bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Mass Spectrometry-Based Panel of Nine Thyroid Hormone Metabolites in Human Serum
Authors: Jongejan Rutchanna M S , Klein Theo , Meima Marcel E , Visser W Edward , van Heerebeek Ramona E A , Luider Theo M , Peeters Robin P , de Rijke Yolanda B 
Published: January 2020

Abstract

Background
While thyroxine (T4), 3,3’,5-triiodothyronine (T3), and 3,3’,5’-triiodothyronine (rT3) have routine methods available for evaluating patients with suspected thyroid disease, appropriate methods for the measurement of other thyroid hormone metabolites (THMs) are lacking. The effects of other iodothyronines or iodothyroacetic acids are therefore less explored. To better understand the (patho)physiological role of THMs, a robust method to measure iodothyronines and iodothyroacetic acids in serum in a single analysis is needed, including associated reference intervals.

Methods
Clinical and Laboratory Standards Institute guidelines, European Medicines Agency guidelines, and the National Institute of Standards and Technology protocol were used for the method validation and reference intervals. Reference intervals were determined in 132 healthy males and 121 healthy females. Serum samples were deproteinized with acetonitrile, followed by anion-exchange solid phase extraction and analysis with LC-MS/MS, using eight 13C6-internal standards

Results
The analytical method validation was performed for all nine THMs. Reference intervals (2.5th to 97.5th percentile) were determined for L-thyronine (4.9–11.3 ng/dL), 3-monoiodothyronine (0.06 --0.41 ng/dL), 3,5-diiodothyronine (&lt;0.13 ng/dL), 3,3’-diiodothyronine (0.25--0.77 ng/dL), T3 (66.4--129.9 ng/dL), rT3 (15.0--64.1 ng/dL), T4 (4.3--10.0 µg/dL), triac/3,3’,5-triiodothyroacetic acid (not detected), and tetrac/3,3’,5,5’-tetraiodothyroacetic acid (2.2--27.2 ng/dL).

Conclusions
A broad dynamic concentration range exists among the nine THMs. This method should help to develop a better understanding of the clinical relevance of other THMs, as well as an understanding of thyroid hormone metabolism in health and disease.
MapReduce and Optimized Deep Network for Rainfall Prediction in Agriculture
Authors: S Oswalt Manoj , J P Ananth 
Published: January 2020

Abstract
Rainfall prediction is the active area of research as it enables the farmers to move with the effective decision-making regarding agriculture in both cultivation and irrigation. The existing prediction models are scary as the prediction of rainfall depended on three major factors including the humidity, rainfall and rainfall recorded in the previous years, which resulted in huge time consumption and leveraged huge computational efforts associated with the analysis. Thus, this paper introduces the rainfall prediction model based on the deep learning network, convolutional long short-term memory (convLSTM) system, which promises a prediction based on the spatial-temporal patterns. The weights of the convLSTM are tuned optimally using the proposed Salp-stochastic gradient descent algorithm (S-SGD), which is the integration of Salp swarm algorithm (SSA) in the stochastic gradient descent (SGD) algorithm in order to facilitate the global optimal tuning of the weights and to assure a better prediction accuracy. On the other hand, the proposed deep learning framework is built in the MapReduce framework that enables the effective handling of the big data. The analysis using the rainfall prediction database reveals that the proposed model acquired the minimal mean square error (MSE) and percentage root mean square difference (PRD) of 0.001 and 0.0021.
The transcriptome of Escherichia coli O157: H7 reveals a role for oxidative stress resistance in its survival from predation by Tetrahymena
Authors: George Andree Sherlon , Rehfuss Marc Yi Ming , Parker Craig Thomas , Brandl Maria Theresa 
Published: January 2020

