bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of Immune Checkpoint Inhibitors in Gastrointestinal Malignancies
Authors: Mazloom Anita , Ghalehsari Nima , Gazivoda Victor , Nimkar Neil , Paul Sonal , Gregos Peter , Rateshwar Janice , Khan Uqba
Published: August 2020

Immune checkpoint inhibitors (ICIs) have revolutionized the treatment of several solid and hematological malignancies. ICIs are not only able to produce long and durable responses, but also very well tolerated by patients. There are several approved indications of use of ICIs in treatment of metastatic gastrointestinal malignancies including gastric, esophageal, colorectal and hepatocellular carcinoma. In addition, ICIs can be used in microsatellite instability-high (MSI-H) and high tumor mutational burden (TMB) tumors in chemotherapy-resistant setting. Despite having good efficacy and superior safety profile, ICIs are clinically active in small subset of patients, therefore, there is a huge unmet need to enhance their efficacy and discover new predictive biomarkers. There are several ongoing clinical trials that are exploring the role of ICIs in various gastrointestinal cancers either as single agent or in combination with chemotherapy, radiation therapy, targeted agents or other immunotherapeutic agents. In this review, we discuss the published and ongoing trials for ICIs in gastrointestinal malignancies, including esophageal, gastric cancer, pancreatic, hepatocellular, biliary tract, colorectal and anal cancers. Specifically, we focus on the use of ICIs in each line of therapy and discuss the future directions of these agents in each type of gastrointestinal cancer.
Investigation of the PD-1 and PD-L1 Immune Checkpoint Molecules Throughout Healthy Human Pregnancy and in Nonpregnant Women
Authors: Meggyes Matyas , Nagy David U. , Szereday Laszlo
Published: August 2020

Background: A growing body of evidence supports the importance of PD-1 and PD-L1, especially in the materno-fetal interface, although limited information is available about the peripheral expression of these molecules during the trimesters of pregnancy. Methods: 13 healthy women were enrolled from the 1st, 10 from the 2nd and 12 from the 3rd trimester of pregnancy at the same time, 10 healthy, age-matched nonpregnant women formed the control group. From peripheral blood, mononuclear cells were separated and stored at –80 °C. From freshly thawed samples, surface and intracellular staining were performed for flow cytometric analyses. CD107a degranulation assay was used to evaluate the cytotoxicity. Results: significant alternation was detected in PD-1 expression by CD8+T cells and in PD-L1 expression by CD8+T, CD4+T and Treg cells. An interesting relationship was revealed between the PD-1 and PD-L1 expression by the investigated subpopulations in 2nd trimester of pregnancy. Different expression patterns of an activation receptor NKG2D by the PD-1+ CD8+T cells was observed during pregnancy. The notable relationship was further determined in cytotoxicity between PD-1+ and NKG2D+ CD8+T cells throughout pregnancy. Conclusions: the different PD-1 presence and the relationship with NKG2D could contribute to the dynamic changes of the Th1 and Th2 predominance throughout the three trimesters of a healthy pregnancy.
Deep Learning-Based Segmentation and Quantification of Retinal Capillary Non-Perfusion on Ultra-Wide-Field Retinal Fluorescein Angiography
Authors: Nunez do Rio Joan M. , Sen Piyali , Rasheed Rajna , Bagchi Akanksha , Nicholson Luke , Dubis Adam M. , Bergeles Christos , Sivaprasad Sobha
Published: August 2020

Reliable outcome measures are required for clinical trials investigating novel agents for preventing progression of capillary non-perfusion (CNP) in retinal vascular diseases. Currently, accurate quantification of topographical distribution of CNP on ultrawide field fluorescein angiography (UWF-FA) by retinal experts is subjective and lack standardisation. A U-net style network was trained to extract a dense segmentation of CNP from a newly created dataset of 75 UWF-FA images. A subset of 20 images was also segmented by a second expert grader for inter-grader reliability evaluation. Further, a circular grid centred on the FAZ was used to provide standardised CNP distribution analysis. The model for dense segmentation was five-fold cross-validated achieving area under the receiving operating characteristic of 0.82 (0.03) and area under precision-recall curve 0.73 (0.05). Inter-grader assessment on the 20 image subset achieves: precision 59.34 (10.92), recall 76.99 (12.5), and dice similarity coefficient (DSC) 65.51 (4.91), and the centred operating point of the automated model reached: precision 64.41 (13.66), recall 70.02 (16.2), and DSC 66.09 (13.32). Agreement of CNP grid assessment reached: Kappa 0.55 (0.03), perfused intraclass correlation (ICC) 0.89 (0.77, 0.93), non-perfused ICC 0.86 (0.73, 0.92), inter-grader agreement of CNP grid assessment values are Kappa 0.43 (0.03), perfused ICC 0.70 (0.48, 0.83), non-perfused ICC 0.71 (0.48, 0.83). Automated dense segmentation of CNP in UWF-FA images achieves performance levels comparable to inter-grader agreement values. A grid placed on the deep learning-based automatic segmentation of CNP generates a reliable and quantifiable method of measurement of CNP, to overcome the subjectivity of human graders.
Second Update for Anaesthetists on Clinical Features of COVID-19 Patients and Relevant Management
Authors: Weenink Robert P. , Preckel Benedikt , Hulst Abraham H. , Hermanides Jeroen , de Jong Menno D. , Schlack Wolfgang S. , Stevens Markus F. , Sperna Weiland Nicolaas H. , Hollmann Markus W.
Published: August 2020

