bluuebunny/crossref_metadata_2025 huggingface dataset:
A Negative (1,3)-β-D-Glucan Result Alone Is Not Sufficient to Rule Out a Diagnosis of Pneumocystis Pneumonia in Patients With Hematological Malignancies
Authors: Damiani Céline , Demey Baptiste , Pauc Cécile , Le Govic Yohann , Totet Anne
Published: August 2021

Background: Serum (1,3)-β-D-glucan (BG) testing is increasingly being used in the diagnostic armamentarium for invasive fungal diseases. Given its high sensitivity, some studies suggest that a negative BG result contributes to rule out a diagnosis of Pneumocystis pneumonia (PCP). However, recent reports described a suboptimal sensitivity in HIV-negative immunocompromised patients. In this study, we evaluated the performance of BG assay for PCP diagnosis in HIV-negative patients with diverse PCP risk factors. We also assessed the correlation between Pneumocystis jirovecii load in pulmonary samples and serum BG levels.

Methods: We retrospectively included HIV-negative patients with microscopically proven PCP and for whom a BG result was available. We also enrolled patients colonized by Pneumocystis as control group. Colonized patients were matched with PCP patients based on their underlying condition that exposed to PCP. Pulmonary fungal loads were determined by an in-house real-time PCR, and BG levels were measured by using the Fungitell® kit (Associates of Cape Cod, Inc.).

Results: Thirty-nine patients were included in each of the two groups. Thirty-four of 39 PCP patients and one of 39 colonized patient had a positive BG test, resulting in a sensitivity of 0.87 (95% CI: 0.73–0.94), a specificity of 0.97 (95% CI: 0.87–0.99), a positive predictive value of 0.97 (95% CI: 0.85–0.99), and a negative predictive value of 0.88 (95% CI: 0.75–0.95) for BG assay. Nonetheless, median BG level differed according to the underlying condition. Among the PCP group, the lowest median level of 211 pg/ml was observed in patients with hematological malignancy (HM) and differed significantly from that observed either in solid organ transplants (3,473 pg/ml) or in patients with autoimmune or inflammatory disorder (3,480 pg/ml). Indeed, the sensitivity of BG assay was estimated at 0.64 (95% CI: 0.35–0.85) in HM patients and was lower than the one observed in the whole PCP group. Furthermore, BG level and fungal burden correlated poorly among all PCP patients.

Conclusion: BG is not a reliable biomarker for ruling out PCP in HIV-negative patients with HM. Interpretation of a negative BG result should take into account, but not be limited to, the underlying condition predisposing to PCP.
Recent Developments in Free Energy Calculations for Drug Discovery
Authors: King Edward , Aitchison Erick , Li Han , Luo Ray
Published: August 2021

The grand challenge in structure-based drug design is achieving accurate prediction of binding free energies. Molecular dynamics (MD) simulations enable modeling of conformational changes critical to the binding process, leading to calculation of thermodynamic quantities involved in estimation of binding affinities. With recent advancements in computing capability and predictive accuracy, MD based virtual screening has progressed from the domain of theoretical attempts to real application in drug development. Approaches including the Molecular Mechanics Poisson Boltzmann Surface Area (MM-PBSA), Linear Interaction Energy (LIE), and alchemical methods have been broadly applied to model molecular recognition for drug discovery and lead optimization. Here we review the varied methodology of these approaches, developments enhancing simulation efficiency and reliability, remaining challenges hindering predictive performance, and applications to problems in the fields of medicine and biochemistry.
Multifunctional Fructose 1,6-Bisphosphate Aldolase as a Therapeutic Target
Authors: Pirovich David B. , Da’dara Akram A. , Skelly Patrick J.
Published: August 2021

Fructose 1,6-bisphosphate aldolase is a ubiquitous cytosolic enzyme that catalyzes the fourth step of glycolysis. Aldolases are classified into three groups: Class-I, Class-IA, and Class-II; all classes share similar structural features but low amino acid identity. Apart from their conserved role in carbohydrate metabolism, aldolases have been reported to perform numerous non-enzymatic functions. Here we review the myriad “moonlighting” functions of this classical enzyme, many of which are centered on its ability to bind to an array of partner proteins that impact cellular scaffolding, signaling, transcription, and motility. In addition to the cytosolic location, aldolase has been found the extracellular surface of several pathogenic bacteria, fungi, protozoans, and metazoans. In the extracellular space, the enzyme has been reported to perform virulence-enhancing moonlighting functions e.g., plasminogen binding, host cell adhesion, and immunomodulation. Aldolase’s importance has made it both a drug target and vaccine candidate. In this review, we note the several inhibitors that have been synthesized with high specificity for the aldolases of pathogens and cancer cells and have been shown to inhibit classical enzyme activity and moonlighting functions. We also review the many trials in which recombinant aldolases have been used as vaccine targets against a wide variety of pathogenic organisms including bacteria, fungi, and metazoan parasites. Most of such trials generated significant protection from challenge infection, correlated with antigen-specific cellular and humoral immune responses. We argue that refinement of aldolase antigen preparations and expansion of immunization trials should be encouraged to promote the advancement of promising, protective aldolase vaccines.
Toward More Robust Hand Gesture Recognition on EIT Data
Authors: Leins David P. , Gibas Christian , Brück Rainer , Haschke Robert
Published: August 2021

