bluuebunny/crossref_metadata_2025_split huggingface dataset:
Erianin, a novel dibenzyl compound in Dendrobium extract, inhibits lung cancer cell growth and migration via calcium/calmodulin-dependent ferroptosis
Authors: Chen Peng , Wu Qibiao , Feng Jiao , Yan Lili , Sun Yitian , Liu Shuiping , Xiang Yu , Zhang Mingming , Pan Ting , Chen Xiaying , Duan Ting , Zhai Lijuan , Zhai Bingtao , Wang Wengang , Zhang Ruonan , Chen Bi , Han Xuemeng , Li Yicong , Chen Liuxi , Liu Ying , Huang Xingxing , Jin Ting , Zhang Wenzheng , Luo Hong , Chen Xiaohui , Li Yongqiang , Li Qiujie , Li Guohua , Zhang Qin , Zhuo Lvjia , Yang Zuyi , Tang Huifen , Xie Tian , Ouyang Xiaoping , Sui Xinbing 
Published: May 2020

AbstractFerroptosis, a novel form of programmed cell death, is characterized by iron-dependent lipid peroxidation and has been shown to be involved in multiple diseases, including cancer. Stimulating ferroptosis in cancer cells may be a potential strategy for cancer therapy. Therefore, ferroptosis-inducing drugs are attracting more attention for cancer treatment. Here, we showed that erianin, a natural product isolated from Dendrobium chrysotoxum Lindl, exerted its anticancer activity by inducing cell death and inhibiting cell migration in lung cancer cells. Subsequently, we demonstrated for the first time that erianin induced ferroptotic cell death in lung cancer cells, which was accompanied by ROS accumulation, lipid peroxidation, and GSH depletion. The ferroptosis inhibitors Fer-1 and Lip-1 but not Z-VAD-FMK, CQ, or necrostatin-1 rescued erianin-induced cell death, indicating that ferroptosis contributed to erianin-induced cell death. Furthermore, we demonstrated that Ca2+/CaM signaling was a critical mediator of erianin-induced ferroptosis and that blockade of this signaling significantly rescued cell death induced by erianin treatment by suppressing ferroptosis. Taken together, our data suggest that the natural product erianin exerts its anticancer effects by inducing Ca2+/CaM-dependent ferroptosis and inhibiting cell migration, and erianin will hopefully serve as a prospective compound for lung cancer treatment.
EPIC STAR: a reliable and efficient approach for phonon- and impurity-limited charge transport calculations
Authors: Deng Tianqi , Wu Gang , Sullivan Michael B. , Wong Zicong Marvin , Hippalgaonkar Kedar , Wang Jian-Sheng , Yang Shuo-Wang 
Published: May 2020

AbstractA computationally efficient first-principles approach to predict intrinsic semiconductor charge transport properties is proposed. By using a generalized Eliashberg function for short-range electron–phonon scattering and analytical expressions for long-range electron–phonon and electron–impurity scattering, fast and reliable prediction of carrier mobility and electronic thermoelectric properties is realized without empirical parameters. This method, which is christened “Energy-dependent Phonon- and Impurity-limited Carrier Scattering Time AppRoximation (EPIC STAR)” approach, is validated by comparing with experimental measurements and other theoretical approaches for several representative semiconductors, from which quantitative agreement for both polar and non-polar, isotropic and anisotropic materials is achieved. The efficiency and robustness of this approach facilitate automated and unsupervised predictions, allowing high-throughput screening and materials discovery of semiconductor materials for conducting, thermoelectric, and other electronic applications.
MetaGeneHunt for protein domain annotation in short-read metagenomes
Authors: Berlemont R. , Winans N. , Talamantes D. , Dang H. , Tsai H-W. 
Published: May 2020

