bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probabilistic Boolean Modeling of Pre‐clinical Tumor Models for Biomarker Identification in Cancer Drug Development
Authors: Berlow Noah E. 
Published: October 2021

AbstractAs high‐throughput sequencing experiments become more widely used in pre‐clinical and clinical settings, pharmacogenetic and pharmacogenomic biomarker development plays an increasingly important role in oncology drug development pipelines and programs. Consequently, computer‐based learning approaches have entered into use at multiple stages in pre‐clinical and clinical pipelines. However, few approaches are available to identify interpretable and implementable biomarkers of response early in the drug development process when only small pre‐clinical data packages are available. To address the need for early‐stage biomarker development using pre‐clinical tumor models, we have adapted the previously published Probabilistic Target Inhibitor Map (PTIM) platform to the challenge of biomarker hypothesis development, and denoted this approach the Probabilistic Target Map‐Biomarker (PTM‐Biomarker). In this article, we detail the history and design philosophy of PTM‐Biomarker, and present two case studies using the biomarker discovery tool to illustrate its utility in guiding cancer drug development. © 2021 Wiley Periodicals LLC.
QTL analysis of flowering‐related traits by specific length amplified fragment sequencing in melon
Authors: Wang Guichao , Dai Dongyang , Wang Ling , Sheng Yunyan , Wang Di , Li Dandan , Tian Limei , Luan Feishi 
Published: October 2021

AbstractMelon (Cucumis melo L., 2n = 24) belongs to the family Cucurbitaceae and is an important vegetable crop. This study aimed to investigate the quantitative trait loci (QTL) of flowering‐related traits to understand the genetic inheritance and candidate gene of flowering‐related traits. The specific length amplified fragment sequencing (SLAF‐seq) technology was used to construct a genetic map of 115 individual plants in the melon F2 population. A total of 82.6 Gb of data were generated using SLAF‐seq. A genetic map was constructed with 10,596 specific length amplified fragment markers in 12 linkage groups, which spanned 1,383.88 cM with an average distance of 0.13 cM between markers. Ten QTL of flowering‐related traits were detected, which explained 2.16–19.34% of the phenotypic variance. The logarithm of the odds (LOD) values ranged from 3.5 to 24.9. Ninety‐four F2:3 families were used for mapping mft and fft in candidate regions by simple sequence repeat (SSR) and cleaved amplified polymorphic sequences (CAPS) markers. The mapping results showed that mft2.1 and fft2.1 were located in the same region, between CmSSR07071 and CmSSR07102. By gene annotation, 36 candidate genes were detected in this region, 26 of which were annotated. Quantitative reverse transcription–polymerase chain reaction (PCR) showed that candidate genes, including WRKY transcription factor and AP2/ERF and B3 domain‐containing transcription factor, were differentially expressed in female and male flowers in the flower budding stages. These genes may provide the theoretical foundation for gene cloning and genetic transformation in melons.
Bifunctional Janus Silica Spheres for Pickering Interfacial Tandem Catalysis
Authors: Chang Fuqiang , Vis Carolien M. , Bergmeijer Menno , Howes Stuart C. , Bruijnincx Pieter C. A. 
Published: October 2021

AbstractNature provides much inspiration for the design of multistep conversion processes, with numerous reactions running simultaneously and without interference in cells, for example. A key challenge in mimicking nature's strategies is to compartmentalize incompatible reagents and catalysts, for example, for tandem catalysis. Here, we present a new strategy for antagonistic catalyst compartmentalization. The synthesis of bifunctional Janus catalyst particles carrying acid and base groups on the particle's opposite patches is reported as is their application as acid‐base catalysts in oil/water emulsions. The synthesis strategy involved the use of monodisperse, hydrophobic and amine‐functionalized silica particles (SiO2−NH2−OSi(CH3)3) to prepare an oil‐in‐water Pickering emulsion (PE) with molten paraffin wax. After solidification, the exposed patch of the silica particles was selectively etched and refunctionalized with acid groups to yield acid‐base Janus particles (Janus A–B). These materials were successfully applied in biphasic Pickering interfacial catalysis for the tandem dehydration‐Knoevenagel condensation of fructose to 5‐(hydroxymethyl)furfural‐2‐diethylmalonate (5‐HMF‐DEM) in a water/4‐propylguaiacol PE. The results demonstrate the advantage of rapid extraction of 5‐hydroxymethylfurfural (5‐HMF), a prominent platform molecule prone to side product formation in acidic media. A simple strategy to tune the acid/base balance using PE with both Janus A–B and monofunctional SiO2−NH2−OSi(CH3)3 base catalysts proved effective for antagonistic tandem catalysis.
A call for discovery: Re‐envisioning The Cancer Genome Atlas as a blueprint for a TCGA2.0—The COVID‐19 Genome Atlas
Authors: Hargadon Kristian M. 
Published: October 2021