Striving for more robust and natural control of multi-fingered hand prostheses, we are studying electrical impedance tomography (EIT) as a method to monitor residual muscle activations. Previous work has shown promising results for hand gesture recognition, but also lacks generalization across multiple sessions and users. Thus, the present paper aims for a detailed analysis of an existing EIT dataset acquired with a 16-electrode wrist band as a prerequisite for further improvements of machine learning results on this type of signal. The performed t-SNE analysis confirms a much stronger inter-session and inter-user variance compared to the expected in-class variance. Additionally, we observe a strong drift of signals within a session. To handle these challenging problems, we propose new machine learning architectures based on deep learning, which allow to separate undesired from desired variation and thus significantly improve the classification accuracy. With these new architectures we increased cross-session classification accuracy on 12 gestures from 19.55 to 30.45%. Based on a fundamental data analysis we developed three calibration methods and thus were able to further increase cross-session classification accuracy to 39.01, 55.37, and 56.34%, respectively.
Serum Cystatin C Predicts Stroke Clinical Outcomes at 1 Year Independent of Renal Function
Authors: Ding Yarong , Liu Liping , Chen Zimo , Li Hao , Pan Yuesong , Wang Junfeng , Meng Xia , Lin Jinxi , Jing Jing , Xie Xuewei , Xiang Xianglong , Wang Yongjun
Published: August 2021

Objective: Serum cystatin C (CysC) is a sensitive marker of renal function to predict cardiovascular diseases. We aimed to investigate the predictive value of CysC for clinical outcomes independent of renal function in patients with acute ischemic stroke (AIS).

Methods: We measured serum CysC levels in 10,256 AIS patients from Third China National Stroke Registry (CNSR-III). The primary outcome was a combination of all-cause mortality and major disability (modified Rankin scale score, 3–6). Secondary outcomes included stroke recurrence and combined vascular events at 1 year. Outcomes were analyzed using logistic regression and Cox proportional hazards models, respectively.

Results: The median CysC of included patients was 0.95 mg/l (interquartile range, 0.83–1.10 mg/l). A U-shaped association was observed between CysC and primary outcome (all-cause mortality or major disability) [quartile (Q)1 vs. Q2: adjusted odds ratio (aOR) 1.29, 95% CI 1.06–1.58, p = 0.012; Q3 vs. Q2: aOR 1.12, 95% CI 0.93–1.35, p = 0.242; Q4 vs. Q2: aOR 1.35, 95% CI 1.10–1.65, p = 0.004]. A similar trend also existed in “preserved renal function” patients. Adding CysC to a model containing conventional risk factors improved the model performance with integrated discrimination improvement (IDI) of 0.13% (p = 0.016) and net reclassification index (NRI) of 13.10% (p <0.001) for primary outcome. No significant association was observed for stroke recurrence or combined vascular event rate in different CysC quartiles.

Conclusions: CysC showed a U-shaped correlation with 1-year stroke clinical outcome, suggesting that serum CysC may not only be a simple candidate marker of renal function.
Long-Term Vestibular Outcomes in Cochlear Implant Recipients
Authors: Rasmussen Kasper Møller Boje , West Niels , Tian Luchen , Cayé-Thomasen Per
Published: August 2021

Background: Vestibular dysfunction is likely the most common complication to cochlear implantation (CI) and may, in rare cases, result in persistent severe vertigo. Literature on long-term vestibular outcomes is scarce.

Objective: This paper aims to evaluate vestibular dysfunction before and after cochlear implantation, the long-term vestibular outcomes, and follows up on previous findings of 35 consecutive adult cochlear implantations evaluated by a battery of vestibular tests.

Methods: A prospective observational longitudinal cohort study was conducted on 35 CI recipients implanted between 2018 and 2019; last follow-up was conducted in 2021. At the CI work-up (T0) and two postoperative follow-ups (T1 and T2), 4 and 14 months following implantation, respectively, all patients had their vestibular function evaluated. Evaluation with a vestibular test battery, involving video head impulse test (vHIT), cervical vestibular evoked myogenic potentials (cVEMP), caloric irrigation test, and dizziness handicap inventory (DHI), were performed at all evaluations.

Results: vHIT testing showed that 3 of 35 ears had abnormal vHIT gain preoperatively, which increased insignificantly to 4 of 35 at the last follow-up (p = 0.651). The mean gain in implanted ears decreased insignificantly from 0.93 to 0.89 (p = 0.164) from T0 to T2. Preoperatively, 3 CI ears had correction saccades, which increased to 11 at T2 (p = 0.017). Mean unilateral weakness increased from 19 to 40% from T0 to T2 (p < 0.005), and the total number of patients with either hypofunctioning or areflexic semicircular canals increased significantly from 7 to 17 (p < 0.005). Twenty-nine percent of CI ears showed cVEMP responses at T0, which decreased to 14% (p = 0.148) at T2. DHI total mean scores increased slightly from 10.9 to 12.8 from T0 to T1 and remained at 13.0 at T2 (p = 0.368). DHI scores worsened in 6 of 27 patients and improved in 4 of 27 subjects from T0 to T2.

Conclusion: This study reports significant deterioration in vestibular function 14 months after cochlear implantation, in a wide range of vestibular tests. vHIT, caloric irrigation, and cVEMP all measured an overall worsening of vestibular function at short-term postoperative follow-up. No significant deterioration or improvement was measured at the last postoperative follow-up; thus, vestibular outcomes reached a plateau. Despite vestibular dysfunction, most of the patients report less or unchanged vestibular symptoms.
Using Different Cutoffs to Define Tinnitus and Assess Its Prevalence—A Survey in the Dutch General Population
Authors: Rademaker Maaike M. , Smit Adriana L. , Brabers Anne E. M. , de Jong Judith D. , Stokroos Robert J. , Stegeman Inge
Published: August 2021

Introduction: Tinnitus prevalence numbers in the literature range between 5 and 43%, depending on the studied population and definition. It is unclear when tinnitus becomes pathologic.

