature range of −50 °C to 70 °C were investigated by uniaxial tensile test with different strain rates varying from 0.5 min−1to 10 min−1. The scanning electron microscopy (SEM) was used to observe the fractured surface of HTPE/PCL propellant, and the dynamic mechanical analysis (DMA) was employed to analyze its strain induced crystallization at low temperature. It reveals that the temperature and strain rate have great influence on the mechanical properties of HTPE/PCL propellant. As the temperature increasing or the strain rate decreasing, the maximum tensile strength gradually reduces, but the elongation at break increases first and then decreases. The fracture of HTPE/PCL propellant changes from the part dewetting and brittle fracture at low temperature to the fracture caused by dewetting at high temperature. The master curves for mechanical properties of HTPE/PCL propellant at the wide temperature of −50 °C to 70 °C with the strain rate of 0.5 min−1to 10 min−1were obtained, the prediction of maximum tensile strength and elastic modulus can be achieved.
DeepCys: Structure‐based multiple cysteine function prediction method trained on deep neural network: Case study on domains of unknown functions belonging to COX2 domains
Authors: Nallapareddy Vamsi , Bogam Shubham , Devarakonda Himaja , Paliwal Shubham , Bandyopadhyay Debashree
Published: February 2021

Cysteine (Cys) is the most reactive amino acid participating in a wide range of biological functions. In‐silico predictions complement the experiments to meet the need of functional characterization. Multiple Cys function prediction algorithm is scarce, in contrast to specific function prediction algorithms. Here we present a deep neural network‐based multiple Cys function prediction, available on web‐server (DeepCys) (https://deepcys.herokuapp.com/). DeepCys model was trained and tested on two independent datasets curated from protein crystal structures. This prediction method requires three inputs, namely, PDB identifier (ID), chain ID and residue ID for a given Cys and outputs the probabilities of four cysteine functions, namely, disulphide, metal‐binding, thioether and sulphenylation and predicts the most probable Cys function. The algorithm exploits the local and global protein properties, like, sequence and secondary structure motifs, buried fractions, microenvironments and protein/enzyme class. DeepCys outperformed most of the multiple and specific Cys function algorithms. This method can predict maximum number of cysteine functions. Moreover, for the first time, explicitly predicts thioether function. This tool was used to elucidate the cysteine functions on domains of unknown functions belonging to cytochrome C oxidase subunit‐II like transmembrane domains. Apart from the web‐server, a standalone program is also available on GitHub (https://github.com/vam-sin/deepcys).
A novel robust event‐triggered fault tolerant automatic steering control approach of autonomous land vehicles under in‐vehicle network delay
Authors: Zhang Jie , Zhang Bangji , Zhang Nong , Wang Chenyang , Chen Yuanchang
Published: February 2021

This paper proposes a novel robust event‐triggered fault tolerant automatic steering control strategy for autonomous land vehicles to achieve path tracking and vehicle lateral motion control under in‐vehicle network delay. From the practical point of view, the parameter uncertainties, time delay, and actuator fault are simultaneously introduced to make the designed controller robust to more extensive and challenging driving conditions. A novel polytope reduction and norm‐bounded uncertainty reduction method is used to effectively handle the time‐varying velocity and tire cornering stiffness uncertainties. Then, the uncertain vehicle model can be reconstructed as an uncertain network control system model with time delay and actuator fault. Due to the inevitable time delay and actuator fault, a new cubic absolute‐value Lyapunov function is developed to guarantee the asymptotical stability of the closed control system with the H∞ performance, and the modified project‐based adaptive law is applied to strengthen the fault tolerant ability. Furthermore, a progressive event‐triggered mechanism is proposed for the collaborative design of robust fault tolerant automatic steering controller, which can signally improve the communication resource utilization of the limited bandwidth in‐vehicle network. Finally, the performance comparisons of different controllers are presented. These results prove that the proposed controller can simultaneously guarantee the path tacking performance and lateral dynamics stability, and save the communication resource of the in‐vehicle network.
Use cases and testbed solutions for 5G cellular backhauling via satellite
Authors: Politis Christos , Liolis Konstantinos , Grønsund Pål , Heck Stefan
Published: February 2021

This paper describes the use cases and testbed solutions for 5G cellular backhauling via satellite developed within the H2020 5G‐Public Private Partnership (PPP) Phase III project “5G‐VINNI” (5G Verticals Innovation Infrastructure). It presents the end‐to‐end design of the 5G‐VINNI Norway and Luxembourg Facility Sites and aims to showcase the satellite integration into 5G with focus on satellite backhauling solutions. It elaborates on the satellite transport network between the 5G Radio Access Network (RAN) and the 5G Core Network (5GC), where design aspects on the satellite network integration into the standard 3GPP 5GC architecture are detailed. It also addresses the split of the 5GC between the Central Node and the Edge Node, where the Edge Node can be fixed and nomadic. The paper describes also the Management and Orchestration (MANO) and Network Functions Virtualisation Infrastructure (NFVI) features of the 5G‐VINNI Norway and Luxembourg Facility Sites.
Gelatin expression from an engineered Saccharomyces cerevisiae CUP1 promoter in Pichia pastoris
Authors: Williams Kim E. , Olsen David R.
Published: February 2021

The 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

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

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

Models 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

Background

The 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.

Methods

A 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).

Results

A 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.

Conclusion

The 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

Precision 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

In-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

Lake 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

In 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

In 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

Microorganisms 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

Migration 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

Archaea 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

Coronaviruses 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.