AbstractThe COVID‐19 pandemic has impacted the health of millions and had a myriad of devastating consequences for global societies since its emergence in 2019. Noting parallels between the impact of COVID‐19 and cancer as diseases of global health significance, and as a way of building off the successes of The Cancer Genome Atlas (TCGA) as a comprehensive, multiomics approach to understand and combat cancer, this Call For Discovery provides a vision for creating a new TCGA2.0 (The COVID‐19 Genome Atlas) as a tool that will benefit researchers, clinicians, and patients alike as the scientific community works to better understand not only the various determinants of COVID‐19 disease outcome but also the most effective ways to manage and treat COVID‐19 disease complications.
Alteration of Endogenous Fatty Acids Profile and Lipid Metabolism in Rats Caused by a High‐Colleseed Oil and a High‐Sunflower Oil Diet
Authors: Li Ruizhi , Tan Chin Ping , Xu Yong‐Jiang , Liu Yuanfa 
Published: October 2021

AbstractDietary fat has an important influence on mammalian lipid homeostasis. However, the relationship between dietary fat types and endogenous fatty acids (FAs) in organs as well as lipid homeostasis remains unclear enough. In this study, rats are randomly divided into a control group (CN), a high‐colleseed oil group (COG), and a high‐sunflower oil group (SOG). FAs profile in liver and visceral fats of rats in two high‐fat (HF) diet groups is compared with that in CN. Oleic, γ‐linolenic, eicosadienoic, and arachidonic acid accumulate in COG liver or visceral fats, but the levels of linoleic, eicosadienoic, docosanoic, and dihomo‐γ‐linolenic acid decrease in COG visceral fats. However, these FAs levels increased in SOG liver or visceral fats except dihomo‐γ‐linolenic and arachidonic acid which changed insignificantly. The trend of initial upregulation and then downregulation of lipid metabolism‐related genes expression is noted in COG liver, including stearoyl‐CoA desaturase. Upregulation of adiponectin (ADPN) expression in visceral fats and downregulation of ADPN receptor 2 (Adipo‐R2) expression in livers of both HF groups are observed. Correlation analysis revealed positive correlations between specific FAs content and ADPN expression level. Negative correlations are observed between Adipo‐R2 expression and the content of oleic, linoleic, and γ‐linolenic acid in the SOG liver.Practical applications: Dietary fat not only provides energy but is also associated with lipid homeostasis. In this work, the authors investigate the distribution of fatty acids (FAs) in vivo and their influence on genes related to lipid metabolism induced by diets enriched in oleic acid or linoleic acid. The study suggests that dietary fats modulate lipid homeostasis not only by regulating endogenous FAs levels but also by affecting the expression of genes related to lipid metabolism. This study may support the research in lipid nutrition and rational intake of dietary fat.
Performance Comparison of single‐slope solar still loaded with various nanofluids
Authors: Dhindsa G. S. , Kumar Vijay , Mittal M. K. , Sokhal G.S. , Khalilpoor Nima , Sharifpur Mohsen , Issakhov Alibek , Tonk Ravinder 
Published: October 2021

AbstractNanofluids are great heat transfer carriers for collecting thermal energy in solar thermal applications. In the present study, a theoretical study of single‐slope solar still (passive type) has been carried out by incorporating CuO, Al2O3, Ag, Fe2O3, and SiC‐water nanofluids at different volume concentrations (0.02, 0.05, 0.08, 0.12, and 0.2). This analysis has been carried out with an optimum water depth of 0.02m as obtained from the experimental and theoretical studies. In order to validate the model, the experiments were conducted on solar still and then performance of still was compared. The analytical expression of the characteristic equation using Runga‐Kutta ODE, for passive single slope solar still was found to be in good agreement with experiments carried out in Patiala, India. The total deviation for both experimental and theoretical distillate output of a still for a day was found to be 12.24%. Daily production for Al2O3‐water‐based nanofluid was found to be (14.22%) higher than simple solar still without nanofluid, followed by CuO (10.82%), Ag (8.11%), Fe2O3 (7.63%) and SiC (7.61%).
Prevalence of iron deficiency in pregnant women: A prospective cross‐sectional Austrian study
Authors: Zeisler Harald , Dietrich Wolf , Heinzl Florian , Klaritsch Philipp , Humpel Victoria , Moertl Manfred , Obruca Christian , Wimazal Friedrich , Ramoni Angela , Tiechl Johanna , Wentzel‐Schwarz Elisabeth 
Published: October 2021