Objectives: To assess the tinnitus prevalence in the Dutch general population with different cutoffs for definition.

Methods: In this cross-sectional study, a questionnaire was sent to a sample (n = 2,251) of the Nivel (Netherlands Institute for Health Services Research) Dutch Health Care Consumer Panel. Three questions were asked to assess the presence of tinnitus, duration, and frequency of the complaint. We classified people as having pathologic tinnitus when participants experienced it for 5–60 min (daily or almost daily or weekly), or tinnitus for >60 min or continuously (daily or almost daily or weekly or monthly), so tinnitus impact on daily life was measured with the Tinnitus Functional Index (TFI) and a single-item question. Answers were stratified to mid-decade years of age. Prevalence numbers were weighted by gender and age to match the Dutch population.

Results: Nine hundred thirty-two of 2,251 participants (41%) filled out the questionnaire. The median age was 67.0 (IQR 17) years. Three hundred thirty-eight of 932 (36%) experienced tinnitus for an undefined amount of time during the last year. Two hundred sixteen of 932 (23%) met our definition of having pathologic tinnitus (21% when weighted for age and gender). The median TFI score for all pathologic tinnitus participants was 16.6 (IQR 21.8). A percentage of 50.4% of the pathologic tinnitus participants had a TFI in the range 0–17, which can be interpreted as not a problem.

Conclusion: Twenty-three percent (unweighted) or 21% (weighted) of our sample met our definition of pathologic tinnitus, which was based on a combination of duration and frequency over the last year. The TFI score of 47.7% of the pathologic tinnitus participants is ≥18. This indicates that they consider the tinnitus to be at least “a small problem” [11.1% (unweighted) or 8.9% (weighted) of the total study group]. This study illustrates the difficulties with defining pathologic tinnitus. In addition, it demonstrates that tinnitus prevalence numbers vary with different definitions and, consequently, stresses the importance of using a uniform definition of tinnitus.
Could Brain–Computer Interface Be a New Therapeutic Approach for Body Integrity Dysphoria?
Authors: Chakraborty Stuti , Saetta Gianluca , Simon Colin , Lenggenhager Bigna , Ruddy Kathy
Published: August 2021

Patients suffering from body integrity dysphoria (BID) desire to become disabled, arising from a mismatch between the desired body and the physical body. We focus here on the most common variant, characterized by the desire for amputation of a healthy limb. In most reported cases, amputation of the rejected limb entirely alleviates the distress of the condition and engenders substantial improvement in quality of life. Since BID can lead to life-long suffering, it is essential to identify an effective form of treatment that causes the least amount of alteration to the person’s anatomical structure and functionality. Treatment methods involving medications, psychotherapy, and vestibular stimulation have proven largely ineffective. In this hypothesis article, we briefly discuss the characteristics, etiology, and current treatment options available for BID before highlighting the need for new, theory driven approaches. Drawing on recent findings relating to functional and structural brain correlates of BID, we introduce the idea of brain–computer interface (BCI)/neurofeedback approaches to target altered patterns of brain activity, promote re-ownership of the limb, and/or attenuate stress and negativity associated with the altered body representation.
Clinical Use of a Real-World Low Carbohydrate Diet Resulting in Reduction of Insulin Dose, Hemoglobin A1c, and Weight
Authors: Wolver Susan , Fadel Kristen , Fieger Ethan , Aburish Zein , O'Rourke Brennen , Chandler Toni-Marie , Shimotani Dorian , Clingempeel Natasha , Jain Shuchi , Jain Aashish , Puri Puneet
Published: August 2021

Introduction: Type 2 Diabetes Mellitus (T2DM) is increasing in epidemic proportions. In addition to the morbidity and mortality, for those treated with insulin, the physical, psychological, and financial tolls are often greater. Our real-world study evaluated a Low Carbohydrate Diet (LCD) in patients with T2DM on insulin with respect to glycemic control, insulin reduction, and weight loss.

Materials and Methods: A prospective cohort study was conducted via an Electronic Medical Record search for patients attending the Virginia Commonwealth University Medical Weight Loss Program from 2014 to 2020 with Type 2 Diabetes Mellitus who initially presented on insulin. Data was extracted for 1 year after enrollment. The weight loss program focuses on a LCD.

Results: Of 185 participants, the mean (± SD) age was 56.1 (9.9) years. Seventy percent were female and 63% were black. Eighty-five completed 12 months (45.9%), reduced their median (25–75% interquartile range, IQR) insulin dose from 69 to 0 units (0–18, p < 0.0001), HbA1c from 8 to 6.9% (6.2–7.8, p < 0.0001), and weight from 116 to 99 kg (85–120, p < 001). Eighty six percent who completed 12 months were able to reduce or discontinue insulin, with 70.6% completely discontinuing. Among all participants who completed 3, 6, or 12 months, 97.6% were able to reduce or eliminate insulin use.