The COVID-19 pandemic poses great challenges for healthcare workers around the world, including perioperative specialists. Previously, we provided a first overview of available literature on SARS-CoV-2 and COVID-19, relevant for anaesthetists and intensivists. In the current review, we provide an update of this topic, after a literature search current through May 2020. We discuss the evidence on perioperative risk for COVID-19 patients presenting for surgery, the risk of transmission of SARS-CoV-2 in the operating room, and the current literature on laboratory diagnostics. Furthermore, cardiovascular and nervous system involvement in COVID-19 are discussed, as well as considerations in diabetic patients. Lastly, the latest evidence on pharmacological treatment is summarised.
Clinical and Radiologic Outcomes of Combined Use of Biocomposite and PEEK Suture Anchors during Arthroscopic Rotator Cuff Repair: A Prospective Observational Study
Authors: Lee Jae-Hoo , Lee Yong-Beom
Published: August 2020

The aim of the current study was to evaluate the functional and radiologic outcomes of biocompatible non-absorbable PEEK (polyetheretherketone) and biocomposite (poly-L-lactic acid/poly(lactic-co-glycolic acid) 70% + β-tricalcium phosphate) anchors, especially in terms of perianchor cyst formation during the first six months postoperatively. We prospectively analysed 29 patients who underwent arthroscopic rotator cuff repair between March and May 2019. Both PEEK and biocomposite suture anchors were used as lateral anchors in one body. Clinical outcomes were assessed using the shoulder range of motion (ROM), visual analogue scale (VAS) for pain and satisfactory score, American Shoulder and Elbow Surgeons (ASES) score, and Simple Shoulder Test (SST). All these were obtained in patients preoperatively at 3 and 6 months after surgery. The imaging evaluation included perianchor cyst formation, anchor absorption, repaired cuff integrity, and retear pattern. All functional outcomes significantly improved over time. The biocomposite anchor had a statistically significant tendency to form higher grades of fluid collection at 3 months after surgery. However, the perianchor cyst reduced by the sixth postoperative month. Six months postoperatively, the functional outcomes were improved after rotator cuff repair and similar degrees of perianchor cyst formation were observed, regardless of the suture anchor material used.
The Role of Imaging Techniques to Define a Peri-Prosthetic Hip and Knee Joint Infection: Multidisciplinary Consensus Statements
Authors: Romanò Carlo Luca , Petrosillo Nicola , Argento Giuseppe , Sconfienza Luca Maria , Treglia Giorgio , Alavi Abass , Glaudemans Andor W.J.M. , Gheysens Olivier , Maes Alex , Lauri Chiara , Palestro Christopher J. , Signore Alberto
Published: August 2020

Diagnosing a peri-prosthetic joint infection (PJI) remains challenging despite the availability of a variety of clinical signs, serum and synovial markers, imaging techniques, microbiological and histological findings. Moreover, the one and only true definition of PJI does not exist, which is reflected by the existence of at least six different definitions by independent societies. These definitions are composed of major and minor criteria for defining a PJI, but most of them do not include imaging techniques. This paper highlights the pros and cons of available imaging techniques—X-ray, ultrasound, computed tomography (CT), Magnetic Resonance Imaging (MRI), bone scintigraphy, white blood cell scintigraphy (WBC), anti-granulocyte scintigraphy, and fluorodeoxyglucose positron emission tomography/computed tomography (FDG-PET/CT), discusses the added value of hybrid camera systems—single photon emission tomography/computed tomography (SPECT/CT), PET/CT and PET/MRI and reports consensus answers on important clinical questions that were discussed during the Third European Congress on Inflammation/Infection Imaging in Rome, December 2019.
Diagnostic and Clinical Impact of 18F-FDG PET/CT in Staging and Restaging Soft-Tissue Sarcomas of the Extremities and Trunk: Mono-Institutional Retrospective Study of a Sarcoma Referral Center
Authors: Annovazzi Alessio , Rea Sandra , Zoccali Carmine , Sciuto Rosa , Baldi Jacopo , Anelli Vincenzo , Petrongari Maria G. , Pescarmona Edoardo , Biagini Roberto , Ferraresi Virginia
Published: August 2020

Background: Soft-tissue sarcomas (STS) represent a wide heterogeneous class of rare tumors. The exact role 18F-fluorodeoxyglucose positron emission/computed tomography (18F-FDG PET/CT) in the evaluation of STS is not well established. The aim of the present study was to evaluate how the use of 18F-FDG PET/CT in STS could influence patient therapy planning, looking for a possible added value over computed tomography and magnetic resonance imaging—the most used modalities in the study of STS. Differences in SUVmax according to histologic subtype and tumor grade were also considered. Methods: a total of 345 consecutive 18F-FDG PET/CT scans performed for initial staging (n = 171) or for suspected disease relapse (n = 174) in 282 patients with STS extracted from the local Information System database were retrospectively reviewed. Results: 18F-FDG PET/CT altered therapy planning in 80 cases (16.4% for staging and 29.9% in restaging), both for disease upstaging (58.8%) and downstaging (41.2%) Conclusions: 18F-FDG PET/CT could significantly influence management of patients with STS, particularly for restaging.
Endometrial Carcinomas with Intestinal-Type Metaplasia/Differentiation: Does Mismatch Repair System Defects Matter? Case Report and Systematic Review of the Literature
Authors: Ardighieri Laura , Palicelli Andrea , Ferrari Federico , Bugatti Mattia , Drera Emma , Sartori Enrico , Odicino Franco
Published: August 2020