ABSTRACTPathogenic E. coli remains undigested upon phagocytosis by Tetrahymena and is egested from the ciliate as viable cells in its fecal pellets. Factors that are involved in the survival of Shiga toxin-producing E. coli serovar O157: H7 (EcO157) from digestion by Tetrahymena were identified by microarray analysis of its transcriptome in the protozoan phagosome. Numerous genes belonging to anaerobic metabolism and various stress responses were upregulated significantly ≥ 2-fold in EcO157 cells in the food vacuoles compared with in planktonic cells that remained uningested by the protist. Among these were the oxidative stress response genes, ahpF and katG. Fluorescence microscopy and staining with CellROX® Orange confirmed the presence of reactive oxygen species in food vacuoles containing EcO157 cells. Frequency distribution analysis of the percentage of EcO157 viable cells in Tetrahymena fecal pellets revealed that the ΔahpCF and ΔahpCFΔkatG mutants were less fit than the wild type strain and ΔkatG mutant after passage through the protist. Given the broad use of oxidants as sanitizers in the food industry, our observation of the oxidative stress response in EcO157 during its interaction with Tetrahymena emphasizes the importance of furthering our knowledge of the physiology of this human pathogen in environments relevant to its ecology and to food safety.
Optimizing Small World Initiative service learning by focusing on antibiotics-producing actinomycetes from soil
Authors: de Groot Piet W J , Fernández-Pereira Jordan , Sabariegos Rosario , Clemente-Casares Pilar , Parra-Martínez Javier , Cid Víctor J , Moreno Diego A 
Published: January 2020

ABSTRACT
Small World Initiative and Tiny Earth are popular citizen science programs that are implemented worldwide in response to the global antibiotic resistance crisis. When starting up the program in Albacete (Spain), we noted that rates of isolated antibiotic-producing bacteria are generally low. To make the activity more stimulating for participating students, we modified the protocol to obtain more positive results by focusing on isolation of actinomycetes, the main producers of most clinically used antibiotics. Adaptations involved redesigning culture media, incubation times and temperatures, and modification of the ESKAPE antibiosis experiment by employing an agar-transplantation step. Of 390 bacterial isolates tested, almost 6% tested positive in antibiosis experiments and DNA sequence analysis confirmed that all positives are actinomycetes, demonstrating that our protocol is efficient toward isolating antibiotic-producing actinomycetes from soil. Evaluation forms filled by participating students indicated that the program was received very positively and that our modifications contribute to make this educational program more stimulating and efficient.
Dynamic Evolution of the Cthrc1 Genes, a Newly Defined Collagen-Like Family
Authors: Leclère Lucas , Nir Tal S , Bazarsky Michael , Braitbard Merav , Schneidman-Duhovny Dina , Gat Uri 
Published: January 2020

Abstract
Collagen triple helix repeat containing protein 1 (Cthrc1) is a secreted glycoprotein reported to regulate collagen deposition and to be linked to the Transforming growth factor β/Bone morphogenetic protein and the Wnt/planar cell polarity pathways. It was first identified as being induced upon injury to rat arteries and was found to be highly expressed in multiple human cancer types. Here, we explore the phylogenetic and evolutionary trends of this metazoan gene family, previously studied only in vertebrates. We identify Cthrc1 orthologs in two distant cnidarian species, the sea anemone Nematostella vectensis and the hydrozoan Clytia hemisphaerica, both of which harbor multiple copies of this gene. We find that Cthrc1 clade-specific diversification occurred multiple times in cnidarians as well as in most metazoan clades where we detected this gene. Many other groups, such as arthropods and nematodes, have entirely lost this gene family. Most vertebrates display a single highly conserved gene, and we show that the sequence evolutionary rate of Cthrc1 drastically decreased within the gnathostome lineage. Interestingly, this reduction coincided with the origin of its conserved upstream neighboring gene, Frizzled 6 (FZD6), which in mice has been shown to functionally interact with Cthrc1. Structural modeling methods further reveal that the yet uncharacterized C-terminal domain of Cthrc1 is similar in structure to the globular C1q superfamily domain, also found in the C-termini of collagens VIII and X. Thus, our studies show that the Cthrc1 genes are a collagen-like family with a variable short collagen triple helix domain and a highly conserved C-terminal domain structure resembling the C1q family.
Maximum Likelihood Estimation of Species Trees from Gene Trees in the Presence of Ancestral Population Structure
Authors: Koch Hillary , DeGiorgio Michael 
Published: January 2020