Conclusion: In patients with T2DM on a LCD, it is possible to reduce and even discontinue insulin use while facilitating weight loss and achieving glycemic control. A Low Carbohydrate Diet should be offered to all patients with diabetes, especially those using insulin.
Viability, Sublethal Injury, and Release of Cellular Components From Alicyclobacillus acidoterrestris Spores and Cells After the Application of Physical Treatments, Natural Extracts, or Their Components
Authors: Bevilacqua Antonio , Petruzzi Leonardo , Speranza Barbara , Campaniello Daniela , Ciuffreda Emanuela , Altieri Clelia , Sinigaglia Milena , Corbo Maria Rosaria
Published: August 2021

Alicyclobacillus acidoterrestris is a spoiling microorganism regarded as one of the most important causes of spoilage of fruit juices and acidic products. In this paper, four strains of A. acidoterrestris (type strain-DSM 3922; two wild strains isolated from soil-C8 and C24; wild strain isolated from a spoiled pear juice CB1) were treated through natural extracts/active compounds from essential oils (EOs), and physical treatments were used to assess their susceptibility and the presence of sublethal injury. The characterization of damage was also performed. The results suggest that it is possible to control A. acidoterrestris through alternative approaches, although the effect relied upon the age of spores. In addition to the mere antimicrobial effect, some treatments could cause a sublethal injury on spores. Lemon extract was the most effective treatment for both the antimicrobial effect and the sublethal injury, as evidenced by the release of proteins, and calcium dipicolinate [dipicolinic acid (DPA)] by fresh spores and only DPA (with an exception for C8) by old spores. A sublethal injury with protein release was also found for physical treatments [US (ultrasound) or heating]. For the first time, this paper reports on the existence of a sublethal injury for A. acidoterrestris, and this evidence could also be a challenge, because injured microorganisms could restore their metabolism, or an opportunity to design new preserving treatments.
The Gut Microbiota Activates AhR Through the Tryptophan Metabolite Kyn to Mediate Renal Cell Carcinoma Metastasis
Authors: Dai Guoyu , Chen Xiang , He Yao
Published: August 2021

Background: The incidence of renal cell carcinoma (RCC) is increasing year by year. It is difficult to have complete treatment so far. Studies have shown that tryptophan metabolite Kynurenine (Kyn) affects cell proliferation, migration, apoptosis, adhesion, and differentiation. Our aim is to explore whether Kyn activates aromatic hydrocarbon receptor (AhR) to mediate RCC metastasis.

Methods: We collected RCC tissues and feces from RCC patients. 16S rRNA technology was performed to analyze the gut microbial composition of RCC patients. LC-MS/MS was used to analyze the gut microbial metabolites. The AhR was inhibited and treated with Kyn. Immunofluorescence was used to measure the degree of AhR activation. The migration and invasion ability of 786-O cells was tested by Transwell assay. Flow cytometry and cell cycle assay were utilized to observe the apoptosis and cycle of 786-O cells. CCK-8 assay was used to detect 786-O cells proliferation. qRT-PCR and Western blot were used to detect AhR and EMT-related genes expression level.

Results: AhR expression was up-regulated in RCC tissues. RCC gut microbiota was disordered. The proportion of Kyn was increased in RCC. After being treated with Kyn, the migration, invasion, and proliferation ability of 786-O cells were decreased. Furthermore, the expression of EMT-related protein E-cadherin decreased, and the expression of N-cadherin and Vimentin increased. The proportion of 786-O cells in the S phase increased. The apoptosis rate of 786-O cells was inhibited.

Conclusion: The tryptophan metabolite Kyn could activate AhR. Kyn could promote 786-O cells migration and invasion. Gut microbiota could activate AhR through its tryptophan metabolite Kyn to mediate RCC metastasis.
Review of Mendelian Randomization Studies on Ovarian Cancer
Authors: Guo Jian-Zeng , Xiao Qian , Gao Song , Li Xiu-Qin , Wu Qi-Jun , Gong Ting-Ting
Published: August 2021

Ovarian cancer (OC) is one of the deadliest gynecological cancers worldwide. Previous observational epidemiological studies have revealed associations between modifiable environmental risk factors and OC risk. However, these studies are prone to confounding, measurement error, and reverse causation, undermining robust causal inference. Mendelian randomization (MR) analysis has been established as a reliable method to investigate the causal relationship between risk factors and diseases using genetic variants to proxy modifiable exposures. Over recent years, MR analysis in OC research has received extensive attention, providing valuable insights into the etiology of OC as well as holding promise for identifying potential therapeutic interventions. This review provides a comprehensive overview of the key principles and assumptions of MR analysis. Published MR studies focusing on the causality between different risk factors and OC risk are summarized, along with comprehensive analysis of the method and its future applications. The results of MR studies on OC showed that higher BMI and height, earlier age at menarche, endometriosis, schizophrenia, and higher circulating β-carotene and circulating zinc levels are associated with an increased risk of OC. In contrast, polycystic ovary syndrome; vitiligo; higher circulating vitamin D, magnesium, and testosterone levels; and HMG-CoA reductase inhibition are associated with a reduced risk of OC. MR analysis presents a2 valuable approach to understanding the causality between different risk factors and OC after full consideration of its inherent assumptions and limitations.
The Fibrosis-Targeted Collagen/Integrins Gene Profile Predicts Risk of Metastasis in Pulmonary Neuroendocrine Neoplasms
Authors: Prieto Tabatha Gutierrez , Machado-Rugolo Juliana , Baldavira Camila Machado , Velosa Ana Paula Pereira , Teodoro Walcy Rosolia , Saber Alexandre Muxfeldt Ab´ , Capelozzi Vera Luiza
Published: August 2021

