bluuebunny/crossref_metadata_2025_split huggingface dataset:
A generalized machine‐learning aided method for targeted identification of industrial enzymes from metagenome: A xylanase temperature dependence case study
Authors: Foroozandeh Shahraki Mehdi , Farhadyar Kiana , Kavousi Kaveh , Azarabad Mohammad H. , Boroomand Amin , Ariaeenejad Shohreh , Hosseini Salekdeh Ghasem 
Published: October 2020

AbstractGrowing industrial utilization of enzymes and the increasing availability of metagenomic data highlight the demand for effective methods of targeted identification and verification of novel enzymes from various environmental microbiota. Xylanases are a class of enzymes with numerous industrial applications and are involved in the degradation of xylose, a component of lignocellulose. The optimum temperature of enzymes is an essential factor to be considered when choosing appropriate biocatalysts for a particular purpose. Therefore, in silico prediction of this attribute is a significant cost and time‐effective step in the effort to characterize novel enzymes. The objective of this study was to develop a computational method to predict the thermal dependence of xylanases. This tool was then implemented for targeted screening of putative xylanases with specific thermal dependencies from metagenomic data and resulted in the identification of three novel xylanases from sheep and cow rumen microbiota. Here we present thermal activity prediction for xylanase, a new sequence‐based machine learning method that has been trained using a selected combination of various protein features. This random forest classifier discriminates non‐thermophilic, thermophilic, and hyper‐thermophilic xylanases. The model's performance was evaluated through multiple iterations of sixfold cross‐validations as well as holdout tests, and it is freely accessible as a web‐service at arimees.com.
Incidence and survival for oropharynx and non‐oropharynx head and neck cancers among veterans living with HIV
Authors: Mazul Angela L. , Hartman Christine , Kramer Jennifer , White Donna L. , Royse Kathryn , Raychaudhury Suchismita , Sandulache Vlad , Ahmed Sarah T. , Richardson Peter , Sikora Andrew G. , Chiao Elizabeth 
Published: October 2020

AbstractBackgroundPeople living with HIV/AIDS (PLWH) have an excess risk for head and neck squamous cell carcinoma (HNSCC) compared to the general U.S. population, but little is known about HIV‐specific risk factors associated with the incidence and outcomes HNSCC. We aim to identify clinical and HIV‐specific risk factors associated with oropharyngeal and non‐oropharyngeal HNSCC incidence and outcomes separately.MethodsWe constructed a retrospective cohort study of 45,052 PLWH aged 18 or above from the national Veteran Affairs (VA) Corporate Data from 1999 to 2015. We extracted demographic data and risk factor information, including history of alcohol abuse, smoking, CD4 count (cells/μl), and percent of follow‐up time with undetectable HIV viral load as time‐updated variables. We calculated the age‐standardized incidence rates of oropharyngeal and non‐oropharyngeal HNSCC and estimated adjusted hazard ratios (HR). We also examined overall survival using Kaplan–Meier curves and adjusted HR.ResultsThe standardized incidence rate of oropharyngeal and non‐oropharyngeal HNSCC in this veteran cohort of PLWH is 23.0 (95% confidence intervals (CIs): 17.1‐28.9) and 55.4 (95% CI: 46.5‐64.3) per 100,000 person‐years, respectively. Nadir CD4 count ≤200 was associated with an increased risk of non‐oropharyngeal HNSCC (HR: 1.78; 95% CI: 1.31‐2.30 vs >200). Five‐year overall survival of OPSCC (37.0%) was significantly lower than non‐oropharyngeal HNSCC (49.1%).ConclusionsPLWH who receive care in the VA had higher age‐adjusted HNSCC incidence rates than reported in the general population, suggesting that HIV and immunosuppression play a role. Additional studies should be conducted to study the interaction between HPV and HIV.
Quinone Methide‐Based Organophosphate Hydrolases Inhibitors: Trans Proximity Labelers versus Cis Labeling Activity‐Based Probes
Authors: Dubovetskyi Artem , Cherukuri Kesava Phaneendra , Ashani Yacov , Meshcheriakova Anna , Reuveny Eitan , Ben‐Nissan Gili , Sharon Michal , Fumagalli Laura , Tawfik Dan S. 
Published: October 2020