AbstractThe annotation of short-reads metagenomes is an essential process to understand the functional potential of sequenced microbial communities. Annotation techniques based solely on the identification of local matches tend to confound local sequence similarity and overall protein homology and thus don’t mirror the complex multidomain architecture and the shuffling of functional domains in many protein families. Here, we present MetaGeneHunt to identify specific protein domains and to normalize the hit-counts based on the domain length. We used MetaGeneHunt to investigate the potential for carbohydrate processing in the mouse gastrointestinal tract. We sampled, sequenced, and analyzed the microbial communities associated with the bolus in the stomach, intestine, cecum, and colon of five captive mice. Focusing on Glycoside Hydrolases (GHs) we found that, across samples, 58.3% of the 4,726,023 short-read sequences matching with a GH domain-containing protein were located outside the domain of interest. Next, before comparing the samples, the counts of localized hits matching the domains of interest were normalized to account for the corresponding domain length. Microbial communities in the intestine and cecum displayed characteristic GH profiles matching distinct microbial assemblages. Conversely, the stomach and colon were associated with structurally and functionally more diverse and variable microbial communities. Across samples, despite fluctuations, changes in the functional potential for carbohydrate processing correlated with changes in community composition. Overall MetaGeneHunt is a new way to quickly and precisely identify discrete protein domains in sequenced metagenomes processed with MG-RAST. In addition, using the sister program “GeneHunt” to create custom Reference Annotation Table, MetaGeneHunt provides an unprecedented way to (re)investigate the precise distribution of any protein domain in short-reads metagenomes.
Prediction of prostate cancer Gleason score upgrading from biopsy to radical prostatectomy using pre-biopsy multiparametric MRI PIRADS scoring system
Authors: Alqahtani Saeed , Wei Cheng , Zhang Yilong , Szewczyk-Bieda Magdalena , Wilson Jennifer , Huang Zhihong , Nabi Ghulam 
Published: May 2020

AbstractAn increase or ‘upgrade’ in Gleason Score (GS) in prostate cancer following Transrectal Ultrasound (TRUS) guided biopsies remains a significant challenge to overcome. to evaluate whether MRI has the potential to narrow the discrepancy of histopathological grades between biopsy and radical prostatectomy, three hundred and thirty men treated consecutively by laparoscopic radical prostatectomy (LRP) between July 2014 and January 2019 with localized prostate cancer were included in this study. Independent radiologists and pathologists assessed the MRI and histopathology of the biopsies and prostatectomy specimens respectively. A multivariate model was constructed using logistic regression analysis to assess the ability of MRI to predict upgrading in biopsy GS in a nomogram. A decision-analysis curve was constructed assessing impact of nomogram using different thresholds for probabilities of upgrading. PIRADS scores were obtained from MRI scans in all the included cases. In a multivariate analysis, the PIRADS v2.0 score significantly improved prediction ability of MRI scans for upgrading of biopsy GS (p = 0.001, 95% CI [0.06–0.034]), which improved the C-index of predictive nomogram significantly (0.90 vs. 0.64, p < 0.05). PIRADS v2.0 score was an independent predictor of postoperative GS upgrading and this should be taken into consideration while offering treatment options to men with localized prostate cancer.
Raman spectroscopic signatures of carotenoids and polyenes enable label-free visualization of microbial distributions within pink biofilms
Authors: Horiue Hiroto , Sasaki Mai , Yoshikawa Yuki , Toyofuku Masanori , Shigeto Shinsuke 
Published: May 2020

AbstractPink biofilms are multispecies microbial communities that are commonly found in moist household environments. The development of this pink stain is problematic from an aesthetic point of view, but more importantly, it raises hygienic concerns because they may serve as a potential reservoir of opportunistic pathogens. Although there have been several studies of pink biofilms using molecular analysis and confocal laser scanning microscopy, little is known about the spatial distributions of constituent microorganisms within pink biofilms, a crucial factor associated with the characteristics of pink biofilms. Here we show that Raman spectroscopic signatures of intracellular carotenoids and polyenes enable us to visualize pigmented microorganisms within pink biofilms in a label-free manner. We measured space-resolved Raman spectra of a pink biofilm collected from a bathroom, which clearly show resonance Raman bands of carotenoids. Multivariate analysis of the Raman hyperspectral imaging data revealed the presence of typical carotenoids and structurally similar but different polyenes, whose spatial distributions within the pink biofilm were found to be mutually exclusive. Raman measurements on individual microbial cells isolated from the pink biofilm confirmed that these distributions probed by carotenoid/polyene Raman signatures are attributable to different pigmented microorganisms. The present results suggest that Raman microspectroscopy with a focus on microbial pigments such as carotenoids is a powerful nondestructive method for studying multispecies biofilms in various environments.
The Antioxidants Glutathione, Ascorbic Acid and Uric Acid Maintain Butyrate Production by Human Gut Clostridia in The Presence of Oxygen In Vitro
Authors: Million Matthieu , Armstrong Nicholas , Khelaifia Saber , Guilhot Elodie , Richez Magali , Lagier Jean-Christophe , Dubourg Gregory , Chabriere Eric , Raoult Didier 
Published: May 2020