Recently, collagen/integrin genes have shown promise as predictors of metastasis mainly in non-small cell lung cancer and breast cancer. However, it is unknown if these gene expression profiling differ in metastatic potential of pulmonary neuroendocrine neoplasms (PNENs). In this study, we sought to identify differentially expressed collagen/integrin genes in PNENs in order to understand the molecular mechanisms underlying the development of stroma-associated fibrosis for invasion and metastasis. We compared collagen/integrin gene expression profiling between PNE tumors (PNETs) and PNE carcinomas (PNECs) using a two-stage design. First, we used PCR Array System for 84 ECM-related genes, and among them, we found COL1A2, COL3A1, COL5A2, ITGA5, ITGAV, and ITGB1 functionally involved in the formation of the stroma-associated fibrosis among PNENs histological subtypes. Second, we examined the clinical association between the six collagen/integrin genes in tumor tissues from 24 patients with surgically excised PNENs. However, the pathological exam of their resected tissues demonstrated that 10 developed lymph node metastasis and 7 distant metastasis. We demonstrated and validated up regulation of the six fibrogenic genes in PNECs and down regulation in PNETs that were significantly associated with metastasis-free and overall survival (P<0.05). Our study implicates up regulation of fibrogenic genes as a critical molecular event leading to lymph node and distant metastasis in PNENs.
N6-Methylandenosine-Related lncRNAs Predict Prognosis and Immunotherapy Response in Bladder Cancer
Authors: Zhang Yuying , Zhu Baoyi , He Minghui , Cai Yi , Ying Xiaoling , Jiang Chonghe , Ji Weidong , Zeng Jianwen
Published: August 2021

Both lncRNAs and the N6-methyladenosine (m6A) modification are key regulators of tumorigenesis and innate immunity. However, little is known about the m6A modification of lncRNAs and their clinical and immune relevance in bladder cancer. In this study, we identified m6A-related lncRNAs using Pearson correlation analysis in The Cancer Genome Atlas (TCGA) and the IMvigor210 datasets. Next, univariate Cox regression was performed using the TCGA dataset to filter prognostic m6A-related lncRNAs, which were further subjected to the least absolute shrinkage and selection operator (LASSO) Cox regression to establish a 12 m6A-related lncRNA prognostic score (m6A-LRS). The m6A-LRS was validated in the IMvigor210 dataset. In addition, high m6A-LRS tumors, characterized by decreased tumor mutation load and neoantigen load, showed poorer response to immunotherapy than those with low m6A-LRS in the IMvigor210 dataset. Further, we constructed an m6A-LRS-based nomogram that demonstrated a strong ability to predict overall survival in patients with bladder cancer. Moreover, enrichment analysis revealed that tumor-associated biological processes, oncogenic signaling, and tumor hallmarks were commonly associated with a high m6A-LRS. Gene set variation analysis also indicated that high m6A-LRS was associated with activation of canonical oncogenic signatures, such as the epithelial-to-mesenchymal transition, cell cycle regulators, and DNA replication, as well as activation of immunosuppressive signatures, such as the T-cell exhaustion and pan-fibroblast-TGF-β response signatures. Furthermore, we observed distinct tumor microenvironment cell infiltration characteristics between high- and low-risk tumors. High m6A-LRS tumors showed reduced infiltration of CD8+ T-cells and enhanced infiltration of macrophages and fibroblasts. Additionally, we established a competing endogenous RNA network based on the12 m6A-related lncRNAs. Finally, three lncRNAs (SNHG16, SBF2-AS1, and BDNF-AS) were selected for further validation. The qualitative PCR assay on 10 pairs of bladder cancer and adjacent normal control samples validated the differential expression, and methylated RNA immunoprecipitation (MeRIP) analysis demonstrated a robust m6A enrichment in T24 bladder cancer cells compared with normal uroepithelial cells (SVHUC-1). In conclusion, this study introduced an m6A-related lncRNA signature that identified a subgroup of patients with poor prognoses and suboptimal immune responses, thus providing novel approaches for treatment response prediction and patient stratification in bladder cancer.
Prognostic Analysis of Gastric Signet Ring Cell Carcinoma and Hepatoid Adenocarcinoma of the Stomach: A Propensity Score-Matched Study
Authors: Yang Yu , Li Yuxuan , Du Xiaohui
Published: August 2021

Background

Hepatoid adenocarcinoma of the stomach (HAS) is a rare type of primary gastric cancer, and most previous studies have reported that HAS has a poor prognosis due to its aggressive biological behavior. The aim of this study was to compare the prognosis of HAS to that of gastric signet ring cell carcinoma (SRC).

Methods

This was a single-center, retrospective, observational cohort study (January 2010 to January 2016) of gastric cancer patients with pathological HAS and SRC. Overall survival was compared between HAS and SRC patients. We used univariate Cox regression, multivariate Cox regression, propensity score matching (PSM), inverse probability of treatment weighting, standardized mortality ratio weighting, standardized mortality ratio weighting, and overlap weighting to perform a prognostic analysis.

Results

A total of 725 (672 SRC and 53 HAS) patients were included. After nearest-neighbor 1:4 PSM, 200 SRC patients and 50 HAS patients were matched. Only in univariate Cox regression analysis with the cohort before PSM did HAS show a significantly worse prognosis than SRC [hazard ratio (HR), 1.66; 95% confidence interval (CI), 1.02–2.69, p = 0.040]. However, in the analysis of multivariate Cox regression with the cohort before PSM and series analysis based on the propensity score, all of the results indicated that there was no statistically significant difference in overall survival between HAS and SRC (all p > 0.05). Furthermore, in the subgroup of proximal location (p = 0.027), T stage 4a & 4b (p = 0.001), N stage 3a & 3b (p = 0.022), with cancer nodules (p = 0.026), serum CEA higher than the normal value (p = 0.038), and serum CA199 higher than the normal value (p = 0.023), the prognosis of HAS was significantly worse than that of SRC.