AbstractThe aim of the study was to determine, for the first time, in a prospective cross‐sectional multicenter study, the prevalence of iron deficiency (ID) in an Austrian pregnant population. A cohort of 425 pregnant women was classified into four groups of different weeks of gestation. Group 1 was monitored longitudinally, while groups 2–4, iron status, were sampled only once. Evaluation of the prevalence of ID was performed by comparing the diagnostic criteria of the WHO to the cutoff proposed by Achebe MM and Gafter‐Gvili A (Achebe) and the Austrian Nutrition Report (ANR). In comparison with the ANR, the prevalence of ID was lower in group 1 and higher in groups 2–4 (17.2% vs. 12.17%, 25.84%, 35.29%, and 41.76%, respectively) (p‐values < .01 except group 1). According to WHO, the prevalence in group 1 was 12.17% at inclusion, 2 months later 31.7%, and further 2 months later 65.71%, respectively. According to Achebe, the number of cases doubled; for group 1, the number of cases rose from 13 to 42 (115 patients total); for groups 2–4, we observed an increase from 112 to 230 (340 patients total). This study reported a prevalence of around 12% at the beginning of pregnancy, which increased during pregnancy up to 65%. ID can have a massive impact on quality of life, justifying screening, as iron deficiency would be easy to diagnose and treat.
Evaluation of Sustainability of a Prune Production Process from Farm to Fork Approach based on Thermodynamic Principles and Actual Operational Data
Authors: Nadi Fatemeh , Hepbasli Arif 
Published: October 2021

AbstractThe main objective of the present study is to investigate energy consumption, exergy and greenhouse gas (GHG) emissions from prune production in both the garden and plant sectors. Both energy and exergy analysis methods are used while some sustainability indicators such as the cumulative degree of perfection (CDP) and the renewability indicator (RI) as well environmental aspects are considered. The analysis is based on the actual operational data. The high energy consumption, exergy and GHG emissions are related to the post‐harvest and the factory operations. Natural gas is determined to be the most effective input to energy consumption, exergy and GHG emissions in the whole process of producing prunes. Based on the sustainability indicators used, the agricultural operation of the plum production process is partially renewable while the factory operation of the prune production process is highly non‐renewable. In cases where the production process of prunes includes the use of renewable energy and plum waste, CDP increases from 0.32 to 2.88 and RI from ‐2.16 to 0.65. The use of renewable sources in producing one ton of prune annually reduces GHG emissions by 362.55 tons and energy consumption by 7.45 TJ worldwide. The use of plum waste would also produce 402.8 TJ of energy per year.
Safety and efficacy of a mucoadhesive phytomedication containing curcuminoids and Bidens pilosa L. extract in the prevention and treatment of radiochemotherapy‐induced oral mucositis: Triple‐blind, randomized, placebo‐controlled, clinical trial
Authors: Arantes Diego Antônio Costa , da Silva Artur Christian Garcia , Freitas Nilceana Maya Aires , Lima Eliana Martins , de Oliveira Aline Carlos , Marreto Ricardo Neves , Mendonça Elismauro Francisco , Valadares Marize Campos 
Published: October 2021

AbstractBackgroundOral mucositis (OM) is the significant complication of radio/chemotherapy treatment. This study evaluated the safety and efficacy of a mucoadhesive phytomedication containing curcuminoids and Bidens pilosa L. (FITOPROT) in the prevention/treatment of OM.MethodsSixty‐two patients were randomized into the group's intervention and placebo. Adverse effect assessment, OM grading, pain, and saliva collection were carried at the 1st, 15th, 21st, and final of radiotherapy (RT). Inflammatory salivary mediators were measured.ResultsFITOPROT decreased the severity of OM from the 15th to the final RT, while the placebo showed an increase in the severity (p < 0.05). Intervention group had a lower number of patients with ulcerated OM at the final RT (p < 0.05). Phytomedication prevented increases of IL‐8 levels and reduced the salivary nitrite during RT.ConclusionsFITOPROT does not promote adverse effects, it appears to be effective at reducing the severity of OM, and it controls the concentration of pro‐inflammatory mediators.
Autophagy and cancer metabolism—The two‐way interplay
Authors: Yan Reui‐Liang , Chen Ruey‐Hwa 
Published: October 2021