AbstractQuinone methide (QM) chemistry is widely applied including in enzyme inhibitors. Typically, enzyme‐mediated bond breaking releases a phenol product that rearranges into an electrophilic QM that in turn covalently modifies protein side chains. However, the factors that govern the reactivity of QM‐based inhibitors and their mode of inhibition have not been systematically explored. Foremost, enzyme inactivation might occur in cis, whereby a QM molecule inactivates the very same enzyme molecule that released it, or by trans if the released QMs diffuse away and inactivate other enzyme molecules. We examined QM‐based inhibitors for enzymes exhibiting phosphoester hydrolase activity. We tested different phenolic substituents and benzylic leaving groups, thereby modulating the rates of enzymatic hydrolysis, phenolate‐to‐QM rearrangement, and the electrophilicity of the resulting QM. By developing assays that distinguish between cis and trans inhibition, we have identified certain combinations of leaving groups and phenyl substituents that lead to inhibition in the cis mode, while other combinations gave trans inhibition. Our results suggest that cis‐acting QM‐based substrates could be used as activity‐based probes to identify various phospho‐ and phosphono‐ester hydrolases, and potentially other hydrolases.
Characterization of New DNA Aptamers for Anti‐HIV‐1 Reverse Transcriptase
Authors: Ratanabunyong Siriluk , Aeksiri Niran , Yanaka Saeko , Yagi‐Utsumi Maho , Kato Koichi , Choowongkomon Kiattawee , Hannongbua Supa 
Published: October 2020

AbstractHIV‐1 RT is a necessary enzyme for retroviral replication, which is the main target for antiviral therapy against AIDS. Effective anti‐HIV‐1 RT drugs are divided into two groups; nucleoside inhibitors (NRTI) and non‐nucleoside inhibitors (NNRTI), which inhibit DNA polymerase. In this study, new DNA aptamers were isolated as anti‐HIV‐1 RT inhibitors. The selected DNA aptamer (WT62) presented with high affinity and inhibition against wild‐type (WT) HIV‐1 RT and gave a KD value of 75.10±0.29 nM and an IC50 value of 84.81±8.54 nM. Moreover, WT62 decreased the DNA polymerase function of K103 N/Y181 C double mutant (KY) HIV‐1 RT by around 80 %. Furthermore, the ITC results showed that this aptamer has small binding enthalpies with both WT and KY HIV‐1 RTs through which the complex might form a hydrophobic interaction or noncovalent bonding. The NMR result also suggested that the WT62 aptamer could bind with both WT and KY mutant HIV‐1 RTs at the connection domain.
Cysteine‐Rich Peptides: Hyperstable Scaffolds for Protein Engineering
Authors: González‐Castro Rafael , Gómez‐Lim Miguel A. , Plisson Fabien 
Published: October 2020

AbstractCysteine‐rich peptides (CRPs) are small proteins of less than 100 amino acids in length characterized by the presence of disulfide bridges and common end‐to‐end macrocyclization. These properties confer hyperstability against high temperatures, salt concentration, serum presence, and protease degradation to CRPs. Moreover, their intercysteine domains (loops) are susceptible to residue hypervariability. CRPs have been successfully applied as stable scaffolds for molecular grafting, a protein engineering process in which cysteine‐rich structures provide higher thermodynamic and metabolic stability to an epitope and acquire new biological function(s). This review describes the successes and limitations of seven cysteine‐rich scaffolds, their bioactive epitopes, and the resulting grafted peptides.
Fabrication of Graphitic Carbon Nitride‐Based Film: An Emerged Highly Efficient Catalyst for Direct C—H Arylation under Solar Light
Authors: Chaubey Surabhi , Yadav Rajesh K. , Kim Tae Wu , Yadav Tara Chand , Kumar Abhishek , Dwivedi D. K. , Pandey B. K. , Singh Atul P. 
Published: October 2020