AbstractUncontrolled oxidative stress, reported in Salmonella and HIV infections, colorectal cancer or severe acute malnutrition, has been associated with anaerobic gut microbiome alteration, impaired butyrate production, mucosal immunity dysregulation and disruption of host-bacterial mutualism. However, the role of major antioxidant molecules in the human body, such as glutathione, ascorbic acid and uric acid, has been neglected in this context. Here, we performed an in vitro metabolomics study of the 3 most odorous anaerobic microbes isolated from the human gut in our laboratory (Clostridium sporogenes, Clostridium subterminale and Romboutsia lituseburensis) when grown in anaerobiosis or in aerobiosis with these 3 antioxidant molecules via gas and liquid chromatography-mass spectrometry (GC/MS and LC/MS). There was no growth or volatile organic compound production in aerobic cultures without the 3 antioxidant molecules. In anaerobiosis, the major metabolic products of the bacteria were thiols, alcohols and short-chain fatty acid esters. The production of alkanes, cycloheptatriene and, paradoxically, increased butyrate production, was observed in the cultures grown in aerobiosis with the 3 antioxidant molecules. The qualitative shift suggests specific molecular mechanisms that remain to be elucidated. The increased production of butyrate, but also isobutyrate and isovalerate in vitro suggests that these 3 antioxidant molecules contributed to the maintenance and active resilience of host-bacterial mutualism against mucosal oxygen and uncontrolled oxidative stress in vivo.
Deep learning-enabled point-of-care sensing using multiplexed paper-based sensors
Authors: Ballard Zachary S. , Joung Hyou-Arm , Goncharov Artem , Liang Jesse , Nugroho Karina , Di Carlo Dino , Garner Omai B. , Ozcan Aydogan 
Published: May 2020

AbstractWe present a deep learning-based framework to design and quantify point-of-care sensors. As a use-case, we demonstrated a low-cost and rapid paper-based vertical flow assay (VFA) for high sensitivity C-Reactive Protein (hsCRP) testing, commonly used for assessing risk of cardio-vascular disease (CVD). A machine learning-based framework was developed to (1) determine an optimal configuration of immunoreaction spots and conditions, spatially-multiplexed on a sensing membrane, and (2) to accurately infer target analyte concentration. Using a custom-designed handheld VFA reader, a clinical study with 85 human samples showed a competitive coefficient-of-variation of 11.2% and linearity of R2 = 0.95 among blindly-tested VFAs in the hsCRP range (i.e., 0–10 mg/L). We also demonstrated a mitigation of the hook-effect due to the multiplexed immunoreactions on the sensing membrane. This paper-based computational VFA could expand access to CVD testing, and the presented framework can be broadly used to design cost-effective and mobile point-of-care sensors.
SwiftReg cluster registration automatically reduces flow cytometry data variability including batch effects
Authors: Rebhahn Jonathan A. , Quataert Sally A. , Sharma Gaurav , Mosmann Tim R. 
Published: May 2020

AbstractBiological differences of interest in large, high-dimensional flow cytometry datasets are often obscured by undesired variations caused by differences in cytometers, reagents, or operators. Each variation type requires a different correction strategy, and their unknown contributions to overall variability hinder automated correction. We now describe swiftReg, an automated method that reduces undesired sources of variability between samples and particularly between batches. A high-resolution cluster map representing the multidimensional data is generated using the SWIFT algorithm, and shifts in cluster positions between samples are measured. Subpopulations are aligned between samples by displacing cell parameter values according to registration vectors derived from independent or locally-averaged cluster shifts. Batch variation is addressed by registering batch control or consensus samples, and applying the resulting shifts to individual samples. swiftReg selectively reduces batch variation, enhancing detection of biological differences. swiftReg outputs registered datasets as standard .FCS files to facilitate further analysis by other tools.
Characterization of a toxin-antitoxin system in Mycobacterium tuberculosis suggests neutralization by phosphorylation as the antitoxicity mechanism
Authors: Yu Xia , Gao Xiaopan , Zhu Kaixiang , Yin Han , Mao Xujian , Wojdyla Justyna Aleksandra , Qin Bo , Huang Hairong , Wang Meitian , Sun Yi-Cheng , Cui Sheng 
Published: May 2020