AbstractAutophagy is an intracellular catabolic process that degrades cytoplasmic components for recycling in response to stressed conditions, such as nutrient deprivation. Dysregulation of autophagy is associated with various diseases, including cancer. Although autophagy plays dichotomous and context‐dependent roles in cancer, evidence has emerged that cancer cells exploit autophagy for metabolic adaptation. Autophagy is upregulated in many cancer types through tumor cell‐intrinsic proliferation demands and the hypoxic and nutrient‐limited tumor microenvironment (TME). Autophagy‐induced breakdown products then fuel into various metabolic pathways to supply tumor cells with energy and building blocks for biosynthesis and survival. This bidirectional regulation between autophagy and tumor constitutes a vicious cycle to potentiate tumor growth and therapy resistance. In addition, the pro‐tumor functions of autophagy are expanded to host, including cells in TME and distant organs. Thus, inhibition of autophagy or autophagy‐mediated metabolic reprogramming may be a promising strategy for anticancer therapy. Better understanding the metabolic rewiring mechanisms of autophagy for its pro‐tumor effects will provide insights into patient treatment.
Euxanthone inhibits lipopolysaccharide‐induced injury, inflammatory response, and MUC5AC hypersecretion in human airway epithelial cells by the TLR4/MyD88 pathway
Authors: Shen Wen , Yin Yuyao , Li Tiantian , Cao Gang 
Published: October 2021

AbstractAsthma progression is involved in airway epithelial dysfunction, airway inflammatory response, and mucus hypersecretion. Euxanthone has been found to exhibit cytotoxic activity on several human diseases, such as neurological disorders and cancers. Our study aimed to explore the influence of euxanthone on lipopolysaccharide (LPS)‐induced injury, inflammatory response, and mucin 5AC (MUC5AC) hypersecretion in human airway epithelial cells (AECs). Network pharmacology analysis was carried out to analyze the drug targets and key pathways of euxanthone against asthma. Cell injury was evaluated by CCK‐8, Lactate dehydrogenase (LDH) release assay, and terminal deoxynucleotidyl transferase‐mediated dUTP nick end‐labeling (TUNEL) assay. The production of interleukin (IL)‐6, IL‐8, monocyte chemoattractant protein‐1 (MCP‐1), and MUC5AC was measured using enzyme‐linked immunosorbent assay (ELISA). MUC5AC mRNA expression was detected by qRT‐PCR. Toll‐like receptor 4 (TLR4) and myeloid differentiation factor 88 (MyD88) protein expression was examined by western blot analysis. Venn diagram showed 14 overlapping targets between euxanthone and asthma. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, we focused on TLR signaling pathway. LPS exposure evoked viability reduction, increased LDH release and apoptosis, and induced production of inflammatory cytokines (IL‐6, IL‐8, and MCP‐1) and MUC5AC hypersecretion in human AECs, which were alleviated by euxanthone. Mechanistically, we validated that euxanthone attenuated LPS‐induced activation of TLR4/MyD88 pathway in AECs. Moreover, inhibition of the TLR4/MyD88 pathway enhanced the inhibitory effect of euxanthone on LPS‐induced cell injury, inflammatory response and MUC5AC expression. In conclusion, euxanthone attenuated LPS‐induced cell injury, inflammatory response, and MUC5AC expression in AECs by inhibiting the activation of TLR4/MyD88 pathway.
Movement correction method for laser speckle contrast imaging of cerebral blood flow in cranial windows in rodents
Authors: Guilbert Jérémie , Desjardins Michèle 
Published: October 2021

AbstractLaser speckle contrast imaging (LSCI) is used in clinical research to dynamically image blood flow. One drawback is its susceptibility to movement artifacts. We demonstrate a new, simple method to correct motion artifacts in LSCI signals measured in awake mice with cranial windows during sensory stimulation. The principle is to identify a region in the image in which speckle contrast (SC) is independent of blood flow and only varies with animal movement, then to regress out this signal from the data. We show that (1) the regressed signal correlates well with mouse head movement, (2) the corrected signal correlates better with independently measured blood volume and (3) it has a (59 ± 6)% higher signal‐to‐noise ratio. Compared to three alternative correction methods, ours has the best performance. Regressing out flow‐independent global variations in SC is a simple and accessible way to improve the quality of LSCI measurements.
Effect of selenium‐free parenteral nutrition on serum selenium of neonates and infants maintained on long‐term parenteral nutrition
Authors: Lee Ji Young , Shin Hyun Jung , Bae Hye Jung , Jo Yun Hee , Cho Yoon Sook , Shin Seung Han , Kim Ee‐Kyung , Kim Han‐Suk 
Published: October 2021