Main observation and conclusionPhotoredox C—H bond formation can proceed in aerobic environment under solar light and has therefore become attractive. Nowadays, different types of expensive novel metal complexes and nanomaterials have been urbanized as photocatalysts for direct C—H bond formation in between derivatives of heteroarenes (HAs) and aryl diazonium salts. These photocatalysts, however, still suffer from poor stability, high cost, and decay. Herein, a graphitic carbon nitride‐based fluorescein isothiocyanate (g‐C3N4–FITC) film photocatalyst has been reported, which shows excellent light harvesting ability, and band gap suitability to catalyze the metal free direct C—H arylation of HAs under solar light at ambient temperature. Moreover, the g‐C3N4–FITC film photocatalyst can be reused four times without significant loss of activity, confirming the excellent photocatalytic stability. The current strategy to construct a g‐C3N4–FITC film photocatalyst for direct C—H arylation opens a new path towards replacing metal‐based catalysts in fine chemical synthesis.
Acute monocytic leukemia presenting as generalized lymphadenopathy and skin rash in a toddler: highlighting the clinicopathologic mimics
Authors: Jain Aleena , Gupta Parikshaa , Gupta Nalini , Senguttuvan Gnanamani , Kapadia Alpeshkumar Bipinbhai , Thirunavukkarasu Balamurugan , Nada Ritambhra , Varma Neelam 
Published: October 2020

AbstractAcute myeloid leukemia (AML) is the fifth most common malignancy in children. Extramedullary involvement in acute myeloid leukemia is rare and can be seen in soft tissues, central nervous system, skin and lymphoreticular organs. The clinical presentations can often be non‐specific and hence, the diagnosis can be very challenging, especially in cases without a prior hematologic diagnosis. We report a case of pediatric acute monocytic leukemia presenting with generalized lymphadenopathy and cutaneous rash. Fine‐needle aspiration was performed from the lymph nodes and a cytologic diagnosis of infiltration by a lymphoreticular malignancy was suggested. Peripheral blood, bone marrow and cerebrospinal fluid involvement were noted subsequently. Flow cytometry on the bone marrow aspirate confirmed a diagnosis of acute monocytic leukemia. The index case besides highlighting an uncommon presentation of acute monocytic leukemia in a toddler, also emphasizes the need to consider acute monocytic leukemia as a cytomorphologic differential in such presentations.
An approach to increasing forecast‐combination accuracy through VAR error modeling
Authors: Weigt Till , Wilfling Bernd 
Published: October 2020

AbstractWe consider a situation in which the forecaster has available M individual forecasts of a univariate target variable. We propose a 3‐step procedure designed to exploit the interrelationships among the M forecast‐error series (estimated from a large time‐varying parameter VAR model of the errors, using past observations) with the aim of obtaining more accurate predictions of future forecast errors. The refined future forecast‐error predictions are then used to obtain M new individual forecasts that are adapted to the information from the estimated VAR. The adapted M individual forecasts are ultimately combined and any potential accuracy gains from the adapted combination forecasts analyzed. We evaluate our approach in an out‐of‐sample forecasting analysis, using a well‐established 7‐country data set on output growth. Our 3‐step procedure yields substantial accuracy gains (in terms of loss reductions of up to 18%) for the simple average and three time‐varying‐parameter combination forecasts.
The use of lithic raw materials at the Early Mesolithic open‐air site Feuersteinacker (Vogelsbergkreis, Germany)
Authors: Hess Thomas , Riede Felix 
Published: October 2020

AbstractThe open‐air site Feuersteinacker near Stumpertenrod has yielded one of the largest lithic assemblages in Central Germany. It repeatedly served as a workshop for the production of stone tools during an early phase of the Mesolithic. The range of lithic raw materials is extremely diverse, but until today, there is only a limited number of archaeological studies on the occurrence of lithic resources in the area. The following study presents the first in‐depth investigation of the use of different rock types by Mesolithic hunter–fisher–gatherers at the site. Provenance analyses using petrographic methods permit raw materials to be assigned to a specific source and provide new insights into their formation. Furthermore, this study explores the way in which the materials were processed throughout the reduction sequence. A comparison of topographic parameters suggests that the location was situated on an important transit route during prehistoric times. The presented results contribute to a better understanding of mobility patterns and subsistence strategies of Early Mesolithic groups in Central Germany.
Oral health in patients with dementia: A meta‐analysis of comparative and observational studies
Authors: Zeng Liang‐Nan , Zong Qian‐Qian , Xu Shi‐Wei , An Feng‐Rong , Ungvari Gabor S. , Bressington Daniel T. , Cheung Teris , Qin Ming‐Zhao , Chen Li‐Gang , Xiang Yu‐Tao 
Published: October 2020