Conclusion

Based on our study, there was no statistically significant difference in overall survival between HAS and gastric SRC patients. However, in patients with an advanced tumor stage, HAS may have a worse overall survival than SRC.
A Nano-Pharmaceutical Formula of Quercetin Protects from Cardiovascular Complications Associated with Metabolic Syndrome
Authors: Ahmed Osama A. A. , Hassan Noura A. , Azhar Ahmad S. , El-Mas Mahmoud M. , El-Bassossy Hany M.
Published: August 2021

Metabolic syndrome (MetS) is closely associated with the development of cardiovascular diseases. We recently developed a nano-preparation of the flavonoid quercetin (QU) in a self-nanoemulsifying drug delivery system (SNEDDS). The latter comprised a mixture composed of pumpkin seed oil, D-α-Tocopherol polyethylene glycol 1,000 succinate and polyethylene glycol. The QU SNEDDS preparations exhibited a considerably higher bioavailability compared with the standard quercetin suspension. Here, we investigated whether the quercetin loaded SNEDDS could offer better protection compared with the standard formulation against cardiovascular complications of MetS in rats. MetS was induced by high fructose, high salt and high fat diet for 12 weeks while the nano-preparation or the standard suspension of quercetin was orally administered for the last 6 weeks. Compared to little effect for the standard quercetin suspension (MQ), the treatment of MetS rats with the quercetin loaded SNEDDS (MNQ) virtually abolished the depressant effect of MetS on contractility index (control, 114 ± 4; MetS, 92 ± 3; MQ, 100 ± 2; MNQ, 114 ± 6 1/s) and rate of rise in left ventricular pressure (dP/dtmax) (control, 8,171 ± 274; MetS, 6,664 ± 135; MQ, 6,776 ± 108; MNQ, 7,498 ± 303 mmHg/s). Likewise, the prolongation by MetS of electrocardiographic markers of arrhythmogenesis (QTc, JT, and Tpeak-to-Tend intervals) and concomitant rises in dicrotic notch pressure were preferentially reversed by quercetin nano-preparation. On the other hand, the rises in the isovolumic relaxation constant (Tau, denotes diastolic dysfunction), blood pressure, pulse pressure, and difference between systolic and dicrotic pressure (SDP difference) were equally improved by the two preparations of quercetin. Additionally, no differences were noted in the ability of the two quercetin preparations in abrogating the elevated oxidative (MDA) and inflammatory (TNFα) markers in cardiac tissues of MetS rats. Histopathological, microscopical signs of necrosis, inflammatory cell infiltration, and vascular congestion in MetS hearts were more markedly inhibited by the nano-preparation, compared with the standard preparation of quercetin. In conclusion, the quercetin loaded SNEDDS is evidently more advantageous than the standard preparation of the drug in alleviating functional and histopathological manifestations of cardiac damage incited by MetS.
A Birds-Eye (Re)View of Acid-Suppression Drugs, COVID-19, and the Highly Variable Literature
Authors: Mura Cameron , Preissner Saskia , Preissner Robert , Bourne Philip E.
Published: August 2021

This Perspective examines a recent surge of information regarding the potential benefits of acid-suppression drugs in the context of COVID-19, with a particular eye on the great variability (and, thus, confusion) that has arisen across the reported findings, at least as regards the popular antacid famotidine. The degree of inconsistency and discordance reflects contradictory conclusions from independent, clinical-based studies that took roughly similar approaches, in terms of both experimental design (retrospective, observational, cohort-based, etc.) and statistical analysis workflows (propensity-score matching and stratification into sub-cohorts, etc.). The contradictions and potential confusion have ramifications for clinicians faced with choosing therapeutically optimal courses of intervention: e.g., do any potential benefits of famotidine suggest its use in a particular COVID-19 case? (If so, what administration route, dosage regimen, duration, etc. are likely optimal?) As succinctly put this March in Freedberg et al. (2021), “…several retrospective studies show relationships between famotidine and outcomes in COVID-19 and several do not.” Beyond the pressing issue of possible therapeutic indications, the conflicting data and conclusions related to famotidine must be resolved before its inclusion/integration in ontological and knowledge graph (KG)–based frameworks, which in turn are useful for drug discovery and repurposing. As a broader methodological issue, note that reconciling inconsistencies would bolster the validity of meta-analyses which draw upon the relevant data-sources. And, perhaps most broadly, developing a system for treating inconsistencies would stand to improve the qualities of both 1) real world evidence-based studies (retrospective), on the one hand, and 2) placebo-controlled, randomized multi-center clinical trials (prospective), on the other hand. In other words, a systematic approach to reconciling the two types of studies would inherently improve the quality and utility of each type of study individually.
Preclinical Characterization of a Novel Anti-Cancer PD-L1 Inhibitor RPH-120
Authors: Kulikov Andrey , Shipaeva Elena , Dmitrieva Anastasia , Batrak Vera , Shipunov Georgy , Guy Colin , Smith Jill , Zhang Ran , Zhang Michael , Duan Jeff , Chestukhin Anton , Barbashov Sergei , Samsonov Mikhail , Lavrovsky Yan
Published: August 2021

