bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing optimal: inequalities in codon optimization algorithms
Authors: Ranaghan Matthew J. , Li Jeffrey J. , Laprise Dylan M. , Garvie Colin W.
Published: February 2021

Background

Custom genes have become a common resource in recombinant biology over the last 20 years due to the plummeting cost of DNA synthesis. These genes are often “optimized” to non-native sequences for overexpression in a non-native host by substituting synonymous codons within the coding DNA sequence (CDS). A handful of studies have compared native and optimized CDSs, reporting different levels of soluble product due to the accumulation of misfolded aggregates, variable activity of enzymes, and (at least one report of) a change in substrate specificity. No study, to the best of our knowledge, has performed a practical comparison of CDSs generated from different codon optimization algorithms or reported the corresponding protein yields.

Results

In our efforts to understand what factors constitute an optimized CDS, we identified that there is little consensus among codon-optimization algorithms, a roughly equivalent chance that an algorithm-optimized CDS will increase or diminish recombinant yields as compared to the native DNA, a near ubiquitous use of a codon database that was last updated in 2007, and a high variability of output CDSs by some algorithms. We present a case study, using KRas4B, to demonstrate that a median codon frequency may be a better predictor of soluble yields than the more commonly utilized CAI metric.

Conclusions

We present a method for visualizing, analyzing, and comparing algorithm-optimized DNA sequences for recombinant protein expression. We encourage researchers to consider if DNA optimization is right for their experiments, and work towards improving the reproducibility of published recombinant work by publishing non-native CDSs.
The fly liquid-food electroshock assay (FLEA) suggests opposite roles for neuropeptide F in avoidance of bitterness and shock
Authors: Mishra Puskar , Yang Shany E. , Montgomery Austin B. , Reed Addison R. , Rodan Aylin R. , Rothenfluh Adrian
Published: February 2021

Background

Proper regulation of feeding is important for an organism’s well-being and survival and involves a motivational component directing the search for food. Dissecting the molecular and neural mechanisms of motivated feeding behavior requires assays that allow quantification of both motivation and food intake. Measurements of motivated behavior usually involve assessing physical effort or overcoming an aversive stimulus. Food intake in Drosophila can be determined in a number of ways, including by measuring the time a fly’s proboscis interacts with a food source associated with an electrical current in the fly liquid-food interaction counter (FLIC). Here, we show that electrical current flowing through flies during this interaction is aversive, and we describe a modified assay to measure motivation in Drosophila.

Results

Food intake is reduced during the interaction with FLIC when the electrical current is turned on, which provides a confounding variable in studies of motivated behavior. Based on the FLIC, we engineer a novel assay, the fly liquid-food electroshock assay (FLEA), which allows for current adjustments for each feeding well. Using the FLEA, we show that both external incentives and internal motivational state can serve as drivers for flies to overcome higher current (electric shock) to obtain superior food. Unlike similar assays in which bitterness is the aversive stimulus for the fly to overcome, we show that current perception is not discounted as flies become more food-deprived. Finally, we use genetically manipulated flies to show that neuropeptide F, an orthologue of mammalian NPY previously implicated in regulation of feeding motivation, is required for sensory processing of electrical current.

Conclusion

The FLEA is therefore a novel assay to accurately measure incentive motivation in Drosophila. Using the FLEA, we also show that neuropeptide F is required for proper perception or processing of an electroshock, a novel function for this neuropeptide involved in the processing of external and internal stimuli.
Serum transferrin as a biomarker of hepatocyte nuclear factor 4 alpha activity and hepatocyte function in liver diseases
Authors: Guldiken Nurdan , Argemi Josepmaria , Gurbuz Berivan , Atkinson Stephen R. , Oliverius Martin , Fila Petr , Hamesch Karim , Bruns Tony , Cabezas Joaquín , Lozano Juan J. , Mann Jelena , Cao Sheng , Mathurin Philippe , Shah Vijay H. , Trautwein Christian , Thursz Mark R. , Bataller Ramon , Strnad Pavel
Published: February 2021

Background

Serum transferrin levels represent an independent predictor of mortality in patients with liver failure. Hepatocyte nuclear factor 4 alpha (HNF4α) is a master regulator of hepatocyte functions. The aim of this study was to explore whether serum transferrin reflects HNF4α activity.

Methods

Factors regulating transferrin expression in alcoholic hepatitis (AH) were assessed via transcriptomic/methylomic analysis as well as chromatin immunoprecipitation coupled to DNA sequencing. The findings were corroborated in primary hepatocytes. Serum and liver samples from 40 patients with advanced liver disease of multiple etiologies were also studied.

Results

In patients with advanced liver disease, serum transferrin levels correlated with hepatic transferrin expression (r = 0.51, p = 0.01). Immunohistochemical and biochemical tests confirmed reduced HNF4α and transferrin protein levels in individuals with cirrhosis. In AH, hepatic gene-gene correlation analysis in liver transcriptome revealed an enrichment of HNF4α signature in transferrin-correlated transcriptome while transforming growth factor beta 1 (TGFβ1), tumor necrosis factor α (TNFα), interleukin 1 beta (IL-1β), and interleukin 6 (IL-6) negatively associated with transferrin signature. A key regulatory region in transferrin promoter was hypermethylated in patients with AH. In primary hepatocytes, treatment with TGFβ1 or the HNF4α inhibitor BI6015 suppressed transferrin production, while exposure to TNFα, IL-1β, and IL-6 had no effect. The correlation between hepatic HNF4A and transferrin mRNA levels was also seen in advanced liver disease.