AbstractObjectivePoor oral health is common in dementia, but findings of epidemiological studies have been inconsistent. This meta‐analysis examined oral health in patients with dementia diagnosed according to standardized diagnostic criteria.MethodsSix international databases (PubMed, EMBASE, PsycINFO, Medline, Cochrane Library, and Web of Science) were searched from their commencement date until 8 November 2018. Oral health was measured by the Remaining Teeth (RT) and Decayed, Missing, and Filled Teeth (DMFT) Index. The mean differences (MD) and 95% confidence intervals (CI) of DMFT Index total and component scores were calculated using a random‐effect model.ResultsTwenty‐four studies were included for analyses. The pooled DMFT Index was 23.48 (95% CI: 22.34, 24.62), while the pooled score for each component was 2.38 (95% CI: 1.56, 3.20) in decayed teeth (DT), 18.39 (95% CI: 15.92, 20.87) in missing teeth (MT), 2.29 (95% CI: 0.62, 3.95) in filled teeth (FT), and 11.59 (95% CI: 9.14, 14.05) in RT. Compared to controls, people with dementia had significantly a higher DMFT Index total score (MD = 3.80, 95% CI: 2.21, 5.39, p < 0.00,001), and significantly lower number of RT (MD = −3.15, 95% CI: −4.23, −2.06, p < 0.00,001). Subgroup analyses revealed that higher DMFT Index score was significantly associated with year of survey (>2010), study design (case‐control study), percentage of females (≤54.3), and the Mini Mental State Examination score (≤18.2). Higher MT score was significantly associated with study design (cross‐sectional study), and lower FT score was significantly associated with year of survey (>2010).ConclusionsOral health was significantly poorer in people with dementia compared with controls. Regular screening and effective treatment should be implemented for this population.
Hypomagnesemia and incidence of osteoradionecrosis in patients with head and neck cancers
Authors: Liu Wenli , Qdaisat Aiham , Zhou Shouhao , Fuller Clifton D. , Ferrarotto Renata , Guo Ming , Lai Stephen Y. , Cardoso Richard , Mohamed Abdallah S. R. , Lopez Gabriel , Narayanan Santhosshi , van Dijk Lisanne V. , Cohen Lorenzo , Bruera Eduardo , Yeung Sai‐Ching J. , Hanna Ehab Y. 
Published: October 2020

AbstractBackgroundWe aimed to determine whether hypomagnesemia predicts osteoradionecrosis development in patients with squamous cell carcinoma of the oropharynx and oral cavity who received platinum‐based concurrent chemoradiation with or without induction therapy.MethodsWe reviewed data from patients with head and neck cancers who had undergone chemoradiation with weekly cisplatin/carboplatin between January 1, 2010 and December 31, 2014 at our institution. Pathologic features, laboratory test results, disease stage, and social histories were recorded. The association between hypomagnesemia and osteoradionecrosis was analyzed controlling for known confounding factors.ResultsHypomagnesemia during cancer treatment was associated with osteoradionecrosis development (HR = 2.72, P = .037) independent of total radiation dose (HR = 1.07, P = .260) and smoking history (HR = 2.05, P = .056) among the patients who received platinum‐based induction chemotherapy followed by concurrent chemoradiation.ConclusionsHypomagnesemia was predictive of the development of osteoradionecrosis in patients with cancers of the oropharynx and oral cavity receiving platinum‐based induction followed by concurrent chemoradiation.
The tumor microenvironment of lymphomas: Insights into the potential role and modes of actions of checkpoint inhibitors
Authors: Menter Thomas , Tzankov Alexandar , Dirnhofer Stefan 
Published: October 2020

AbstractThe tumor microenvironment (TME) – a term comprising non‐neoplastic cells and extracellular matrix as well as various cytokines, chemokines, growth factors, and other substances in the vicinity of tumor cells – is an integrative part of most tumors including lymphomas. Interactions between lymphoma cells and the TME are vital for survival and proliferation of the former. In addition, lymphoma cells often reprogram the TME to protect them from defense mechanisms of the host's immune system. In this review, we will introduce the role of the tumor microenvironment (TME) for lymphoma cells looking at direct cell–cell interactions as well as cytokine‐related communications. The immunomodulative/immunosuppressive role of the TME is more and more coming into the focus of potential new targeted therapies, and thus a special attention will be given to the interactions of immune checkpoints such as programed cell death protein 1 and L1 (PD‐1/PD‐L1), T‐cell immunoglobulin and mucin‐domain containing protein‐3 (TIM‐3), lymphocyte‐activation gene 3 (LAG‐3), and cytotoxic T‐lymphocyte‐associated protein‐4 (CTLA4) with the TME, as well as their expression by both lymphoma cells and cells of the TME. Aspects of the TME will be discussed for indolent and aggressive B‐cell lymphomas, Hodgkin lymphomas, and T‐cell lymphomas. In addition, the potential influence of other immunomodulators such as lenalidomide will be briefly touched. The complex role of the TME is in the focus of new therapeutic options. In order to exploit its full therapeutic potential, however, a thorough understanding of TME biology and interaction between lymphoma cells and the TME, as well as the host's immune system and the TME is necessary.
Cointegration tests at the quantiles
Authors: Furno Marilena 
Published: October 2020

