bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biomass soft sensor for aPichia pastorisfed‐batch process based on phase detection and hybrid modeling
Authors: Brunner Vincent , Siegl Manuel , Geier Dominik , Becker Thomas 
Published: June 2020

AbstractA common control strategy for the production of recombinant proteins inPichia pastorisusing the alcohol oxidase 1 (AOX1) promotor is to separate the bioprocess into two main phases: biomass generation on glycerol and protein production via methanol induction. This study reports the establishment of a soft sensor for the prediction of biomass concentration that adapts automatically to these distinct phases. A hybrid approach combining mechanistic (carbon balance) and data‐driven modeling (multiple linear regression) is used for this purpose. The model parameters are dynamically adapted according to the current process phase using a multilevel phase detection algorithm. This algorithm is based on the online data of CO2in the off‐gas (absolute value and first derivative) and cumulative base feed. The evaluation of the model resulted in a mean relative prediction error of 5.52% andR²of .96 for the entire process. The resulting model was implemented as a soft sensor for the online monitoring of theP. pastorisbioprocess. The soft sensor can be used for quality control and as input to process control systems, for example, for methanol control.
Effect of abiotic stress on bioactive compound production in germinated brown rice
Authors: Nascimento Lucas Ávila do , Avila Bianca Pio , Colussi Rosana , Elias Moacir Cardoso 
Published: June 2020

AbstractBackground and objectivesThe objective of this study was to evaluate the effect of germination and various abiotic stresses on the technological, nutritional, and sensorial characteristics of brown rice. The seeds were soaked at 40°C and 30% humidity. The soaked seeds were allowed to germinate at 30°C for 36 hr in BOD chamber. The soaked rice grains were subjected to stress conditions in the last 4 hr of germination using saline (SBR/S), low temperature (4°C) (SBR/C), or a combination of saline and low temperature (SBR/B) and, after, it was analyzed the effect of germination and those abiotic stresses on the technological, nutritional, and sensorial characteristics of brown rice by the color parameters, texture profile, γ‐aminobutyric acid content, protein, and starch digestibilities.FindingsThe sprouted grains (SBR) were darker than the brown rice. The germinated rice grains exposed to cold stress were more resistant to crushing and chewing compared to grains exposed to salinity stress and those exposed to both cold and salinity stresses. Germination enhanced the γ‐aminobutyric acid (GABA) content and starch digestibility. The GABA content increased further, whereas the protein digestibility decreased in the germinated grains upon exposure to abiotic stresses.ConclusionsThe best conditions for germination and alternative processes that can help them to intensify the nutritional value of germinated grains must be elucidated. The results of this study were satisfactory for the nutritional and technological parameters, and thus, exposure of germinated grains to abiotic stress can be an alternative method for enriched rice production.Significance and noveltyColor and texture parameters change with germination and vary according to abiotic stresses. For the same reason, the content of GABA is increased. Protein digestibility is reduced, differently about the starch digestibility.
A case of secretory carcinoma of the submandibular gland with unusual immunohistochemical staining
Authors: Karabachev Alexander , Aulet Ricardo , Sajisevi Mirabelle , Ciolino Allison 
Published: June 2020

AbstractMammaglobin negative secretory carcinoma may be overlooked. It is important to assess the possibility of diagnosis when histology is suggestive and immunohistochemical staining for S‐100 is positive even when staining for mammaglobin is negative.
Start‐Up Study on Biohydrogen from Palm Oil Mill Effluent in a Pilot‐Scale Reactor
Authors: Akhbari Azam , Chuen Onn Chiu , Zinatizadeh Ali Akbar , Ibrahim Shaliza 
Published: June 2020

