bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of nuclear magnetic resonance permeability models in tight reservoirs
Authors: Solatpour Razieh , Kantzas Apostolos 
Published: October 2018

AbstractTight reservoir permeability with values ranging from a few nD–0.1 mD is a challenging parameter to measure. Since the 1970s, many correlations were applied to estimate the permeability of tight formations using the nuclear magnetic resonance (NMR) technique. Due to increasing interest in tight reservoir recovery, each year many papers are published on the Timur‐Coates and Kenyon models and their modification on estimating the NMR permeability of tight reservoirs. It brings up the question of which is the most accurate, reliable, and feasible model to be used for predicting tight NMR permeability.The first part of this paper is dedicated to introducing the existing models for NMR‐based estimates of tight reservoir permeability. The second part compares these models by applying them on tight reservoirs from North America, Asia, and Europe. NMR experiments were conducted on 150 cores. NMR T2 relaxation times were measured and effective and total porosities, the geometric mean of relaxation time (T2gm), irreducible bulk volume (BVI), and free fluid index (FFI) were calculated. For validation of the models, the cross plots of NMR permeability versus the Klinkenberg gas permeability are presented. Comparison of the model is based on the calculated standard error of these two independently measured permeabilities.This paper is beneficial in understanding existing tight reservoir NMR permeability models. The results can be used as a guide for choosing the best NMR permeability estimation model for tight reservoirs data.
11‐Aza‐artemisinin Derivatives Exhibit Anticancer Activities by Targeting the Fatty Acid Binding Protein 6 (FABP6)
Authors: Chen Xin‐Ya , Yin Yue , Xi Jie , Yuan Yi , Li Yan , Li Qing , Wang Ren‐Xiao , Yao Zhu‐Jun , Tang Gong‐Li 
Published: October 2018

AbstractArtemisinin (Qinghaosu), a sesquiterpene lactone isolated from the Chinese medicinal herb Artemisia annua, is famous as the first‐line antimalarial drug, and reported to also possess anticancer properties. Though many studies have proceeded focusing on artemisinin and bioactive derivatives in clinic or laboratory, their cellular targets and mechanism of actions have still remained obscure. Here, two new 11‐aza‐artemisinin derivatives AAD1 and AAD2, which displayed cytotoxity against multiple cancer cell lines, were synthesized and applied as the probes for target identification and anticancer mechanism research. Using T7 phage display screen method, fatty acid binding protein 6 (FABP6) was identified and verified as one of the potential targets. Further studies showed FABP6 is a direct binding protein of AAD1 and AAD2, and mediated the corresponding anticancer activities of these artemisinin derivatives.
Frequent PTEN loss and differential HER2/PI3K signaling pathway alterations in salivary duct carcinoma: Implications for targeted therapy
Authors: Saintigny Pierre , Mitani Yoshitsugu , Pytynia Kristen B. , Ferrarotto Renata , Roberts Dianna B. , Weber Randal S. , Kies Merrill S. , Maity Sankar N. , Lin Sue‐Hwa , El‐Naggar Adel K. 
Published: October 2018