Background: Intestinal metaplasia/differentiation in primary endometrial carcinomas is an uncommon phenomenon, with only few cases described. Material and Methods: We performed a systematic review of endometrial carcinomas with intestinal metaplasia/differentiation interrogating the electronic databases Pubmed, Web of Science, and Scopus, and we reported an additional case arising in a 49-year-old woman. Results: We identified only eight patients diagnosed with endometrial carcinomas exhibiting intestinal metaplasia/differentiation, and additionally our case. Endometrial carcinomas with intestinal-type features can present in pure or mixed forms in association with usual-type endometrioid carcinomas; in mixed forms, the two neoplastic components may derive from a common neoplastic progenitor, as evidenced by the concomitant loss of MSH2 and MSH6 protein expression in our case. Disease recurrences occur in a significant fraction of the cases, including patients diagnosed in low-stage disease. Conclusions: Endometrial carcinomas with intestinal metaplasia/differentiation are rare and they may represent a more aggressive tumor variant, thus requiring a proper treatment despite the low-tumor stage. The ProMise classification should be performed also in these unusual tumors, since they can be associated with mismatch repair system defects.
Selective Laser Sintering of PA6: Effect of Powder Recoating on Fibre Orientation
Authors: Heckner Tobias , Seitz Michael , Raisch Sven Robert , Huelder Gerrit , Middendorf Peter
Published: August 2020

In Selective Laser Sintering, fibres are strongly orientated during the powder recoating process. This effect leads to an additional increase of anisotropy in the final printed parts. This study investigates the influence of process parameter variation on the mechanical properties and the fibre orientation. A full factorial design of experiment was created to evaluate the processing parameters of recoating speed, layer thickness and laser power on the part’s modulus of elasticity. Based on the mechanical testing, computed tomography was applied to selected samples to investigate the process-induced fibre microstructure, and calculate the fibre orientation tensors. The results show increasing part stiffness in the deposition direction, with decreasing layer thickness and increasing laser power, while the recoating speed only shows little effect on the mechanical performance. This complies with computed tomography imaging results, which show an increase in fibre orientation with smaller layer thickness. With thinner layers, and hence smaller shear gaps, shear stresses induced by the roller during recoating increase significantly, leading to excessive fibre reorientation and alignment. The high level of fibre alignment implies an increase of strength and stiffness in the recoating direction. In addition, thinner layer thickness under constant laser energy density results in improved melting behaviour, and thus improved fibre consolidation, consequently further increasing the mechanical properties. Meanwhile, the parameters of recoating speed and laser power do not have a significant impact on fibre orientation within their applicable process windows.
Data-Driven, Multi-Model Workflow Suggests Strong Influence from Hurricanes on the Generation of Turbidity Currents in the Gulf of Mexico
Authors: Harris Courtney , Syvitski Jaia , Arango H.G. , Meiburg E.H. , Cohen Sagy , Jenkins C.J. , Birchler Justin , Hutton E.W.H. , Kniskern T.A. , Radhakrishnan S. , Auad Guillermo
Published: August 2020

Turbidity currents deliver sediment rapidly from the continental shelf to the slope and beyond; and can be triggered by processes such as shelf resuspension during oceanic storms; mass failure of slope deposits due to sediment- and wave-pressure loadings; and localized events that grow into sustained currents via self-amplifying ignition. Because these operate over multiple spatial and temporal scales, ranging from the eddy-scale to continental-scale; coupled numerical models that represent the full transport pathway have proved elusive though individual models have been developed to describe each of these processes. Toward a more holistic tool, a numerical workflow was developed to address pathways for sediment routing from terrestrial and coastal sources, across the continental shelf and ultimately down continental slope canyons of the northern Gulf of Mexico, where offshore infrastructure is susceptible to damage by turbidity currents. Workflow components included: (1) a calibrated simulator for fluvial discharge (Water Balance Model - Sediment; WBMsed); (2) domain grids for seabed sediment textures (dbSEABED); bathymetry, and channelization; (3) a simulator for ocean dynamics and resuspension (the Regional Ocean Modeling System; ROMS); (4) A simulator (HurriSlip) of seafloor failure and flow ignition; and (5) A Reynolds-averaged Navier–Stokes (RANS) turbidity current model (TURBINS). Model simulations explored physical oceanic conditions that might generate turbidity currents, and allowed the workflow to be tested for a year that included two hurricanes. Results showed that extreme storms were especially effective at delivering sediment from coastal source areas to the deep sea, at timescales that ranged from individual wave events (~hours), to the settling lag of fine sediment (~days).
Wave Interaction with Single and Twin Vertical and Sloped Slotted Walls
Authors: Alkhalidi Mohamad , Alanjari Noor , Neelamani S.
Published: August 2020