AbstractA start‐up study for biohydrogen production from palm oil mill effluent (POME) is carried out in a pilot‐scale up‐flow anaerobic sludge blanket fixed‐film reactor (UASFF). A substrate with a chemical oxygen demand (COD) of 30 g L−1 is used, starting with molasses solution for 30 days and followed by a 10% v/v increment of POME/molasses ratio. At 100% POME, a hydrogen content of 80%, hydrogen production rate of 36 L H2 per day, and maximum COD removal of 48.7% are achieved. Bio‐kinetic coefficients of Monod, first‐order, Grau second‐order, and Stover‐Kincannon kinetic models are calculated to describe the performance of the system. The steady‐state data with 100% POME shows that Monod and Stover‐Kincannon models with bio‐kinetic coefficients of half‐velocity constant (Ks) of 6000 mg COD L−1, microbial decay rate (Kd) of 0.0015 per day, growth yield constant (Y) of 0.786 mg volatile suspended solids (VSS)/mg COD, specific biomass growth rate (μmax) of 0.568 per day, and substrate consumption rate of (Umax) 3.98 g/L day could be considered as superior models with correlation coefficients (R2) of 0.918 and 0.989, respectively, compared to first‐order and Grau's second‐order models with coefficients of K1 1.08 per day, R2 0.739, and K2s 1.69 per day, a = 7.0 per day, b = 0.847.
Influence of Protein Modification and Glycosylation in the Catalytic Hydrogen Evolution Reaction of Avidin and Neutravidin: An Electrochemical Analysis
Authors: Izadi Nasim , Černocká Hana , Trefulka Mojmír , Ostatná Veronika 
Published: June 2020

AbstractTo investigate glycans’ influence on the behavior of glycoproteins on charged surfaces, avidin and its nonglycosylated and neutralized version neutravidin were studied by label‐free chronopotentiometric stripping (CPS) analysis and alternating current voltammetry combined with a mercury electrode. Despite neutravidin's and avidin's similar size and structure, their CPS responses differed due to the different amounts of catalytically active free amino groups of lysine and arginine residues. Acetylation of the proteins resulted in the suppression of their CPS responses by almost four times for avidin and by about 50 % for neutravidin, respectively. On the other hand, the presence of glycans in the acetylated avidin induced about 30 % higher chronopotentiometric response compared to the acetylated neutravidin. We suggest that the presence, size and composition of the glycans influenced the CPS signal due to differences in the orientation at a charged surface. The obtained results can be utilized in glycoprotein research.
Root and axillary shoot development of hairy vetch stem cuttings and cessation of flower development under a short photoperiod
Authors: Wiering Nicholas , Gardner Gary , Sheaffer Craig C. , Ehlke Nancy J. 
Published: June 2020

AbstractClonal propagation is a valuable tool for plant breeders to maintain heterozygous genotypes in crop species that are not amenable to self‐pollination or apomixis. An example is the drought‐tolerant forage and N‐fixing cover crop hairy vetch (Vicia villosa Roth), which primarily outcrosses and is developed into composite cultivars by plant breeders. The ability to obtain clones of desirable genotypes in breeding nurseries would enable the maintenance of heterozygous genotypes for genetic study or the ability to reconstitute a true synthetic cultivar. We developed an efficient method of clonal propagation from stem cuttings to maintain genotypes in a vegetative state for a minimum of 2 yr, even when obtained from flowering parental plants. The long‐term viability of such clones is unknown, however. We determined that hairy vetch, which flowers under long days, exhibits a form of partial flowering where vegetative meristems are maintained during conditions that induce flowering. Clones obtained from flowering parents would resume reproductive growth and eventually senesce if kept in inductive conditions. However, if clones were grown under a continuous 6‐h photoperiod, reproductive development would cease and vegetative growth would resume indefinitely.
T‐cell activation and immune memory enhancement induced by irreversible electroporation in pancreatic cancer
Authors: He Chaobin , Huang Xin , Zhang Yu , Lin Xiaojun , Li Shengping 
Published: June 2020