BACKGROUNDPatients with advanced primary and recurrent salivary duct carcinoma (SDC), a rare and lethal malignancy, have limited therapeutic options. Novel small‐molecule agents aimed at targeting critical signaling associated with SDC tumorigenesis may lead to new therapeutic options for patients with these tumors. The human epidermal growth factor receptor 2 (HER2)/phosphoinositide 3‐kinase (PI3K) axis, an important oncogenic pathway, has been targeted for therapy in several solid tumors. Currently, little is known about the role and clinical implications of alterations of the HER2/PI3K pathway in patients with SDC.METHODSThe authors investigated the clinicopathologic features, genetic alterations, and expression of key members of the HER2/PI3K pathway in 43 primary tumors and conducted in vitro functional and targeted drug‐response analyses on cell lines derived from salivary epithelial carcinomas.RESULTSIn primary tumors, loss of phosphatase and tensin homolog (PTEN) expression was identified in 22 of 43 tumors (51%), overexpression of HER2 was observed in 12 of 43 tumors (28%), and phosphatidylinositol‐4,5‐bisphosphate 3‐kinase catalytic subunit alpha (PIK3CA) mutations were identified in 12 of 43 tumors (28%). Phosphorylated protein kinase B (p‐AKT) was highly expressed in most tumors. Most tumors (70%) displayed mutually exclusive alterations of PI3K members, whereas 8 tumors (19%) had 2 or more concurrent abnormalities. In vitro studies demonstrated a direct association between PTEN loss and PI3K pathway activation and evidence of response to combined PI3Kα and PI3Kβ and/or pan‐PI3K inhibitors.CONCLUSIONSThe current analyses reveal frequent PTEN loss and mutually exclusive alterations of key PI3K pathway members in SDC and demonstrate in vitro evidence of a response to pan‐PI3K inhibitors. These results provide a framework for a biomarker‐based substratification of patients with SDC in future targeted therapy. Cancer 2018;124:3523‐32. © 2018 American Cancer Society.
Self‐reported fatigue in children with advanced cancer: Results of the PediQUEST study
Authors: Ullrich Christina K. , Dussel Veronica , Orellana Liliana , Kang Tammy I. , Rosenberg Abby R. , Feudtner Chris , Wolfe Joanne 
Published: October 2018

BACKGROUNDPediatric cancer‐related fatigue is prevalent and significantly impairs health‐related quality of life, yet its patterns and correlates are poorly understood. The objectives of this study were to describe fatigue as prospectively reported by children with advanced cancer and to identify the factors associated with fatigue and associated distress.METHODSChildren (age ≥2 years) with advanced cancer (N = 104) or their parents at 3 academic hospitals reported symptoms at most weekly over 9 months using the computer‐based Pediatric Quality of Life Evaluation of Symptoms Technology (PediQUEST) system. PediQUEST administered a modified version of the Memorial Symptom Assessment Scale (PQ‐MSAS) as part of a randomized controlled trial. Clinical information was abstracted from medical records. Primary outcomes were: 1) fatigue prevalence (yes/no response to PQ‐MSAS fatigue item) and 2) fatigue distress (composite score of severity, frequency, and bother). Multivariable models were constructed to identify factors independently associated with fatigue prevalence and scores reflecting fatigue distress (ie, burden).RESULTSOf 920 reports, 46% (n = 425) noted fatigue. When reported, fatigue was of high frequency in 41% of respondents (n = 174), severity in 25%of respondents (n = 107), and bother in 34%of respondents (n = 143). Most reports (84%; n = 358) were associated with scores indicating fatigue distress. In multivariable analyses, fatigue was associated with older age, lower hemoglobin, and distress from particular symptoms (anorexia, nausea, sleep disturbance, sadness, and irritability). In contrast, fatigue distress was associated with distress from nausea, cough, and pain.CONCLUSIONSFatigue is common among children with advanced cancer and is often highly distressing. Interventions focused on uncontrolled symptoms may ease fatigue distress in children with advanced cancer.
Phase 1 study of EGFR‐antisense DNA, cetuximab, and radiotherapy in head and neck cancer with preclinical correlatives
Authors: Bauman Julie E. , Duvvuri Umamaheswar , Thomas Sufi , Gooding William E. , Clump David A. , Karlovits Brian , Wehbe Ahmad , Miller Frank R. , Kim Seungwon , Sen Malabika , Heron Dwight E. , Grandis Jennifer R. , Argiris Athanassios 
Published: October 2018