Conclusions

Serum transferrin levels constitute a prognostic and mechanistic biomarker. Consequently, they may serve as a surrogate of impaired hepatic HNF4α signaling and liver failure.
Lower iodine storage in the placenta is associated with gestational diabetes mellitus
Authors: Neven Kristof Y. , Cox Bianca , Cosemans Charlotte , Gyselaers Wilfried , Penders Joris , Plusquin Michelle , Roels Harry A. , Vrijens Karen , Ruttens Ann , Nawrot Tim S.
Published: February 2021

Background

The micronutrient iodine is essential for a healthy intrauterine environment and is required for optimal fetal growth and neurodevelopment. Evidence linking urinary iodine concentrations, which mainly reflects short-term iodine intake, to gestational diabetes mellitus (GDM) is inconclusive. Although the placental concentrations would better reflect the long-term gestational iodine status, no studies to date have investigated the association between the placental iodine load and the risk at GDM. Moreover, evidence is lacking whether placental iodine could play a role in biomarkers of insulin resistance and β-cell activity.

Methods

We assessed the incidence of GDM between weeks 24 and 28 of gestation for 471 mother-neonate pairs from the ENVIRONAGE birth cohort. In placentas, we determined the iodine concentrations. In maternal and cord blood, we measured the insulin concentrations, the Homeostasis Model Assessment (HOMA) for insulin resistance (IR) index, and β-cell activity. Logistic regression was used to estimate the odds ratios (OR) of GDM, and the population attributable factor (PAF) was calculated. Generalized linear models estimated the changes in insulin, HOMA-IR, and β-cell activity for a 5 μg/kg increase in placental iodine.

Results

Higher placental iodine concentrations decreased the risk at GDM (OR = 0.82; 95%CI 0.72 to 0.93; p = 0.003). According to the PAF, 54.2% (95%CI 11.4 to 82.3%; p = 0.0006) of the GDM cases could be prevented if the mothers of the lowest tertile of placental iodine would have placental iodine levels as those belonging to the highest tertile. In cord blood, the plasma insulin concentration was inversely associated with the placental iodine load (β = − 4.8%; 95%CI − 8.9 to − 0.6%; p = 0.026).

Conclusions

Higher concentrations of placental iodine are linked with a lower incidence of GDM. Moreover, a lower placental iodine load is associated with an altered plasma insulin concentration, HOMA-IR index, and β-cell activity. These findings postulate that a mild-to-moderate iodine deficiency could be linked with subclinical and early-onset alterations in the normal insulin homeostasis in healthy pregnant women. Nevertheless, the functional link between gestational iodine status and GDM warrants further research.
Prevalence of commonly diagnosed disorders in UK dogs under primary veterinary care: results and applications
Authors: O’Neill Dan G. , James Hannah , Brodbelt Dave C. , Church David B. , Pegram Camilla
Published: February 2021

Background

Although dogs are a commonly owned companion animal in the UK, the species experiences many health problems that are predictable from demographic information. This study aimed to use anonymised veterinary clinical data from the VetCompass™ Programme to report the frequency of common disorders of dogs under primary veterinary care in the UK during 2016 and to explore effects associated with age, sex and neuter status.

Results

From an available population of 905,543 dogs under veterinary care at 886 veterinary clinics during 2016, the current study included a random sample of 22,333 (2.47 %) dogs from 784 clinics. Prevalence for each disorder was calculated at the most refined level of diagnostic certainty (precise-level precision) and after grouping to a more general level of diagnostic precision (grouped-level precision). The most prevalent precise-level precision disorders recorded were periodontal disease (prevalence 12.52 %, 95 % CI: 12.09–12.97), otitis externa (7.30 %, 95 % CI: 6.97–7.65) and obesity (7.07 %, 95 % CI: 6.74–7.42). The most prevalent grouped-level disorders were dental disorder (14.10 %, 95 % CI: 13.64–14.56), skin disorder (12.58 %, 95 % CI: 12.15–13.02) and enteropathy (10.43 %, 95 % CI: 10.04–10.84). Associations were identified for many common disorders with age, sex and neuter.

Conclusions

The overall findings can assist veterinarians and owners to prioritise preventive care and to understand demographic risk factors in order to facilitate earlier diagnosis of common disorders in dogs. The information on associations with age, sex and neuter status provides additional contextual background to the complexity of disorder occurrence and supports targeted health controls for demographic subsets of dogs.
Use of immune repertoire sequencing to resolve discordant microscopic and immunochemical findings in a case of T cell-rich large B cell lymphoma in a young dog
Authors: Lee Gary Kwok Cheong , Bienzle Dorothee , Keller Stefan Matthias , Hwang Mei-Hua , Darzentas Nikos , Chang Haiyang , Rätsep Emily , Egan Rebecca , Beeler-Marfisi Janet
Published: February 2021

Background

Lymphocytic neoplasms with frequent reactive lymphocytes are uncommonly reported in dogs, and can pose a diagnostic challenge. Different diagnostic modalities such as cytology, flow cytometry, histopathology, immunohistochemistry, and clonality testing, are sometimes required for a diagnosis. This report illustrates the value of using a multi-modal diagnostic approach to decipher a complex lymphocytic tumor, and introduces immune repertoire sequencing as a diagnostic adjunct.