AbstractBackgroundIrreversible electroporation is shown to induce immune changes in pancreatic cancer while the histology evidences are still lacking. The aim of this study is to show the immune changes in histology and explore whether irreversible electroporation (IRE) can induce immunogenic cell death (ICD) of tumor cells and activate specific immune responses.MethodsSubcutaneous and orthotopic pancreatic cancer models were established and used to evaluate the effect of immune modulation of IRE. The infiltration of T cells was assessed in several tissue samples before and after IRE. Abscopal effect was then assessed by comparing the tumor growth of subcutaneous tumors after in situ ablation with IRE or exposure to tumor culture supernatant (TSN) of IRE‐treated Pan02. The expression of damage‐associated molecular patterns (DAMPs) of tumor cells after IRE was detected in vitro.ResultsIRE could significantly suppress the tumor growth and increase the infiltration of CD8+ T cells. After ablation with IRE or stimulation with TSN of Pan02 treated by IRE, the growth of untreated tumor was suppressed and the effector CD8+ T cells and memory T cells increased significantly in mice. Additionally, the inhibition effect of tumor growth increased along with the increasing strength levels of electroporation. IRE induced ICD of tumor cells by increasing the synthesis and secretion of DAMPs.ConclusionsIRE induced local immunomodulation by increasing specific T cells infiltration. Through enhancing specific immune memory, IRE not only led a complete tumor regression in suit, but also induced abscopal effect, suppressing the growth of the latent lesions.
Oxidative stress induces monocyte‐to‐myofibroblast transdifferentiation through p38 in pancreatic ductal adenocarcinoma
Authors: Huang Xin , He Chaobin , Hua Xin , Kan Anna , Mao Yize , Sun Shuxin , Duan Fangting , Wang Jun , Huang Peng , Li Shengping 
Published: June 2020

AbstractBackgroundCancer‐associated fibroblasts (CAFs) are among the most prominent cells during the desmoplastic reaction in pancreatic ductal adenocarcinoma (PDAC). However, CAFs are heterogeneous and the precise origins are not fully elucidated. This study aimed to explore whether monocytes can transdifferentiate into fibroblasts in PDAC and evaluate the clinical significance of this event.MethodsCD14+ monocytes were freshly isolated from human peripheral blood. Immunofluorescence, reverse transcription‐quantitative PCR, western blot, flow cytometry and enzyme‐linked immunosorbent assay were used to detect the expression of αSMA, fibronectin, and other relevant molecules. In addition, latex beads with a mean particle size of 2.0 µm were used to assess the phagocytic capacity. Moreover, RNA sequencing (RNA‐seq) was performed to identify the differences induced by H2O2 and the underlying mechanisms.ResultsImmunofluorescence identified αSMA and fibroblast‐specific protein 1 expression by tumor‐associated macrophages in PDAC. The in vitro experiment revealed that oxidative stress (H2O2 or radiation) induced monocyte‐to‐myofibroblast transdifferentiation (MMT), as identified by upregulated αSMA expression at both the RNA and protein levels. In addition, compared with freshly isolated monocytes, human monocyte‐derived macrophages increased fibronectin expression. RNA‐seq analysis identified p53 activation and other signatures accompanying this transdifferentiation; however, the p53 stabilizer nutlin‐3 induced αSMA expression through reactive oxygen species generation but not through the p53 transcription/mitochondria‐dependent pathway, whereas the p38 inhibitor SB203580 could partially inhibit αSMA expression. Finally, MMT produced a unique subset of CAFs with reduced phagocytic capacity that could promote the proliferation of pancreatic cancer cells.ConclusionsOxidative stress in the tumor microenvironment could induce MMT in PDAC, thus inducing reactive stroma, modulating immunosuppression, and promoting tumor progression. Reducing oxidative stress may be a promising future therapeutic regimen.
COVID‐19 critical illness pathophysiology driven by diffuse pulmonary thrombi and pulmonary endothelial dysfunction responsive to thrombolysis
Authors: Poor Hooman D. , Ventetuolo Corey E. , Tolbert Thomas , Chun Glen , Serrao Gregory , Zeidman Amanda , Dangayach Neha S. , Olin Jeffrey , Kohli‐Seth Roopa , Powell Charles A. 
Published: June 2020

AbstractPatients with severe COVID‐19 disease have been characterized as having the acute respiratory distress syndrome (ARDS). Critically ill COVID‐19 patients have relatively well‐preserved lung mechanics despite severe gas exchange abnormalities, a feature not consistent with classical ARDS but more consistent with pulmonary vascular disease. Many patients with severe COVID‐19 also demonstrate markedly abnormal coagulation, with elevated d‐dimers and higher rates of venous thromboembolism. We present four cases of patients with severe COVID‐19 pneumonia with severe respiratory failure and shock, with evidence of markedly elevated dead‐space ventilation who received tPA. All showed post treatment immediate improvements in gas exchange and/or hemodynamics. We suspect that severe COVID‐19 pneumonia causes respiratory failure via pulmonary microthrombi and endothelial dysfunction. Treatment for COVID‐19 pneumonia may warrant anticoagulation for milder cases and thrombolysis for more severe disease.
Next‐generation sequencing in residual liquid‐based cytology specimens for cancer genome analysis
Authors: Yamaguchi Tomomi , Akahane Toshiaki , Harada Ohi , Kato Yasutaka , Aimono Eriko , Takei Hidehiro , Tasaki Takashi , Noguchi Hirotsugu , Nishihara Hiroshi , Kamata Hajime , Tanimoto Akihide 
Published: June 2020