AbstractThough large multilocus genomic data sets have led to overall improvements in phylogenetic inference, they have posed the new challenge of addressing conflicting signals across the genome. In particular, ancestral population structure, which has been uncovered in a number of diverse species, can skew gene tree frequencies, thereby hindering the performance of species tree estimators. Here we develop a novel maximum likelihood method, termed TASTI (Taxa with Ancestral structure Species Tree Inference), that can infer phylogenies under such scenarios, and find that it has increasing accuracy with increasing numbers of input gene trees, contrasting with the relatively poor performances of methods not tailored for ancestral structure. Moreover, we propose a supertree approach that allows TASTI to scale computationally with increasing numbers of input taxa. We use genetic simulations to assess TASTI’s performance in the three- and four-taxon settings and demonstrate the application of TASTI on a six-species Afrotropical mosquito data set. Finally, we have implemented TASTI in an open-source software package for ease of use by the scientific community.
Alternative techniques of right ventricular outflow tract reconstruction for surgical repair of truncus arteriosus
Authors: Padalino Massimo A , Çelmeta Bleri , Vedovelli Luca , Castaldi Biagio , Vida Vladimiro L , Stellin Giovanni 
Published: January 2020

Abstract

OBJECTIVES
This study aimed to evaluate the outcomes and feasibility of different techniques of reconstruction of the right ventricular outflow tract (RVOT) in surgical repair of truncus arteriosus.

METHODS
We retrospectively reviewed all consecutive patients with truncus arteriosus who underwent successful surgical repair in our centre between 1994 and 2017. We analysed late results according to the type of RVOT repair.

RESULTS
We collected data from 29 survivors after truncus arteriosus repair. Six (20%) of them were affected by DiGeorge syndrome. The RVOT reconstruction was achieved using a valved conduit in 58.6%, while a direct right ventricle–pulmonary artery (RV–PA) anastomosis, with or without the interposition of the left atrial appendage, was performed in the remaining. At a median follow-up time of 7.9 years (interquartile range 1.8–13.1), 6 patients (3 affected by DiGeorge syndrome) died. Between the 2 groups, there were no differences in terms of the late mortality and onset of adverse events. However, the use of a conduit seemed more prone to reintervention and onset of adverse events.

CONCLUSIONS
Different RVOT reconstruction techniques are safe and have similar late outcomes. However, use of a direct RV–PA anastomosis and left atrial appendage interposition may reduce the need for reoperation in the long term.
The Groupoids of Adaptable Separated Graphs and Their Type Semigroups
Authors: Ara Pere , Bosa Joan , Pardo Enrique , Sims Aidan 
Published: January 2020

AbstractGiven an adaptable separated graph, we construct an associated groupoid and explore its type semigroup. Specifically, we first attach to each adaptable separated graph a corresponding semigroup, which we prove is an $E^*$-unitary inverse semigroup. As a consequence, the tight groupoid of this semigroup is a Hausdorff étale groupoid. We show that this groupoid is always amenable and that the type semigroups of groupoids obtained from adaptable separated graphs in this way include all finitely generated conical refinement monoids. The first three named authors will utilize this construction in forthcoming work to solve the realization problem for von Neumann regular rings, in the finitely generated case.
Multiplex gene transfer by genetic transformation between isolated S. pneumoniae cells confined in microfluidic droplets
Authors: Lam Trinh , Maienschein-Cline Mark , Eddington David T , Morrison Donald A 
Published: January 2020

Abstract
Gene exchange via genetic transformation makes major contributions to antibiotic resistance of the human pathogen, Streptococcus pneumoniae (pneumococcus). The transfers begin when a pneumococcal cell, in a transient specialized physiological state called competence, attacks and lyses another cell, takes up fragments of the liberated DNA, and integrates divergent genes into its genome. Recently, it has been demonstrated that the pneumococcal cells can be enclosed in femtoliter-scale droplets for study of the transformation mechanism, offering the ability to characterize individual cell–cell interactions and overcome the limitations of current methods involving bulk mixed cultures. To determine the relevance and reliability of this new method for study of bacterial genetic transformation, we compared recombination events occurring in 44 recombinants recovered after competence-mediated gene exchange between pairs of cells confined in femtoliter-scale droplets vs. those occurring in exchanges in parallel bulk culture mixtures. The pattern of recombination events in both contexts exhibited the hallmarks of the macro-recombination exchanges previously observed within the more complex natural contexts of biofilms and long-term evolution in the human host.
High glucose inhibits osteogenic differentiation of bone marrow mesenchymal stem cells via regulating miR-493-5p/ZEB2 signalling
Authors: Zhai Zhongshu , Chen Wanhong , Hu Qiaosheng , Wang Xin , Zhao Qing , Tuerxunyiming Muhadasi 
Published: January 2020