Case presentation

A 10-month-old Great Dane was referred for marked ascites. Cytologic analysis of abdominal fluid and hepatic aspirates revealed a mixed lymphocyte population including numerous large lymphocytes, yielding a diagnosis of lymphoma. Flow cytometrically, abdominal fluid lymphocytes were highly positive for CD4, CD5, CD18, CD45, and MHC II, consistent with T cell lymphoma. Due to a rapidly deteriorating clinical condition, the dog was euthanized. Post mortem histologic evaluation showed effacement of the liver by aggregates of B cells surrounded by T cells, suggestive of hepatic T cell-rich large B cell lymphoma. Immune repertoire sequencing confirmed the presence of clonal B cells in the liver but not the abdominal fluid, whereas reactive T cells with shared, polyclonal immune repertoires were found in both locations.

Conclusions

T cell-rich large B cell lymphoma is a rare neoplasm in dogs that may be challenging to diagnose and classify due to mixed lymphocyte populations. In this case, the results of histopathology, immunohistochemistry and immune repertoire sequencing were most consistent with a hepatic B cell neoplasm and reactive T cells exfoliating into the abdominal fluid. Immune repertoire sequencing was helpful in delineating neoplastic from reactive lymphocytes and characterizing repertoire overlap in both compartments. The potential pitfalls of equating atypical cytomorphology and monotypic marker expression in neoplasia are highlighted.
A CTSA One Health Alliance guidance on institutional review of veterinary clinical studies
Authors:   CTSA One Health Alliance, Moore S. A. , O’Kell A. , Borghese H. , Garabed R. , O’Meara H. , Baneux P.
Published: February 2021

Harmonized institutional processes and reviewer training are vital to maintain integrity and ethical rigor of the veterinary clinical research pipeline and are a prerequisite to future work that might establish centralized or single-site ethical and regulatory review to ease initiation of multi-center studies. Funded by a CTSA One Health Alliance (COHA) pilot award, a diverse working group of veterinary clinicians and institutional representatives was convened in February 2020 to develop a guidance document detailing broadly agreed upon practices for ethical review and approval of veterinary clinical studies conducted in the United States.

The working group defined key areas of need for consensus, developed a set of associated guidelines, and circulated these for review by COHA’s fifteen member institutions. Six focus areas were identified by the working group and included vital items of protocol review, composition of the review committee, post-approval monitoring and adverse event reporting, consideration of special circumstances such as satellite sites and the use of healthy veterinary subjects in research, and the informed consent process.

This document outlines a broadly agreed-upon framework through which to approach vital items associated with veterinary clinical study protocol review and approval. These approaches represent current best practice in the review and approval of veterinary clinical studies, and can serve as a guidance for veterinary clinician-scientists and regulatory experts, to ensure robust and ethically conducted studies that can contribute to the advancement of both animal and human health.
MicroRNA 219-5p inhibits alveolarization by reducing platelet derived growth factor receptor-alpha
Authors: Freeman Amelia , Qiao Luhua , Olave Nelida , Rezonzew Gabriel , Gentle Samuel , Halloran Brian , Pryhuber Gloria S. , Gaggar Amit , Tipple Trent E. , Ambalavanan Namasivayam , Lal Charitharth Vivek
Published: February 2021

Background

MicroRNA (miR) are small conserved RNA that regulate gene expression post-transcription. Previous genome-wide analysis studies in preterm infants indicate that pathways of miR 219-5p are important in infants with Bronchopulmonary Dysplasia (BPD).

Methods

Here we report a prospective cohort study of extremely preterm neonates wherein infants diagnosed with severe BPD expressed increased airway miR-219-5p and decreased platelet derived growth factor receptor alpha (PDGFR-α), a target of mir-219-5p and a key regulator of alveolarization, compared to post-conception age-matched term infants.

Results

miR-219-5p was highly expressed in the pulmonary epithelial lining in lungs of infants with BPD by in situhybridizationof human infant lungs. In both in vitro and in vivo (mouse) models of BPD, miR-219-5p was increased on exposure to hyperoxia compared with the normoxia control, with a complementary decrease of PDGFR-α. To further confirm the target relationship between miR‐219 and PDGFR-α, pulmonary epithelial cells (MLE12) and lung primary fibroblasts were treated with a mimic of miR-219-5p and a locked nucleic acid (LNA) based inhibitor of miR-219-5p. In comparison with the control group, the level of miR‐219 increased significantly after miR‐219 mimic treatment, while the level of PDGFR-α declined markedly. LNA exposure increased PDGFR-α. Moreover, in BPD mouse model, over-expression of miR-219-5p inhibited alveolar development, indicated by larger alveolar spaces accompanied by reduced septation.

Conclusions

Taken together, our results demonstrate that increased miR-219-5p contributes to the pathogenesis of BPD by targeting and reducing PDGFR-α. The use of specific miRNA antagonists may be a therapeutic strategy for preventing the development of BPD.
The association between hospital length of stay before rapid response system activation and clinical outcomes: a retrospective multicenter cohort study
Authors: Park Jimyung , Lee Yeon Joo , Hong Sang-Bum , Jeon Kyeongman , Moon Jae Young , Kim Jung Soo , Kang Byung Ju , Ahn Jong-Joon , Lee Dong-Hyun , Park Jisoo , Cho Jae Hwa , Lee Sang-Min
Published: February 2021

Background

Rapid response system (RRS) is being increasingly adopted to improve patient safety in hospitals worldwide. However, predictors of survival outcome after RRS activation because of unexpected clinical deterioration are not well defined. We investigated whether hospital length of stay (LOS) before RRS activation can predict the clinical outcomes.