RPH-120 is a novel fully human anti-PD-L1 IgG1 monoclonal antibody with specifically designed Asn300Ala mutation in Fc fragment. Surface plasmon resonance assay showed that affinity of the RPH-120 to the dimeric form of human PD-L1-Fc fusion protein was much higher than affinity to the monomeric His-tagged PD-L1. Further binding studies demonstrated that RPH-120 is able to bind to human and monkey but not mouse PD-L1. Tissue cross-reactivity study showed good comparability of human and Cynomolgus monkeys tissue staining. Bioactivity was assessed using mixed lymphocyte reaction assay. This study revealed that RPH-120 was able to activate T cells preventing PD1/PD-L1 interaction. Antitumor efficacy was analyzed in HCC-827 lung cancer xenografts in humanized CD34+ mice at three dosage levels: 20, 80, and 200 mg/kg. RPH-120 demonstrated significant tumor growth inhibition, and this inhibition was comparable to that of atezolizumab. In a single dose toxicity, toxicokinetic and dose range finding study performed in Cynomolgus monkeys, RPH-120 was administered via intravenous (IV) bolus or 60-min IV infusion, followed by 8-weeks recovery period. An acceptable toxicokinetic profile was demonstrated and administration at doses of up to 200 mg/kg was well tolerated by all animals. In conclusion, RPH-120 revealed promising in vitro and in vivo activity and safety. RPH-120 is a potent anti-PD-L1 drug candidate for cancer immunotherapy.
Self-Medication With Over-the-counter Medicines Among the Working Age Population in Metropolitan Areas of Thailand
Authors: Chautrakarn Sineenart , Khumros Waraporn , Phutrakool Phanupong
Published: August 2021

Background and Objectives: Self-medication with over-the-counter (OTC) medicines is becoming an increasingly popular practice around the world. The global prevalence rate of self-medication ranges from 11.2% to 93.7%, depending on the target population and country. However, there is a lack of data on the prevalence and practices of self-medication among the working-age population, particularly in Thailand metropolitan areas. The current study describes the prevalence of self-medication practices, adverse drug reactions and severity, reasons for self-medication, and basic medication knowledge among people of working age in metropolitan areas in Thailand.

Methods: We conducted an online cross-sectional study between December 2020 and January 2021. Descriptive statistics were used to analyze self-medication data. A chi-square test was used to assess the association between self-medication and sociodemographic characteristics.

Results: This study found high prevalence of self-medication among the working-age population in metropolitan areas of Thailand (88.2%). The most commonly used drug groups were NSAIDs (34.8%) and antibiotics (30.2%). Minor illness and easy access to pharmacies were the most common reasons for self-medication. Almost half of the participants' illnesses (42.6%) for which they self-medicated were not always completely cured, necessitating treatment at a hospital or clinic. Although only a small number of participants (ranged from 0.6 to 6.6%) experienced adverse drug reactions as a result of self-medication, some had severe symptoms that disrupted their daily lives or required hospitalization. In terms of basic medication knowledge, we discovered that study participants misunderstood some antibiotic drug concepts.

Conclusions: According to the study findings, it is recommended that more information about the risks of self-medication, drug adverse reactions, antibiotic stewardship, more supervision of the prohibition of over-the-counter drugs and selling practices, and adequate facilities for peoples access to medical services be provided at the policy level.
Rutin, A Natural Inhibitor of IGPD Protein, Partially Inhibits Biofilm Formation in Staphylococcus xylosus ATCC700404 in vitro and in vivo
Authors: Qu Qianwei , Cui Wenqiang , Xing Xiaoxu , Zou Rongfeng , Huang Xingyu , Wang Xiaozhen , Wu Tong , Bello-Onaghise God’spower , Yuan Shuguang , Li Yanhua
Published: August 2021

Staphylococcus xylosus (S. xylosus) has become an emerging opportunistic pathogen due to its strong biofilm formation ability. Simultaneously, the biofilm of bacteria plays an important role in antibiotic resistance and chronic infection. Here, we confirmed that rutin can effectively inhibit biofilm formation in S. xylosus, of which the inhibition mechanism involves its ability to interact with imidazole glycerol phosphate dehydratase (IGPD), a key enzyme in the process of biofilm formation. We designed experiments to target IGPD and inhibited its activities against S. xylosus. Our results indicated that the activity of IGPD and the amount of histidine decreased significantly under the condition of 0.8 mg/ml rutin. Moreover, the expression of IGPD mRNA (hisB) and IGPD protein was significantly down-regulated. Meanwhile, the results from molecular dynamic simulation and Bio-layer interferometry (BLI) technique showed that rutin could bind to IGPD strongly. Additionally, in vivo studies demonstrated that rutin treatment reduced inflammation and protect mice from acute mastitis caused by S. xylosus. In summary, our findings provide new insights into the treatment of biofilm mediated persistent infections and chronic bacterial infections. It could be helpful to design next generation antibiotics to against resistant bacteria.
Mouse Model of Loeys–Dietz Syndrome Shows Elevated Susceptibility to Periodontitis via Alterations in Transforming Growth Factor-Beta Signaling
Authors: Yamada Satoru , Tsushima Kenichiro , Kinoshita Masaki , Sakashita Hiromi , Kajikawa Tetsuhiro , Fujihara Chiharu , Yuan Hang , Suzuki Shigeki , Morisaki Takayuki , Murakami Shinya
Published: August 2021