AbstractA cointegration test for quantile regressions is proposed and implemented using Italian data. The test relies on auxiliary quantile regression to verify the stationarity of the residuals of the cointegrating equation. According to the problem under analysis, the cointegrating equation may or may not model a structural break, to verify cointegration with or without break. The existing test by Xiao, Journal of Econometrics (2009), 150, 248–260 is a fluctuation type test, which is closely related to Qu, Journal of Econometrics (2008), 146, 170–184 on structural break in quantile regressions. The link between the two tests makes unclear if the fluctuation test verifies cointegration, stability, or possibly cointegration and stability mixed together. Two real data case studies and a Monte Carlo experiment complete the analysis.
Assessment of pulmonary toxicity of potential antioxidant drug PEGylated nanoceria after intratracheal instillation in rats
Authors: Qian Qinqing , Zhang Yun , Chen Yuan , Ye Chenqiao , Feng Qiang , Tu Jinqing , Lu Zhenbo , Xu Yilan , Ran Na , Xing Guiying , Yu Zhangsen 
Published: October 2020

AbstractCerium oxide (CeO2) nanoparticles have unique redox properties and exert excellent antioxidant effects in the biological environment. In recent years, many researchers have focused on the CeO2 nanoparticles as an effective antioxidant drug in the prevention and treatment of various diseases. However, the toxicity of CeO2 nanoparticles in vivo remains controversial and still needs intensive research. Therefore, the objective of this study is to investigate the pulmonary and systemic toxicity in rats after 14 days of exposure to the PEGylated CeO2 nanoparticles (abbreviated as CNPs; exposure dose of 2, 10, or 20 mg/kg) through a single intratracheal instillation (IT). We assessed the indicators of lung injury and the pathological damage degree of lung tissue. The bronchoalveolar lavage fluid (BALF) analysis and lung histopathology revealed the occurrence of slight pulmonary inflammation in the 20‐mg/kg experimental group rats. However, the inflammation factors in the lung tissue of every group rats did not significantly increase, and the levels of superoxide dismutase (SOD) and glutathione (GSH) in lung tissue homogenate rose considerably in the experimental groups. Collectively, these results indicated that pulmonary exposure by the high dose of CNPs could induce mild pulmonary inflammation but did not cause severe systemic toxicity. Moreover, we speculate that the mechanism of pulmonary toxicity of CNPs in rats was due to the autophagic death of healthy lung epithelial cells mediated by endoplasmic reticulum stress. Our results implicate that CNPs can be safely used as an antioxidant drug for the oxidative stress pulmonary diseases.
A critical‐cultural‐relational approach to rupture resolution: A case illustration with a cross‐racial dyad
Authors: Chang Doris F. , Dunn Jordan J. , Omidi Maryam 
Published: October 2020

AbstractRuptures are common in any therapeutic relationship and their successful resolution is associated with positive outcomes. However, therapist and client differences with regard to power, privilege, identity, and culture increase social and cultural distance, contributing to alliance ruptures and complicating the repair process. Informed by critical race theories, cultural psychological perspectives, and relational principles, we highlight how power, privilege, identity, and culture shape the development of ruptures and thus, how analyses of these dynamics should inform the process of repair. We present an expanded critical‐cultural‐relational approach to rupture resolution that emphasizes essential skills of critical self‐awareness, wise affect, and anti‐oppressive interpersonal engagement, and extends Safran and Muran's (2000) general rupture resolution model to emphasize a critical analysis of the rupture and repair processes. We illustrate our approach through a case presentation involving a rupture in a cross‐racial dyad with themes of racism and classism.