Methods

Using a nationwide multicenter RRS database, we identified patients for whom RRS was activated during hospitalization at 9 tertiary referral hospitals in South Korea between January 1, 2016, and December 31, 2017. All information on patient characteristics, RRS activation, and clinical outcomes were retrospectively collected by reviewing patient medical records at each center. Patients were categorized into two groups according to their hospital LOS before RRS activation: early deterioration (LOS < 5 days) and late deterioration (LOS ≥ 5 days). The primary outcome was 28-day mortality and multivariable logistic regression was used to compare the two groups. In addition, propensity score-matched analysis was used to minimize the effects of confounding factors.

Results

Among 11,612 patients, 5779 and 5883 patients belonged to the early and late deterioration groups, respectively. Patients in the late deterioration group were more likely to have malignant disease and to be more severely ill at the time of RRS activation. After adjusting for confounding factors, the late deterioration group had higher 28-day mortality (aOR 1.60, 95% CI 1.44–1.77). Other clinical outcomes (in-hospital mortality and hospital LOS after RRS activation) were worse in the late deterioration group as well, and similar results were found in the propensity score-matched analysis (aOR for 28-day mortality 1.66, 95% CI 1.45–1.91).

Conclusions

Patients who stayed longer in the hospital before RRS activation had worse clinical outcomes. During the RRS team review of patients, hospital LOS before RRS activation should be considered as a predictor of future outcome.
Diabetic phenotype and prognosis of patients with heart failure and preserved ejection fraction in a real life cohort
Authors: Lejeune Sibille , Roy Clotilde , Slimani Alisson , Pasquet Agnès , Vancraeynest David , Vanoverschelde Jean-Louis , Gerber Bernhard L. , Beauloye Christophe , Pouleur Anne-Catherine
Published: February 2021

Background

Heart failure with preserved ejection fraction (HFpEF) is a heterogeneous syndrome, with several underlying etiologic and pathophysiologic factors. The presence of diabetes might identify an important phenotype, with implications for therapeutic strategies. While diabetes is associated with worse prognosis in HFpEF, the prognostic impact of glycemic control is yet unknown. Hence, we investigated phenotypic differences between diabetic and non-diabetic HFpEF patients (pts), and the prognostic impact of glycated hemoglobin (HbA1C).

Methods

We prospectively enrolled 183 pts with HFpEF (78 ± 9 years, 38% men), including 70 (38%) diabetics (type 2 diabetes only). They underwent 2D echocardiography (n = 183), cardiac magnetic resonance (CMR) (n = 150), and were followed for a combined outcome of all-cause mortality and first HF hospitalization. The prognostic impact of diabetes and glycemic control were determined with Cox proportional hazard models, and illustrated by adjusted Kaplan Meier curves.

Results

Diabetic HFpEF pts were younger (76 ± 9 vs 80 ± 8 years, p = 0.002), more obese (BMI 31 ± 6 vs 27 ± 6 kg/m2, p = 0.001) and suffered more frequently from sleep apnea (18% vs 7%, p = 0.032). Atrial fibrillation, however, was more frequent in non-diabetic pts (69% vs 53%, p = 0.028). Although no echocardiographic difference could be detected, CMR analysis revealed a trend towards higher LV mass (66 ± 18 vs 71 ± 14 g/m2, p = 0.07) and higher levels of fibrosis (53% vs 36% of patients had ECV by T1 mapping > 33%, p = 0.05) in diabetic patients.

Over 25 ± 12 months, 111 HFpEF pts (63%) reached the combined outcome (24 deaths and 87 HF hospitalizations). Diabetes was a significant predictor of mortality and hospitalization for heart failure (HR: 1.72 [1.1–2.6], p = 0.011, adjusted for age, BMI, NYHA class and renal function). In diabetic patients, lower levels of glycated hemoglobin (HbA1C < 7%) were associated with worse prognosis (HR: 2.07 [1.1–4.0], p = 0.028 adjusted for age, BMI, hemoglobin and NT-proBNP levels).

Conclusion

Our study highlights phenotypic features characterizing diabetic patients with HFpEF. Notably, they are younger and more obese than their non-diabetic counterpart, but suffer less from atrial fibrillation. Although diabetes is a predictor of poor outcome in HFpEF, intensive glycemic control (HbA1C < 7%) in diabetic patients is associated with worse prognosis.
Prognostic value of soluble suppression of tumorigenesis-2 (sST2) for cardiovascular events in coronary artery disease patients with and without diabetes mellitus
Authors: Li Man , Duan Lei , Cai Yulun , Hao Benchuan , Chen Jianqiao , Li Huiying , Liu Hongbin
Published: February 2021

Background

Soluble suppression of tumorigenesis-2 (sST2) is implicated in myocardial overload and has long been recognized as an inflammatory marker related to heart failure and acute coronary syndrome, but data on the prognostic value of sST2 in patients with coronary artery disease (CAD) remain limited. This study sought to investigate the prognostic value of sST2 in patients with established CAD and its predictive value in CAD patients with and without type 2 diabetes mellitus (T2DM).

Methods

A total of 3641 consecutive patients were included in this prospective cohort study. The primary end point was major adverse cardiovascular events (MACEs). The secondary end point was all-cause death. The association between sST2 and outcomes was investigated using multivariable Cox regression.