Loeys–Dietz syndrome (LDS) is a syndromic connective tissue disorder caused by a heterozygous missense mutation in genes that encode transforming growth factor (TGF)-β receptor (TGFBR) 1 and 2. We encountered a patient with LDS, who had severe periodontal tissue destruction indicative of aggressive periodontitis. The patient had a missense mutation in the glycine and serine-rich domain of TGFBR1 exon 3. This G-to-T mutation at base 563 converted glycine to valine. We established an LDS model knock-in mouse that recapitulated the LDS phenotype. Homozygosity of the mutation caused embryonic lethality and heterozygous knock-in mice showed distorted and ruptured elastic fibers in the aorta at 24 weeks of age and died earlier than wildtype (WT) mice. We stimulated mouse embryonic fibroblasts (MEFs) from the knock-in mouse with TGF-β and examined their responses. The knock-in MEFs showed downregulated Serpine 1 mRNA expression and phosphorylation of Smad2 to TGF-β compared with WT MEFs. To clarify the influence of TGF-β signaling abnormalities on the pathogenesis or progression of periodontitis, we performed pathomolecular analysis of the knock-in mouse. There were no structural differences in periodontal tissues between WT and LDS model mice at 6 or 24 weeks of age. Micro-computed tomography revealed no significant difference in alveolar bone resorption between WT and knock-in mice at 6 or 24 weeks of age. However, TGF-β-related gene expression was increased significantly in periodontal tissues of the knock-in mouse compared with WT mice. Next, we assessed a mouse periodontitis model in which periodontal bone loss was induced by oral inoculation with the bacterial strain Porphyromonas gingivalis W83. After inoculation, we collected alveolar bone and carried out morphometric analysis. P. gingivalis-induced alveolar bone loss was significantly greater in LDS model mice than in WT mice. Peritoneal macrophages isolated from Tgfbr1G188V/+ mice showed upregulation of inflammatory cytokine mRNA expression induced by P. gingivalis lipopolysaccharide compared with WT macrophages. In this study, we established an LDS mouse model and demonstrated that LDS model mice had elevated susceptibility to P. gingivalis-induced periodontitis, probably through TGF-β signal dysfunction. This suggests that TGF-β signaling abnormalities accelerate the pathogenesis or progression of periodontitis.
Development of an in vitro Microtuberization and Temporary Immersion Bioreactor System to Evaluate Heat Stress Tolerance in Potatoes (Solanum tuberosum L.)
Authors: Gautam Sanjeev , Solis-Gracia Nora , Teale Megan K. , Mandadi Kranthi , Silva Jorge A. da , Vales M. Isabel
Published: August 2021

High temperature (heat) stress reduces tuber yield and quality of potatoes. Screening potatoes for heat tolerance is increasingly important, considering the climate change scenario and expansion of potatoes to countries where heat stress is an issue. In vitro screening for tolerance to abiotic stresses offers several advantages, including quick evaluation of numerous genotypes (clones) in reduced space, controlled environmental conditions (temperature and photoperiod), and free from confounding variables inherent to greenhouse and field conditions. In this study, we explored the feasibility of using a temporary immersion bioreactor system for heat tolerance screening of potatoes. We determined the best hormone-free microtuberizing media for this system (MSG with 8% sucrose) to enhance microtuber number and size. Comparisons of microtubers produced at 30°C as heat treatment, with 16°C as normal condition, allowed to identify heat tolerant and susceptible potato clones. The use of bioreactors allowed distinguishing well-formed (non-deformed) from deformed microtubers. Heat stress increased the total biomass of plant tissues in all the clones. However, the effect of heat stress on microtuber number and weight varied among the clones. Incubation at 30°C decreased the weight and number of non-deformed microtubers in all the clones except for Reveille Russet in which the weight of non-deformed microtubers was significantly increased and the count of non-deformed microtubers was not affected. The potato variety Reveille Russet, which was selected under high-temperature field conditions in Texas, had many non-deformed microtubers per explant and the highest microtuber weight among four clones evaluated under heat stress. We described a faster and reliable in vitro microtuberization system for abiotic stress tolerance screening, identified Reveille Russet as a promising heat-tolerant potato variety, and confirmed Russet Burbank and Atlantic as susceptible heat-tolerant checks.
Genome-Wide Identification and Characterization of Calcium Metabolism Related Gene Families in Arabidopsis thaliana and Their Regulation by Bacillus amyloliquefaciens Under High Calcium Stress
Authors: Gong Jiyi , Shi Tianlong , Li Yuke , Wang Hancheng , Li Fei
Published: August 2021

Several gene families involved in calcium signaling have been detected in plants, including calmodulin (CaM), calcium dependent protein kinases (CDPK), calcineurin B-like (CBL) and cyclic nucleotide-gated channels (CNGCs). In our previous study, we demonstrated that Bacillus amyloliquefaciens LZ04 (B. amyloliquefaciens LZ04) regulate genes involved in calcium stress in Arabidopsis thaliana (A. thaliana). Here, we aimed to explore the potential involvement of calcium-related gene families in the response of A. thaliana to calcium stress and the potential regulatory effects of B. amyloliquefaciens LZ04 on these genes. The structure, duplication, synteny, and expression profiles of 102 genes in calcium-related gene families in A. thaliana were investigated. Hidden Markov Models (HMMs) and BLASTP were used to predict candidate genes and conserved domains of the candidate genes were confirmed in SMART and NCBI CDD databases. Gene duplications and synteny were uncovered by BLASTP and phylogenetic analysis. The transcriptome expression profiles of candidate genes were investigated by strand-specific sequencing. Cluster analysis was used to find the expression profiles of calcium-related genes families under different treatment conditions. A total of 102 genes in calcium-related gene families were detected in A. thaliana genome, including 34 CDPK genes, 20 CNGC genes, 18 CIPK genes, 22 IQD genes, and 10 CBP genes. Additionally, of the 102 genes, 33 duplications (32.35%) and 26 gene pairs including 48 genes (47.06%) were detected. Treatment with B. amyloliquefaciens LZ04 enhanced the resistance of A. thaliana under high calcium stress by regulating some of the genes in the calcium-related gene families. Functional enrichment analysis revealed that the genes clustered in the 42nd expression profile which may be B. amyloliquefaciens-responsive genes under calcium stress were enriched in protein phosphorylation and protein modification process. Transcriptome data was validated by RT-PCR and the results generally corroborated the transcriptome sequencing results. These results may be useful for agricultural improvement in high calcium stress regions.