The interaction between waves and slotted vertical walls was experimentally studied in this research to examine the performance of the structure in terms of wave transmission, reflection, and energy dissipation. Single and twin slotted barriers of different slopes and porosities were tested under random wave conditions. A parametric analysis was performed to understand the effect of wall porosity and slope, the number of walls, and the incoming relative wave height and period on the structure performance. The main focus of the study was on wave transmission, which is the main parameter required for coastal engineering applications. The results show that reducing wall porosity from 30% to 10% decreases the wave transmission by a maximum of 35.38% and 38.86% for single and twin walls, respectively, increases the wave reflection up to 47.6%, and increases the energy dissipation by up to 23.7% on average for single walls. For twin-walls, the reduction in wall porosity decreases the wave transmission up to 26.3%, increases the wave reflection up to 40.5%, and the energy dissipation by 13.3%. The addition of a second wall is more efficient in reducing the transmission coefficient than the other wall parameters. The reflection and the energy dissipation coefficients are more affected by the wall porosity than the wall slope or the existence of a second wall. The results show that as the relative wave height increases from 0.1284 to 0.2593, the transmission coefficient decreases by 21.2%, the reflection coefficient decreases by 15.5%, and the energy dissipation coefficient increases by 18.4% on average. Both the transmission and the reflection coefficients increase as the relative wave length increases while the energy dissipation coefficient decreases. The variation in the three coefficients is more significant in deep water than in shallower water.
A Coupled Artificial Compressibility Method for Free Surface Flows
Authors: Ntouras Dimitris , Papadakis George
Published: August 2020

Modeling free surface flows in a CFD context typically requires an incompressible approach along with a formulation to account for the air–water interface. Commonly, pressure-correction algorithms combined with the Volume of Fluid (VOF) method are used to describe these kinds of flows. Pressure-correction algorithms are segregated solvers, which means equations are solved in sequence until convergence is accomplished. On the contrary, the artificial compressibility (AC) method solves a single coupled system of equations. Solving at each timestep a single system of equations obviates the need for segregated algorithms, since all equations converge simultaneously. The goal of the present work is to combine the AC method with VOF formulation and prove its ability to account for unsteady flows of immiscible fluids. The presented system of equations has a hyperbolic nature in pseudo-time, thus the arsenal of the hyperbolic discretization process can be exploited. To this end, a thorough investigation of unsteady flows is presented to demonstrate the ability of the method to accurately describe unsteady flows. Problems of wave propagation on constant and variable bathymetry are considered, as well as a fluid structure interaction problem, where viscous effects have a significant impact on the motion of the structure. In all cases the results obtained are compared with theoretical or experimental data. The straightforward implementation of the method, as well as its accurate predictions, shows that AC method can be regarded as a suitable choice to account for free surface flows.
Blue Light Induced Edible Mushroom (Lentinula edodes) Proteomic Analysis
Authors: Park Youn Jin , Jang Myoung Jun
Published: August 2020

Blue light is an important environmental factor that induces mushroom growth and morphological changes. In this study, after confirming the morphological difference between Lentinula edodes (LE) under blue light condition (BL) and lightless condition (LL), the increase and decrease in LE protein and the expression of RNA of each protein were confirmed under each condition. LE specimens grown in BL and LL were identified by 253 spots in BL through 2D electrophoresis and LC-MSMS analysis, and 22 types of proteins were identified. It was confirmed that 14 types of proteins showed reduced expression in BL compared to LL. On the other hand, eight kinds of proteins with increased expression in blue light compared to LL were identified. As a result of confirming the difference from the expression pattern in 2D electrophoresis through Quantitative Real-Time PCR, it was confirmed that the expression pattern of the two proteins showed a difference. Therefore, this study will be a key study on the changes in mushroom morphology induced by blue light and the proteins that induce it.
Effects of Kinesiology Taping on Shoulder Posture and Peak Torque in Junior Baseball Players with Rounded Shoulder Posture: A Pilot Study
Authors: Yun Hyeong-geun , Lee Jung-Hoon , Choi Im-Rak
Published: August 2020

Rounded shoulder posture (RSP) causes an imbalance of the adjacent joints due to the malalignment of the shoulder joint, and thus affects the strength of the muscles surrounding the shoulder. This study aimed to investigate the effect of rounded shoulder taping (RST) on shoulder posture and muscle strength in junior baseball players. Nineteen junior baseball players participated in the study, which used a crossover design at an interval of 1 week. The participants were randomized to receive rounded shoulder taping (RST) and sham kinesiology taping (SKT) using kinesiology tape. RSP was measured using two 12-inch combination squares, and shoulder peak torques were measured by isokinetic equipment. The results showed that RST led to significant changes in RSP (p < 0.05), but no significant changes were observed with SKT (p < 0.05). RST led to significant changes in the peak torques of external rotation and internal rotation of the shoulder (p < 0.05), but no significant changes were observed with SKT (p < 0.05). These results suggest that RST could help to correct RSP and improve peak torque of external and internal rotation of the shoulders of junior baseball players with RSP.
Approximation Properties of Solutions of a Mean Value-Type Functional Inequality, II
Authors: Jung Soon-Mo , Lee Ki-Suk , Rassias Michael Th. , Yang Sung-Mo
Published: August 2020