AbstractBackgroundCancer genome profiling of cytology specimens using next‐generation sequencing (NGS) requires adequate and good‐quality DNA. Genomic examination of cytology samples was conventionally performed on cell block (CB) or smear specimens than on residual liquid‐based cytology (LBC) specimens, which are high‐quality DNA sources even after long‐term storage.MethodsWe estimated tumor fractions of 37 residual LBC specimens, including 30 fine needle aspiration (FNA) samples from the thyroid (12 papillary thyroid carcinomas and two malignant lymphomas), lymph node (13 metastatic carcinomas and one malignant lymphoma), and breast cancer (one phyllodes tumor and one invasive ductal carcinoma), two pancreatic carcinoma samples, and five liquid (ascites, pleural effusion, and cerebrospinal fluid) samples. The DNA was extracted from all samples and subjected to NGS using a customized cancer gene panel comprising 28 cancer‐related genes.ResultsNGS analysis revealed somatic mutations corresponding to pathological diagnosis with adequate variant allele frequency (VAF) in 24 LBC specimens, which had significantly higher tumor fraction (72.5% ± 4.9%). Ten cases, including the five fluid samples, had very small tumor fractions (7.5% ± 2.3%) to obtain sufficient VAF. Other two samples had high tumor fractions but showed very low VAF, indicating the presence of fusion genes. The remaining one sample yielded no DNA recovery.ConclusionThe residual LBC specimens collected by FNA from the thyroid gland and lymph node were verified to carry high tumor fraction and could serve as an alternate source for molecular testing to screen and diagnose cancers without the use of CB or smears.
Tool for genomic selection and breeding to evolutionary adaptation: Development of a 100K single nucleotide polymorphism array for the honey bee
Authors: Jones Julia C. , Du Zhipei G. , Bernstein Richard , Meyer Monique , Hoppe Andreas , Schilling Elmar , Ableitner Martin , Juling Katrin , Dick Regina , Strauss Anja S. , Bienefeld Kaspar 
Published: June 2020

AbstractHigh‐throughput high‐density genotyping arrays continue to be a fast, accurate, and cost‐effective method for genotyping thousands of polymorphisms in high numbers of individuals. Here, we have developed a new high‐density SNP genotyping array (103,270 SNPs) for honey bees, one of the most ecologically and economically important pollinators worldwide. SNPs were detected by conducting whole‐genome resequencing of 61 honey bee drones (haploid males) from throughout Europe. Selection of SNPs for the chip was done in multiple steps using several criteria. The majority of SNPs were selected based on their location within known candidate regions or genes underlying a range of honey bee traits, including hygienic behavior against pathogens, foraging, and subspecies. Additionally, markers from a GWAS of hygienic behavior against the major honey bee parasite Varroa destructor were brought over. The chip also includes SNPs associated with each of three major breeding objectives—honey yield, gentleness, and Varroa resistance. We validated the chip and make recommendations for its use by determining error rates in repeat genotypings, examining the genotyping performance of different tissues, and by testing how well different sample types represent the queen's genotype. The latter is a key test because it is highly beneficial to be able to determine the queen's genotype by nonlethal means. The array is now publicly available and we suggest it will be a useful tool in genomic selection and honey bee breeding, as well as for GWAS of different traits, and for population genomic, adaptation, and conservation questions.
Breaking barriers? Ethnicity and socioeconomic background impact on early career progression in the fields of ecology and evolution
Authors: Wanelik Klara M. , Griffin Joanne S. , Head Megan L. , Ingleby Fiona C. , Lewis Zenobia 
Published: June 2020