Results

During a median follow-up of 6.4 years, MACEs occurred in 775 patients, and 275 patients died. Multiple Cox regression models showed that a higher level of sST2 was an independent predictor of MACEs development (HR = 1.36, 95% CI 1.17–1.56, p < 0.001) and all-cause death (HR = 2.01, 95% CI 1.56–2.59, p < 0.001). The addition of sST2 to established risk factors significantly improved risk prediction of the composite outcome of MACEs and all-cause death (C-index, net reclassification index, and integrated discrimination improvement, all p < 0.05). In subgroup analysis depending on diabetes status, the diabetes group had a significantly higher level of sST2, which remained a significant predictor of MACEs and all-cause death in patients with and without T2DM in multivariable models. The area under the curve (AUC) of CAD patients with diabetes mellitus was significantly higher than that of those without T2DM. For MACEs, the AUC was 0.737 (patients with T2DM) vs 0.620 (patients without T2DM). For all-cause death, the AUC was 0.923 (patients with T2DM) vs 0.789 (patients without T2DM).

Conclusions

A higher level of sST2 is significantly associated with long-term MACEs and all-cause death in CAD patients with and without T2DM. sST2 has strong predictive value for cardiovascular adverse events in CAD patients with T2DM, and these results provide new evidence for the role of sST2.
Bacillus aryabhattai TFG5-mediated synthesis of humic substances from coir pith wastes
Authors: Muniraj Iniyakumar , Shameer Syed , Ramachandran Priyadharshini , Uthandi Sivakumar
Published: February 2021

Background

Humic substances (HS) form the largest proportion among all the constituents of soil organic matter and are a key component of the terrestrial ecosystem. HS plays a multifunctional role in the environment by controlling the biogeochemical carbon cycle, providing nutrients and bio-stimulants for plant growth, and interacting with inorganic and organic pollutants. The rate of formation of HS in soils determines its productivity and carbon sequestration capacity. Enhancement of HS synthesis in the soil through the microbial route not only increases CO2 sequestration but also mitigates the greenhouse gas emissions in the environment.

Result

In this study, we attempted to understand the mechanism of formation and enhancement of HS from coir pith wastes using the tyrosinase produced by Bacillus aryabhattai TFG5. The bacterium TFG5 isolated from the termite garden produced the tyrosinase (1.34 U mL−1) and laccase (2.1 U mL−1) at 48 h and 60 h of fermentation, respectively. The extracellular tyrosinase from B. aryabhattai TFG5 was designated as TyrB. Homology modeling of TyrB revealed a structure with a predicted molecular mass of 35.23 kDa and two copper ions in the active center with its conserved residues required for the tyrosinase activity. TyrB efficiently transformed and polymerized standard phenols, such as p-cresol, p-hydroxyl benzoic acid, Levo DOPA, and 2,6 DMP, besides transforming free phenols in coir pith wash water (CWW). Additionally, UV–Vis and FT-IR spectra of the degradation products of the coir pith treated with TyrB revealed the formation of HS within 3 days of incubation. Furthermore, the E472/664 ratio of the degradation products revealed a higher degree of condensation of the aromatic carbons and the presence of more aliphatic structures in the HS.

Conclusion

The results confirmed the influence of TyrB for the effective synthesis of HS from coir pith wastes. The results of the present study also confirm the recently accepted theory of humification proposed by the International Humic Substances Society.
Identification of glycolysis related pathways in pancreatic adenocarcinoma and liver hepatocellular carcinoma based on TCGA and GEO datasets
Authors: Li Ji , Zhu Chen , Yue Peipei , Zheng Tianyu , Li Yan , Wang Biao , Meng Xin , Zhang Yao
Published: February 2021

Background

Abnormal energy metabolism is one of the characteristics of tumor cells, and it is also a research hotspot in recent years. Due to the complexity of digestive system structure, the frequency of tumor is relatively high. We aim to clarify the prognostic significance of energy metabolism in digestive system tumors and the underlying mechanisms.

Methods

Gene set variance analysis (GSVA) R package was used to establish the metabolic score, and the score was used to represent the metabolic level. The relationship between the metabolism and prognosis of digestive system tumors was explored using the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Volcano plots and gene ontology (GO) analyze were used to show different genes and different functions enriched between different glycolysis levels, and GSEA was used to analyze the pathway enrichment. Nomogram was constructed by R package based on gene characteristics and clinical parameters. qPCR and Western Blot were applied to analyze gene expression. All statistical analyses were conducted using SPSS, GraphPad Prism 7, and R software. All validated experiments were performed three times independently.

Results

High glycolysis metabolism score was significantly associated with poor prognosis in pancreatic adenocarcinoma (PAAD) and liver hepatocellular carcinoma (LIHC). The STAT3 (signal transducer and activator of transcription 3) and YAP1 (Yes1-associated transcriptional regulator) pathways were the most critical signaling pathways in glycolysis modulation in PAAD and LIHC, respectively. Interestingly, elevated glycolysis levels could also enhance STAT3 and YAP1 activity in PAAD and LIHC cells, respectively, forming a positive feedback loop.

Conclusions

Our results may provide new insights into the indispensable role of glycolysis metabolism in digestive system tumors and guide the direction of future metabolism–signaling target combined therapy.
Prognostic significance of pretreatment controlling nutritional status score in urological cancers: a systematic review and meta‐analysis
Authors: Niu Xinhao , Zhu Zhe , Bao Juan
Published: February 2021

Background

Controlling Nutritional Status (CONUT) score is a novel nutrition-based biomarker that has been reported for predicting survival in various cancers. However, the relationship between CONUT score and prognosis of urological cancers remains unclear. Hence, we performed this meta-analysis to evaluate the prognostic significance of CONUT score for patients with urological cancers.