Let X be a commutative normed algebra with a unit element e (or a normed field of characteristic different from 2), where the associated norm is sub-multiplicative. We prove the generalized Hyers-Ulam stability of a mean value-type functional equation, f(x)−g(y)=(x−y)h(sx+ty), where f,g,h:X→X are functions. The above mean value-type equation plays an important role in the mean value theorem and has an interesting property that characterizes the polynomials of degree at most one. We also prove the Hyers-Ulam stability of that functional equation under some additional conditions.
A Nonlinear Technical Indicator Selection Approach for Stock Markets. Application to the Chinese Stock Market
Authors: Alfonso Gerardo , Ramirez Daniel R.
Published: August 2020

In this paper we present a combinatorial nonlinear technical indicator approach for the identification of appropriate combinations of stock technical indicators as inputs in non-linear models. This approach is illustrated with the example of Chinese stock indexes and 35 different stock technical indicators using neural networks as the chosen non-linear method. Stock market technical indicators can generate contradictory signals regarding the future performance of the stock analyzed. Furthermore, some non-linear methods, such as neural networks, can have poor generalization power when dealing with problems of high dimensionality due to the issue of local minima. Therefore, non-linear approaches that can identify appropriate combinations of input variables are of clear importance. It will be shown that the proposed approach, when using neural networks as classifiers, generates error rates lower than those using directly neural networks without dimensionality reduction. It will also be shown that merely increasing the number of neurons does not increase the accuracy. The approach proposed in this article is illustrated with an application to the stock market using neural networks but it could be applied to other fields and it can also be used with other non-linear techniques such as for instance support vector machines.
Common Attractive Points of Generalized Hybrid Multi-Valued Mappings and Applications
Authors: Chen Lili , Yang Ni , Zhou Jing
Published: August 2020

In this paper, we first propose the concepts of (ζ,η,λ,π)-generalized hybrid multi-valued mappings, the set of all the common attractive points (CAf,g) and the set of all the common strongly attractive points (CsAf,g), respectively for the multi-valued mappings f and g in a CAT(0) space. Moreover, we give some elementary properties in regard to the sets Af, Ff and CAf,g for the multi-valued mappings f and g in a complete CAT(0) space. Furthermore, we present a weak convergence theorem of common attractive points for two (ζ,η,λ,π)-generalized hybrid multi-valued mappings in the above space by virtue of Banach limits technique and Ishikawa iteration respectively. Finally, we prove strong convergence of a new viscosity approximation method for two (ζ,η,λ,π)-generalized hybrid multi-valued mappings in CAT(0) spaces, which also solves a kind of variational inequality problem.
Improvement of the Crack Propagation Resistance in an α + β Titanium Alloy with a Trimodal Microstructure
Authors: Tan Changsheng , Fan Yiduo , Sun Qiaoyan , Zhang Guojun
Published: August 2020

The roles of microstructure in plastic deformation and crack growth mechanisms of a titanium alloy with a trimodal microstructure have been systematically investigated. The results show that thick intragranular α lath and a small number of equiaxed α phases avoid the nucleation of cracks at the grain boundary, resulting in branching and fluctuation of cracks. Based on electron back-scattered diffraction, the strain partition and plastic deformation ahead of the crack tip were observed and analyzed in detail. Due to the toughening effect of the softer equiaxed α phase at the grain boundary, crack arresting and blunting are prevalent, improving the crack growth resistance and generating a relatively superior fracture toughness performance. These results indicate that a small amount of large globular α phases is beneficial to increase the crack propagation resistance and, thus, a good combination of mechanical property is obtained in the trimodal microstructure.
Prediction and Control Technology of Stainless Steel Quarter Buckle in Hot Rolling
Authors: Li Hui , Yao Chihuan , Shao Jian , He Anrui , Zhou Zhou , Li Weigang
Published: August 2020

To obtain the good flatness of hot-rolled stainless-steel strips, high-precision shape control has always been the focus of research. In hot rolling, the quadratic wave (centre buckle and edge wave) can usually be controlled effectively. However, the quarter buckle of the strip is still a challenge to solve. In this paper, a prediction model of roll deflection and material flow is established to study the change rule and control technology of the quarter buckle. The effects of the process parameters on the quarter buckle are analysed quantitatively. The process parameters affect the quarter buckle and the quadratic wave simultaneously. This coupling makes the control of the quarter buckle difficult. The distribution of lateral temperature and the quartic crown of the strip have less effect on the quadratic wave but have a great effect on the quarter buckle. Finally, a new technology for work roll contour is developed to improve the quarter buckle. Through industrial application, the model and the new contour are proved to be effective.
A Multilevel Bayesian Approach to Improve Effect Size Estimation in Regression Modeling of Metabolomics Data Utilizing Imputation with Uncertainty
Authors: Gillies Christopher E. , Jennaro Theodore S. , Puskarich Michael A. , Sharma Ruchi , Ward Kevin R. , Fan Xudong , Jones Alan E. , Stringer Kathleen A.
Published: August 2020