Abstract
Diabetic osteoporosis (DOP) is attributed to the aberrant physiological function of bone marrow mesenchymal stem cells (BMSCs) under high glucose (HG) environment. MicroRNAs (miRNAs) are involved in the pathological processes of DOP. We aimed to explore the underlying mechanism of miRNA in DOP. BMSCs were cultured in osteogenic medium with HG to induce osteogenic differentiation, and the interaction between miR-493-5p and ZEB2 was assessed by luciferase assay. Herein, we found miR-493-5p is gradually reduced during osteogenic differentiation in BMSCs. HG treatment inhibits osteogenic differentiation and induces an up-regulation of miR-493-5p leading to reduced level of its downstream target ZEB2. Inhibition of miR-493-5p attenuates HG-induced osteogenic differentiation defects by upregulation of ZEB2. Mechanistically, miR-493-5p/ZEB2 signalling mediates HG-inhibited osteogenic differentiation by inactivation of Wnt/β-catenin signalling. More importantly, knockdown of miR-493-5p therapeutically alleviated the DOP condition in mice. HG prevents BMSCs osteogenic differentiation via up-regulation of miR-493-5p, which results in reduced level of ZEB2 by directly targeting its 3′-untranslated region of mRNA. Thus, miR-493-5p/ZEB2 is a potential therapeutic target and provides novel strategy for the treatment and management of DOP.
CFD analysis of flashing flow in two-phase geothermal turbine design
Authors: Rane Sham , He Li 
Published: January 2020

Abstract
A thermal power plant for the East African Rift countries is under study for combined energy and freshwater generation using geothermal water, available at above 500 kPa pressure and temperature exceeding 150°C. This article presents the computational fluid dynamics (CFD) model and analysis of the two-phase turbine used for power generation in this total flow thermal plant. Flash boiling was implemented using a two-fluid multiphase model with the thermal phase-change criteria for heat, mass, and momentum transfer in the CFD solver ANSYS CFX. Initially, flashing flow in a converging–diverging nozzle was validated. This stationary nozzle model was then extended to a curved rotating nozzle reaction turbine and the results of flow and power were evaluated against available test data at 400 kPa feed water pressure under subcooled condition of 117°C and a very low backpressure of 6 kPa. Flow through this turbine was predicted within 8% deviation. An overestimate in thermodynamic power by 30–50% was predicted at speeds below 4000 rpm, while at the design speed of 4623 rpm the deviation was less than 5%. Rotor torque and hence power estimate was found to be dependent on the bubble size, bubble number density, and heat transfer parameters prescribed in the CFD model. The vapour dryness fraction at turbine exit was close to an isentropic expansion vapour quality. The isentropic efficiency was 7.5–17% for the analysed speed range.
Mass Rearing, Quality Parameters, and Bioconversion in Drosophila suzukii (Diptera: Drosophilidae) for Sterile Insect Technique Purposes
Authors: Aceituno-Medina Marysol , Ordoñez Alicia , Carrasco Morfa , Montoya Pablo , Hernández Emilio 
Published: January 2020

AbstractThe spotted wing drosophila, Drosophila suzukii Matsumura, has emerged as a major invasive insect pest of small and stone fruits in both the Americas and Europe in the last decade. Females oviposit in ripening fruit, and significant economic losses can occur. Control measures are mainly associated with the use of pesticides, but the sterile insect technique (SIT), an ecologically friendly pest-specific method, could be used against this species. The objective of this study was to estimate the mass rearing, quality control parameters, and bioconversion using four artificial larval diets and their economic aspects oriented to the SIT application. Diets were based on the combination of coconut fiber, corncob powder, Brewer’s and Torula yeast and were used as oviposition substrate and larval development. We found that a life cycle is completed in 10.19 ± 0.35 d and that adults live an average of 33.67 ± 0.76 d. The highest number of pupae per gram of diet and the maximum bioconversion (6%) were associated with flies developed in the coconut fiber + Brewer’s yeast diet. Under our conditions, the establishment of D. suzukii required at least four generations. The use of 30 × 40 × 30 cm Plexiglas cages, each loaded with 5,000 adults and stocked with 500 g of coconut fiber and Brewer’s yeast diet distributed in 15 × 5 × 10 cm plastic trays with a diet layer 3-cm thick, allows a minimum production of 84,000 pupae of D. suzukii per day.
Effect of Tannic Acid on Nutrition and Activities of Detoxification Enzymes and Acetylcholinesterase of the Fall Webworm (Lepidoptera: Arctiidae)
Authors: Yuan Yufei , Li Lusha , Zhao Jingfen , Chen Min 
Published: January 2020