Methods

PubMed, Embase, the Cochrane Library and National Knowledge Infrastructure (CNKI) were systematically searched up to October 2020. The pooled hazard ratios (HRs) with 95% confidence intervals (CIs) were calculated to evaluate the association of CONUT score with overall survival (OS), cancer-specific survival (CSS) and recurrence/disease/progress-free survival (RFS/DFS/PFS) in urological cancers.

Results

A total of 12 articles with 13 studies were included in the analysis. Pooled results indicated that increased CONUT score predicted poor OS (HR: 1.78, 95% CI 1.51–2.09, p < 0.001), CSS (HR: 2.14, 95% CI 1.55–2.97, p < 0.001) and RFS/DFS/PFS (HR: 1.57, 95% CI 1.35–1.84, p < 0.001). Subgroup analysis by cancer type revealed that high CONUT score associated with worse OS in renal cell carcinoma (RCC) and urothelial cancer (UC) (HR: 3.05, 95% CI 2.07–4.50, p < 0.001; HR: 1.58, 95% CI 1.32–1.89, p < 0.001). Similar results could be found in CSS (RCC HR: 2.67, 95% CI 1.87–3.81, p < 0.011; UC HR: 1.68, 95% CI 1.09–2.59, p = 0.011) and in RFS/DFS/PFS (RCC HR: 1.96, 95% CI 1.44–2.66, p < 0.001; UC HR: 1.42, 95% CI 1.18–1.71, p < 0.001).

Conclusions

These results illustrated that the high CONUT score may predict worse survival for patients suffering from urological cancers. Therefore, the CONUT score may represent an effective prognostic indicator in urological cancers.
Identification the ferroptosis-related gene signature in patients with esophageal adenocarcinoma
Authors: Zhu Lei , Yang Fugui , Wang Lingwei , Dong Lin , Huang Zhiyuan , Wang Guangxue , Chen Guohan , Li Qinchuan
Published: February 2021

Background

Ferroptosis is a recently recognized non-apoptotic cell death that is distinct from the apoptosis, necroptosis and pyroptosis. Considerable studies have demonstrated ferroptosis is involved in the biological process of various cancers. However, the role of ferroptosis in esophageal adenocarcinoma (EAC) remains unclear. This study aims to explore the ferroptosis-related genes (FRG) expression profiles and their prognostic values in EAC.

Methods

The FRG data and clinical information were downloaded from The Cancer Genome Atlas (TCGA) database. Univariate and multivariate cox regressions were used to identify the prognostic FRG, and the predictive ROC model was established using the independent risk factors. GO and KEGG enrichment analyses were performed to investigate the bioinformatics functions of significantly different genes (SDG) of ferroptosis. Additionally, the correlations of ferroptosis and immune cells were assessed through the single-sample gene set enrichment analysis (ssGSEA) and TIMER database. Finally, SDG were verified in clinical EAC specimens and normal esophageal mucosal tissues.

Results

Twenty-eight significantly different FRG were screened from 78 EAC and 9 normal tissues. Enrichment analyses showed these SDG were mainly related to the iron-related pathways and metabolisms of ferroptosis. Gene network demonstrated the TP53, G6PD, NFE2L2 and PTGS2 were the hub genes in the biology of ferroptosis. Cox regression analyses demonstrated four FRG (CARS1, GCLM, GLS2 and EMC2) had prognostic values for overall survival (OS) (all P < 0.05). ROC curve showed better predictive ability using the risk score (AUC = 0.744). Immune cell enrichment analysis demonstrated that the types of immune cells and their expression levels in the high-risk group were significant different with those in the low-risk group (all P < 0.05). The experimental results confirmed the ALOX5, NOX1 were upregulated and the MT1G was downregulated in the EAC tissues compared with the normal esophageal mucosal tissues (all P < 0.05).

Conclusions

We identified differently expressed ferroptosis-related genes that may involve in EAC. These genes have significant values in predicting the patients’ OS and targeting ferroptosis may be an alternative for therapy. Further studies are necessary to verify these results of our study.
LncRNA HOXA-AS3 promotes gastric cancer progression by regulating miR-29a-3p/LTβR and activating NF-κB signaling
Authors: Qu Feng , Zhu Bin , Hu Yi-Lin , Mao Qin-Sheng , Feng Ying
Published: February 2021

Background

Gastric cancer (GC) is among the most common and deadliest cancers globally. Many long non-coding RNAs (lncRNAs) are key regulators of GC pathogenesis. This study aimed to define the role of HOXA-AS3 in this oncogenic context.

Methods

Levels of HOXA-AS3 expression in GC were quantified via qPCR. The effects of HOXA-AS3 knockdown on GC cells function were evaluated in vitro using colony formation assays, wound healing assays and transwell assays. Subcutaneous xenograft and tail vein injection tumor model systems were generated in nude mice to assess the effects of this lncRNA in vivo. The localization of HOXA-AS3 within cells was confirmed by subcellular fractionation, and predicted microRNA (miRNA) targets of this lncRNA and its ability to modulate downstream NF-κB signaling in GC cells were evaluated via luciferase-reporter assays, immunofluorescent staining, and western blotting.