To ensure scientific reproducibility of metabolomics data, alternative statistical methods are needed. A paradigm shift away from the p-value toward an embracement of uncertainty and interval estimation of a metabolite’s true effect size may lead to improved study design and greater reproducibility. Multilevel Bayesian models are one approach that offer the added opportunity of incorporating imputed value uncertainty when missing data are present. We designed simulations of metabolomics data to compare multilevel Bayesian models to standard logistic regression with corrections for multiple hypothesis testing. Our simulations altered the sample size and the fraction of significant metabolites truly different between two outcome groups. We then introduced missingness to further assess model performance. Across simulations, the multilevel Bayesian approach more accurately estimated the effect size of metabolites that were significantly different between groups. Bayesian models also had greater power and mitigated the false discovery rate. In the presence of increased missing data, Bayesian models were able to accurately impute the true concentration and incorporating the uncertainty of these estimates improved overall prediction. In summary, our simulations demonstrate that a multilevel Bayesian approach accurately quantifies the estimated effect size of metabolite predictors in regression modeling, particularly in the presence of missing data.
Promoter Architecture and Promoter Engineering in Saccharomyces cerevisiae
Authors: Tang Hongting , Wu Yanling , Deng Jiliang , Chen Nanzhu , Zheng Zhaohui , Wei Yongjun , Luo Xiaozhou , Keasling Jay D.
Published: August 2020

Promoters play an essential role in the regulation of gene expression for fine-tuning genetic circuits and metabolic pathways in Saccharomyces cerevisiae (S. cerevisiae). However, native promoters in S. cerevisiae have several limitations which hinder their applications in metabolic engineering. These limitations include an inadequate number of well-characterized promoters, poor dynamic range, and insufficient orthogonality to endogenous regulations. Therefore, it is necessary to perform promoter engineering to create synthetic promoters with better properties. Here, we review recent advances related to promoter architecture, promoter engineering and synthetic promoter applications in S. cerevisiae. We also provide a perspective of future directions in this field with an emphasis on the recent advances of machine learning based promoter designs.
Spoilage of Chilled Fresh Meat Products during Storage: A Quantitative Analysis of Literature Data
Authors: Luong Ngoc-Du Martin , Coroller Louis , Zagorec Monique , Membré Jeanne-Marie , Guillou Sandrine
Published: August 2020

A literature search was performed on spoilage of fresh meat products by combining keyword query, text mining and expert elicitation. From the 258 collected studies, a quantitative analysis was first performed to identify the methods which are the most used to evaluate spoilage beside the preservation strategies suggested. In a second step focusing on a subset of 24 publications providing quantitative data on spoilage occurrence time, associations between spoilage occurrence time of meat products and specific spoilage indicators were investigated. The analysis especially focused on factors well represented in the 24 publications, i.e., gas packaging (O2 and CO2) and storage temperature. Relationships between spoilage occurrence and several microbiological indicators were also sought. The results point out possible advantages of removing dioxygen in packaging to delay spoilage occurrence, whereas, in the presence of dioxygen, the carbon dioxide proportion in the gas mixtures was shown to influence spoilage occurrence. The collected data clearly reveal a potentially protective role of lactic acid bacteria. Besides, while a spoilage role could be attributed to Pseudomonas spp., the growth of mesophilic aerobic microbes, Brochothrix spp. and Enterobacteriaceae seemed independent of spoilage occurrence time.
Cu Nanoparticle-Loaded Nanovesicles with Antibiofilm Properties. Part I: Synthesis of New Hybrid Nanostructures
Authors: Sarcina Lucia , García-Manrique Pablo , Gutiérrez Gemma , Ditaranto Nicoletta , Cioffi Nicola , Matos Maria , Blanco-López Maria del Carmen
Published: August 2020

Copper nanoparticles (CuNPs) stabilized by quaternary ammonium salts are well known as antimicrobial agents. The aim of this work was to study the feasibility of the inclusion of CuNPs in nanovesicular systems. Liposomes are nanovesicles (NVs) made with phospholipids and are traditionally used as delivery vehicles because phospholipids favor cellular uptake. Their capacity for hydrophilic/hydrophobic balance and carrier capacity could be advantageous to prepare novel hybrid nanostructures based on metal NPs (Me-NPs). In this work, NVs were loaded with CuNPs, which have been reported to have a biofilm inhibition effect. These hybrid materials could improve the effect of conventional antibacterial agents. CuNPs were electro-synthesized by the sacrificial anode electrolysis technique in organic media and characterized in terms of morphology through transmission electron microscopy (TEM). The NVs were prepared by the thin film hydration method in aqueous media, using phosphatidylcholine (PC) and cholesterol as a membrane stabilizer. The nanohybrid systems were purified to remove non-encapsulated NPs. The size distribution, morphology and stability of the NV systems were studied. Different quaternary ammonium salts in vesicular systems made of PC were tested as stabilizing surfactants for the synthesis and inclusion of CuNPs. The entrapment of charged metal NPs was demonstrated. NPs attached preferably to the membrane, probably due to the attraction of their hydrophobic shell to the phospholipid bilayers. The high affinity between benzyl-dimethyl-hexadecyl-ammonium chloride (BDHAC) and PC allowed us to obtain stable hybrid NVs c.a. 700 nm in diameter. The stability of liposomes increased with NP loading, suggesting a charge-stabilization effect in a novel antibiofilm nanohybrid material.
Field Experience of Antibody Testing against Mycoplasma bovis in Adult Cows in Commercial Danish Dairy Cattle Herds
Authors: Petersen Mette Bisgaard , Pedersen Lars , Pedersen Lone Møller , Nielsen Liza Rosenbaum
Published: August 2020