AbstractPlant tannins, polyphenolic plant secondary metabolites are involved in important chemical defense processes in plants. In this study, tannic acid was used as the standard of plant tannins to determine the effects on nutritional indices and activities of glutathione S-transferases (GSTs), cytochrome P450 monooxygenase (CYP450), carboxylesterase (CarE), and acetylcholinesterase (AChE) in fourth-instar larvae of Hyphantria cunea (Drury) by feeding on an artificial diet containing tannic acid under different treatments. We found that tannic acid significantly affected the digestive capacity and food utilization rate of H. cunea larvae. A tannic acid concentration of less than 2.0% promoted feeding and the utilization of undesirable food by H. cunea larvae, while inhibitory effects were observed at high concentrations (&gt;2.5%). Tannic acid had a significant effect on the activity of detoxification enzymes and AChE in H. cunea larvae in concentration-dependent and time-dependent manners (P &lt; 0.05). These results provide new insights into the potential mechanisms underlying detoxification in H. cunea larvae against tannic acid in host plants.
Adjuvant and neoadjuvant treatment for pancreatic adenocarcinoma
Authors: Motoi Fuyuhiko , Unno Michiaki 
Published: January 2020

Abstract
The prognosis of pancreatic adenocarcinoma is dismal. Hence, advances in multidisciplinary treatment strategies, including surgery, are urgently needed. Early recurrence of distant organ metastases suggests that there are occult metastases even in cases with resectable disease. Several randomized controlled trials on adjuvant chemotherapy have been conducted to prolong survival after resection. CONKO-001 study was the first to demonstrate significant improvement in disease-free survival after surgery with gemcitabine administration. The JASPAC-01 study showed the superiority of adjuvant S1 over gemcitabine in survival after resection. Based on the results, adjuvant S1 therapy is the prescribed standard of care in Japan. Recently, the PRODIGE 24/CCTG PA.6 study showed that survival of patients treated with a modified FOLFIRINOX regimen as adjuvant therapy was significantly longer than those treated with adjuvant gemcitabine therapy. Although the evidence from these trials on adjuvant chemotherapy have been the gold-standard treatment for curatively resected and fully recovered patients, resectable disease at diagnosis is not the status, resected disease after curative resection. Currently, neoadjuvant therapy is considered to be a promising alternative to surgery for pancreatic cancer. Although there are many reports regarding neoadjuvant chemoradiotherapy, so far there has been no solid evidence proving the advantage of this strategy versus standard up-front surgery. Newly obtained results from the Prep-02/JSAP05 randomized phase II/III study, comparing neoadjuvant therapy with up-front surgery, revealed significant improvement in overall survival with neoadjuvant chemotherapy by intention-to-treat analysis. Thus, neoadjuvant intervention might become a new standard strategy in cases undergoing planned resection for pancreatic cancer.
Professional employees and professional managers: conflicting logics, hybridity, and restratification
Authors: Adams Tracey L 
Published: January 2020

AbstractA plethora of studies have documented the changing nature of professional work and the organizations in which it takes place. Among the most documented trends are the emergence of managerial–professional hybrid workers and professional (re)stratification. Although the links between these two trends have been noted, their interconnections have not been fully explored. This article analyzes data from a mixed-methods study of professional engineers in Ontario, Canada, to explore the extent to which they experience conflicting logics, hybridity, resistance, and restratification. Findings indicate that many engineers could be classified as hybrid, as they see managerial roles as an extension of engineering. At the same time, many others see managers as oppositional to engineers, with different priorities. On the whole, there is evidence of restratification as the work experiences, professional attitudes, and responses to conflicting logics (hybridity or resistance) vary between managers and employees. This restratification has the potential to undermine professional unity.