AbstractBackgroundThe risk of selenium deficiency increases for infants receiving long‐term parenteral nutrition (PN). This study analyzed selenium deficiency in neonates and infants requiring long‐term PN and evaluated the effect of intravenous (IV) selenium provision.MethodsThis study was a retrospective study of neonates and infants who were admitted to a neonatal intensive care unit from January 2010 to December 2019, received PN for ≥2 weeks, and had their serum selenium concentration measured. Patients were divided into two groups, depending on their serum selenium concentration, a deficient group (n = 55) and a nondeficient group (n = 47).ResultsOf the study participants, 53.9% (55 of 102) were deficient in selenium. No difference in demographic and clinical characteristics existed except bronchopulmonary dysplasia. A subgroup analysis was performed for patients (n = 29). The average dose of IV selenium administered to patients was 2.7 ± 1.0 mcg/kg/day. The average initial serum selenium concentration was 36.5 ± 18.0 mcg/L, and the serum concentration significantly increased to 52.5 ± 19.1 mcg/L after IV selenium administration (P < .001). The correlation between the average IV selenium dose and the change in serum selenium concentrations was statistically significant (r = .423; P = .022).ConclusionSelenium deficiency is common in neonates and infants receiving long‐term PN. Serum selenium concentration increased proportionally as the IV selenium dose increased. Therefore, it is recommended to supply a proper dose of IV selenium depending on the degree of selenium deficiency.
The application of AMSTAR2 in 32 overviews of systematic reviews of interventions for mental and behavioural disorders: A cross‐sectional study
Authors: De Santis Karina Karolina , Lorenz Robert C. , Lakeberg Meret , Matthias Katja 
Published: October 2021

Abstract‘A measurement tool to assess systematic reviews, version 2’ (AMSTAR2) is a 16‐item tool to critically appraise systematic reviews (SRs) of healthcare interventions. This study aimed to assess the methods and outcomes of AMSTAR2 appraisals in overviews of SRs of interventions for mental and behavioural disorders. The cross‐sectional study was conducted using 32 overviews of SRs selected from three electronic databases in January 2021. Data items included overview and SR characteristics and AMSTAR2 appraisal methods and outcomes. Data were extracted by two authors independently and narratively synthesised using descriptive statistics (means ± SD and relative frequencies). SR characteristics were compared based on AMSTAR2 appraisal outcomes using chi‐square tests. The 32 overviews appraised SRs of predominantly non‐pharmacological interventions for mental disorders. AMSTAR2 appraisals were reported as confidence ratings in 25/32 overviews or individual item scores in 24/32 overviews. Most SRs/overview were non‐Cochrane (mean = 94%), included RCTs only (mean = 77%) and were published before AMSTAR2 release (mean = 79%). The confidence ratings derived in 25 overviews for 349 SRs were predominantly critically low (68%). Confidence ratings were similar for SRs with RCTs only versus RCTs+non‐RCTs or SRs published before versus after AMSTAR2 release, while Cochrane SRs received more high+moderate than low+critically low confidence ratings (p < 0.01). Confidence ratings derived based on AMSTAR2 do not differentiate among SRs of healthcare interventions except for Cochrane SRs that fulfil the criteria for high confidence ratings. AMSTAR2 items should be consulted to avoid common weaknesses in future SRs.
Implementation of design of experiments for optimization of forced degradation conditions and development of a stability‐indicating high‐performance liquid chromatography method for sepiwhite
Authors: Davoodi Javid , Majidi Sina , Jahani Maryam , Tayarani‐Najaran Zahra , Golmohammadzadeh Shiva , Kamali Hossein 
Published: October 2021

AbstractSepiwhite is a novel anti‐pigmenting agent that is derived from fatty acid and phenylalanine and used for hyperpigmentation induced by light exposure or inflammation. In this study, a simple and validated high‐performance liquid chromatography method for the quantitation of sepiwhite was developed. Optimized forced degradation of sepiwhite at thermal, acid/base, photolysis, oxidative, and heavy metal ions conditions were evaluated and the effect of each of them on production of specific 10%–30% degradants was studied by the approach of design of experiments. Sepiwhite accelerated study was conducted and toxicity of sepiwhite at each condition was tested. An optimized high‐performance liquid chromatography method was validated by a face‐centered central composition design. Ten different degradants were identified from sepiwhite and degradation behavior under different conditions was studied. Sepiwhite and its degradant products show no cytotoxicity. This optimized high‐performance liquid chromatography method can be applied for quality control assay and sepiwhite degradation behavior may be considered in the manufacturing of sepiwhite products.