AbstractThe academic disciplines of Science, Technology, Engineering and Mathematics (STEM) have long suffered from a lack of diversity. While in recent years there has been some progress in addressing the underrepresentation of women in STEM subjects, other characteristics that have the potential to impact on equality of opportunity have received less attention. In this study, we surveyed 188 early career scientists (ECRs), defined as within 10 years of completing their PhD, in the fields of ecology, evolutionary biology, behaviour, and related disciplines. We examined associations between ethnicity, age, sexual orientation, sex, socioeconomic background, and disability, with measures of career progression, namely publication record, number of applications made before obtaining a postdoc, type of contract, and number of grant applications made. We also queried respondents on perceived barriers to progression and potential ways of overcoming them. Our key finding was that socioeconomic background and ethnicity were associated with measures of career progression. While there was no difference in the number of reported first‐authored papers on PhD completion, ethnic minority respondents reported fewer other‐authored papers. In addition, ECRs from a lower socioeconomic background were more likely to report being in teaching and research positions, rather than research‐only positions, the latter being perceived as more prestigious by some institutions. We discuss our findings in the context of possible inequality of opportunity. We hope that this study will stimulate wider discussion and help to inform strategies to address the underrepresentation of minority groups in the fields of ecology and evolution, and STEM subjects more widely.
Prediction of flotation efficiency of metal sulfides using an original hybrid machine learning model
Authors: Cook Rachel , Monyake Keitumetse Cathrine , Hayat Muhammad Badar , Kumar Aditya , Alagha Lana 
Published: June 2020

AbstractFroth flotation process is extensively used for selective separation of base metal sulfides from uneconomic mineral resources. Reliable prediction of process outcomes (metal recovery and grade) is vital to ensure peak performance. This work employs an innovative hybrid machine learning (ML) model—constructed by combining the random forest model and the firefly algorithm—to predict froth flotation efficiency of galena and chalcopyrite in relation to various experimental process parameters. The hybrid model's prediction performance was rigorously evaluated, and compared against four different standalone ML models. The outcomes of this study illustrate that the hybrid ML model has the prediction ability to process outcomes with high‐fidelity, while consistently outperforming the standalone ML models.
Evaluation of yield and experiences of age‐related molecular investigation for heritable and nonheritable causes of mismatch repair deficient colorectal cancer to identify Lynch syndrome
Authors: Vos Janet R. , Fakkert Ingrid E. , Spruijt Liesbeth , Willems Riki W. , Langenveld Sera , Mensenkamp Arjen R. , Leter Edward M. , Nagtegaal Iris D. , Ligtenberg Marjolijn J. L. , Hoogerbrugge Nicoline ,   FINAL Group
Published: June 2020

AbstractUniversal mismatch repair deficiency (dMMR) testing of colorectal cancer (CRC) is promoted as routine diagnostics to prescreen for Lynch syndrome. We evaluated the yield and experience of age‐related molecular investigation for heritable and nonheritable causes of dMMR in CRC below age 70 to identify Lynch Syndrome. In a prospective cohort of 3602 newly diagnosed CRCs below age 70 from 19 hospitals, dMMR, MLH1 promoter hypermethylation, germline MMR gene and somatic MMR gene testing was assessed in daily practice. Yield was evaluated using data from the Dutch Pathology Registry (PALGA) and two regional genetic centers. Experiences of clinicians were evaluated through questionnaires. Participating clinicians were overwhelmingly positive about the clinical workflow. Pathologists routinely applied dMMR‐testing in 84% CRCs and determined 10% was dMMR, largely due to somatic MLH1 hypermethylation (66%). Of those, 69% with dMMR CRC below age 70 without hypermethylation were referred for genetic testing, of which 55% was due to Lynch syndrome (hereditary) and 43% to somatic biallelic pathogenic MMR (nonhereditary). The prevalence of Lynch syndrome was 18% in CRC < 40, 1.7% in CRC age 40‐64 and 0.7% in CRC age 65‐69. Age 65‐69 represents most cases with dMMR, in which dMMR due to somatic causes (13%) is 20 times more prevalent than Lynch syndrome. In conclusion, up to age 65 routine diagnostics of (non‐)heritable causes of dMMR CRCs effectively identifies Lynch syndrome and reduces Lynch‐like diagnoses. Above age 64, the effort to detect one Lynch syndrome patient in dMMR CRC is high and germline testing rarely needed.