Mycoplasma bovis in cattle is difficult to diagnose. Recently, the ID screen® mycoplasma bovis indirect ELISA (ID screen) was commercially released by IDVet. The objectives of this study were to: (1) gain and share experience of using the ID screen in adult dairy cows under field conditions; (2) determine the correlation between antibody levels in milk and serum and (3) compare the ID screen results with those of the Bio K 302 (BioX 302) ELISA from BioX Diagnostics. Paired serum and milk samples were collected from 270 cows from 12 Danish dairy herds with three categories of M. bovis disease history. The ID screen tested nearly all cows positive in all, but the three non-infected herds, while the BioX 302 tested very few cows positive. The ID screen is therefore a much more sensitive test than the BioX 302. However, cows in five exposed herds without signs of ongoing infection and two herds with no history of M. bovis infection also tested ID screen positive. Therefore, the performance and interpretation of the test must be investigated under field conditions in best practice test evaluation setups. A concordance correlation coefficient of 0.66 (95% CI: 0.59–0.72) between the ID screen serum and milk results indicates that milk samples can replace serum samples for the ID screen diagnosis of M. bovis in adult cows.
Characterization of Cutaneous Bacterial Microbiota from Superficial Pyoderma Forms in Atopic Dogs
Authors: Older Caitlin E. , Rodrigues Hoffmann Aline , Hoover Kathleen , Banovic Frane
Published: August 2020

Although Staphylococcus pseudintermedius is considered the major pathogen associated with superficial canine pyoderma, no study has investigated the entire bacterial community in these lesions with molecular techniques. The objectives of this study were to characterize the bacterial microbiota in two forms of superficial canine pyoderma lesions, superficial bacterial folliculitis (SBF) and epidermal collarette (EC), especially in terms of the staphylococcal community. Swabs from 12 SBF and 9 EC lesions were obtained from eight and six atopic dogs, respectively. Eight samples from the axilla and groin of four healthy dogs served as controls. DNA was extracted for 16S rRNA gene sequencing and quantitative polymerase chain reaction of Staphylococcus spp. and S. pseudintermedius. Healthy skin samples harbored significantly more diverse bacterial communities than pyoderma samples. Healthy samples had communities that were more similar to each other, and were distinct from pyoderma samples. Staphylococcus spp. abundance was increased in pyoderma samples, especially those from EC samples. Although determining species-level identities of staphylococcal sequences revealed many species, S. pseudintermedius was the primary staphylococcal species found in all sample types. As expected, there are many differences in the microbiota when comparing healthy and canine pyoderma lesions samples. These lesions do not seem to be associated with a change in the relative abundance of specific Staphylococcus species, but simply an overall increase in Staphylococcus spp. abundance. The results of this study provide a starting point for future studies investigating how antimicrobial treatments may further change the microbiota associated with these lesions.
What Room for Two-Dimensional Gel-Based Proteomics in a Shotgun Proteomics World?
Authors: Marcus Katrin , Lelong Cécile , Rabilloud Thierry
Published: August 2020

Two-dimensional gel electrophoresis was instrumental in the birth of proteomics in the late 1980s. However, it is now often considered as an outdated technique for proteomics—a thing of the past. Although this opinion may be true for some biological questions, e.g., when analysis depth is of critical importance, for many others, two-dimensional gel electrophoresis-based proteomics still has a lot to offer. This is because of its robustness, its ability to separate proteoforms, and its easy interface with many powerful biochemistry techniques (including western blotting). This paper reviews where and why two-dimensional gel electrophoresis-based proteomics can still be profitably used. It emerges that, rather than being a thing of the past, two-dimensional gel electrophoresis-based proteomics is still highly valuable for many studies. Thus, its use cannot be dismissed on simple fashion arguments and, as usual, in science, the tree is to be judged by the fruit.
Decision Algorithm for the Automatic Determination of the Use of Non-Inclusive Terms in Academic Texts
Authors: Orgeira-Crespo Pedro , Míguez-Álvarez Carla , Cuevas-Alonso Miguel , Doval-Ruiz María Isabel
Published: August 2020

The use of inclusive language, among many other gender equality initiatives in society, has garnered great attention in recent years. Gender equality offices in universities and public administration cannot cope with the task of manually checking the use of non-inclusive language in the documentation that those institutions generate. In this research, an automated solution for the detection of non-inclusive uses of the Spanish language in doctoral theses generated in Spanish universities is introduced using machine learning techniques. A large dataset has been used to train, validate, and analyze the use of inclusive language; the result is an algorithm that detects, within any Spanish text document, non-inclusive uses of the language with error, false positive, and false negative ratios slightly over 10%, and precision, recall, and F-measure percentages over 86%. Results also show the evolution with time of the ratio of non-inclusive usages per document, having a pronounced reduction in the last years under study.
Islamic Studies in Australian Islamic Schools: Learner Voice
Authors: Abdalla Mohamad , Chown Dylan , Memon Nadeem
Published: August 2020