AbstractMycobacterium tuberculosis (Mtb) encodes an exceptionally large number of toxin-antitoxin (TA) systems, supporting the hypothesis that TA systems are involved in pathogenesis. We characterized the putative Mtb Rv1044-Rv1045 TA locus structurally and functionally, demonstrating that it constitutes a bona fide TA system but adopts a previously unobserved antitoxicity mechanism involving phosphorylation of the toxin. While Rv1045 encodes the guanylyltransferase TglT functioning as a toxin, Rv1044 encodes the novel atypical serine protein kinase TakA, which specifically phosphorylates the cognate toxin at residue S78, thereby neutralizing its toxicity. In contrast to previous predictions, we found that Rv1044-Rv1045 does not belong to the type IV TA family because TglT and TakA interact with each other as substrate and kinase, suggesting an unusual type of TA system. Protein homology analysis suggests that other COG5340-DUF1814 protein pairs, two highly associated but uncharacterized protein families widespread in prokaryotes, might share this unusual antitoxicity mechanism.
Rhinological Consequences of Microsurgical Endonasal-Transsphenoidal Surgery for Pituitary Tumors
Authors: Hondronikos Nikolaos , Alomari Ali , Schrader Martin , Knappe Ulrich J 
Published: May 2020

Abstract
Background Transsphenoidal surgery for sellar lesions may affect patency and function of the nasal airways, smell and sinonasal quality of life. Below is our report on otorhinolaryngological data garnered from patients undergoing endonasal transsphenoidal pituitary microsurgery.
Methods In a prospective study, 68 patients scheduled for transsphenoidal operations (32 female, 36 male, age 17–72 years) underwent otorhinolaryngological evaluation of their nasal morphology, a standardized smell test (sniffin’ sticks) and rhinomanometry to analyse nasal breathing function preoperatively, 3–5 days postoperatively (without rhinomanometry), after 3–4 months and after 9 months.
Results Immediately after surgery, a reduction in smell sensation was detected in almost all patients. Within 3 months, this impairment resolved in all cases except one. In 2 patients (3%) with preoperative anosmia, improvement of smell function to>6 out of 12 sniffin’ sticks was observed. At final visit no patient was noted to have new anosmia. Within 3 months, the results of the rhinomanometry revealed that all patients except one, regained their preoperative nasal breathing function. In 6 patients (8.8%) an improvement in their nose breathing abilities compared to the preoperative state was found. Three patients (4.4%) underwent a LASER transection of mucosal synechiae. In one case with persistent nasal obstruction (1.5%), secondary septoplasty had to be performed. There was no case in which perforation of the nasal septum, nasal tip deflection, or saddle nose deformity was observed.
Conclusion Microsurgical resection of pituitary tumors via the endonasal transsphenoidal approach poses an acceptable risk with regards to sinonasal complications. The incidence of secondary rhinosurgical interventions is low. Standardized comparative studies between endoscopic and microsurgical transsphenoidal operations should be undertaken.
Endoscopic treatment of gastroesophageal variceal bleeding after oxaliplatin-based chemotherapy in patients with colorectal cancer
Authors: Huang Xiaoquan , Li Feng , Wang Lifen , Xiao Mei , Ni Liyuan , Jiang Siyu , Ji Yuan , Zhang Chunqing , Zhang Wei , Wang Jian , Chen Shiyao 
Published: May 2020