Results

GC cells and tissues exhibited significant HOXA-AS3 upregulation (P < 0.05), and the levels of this lncRNA were found to be correlated with tumor size, lymph node status, invasion depth, and Helicobacter pylori infection status. Knocking down HOXA-AS3 disrupted GC cell proliferation, migration, and invasion in vitro and tumor metastasis in vivo. At a mechanistic level, we found that HOXA-AS3 was able to sequester miR-29a-3p, thereby regulating the expression of LTβR and modulating NF-κB signaling in GC.

Conclusion

HOXA-AS3/miR-29a-3p/LTβR/NF-κB regulatory axis contributes to the progression of GC, thereby offering novel target for the prognosis and treatment of GC.
Inhibitory role of ATF3 in gastric cancer progression through regulating cell EMT and stemness
Authors: Huang Chuanqian , Chen Renli , Zheng Fangjing , Tang Yirong , Wang Xiukang , Chen Zichun , Lai Xiaolan
Published: February 2021

Background

Gastric cancer (GC) is one of the most common cancers and the third leading cause of cancer related mortality worldwide. The 5-year survival rate is rather low owing to advanced unresectable and distant metastasis. The EMT has been widely implicated in the stemness, metastatic dormancy, and chemoresistance of different solid tumors. Given the fact that activating transcription factor-3 (ATF3) is a member of the ATF/CREB family of transcription factors and its role in regulation of GC recurrence and metastasis remain poorly understood, the aim of the present study was to investigate its potential impact in epithelial–mesenchymal transition (EMT) and cancer stem cell (CSC) properties and GC aggression.

Methods

To elucidate the potential role of ATF3 in gastric cancer, we utilized SGC-7901 and MGC-803 gastric cancer cell lines as research models and constructed stable cell lines overexpressing ATF3. We conducted a series of assays including cell proliferation, colony formation, cell migration, tumorsphere formation, and invasion to investigate the functional roles of ATF3 in stemness of gastric cancer. The possible effect of ATF3 on epithelial–mesenchymal transition (EMT) was assessed through flow cytometry and qRT-PCR. In vivo functional effect of upregulation of ATF3 on tumor growth was examined in a mouse xenograft model.

Results

We found that overexpression of ATF3 inhibited cell proliferation, colony formation, cell migration and invasion. In addition, up-regulation of ATF3 attenuated tumorsphere formation, cell stemness, and potentially decreased expression of EMT markers. Moreover, ATF3 overexpression inhibited tumorigenesis in mouse xenograft model.

Conclusion

Our data suggest a suppressive role of ATF3 in gastric cancer development. Our findings will provide a potential therapeutic strategy and novel drug target for gastric cancer.
Selecting an anti-malarial clinical candidate from two potent dihydroisoquinolones
Authors: Chen Yizhe , Zhu Fangyi , Hammill Jared , Holbrook Gloria , Yang Lei , Freeman Burgess , White Karen L. , Shackleford David M. , O’Loughlin Kathleen G. , Charman Susan A. , Mirsalis Jon C. , Guy R. Kiplin
Published: February 2021

Background

The ongoing global malaria eradication campaign requires development of potent, safe, and cost-effective drugs lacking cross-resistance with existing chemotherapies. One critical step in drug development is selecting a suitable clinical candidate from late leads. The process used to select the clinical candidate SJ733 from two potent dihydroisoquinolone (DHIQ) late leads, SJ733 and SJ311, based on their physicochemical, pharmacokinetic (PK), and toxicity profiles is described.

Methods

The compounds were tested to define their physicochemical properties including kinetic and thermodynamic solubility, partition coefficient, permeability, ionization constant, and binding to plasma proteins. Metabolic stability was assessed in both microsomes and hepatocytes derived from mice, rats, dogs, and humans. Cytochrome P450 inhibition was assessed using recombinant human cytochrome enzymes. The pharmacokinetic profiles of single intravenous or oral doses were investigated in mice, rats, and dogs.

Results

Although both compounds displayed similar physicochemical properties, SJ733 was more permeable but metabolically less stable than SJ311 in vitro. Single dose PK studies of SJ733 in mice, rats, and dogs demonstrated appreciable oral bioavailability (60–100%), whereas SJ311 had lower oral bioavailability (mice 23%, rats 40%) and higher renal clearance (10–30 fold higher than SJ733 in rats and dogs), suggesting less favorable exposure in humans. SJ311 also displayed a narrower range of dose-proportional exposure, with plasma exposure flattening at doses above 200 mg/kg.

Conclusion

SJ733 was chosen as the candidate based on a more favorable dose proportionality of exposure and stronger expectation of the ability to justify a strong therapeutic index to regulators.
Computational flow cytometric analysis to detect epidermal subpopulations in human skin
Authors: Zhang Lidan , Cen Ying , Huang Qiaorong , Li Huifang , Mo Xianming , Meng Wentong , Chen Junjie
Published: February 2021

Background

The detection and dissection of epidermal subgroups could lead to an improved understanding of skin homeostasis and wound healing. Flow cytometric analysis provides an effective method to detect the surface markers of epidermal cells while producing high-dimensional data files.

Methods

A 9-color flow cytometric panel was optimized to reveal the heterogeneous subgroups in the epidermis of human skin. The subsets of epidermal cells were characterized using automated methods based on dimensional reduction approaches (viSNE) and clustering with Spanning-tree Progression Analysis of Density-normalized Events (SPADE).

Results

The manual analysis revealed differences in epidermal distribution between body sites based on a series biaxial gating starting with the expression of CD49f and CD29. The computational analysis divided the whole epidermal cell population into 25 clusters according to the surface marker phenotype with SPADE. This automatic analysis delineated the differences between body sites. The consistency of the results was confirmed with PhenoGraph.