This paper provides insight into senior secondary learners’ views on Islamic Studies (IS) in three large Australian Islamic schools. This study offers a ‘dialogic alternative’ of ‘speaking with’ rather than ‘speaking for’ learners in Islamic educational research, planning, and renewal within K-12 Islamic schools. The study privileges learners’ voice and enables an insight to their experience with one of the most important features of Islamic schools—Islamic Studies. Using phenomenology as a methodological framework, learner voice was elicited through focus groups where 75 learners (years 10, 11, and 12) provided information describing their experience with Islamic Studies. Thematic content analysis of the textual data suggests that learners’ dissatisfaction far outweighs their satisfaction with Islamic Studies. The findings of this paper can benefit Islamic schools in Australia and other Western contexts.
A Comparison of SSEBop-Model-Based Evapotranspiration with Eight Evapotranspiration Products in the Yellow River Basin, China
Authors: Yin Lichang , Wang Xiaofeng , Feng Xiaoming , Fu Bojie , Chen Yongzhe
Published: August 2020

Accurate evapotranspiration (ET) estimation is important in understanding the hydrological cycle and improving water resource management. The operational simplified surface energy balance (SSEBop) model can be set up quickly for the routine monitoring of ET. Several studies have suggested that the SSEBop model, which can simulate ET, has performed inconsistently across the United States. There are few detailed studies on the evaluation of ET simulated by SSEBop in other regions. To explore the potential and application scope of the SSEBop model, more evaluation of the ET simulated by SSEBop is clearly needed. We calculated the SSEBop-model-based ET (ETSSEBopYRB) with land surface temperature product of MOD11A2 and climate variables as inputs for the Yellow River Basin (YRB), China. We also compared the ETSSEBopYRB with eight coarse resolution ET products, including China ETMTE, produced using the upscaling energy flux method; China ETCR, which is generated using the non-linear complementary relationship model; three global products based on the Penman–Monteith logic (ETPMLv2, ETMODIS, and ETBESS), two global ET products based on the surface energy balance (ETSEBS, ETSSEBopGlo), and integrated ET products based on the Bayesian model averaging method (ETGLASS), using the annual ET data derived from the water balance method (WB-ET) for fourteen catchments. We found that ETSSEBopYRB and the other eight ET products were able to explain 23 to 52% of the variability in the water balance ET for fourteen small catchments in the YRB. ETSSEBopYRB had a better agreement with WB-ET than ETSEBS, ETMODIS, ETCR, and ETGLASS, with lower RMSE (88.3 mm yr−1 vs. 121.7 mm yr−1), higher R2 (0.49 vs. 0.43), and lower absolute RPE (−3.3% vs. –19.9%) values for the years 2003–2015. We also found that the uncertainties of the spatial patterns of the average annual ET values and the ET trends were still large for different ET products. Third, we found that the free global ET product derived from the SSEBop model (ETSSEBopGlo) highly underestimated the annual total ET trend for the YRB. The poor performance of the land surface temperature product of MOD11A2 in 2015 caused the large ETSSEBopYRB uncertainty at eight-day and monthly scales. Further evaluation of ET based on the SSEBop model for site measurements is needed.
Monitoring Approach for Tropical Coniferous Forest Degradation Using Remote Sensing and Field Data
Authors: Duarte Efraín , Barrera Juan A. , Dube Francis , Casco Fabio , Hernández Alexander J. , Zagal Erick
Published: August 2020

Current estimates of CO2 emissions from forest degradation are generally based on insufficient information and are characterized by high uncertainty, while a global definition of ‘forest degradation’ is currently being discussed in the scientific arena. This study proposes an automated approach to monitor degradation using a Landsat time series. The methodology was developed using the Google Earth Engine (GEE) and applied in a pine forest area of the Dominican Republic. Land cover change mapping was conducted using the random forest (RF) algorithm and resulted in a cumulative overall accuracy of 92.8%. Forest degradation was mapped with a 70.7% user accuracy and a 91.3% producer accuracy. Estimates of the degraded area had a margin of error of 10.8%. A number of 344 Landsat collections, corresponding to the period from 1990 to 2018, were used in the analysis. Additionally, 51 sample plots from a forest inventory were used. The carbon stocks and emissions from forest degradation were estimated using the RF algorithm with an R2 of 0.78. GEE proved to be an appropriate tool to monitor the degradation of tropical forests, and the methodology developed herein is a robust, reliable, and replicable tool that could be used to estimate forest degradation and improve monitoring, reporting, and verification (MRV) systems under the reducing emissions from deforestation and forest degradation (REDD+) mechanism.
Pay for Individual Performance: Aiding or Harming Sustainable Intrinsic Motivation?
Authors: Cabanas Sara , Proença Teresa , Carozzo-Todaro Mauro
Published: August 2020

This study aims to understand the effect of pay for individual performance (PFIP) on employees’ intrinsic motivation. Although several studies have analyzed this relationship, until now, the role of satisfaction with variable rewards has not been considered. It was hypothesized that employees who are satisfied with variable rewards would find in PFIP a source of feedback that would contribute to the satisfaction of their basic psychological needs. An empirical study was conducted with 184 professionals working in human resource consulting firms. Data were collected using an online survey, and the PROCESS macro for SPSS was used to analyze the proposed hypotheses. The results indicate that, in this context, PFIP has a direct positive effect on intrinsic motivation. It also has an indirect positive effect, which is partially and sequentially mediated by satisfaction with variable rewards and satisfaction of basic psychological needs. Employers should emphasize the informational nature of rewards, and also seek alignment between the objectives of the compensation system and employee expectations and values. The present findings broaden our understanding of how a PFIP system influences a sustainable intrinsic motivation.