Abstract
Background Oxaliplatin, used as first-choice treatment for colorectal cancer (CRC), induces sinusoidal endothelial injury and portal hypertension. This study investigated the characteristics of oxaliplatin-induced portal hypertension and evaluated the efficacy of endoscopic management of gastroesophageal variceal bleeding.
Methods We performed a retrospective, multicenter, case-control study between January 2010 and December 2018. Patients who received oxaliplatin-based chemotherapy after CRC surgery and presented with portal hypertension and gastroesophageal varices were compared with consecutive patients with hepatitis B-related cirrhotic portal hypertension receiving endoscopic treatment for variceal bleeding.
Results 39 patients with oxaliplatin-induced portal hypertension were identified, 35 of whom had a history of variceal bleeding. The median period between start of oxaliplatin-based chemotherapy and the occurrence of varices was 50.4 months (n = 39). A total of 26 patients with oxaliplatin-related portal hypertension and 230 patients with hepatitis B-related portal hypertension underwent endoscopic treatment. Kaplan-Meier analysis revealed that the 1-year rebleeding rate was significantly higher in the oxaliplatin group than in the hepatitis B group (43.3 % vs. 19.0 %, P = 0.001). Multivariable Cox regression analysis showed that oxaliplatin-based chemotherapy was an independent factor for 3-year rebleeding (hazard ratio [HR] 2.46, 95 % confidence interval [CI] 1.24–4.87; P = 0.01) and 3-year overall mortality (HR 9.43, 95 %CI 2.32–38.31; P = 0.002).
Conclusions Oxaliplatin-related portal hypertension was characterized by massive ascites, splenomegaly, gastric varices, concomitant arterioportal fistula, and relatively normal liver function. Endoscopic treatment to prevent variceal rebleeding in these patients was unsatisfactory compared with endoscopic treatment for hepatitis B-related portal hypertension.
Rare heterochronous liver and pancreatic multiple primary cancers: a case report and literature review
Authors: Zhang Wangjun , Xiao Fan , Li Jie , Guo Xiaoyu , Lin Zhitao , Huang Zijian , Mao Ning , Sun Bei , Wang Gang 
Published: May 2020

AbstractIn recent years, with the continuous improvement of medical diagnostic techniques, the incidence of multiple primary carcinoma (MPC) has increased gradually. Elderly patients are at high risk of MPC. However, the risk of developing a second primary malignancy is 1 % for primary liver malignancy 1. The risk of pancreatic cancers as secondary malignancies with primary liver malignancy is very rare. Here, we report a rare case of heterochronous liver and pancreatic MPCs and review the related literature. We report this case to raise the clinician’s attention to the disease because the long-term survival rate can be effectively improved by timely diagnosis and appropriate treatment. For patients with HCV-positive primary cancers, active antiviral therapy should be simultaneously provided with antitumor therapy, thereby effectively reducing the incidence of MPC.
European Federation of Societies for Ultrasound in Medicine and Biology (EFSUMB) Position Statement on Dermatologic Ultrasound
Authors: Alfageme Fernando , Wortsman Ximena , Catalano Orlando , Roustan Gaston , Crisan Maria , Crisan Diana , Gaitini Diana E. , Cerezo Eugenio , Badea Radu 
Published: May 2020

AbstractDermatologic ultrasound is a recent application of ultrasound for the evaluation of healthy skin and appendages and their diseases. Although the scientific literature regarding this application is still not sufficient for evidence-based guidelines, general recommendations issued by scientific societies are necessary. The EFSUMB (European Federation of Societies for Ultrasound in Medicine and Biology) steering committee for dermatologic ultrasound has developed a series of consensus position statements regarding the main fields of dermatologic ultrasound (technical requirement, normal skin and appendages, inflammatory skin diseases, tumoral skin diseases, aesthetic dermatology and practice-training requirements). This document is the foundation for future evidence-based recommendations and guidelines for dermatologic ultrasound practice.
Activation of C–F, Si–F, and S–F Bonds by N-Heterocyclic Carbenes and Their Isoelectronic Analogues
Authors: Lee Eunsung , Pietrasiak Ewa 
Published: May 2020

Reactions involving C–F, Si–F, and S–F bond cleavage with N-heterocyclic carbenes and isoelectronic species are reviewed. Most examples involve activation of aromatic C–F bond via an SNAr pathway and nucleophilic substitution of fluorine in electron-deficient olefins. The mechanism of the C–F bond activation depends on the reaction partners and the reaction can proceed via addition–elimination, oxidative addition (concerted or stepwise) or metathesis. The adducts formed upon substitution find applications in organic synthesis, as ligands and as stable radical precursors, but in most cases, their full potential remains unexplored.1 Introduction1.1 The C–F Bond1.2 C–F Bond Activation: A Short Summary1.3 C–F Bond Activation: A Special Case of SNAr1.4 N-Heterocyclic Carbenes (NHCs)1.5 The Purpose of this Article2 C–F bond Activation in Acyl Fluorides3 Activation of Vinylic C–F Bonds4 Activation of Aromatic C–F Bonds5 X–F Bond Activation (X = S or Si)6 C–F Bond Activation by Main Group Compounds Isoelectronic with NHCs7 Conclusions and Outlook