Conclusion

A multicolor flow cytometry panel with a streamlined computational analysis pipeline is a feasible approach to delineate the heterogeneity of the epidermis in human skin.
Socio-economic factors do also matter: comments on the article “can climatic factors explain the differences in COVID-19 incidence and severity across the SPANISH regions?: an ecological study”
Authors: Cacho Pedro Muñoz , Hernández José L. , López-Hoyos Marcos , Martínez-Taboada Víctor M.
Published: February 2021

Phosri et al., commented on our previous study about the influence of climate variables at the beginning of the SARS-CoV-2 pandemic in Spain. They showed the impact of the association of gross domestic product (GDP) with the cumulative COVID-19 incidence per 105 inhabitants in our country and the rise of several methodologic issues. Here we discussed the main advantages and disadvantages of ecological studies and we advocate to test the hypothesis created in this type of studies using individual-level research designs.
Gold nanoparticles reduce inflammation in cerebral microvessels of mice with sepsis
Authors: Di Bella Davide , Ferreira João P. S. , Silva Renee de Nazare O. , Echem Cinthya , Milan Aline , Akamine Eliana H. , Carvalho Maria H. , Rodrigues Stephen F.
Published: February 2021

Background

Sepsis is an emergency medical condition that can lead to death and it is defined as a life-threatening organ dysfunction caused by immune dysregulation in response to an infection. It is considered the main killer in intensive care units. Sepsis associated-encephalopathy (SAE) is mostly caused by a sepsis-induced systemic inflammatory response. Studies report SAE in 14–63% of septic patients. Main SAE symptoms are not specific and usually include acute impairment of consciousness, delirium and/or coma, along with electroencephalogram (EEG) changes. For those who recover from sepsis and SAE, impaired cognitive function, mobility and quality of life are often observed months to years after hospital discharge, and there is no treatment available today to prevent that. Inflammation and oxidative stress are key players for the SAE pathophysiology. Gold nanoparticles have been demonstrated to own important anti-inflammatory properties. It was also reported 20 nm citrate-covered gold nanoparticles (cit-AuNP) reduce oxidative stress. In this context, we tested whether 20 nm cit-AuNP could alleviate the acute changes caused by sepsis in brain of mice, with focus on inflammation. Sepsis was induced in female C57BL/6 mice by cecal ligation and puncture (CLP), 20 nm cit-AuNP or saline were intravenously (IV) injected 2 h after induction of sepsis and experiments performed 6 h after induction. Intravital microscopy was used for leukocyte and platelet adhesion study in brain, blood brain barrier (BBB) permeability carried out by Evans blue assay, cytokines measured by ELISA and real time PCR, cell adhesion molecules (CAMs) by flow cytometry and immunohistochemistry, and transcription factors, by western blotting.

Results

20 nm cit-AuNP treatment reduced leukocyte and platelet adhesion to cerebral blood vessels, prevented BBB failure, reduced TNF- concentration in brain, and ICAM-1 expression both in circulating polymorphonuclear (PMN) leukocytes and cerebral blood vessels of mice with sepsis. Furthermore, 20 nm cit-AuNP did not interfere with the antibiotic effect on the survival rate of mice with sepsis.

Conclusions

Cit-AuNP showed important anti-inflammatory properties in the brain of mice with sepsis, being a potential candidate to be used as adjuvant drug along with antibiotics in the treatment of sepsis to avoid SAE
Correlates of recent nonfatal overdose among people who inject drugs in West Virginia
Authors: Ahmad N. Jia , Allen Sean T. , White Rebecca Hamilton , Schneider Kristin E. , O’Rourke Allison , Perdue Michelle , Babcock Charles , Kilkenny Michael E. , Sherman Susan G.
Published: February 2021

Aim

Experiencing a nonfatal overdose (NFOD) is a significant risk factor for a subsequent nonfatal or fatal overdose. Overdose mortality rates in rural Appalachian states are some of the highest in the USA, but little is known about correlates of overdose among rural populations of people who inject drugs (PWID). Our study aimed to identify correlates of experiencing a recent (past 6 months) NFOD among rural PWID in Cabell County, West Virginia.

Methods

Using data from a June–July 2018 cross-sectional survey that was designed to estimate the size and characteristics of the PWID population in Cabell County, West Virginia, we used log binomial regression to identify correlates (e.g., structural vulnerabilities and substance use) of NFOD in the past 6 months.

Results

The majority of our sample of 420 PWID were male (61.2%), White, non-Hispanic (83.6%), and reported recent heroin injection (81.0%). More than two-fifths (42.6%) experienced a recent NFOD. Independent correlates of NFOD included witnessing an overdose in the past 6 months (adjusted prevalence ratio [aPR] = 2.28; 95% CI 1.48–3.50), attempting to quit using drugs in the past 6 months (aPR = 1.54; 95% CI 1.11–2.14), and the number of drugs injected (aPR = 1.16; 95% CI 1.10–1.23)

Conclusions

A large proportion of rural PWID in Appalachia reported having recently overdosed. The associations between witnessing an overdose, attempting to quit using drugs, and number of drugs injected with recent nonfatal overdose underscore the need for expanded access to overdose prevention resources that are tailored to the needs of this population. Expanding access to evidence-based overdose prevention strategies—such as take-home naloxone programs, treatment with methadone or buprenorphine, and harm reduction services—may decrease overdose morbidity and mortality among rural PWID in Appalachia.