AbstractBACKGROUNDCetuximab combined with radiation therapy (RT) is an evidence‐based treatment for locally advanced head and neck squamous cell carcinoma (HNSCC); however, locoregional failure remains the primary cause of cancer‐related death in this disease. Intratumoral injection of epidermal growth factor receptor (EGFR)‐antisense plasmid DNA (EGFR‐AS) is safe and has been associated with promising lesional responses in patients who have recurrent/metastatic HNSCC. For the current study, the authors investigated the antitumor effects of cetuximab and EGFR‐AS in preclinical HNSCC models and reported their phase 1 experience adding intratumoral EGFR‐AS to cetuximab RT.METHODSAntitumor mechanisms were investigated in cell line and xenograft models. Phase 1 trial eligibility required stage IVA through IVC HNSCC and a measurable lesion accessible for repeat injections. Patients received standard cetuximab was for 9 weeks. EGFR‐AS was injected weekly until they achieved a lesional complete response. RT was delivered by conventional fractionation for 7 weeks, starting at week 3. Research biopsies were obtained at baseline and week 2.RESULTSWhen added to cetuximab, EGFR‐AS decreased cell viability and xenograft growth compared with EGFR‐sense control, partially mediated by reduced EGFR expression. Six patients were enrolled in the phase 1 cohort. No grade 2 or greater EGFR‐AS–related adverse events occurred. The best lesional response was a complete response (4 patients), and 1 patient each had a partial response and disease progression. EGFR expression decreased in 4 patients who had available paired specimens.CONCLUSIONSIn preclinical models, dual EGFR inhibition with cetuximab and EGFR‐AS enhanced antitumor effects. In a phase 1 cohort, intratumoral EGFR‐AS injections, cetuximab, and RT were well tolerated. A phase 2 trial is needed to conduct an extended evaluation of safety and to establish efficacy.
Toward the potential cure of leukemias in the next decade
Authors: Kantarjian Hagop M. , Keating Michael J. , Freireich Emil J 
Published: October 2018

AbstractHistorically, progress in leukemia research has been slow, but it has accelerated recently as a result of understanding the pathophysiology of leukemias and implementing more effective and targeted therapies. This review summarizes the progress across leukemia subsets and projects the potential cure of most leukemias in the next decade.
Enrollment on clinical trials does not improve survival for children with acute myeloid leukemia: A population‐based study
Authors: Truong Tony H. , Pole Jason D. , Barber Randy , Dix David , Kulkarni Ketan P. , Martineau Emilie , Randall Alicia , Stammers David , Strahlendorf Caron , Strother Douglas , Sung Lillian 
Published: October 2018

BackgroundIt is questionable whether enrollment on clinical trials offers any survival advantage at the population level over standard‐of‐care treatment. The objectives of this study were to describe the impact of trial enrollment on event‐free survival and overall survival in pediatric acute myeloid leukemia (AML) using the Cancer in Young People in Canada (CYP‐C) database.MethodsChildren were included if they had had AML newly diagnosed between ages birth and 14 years from 2001 to 2012. CYP‐C is a national pediatric cancer population‐based database that includes all cases of pediatric cancer diagnosed and treated at 1 of the 17 tertiary pediatric oncology centers in Canada. Univariate and Cox proportional hazards models were used to evaluate the impact of initial trial enrollment on survival.ResultsIn total, 397 eligible children with AML were included in the analysis, of whom 94 (23.7%) were enrolled on a clinical trial at initial diagnosis. The most common reason for non‐enrollment was that no trial was available. The event‐free survival rate at 5 years was 57.8% ± 5.2% for those enrolled versus 54.8% ± 2.9% for those not enrolled (P = .75). The overall survival rate at 5 years was 70.1% ± 4.9% for those enrolled versus 66.3% ± 2.8% for those not enrolled (P = .58). Enrollment on a trial was not associated with improved event‐free or overall survival in multiple regression analyses.ConclusionsEnrollment on a clinical trial was not associated with improved survival for children with AML in a population‐based cohort. Rationale for trial enrollment should not include the likelihood of benefit compared with non‐enrollment.
Individualized survival prediction for patients with oropharyngeal cancer in the human papillomavirus era
Authors: Beesley Lauren J. , Hawkins Peter G. , Amlani Lahin M. , Bellile Emily L. , Casper Keith A. , Chinn Steven B. , Eisbruch Avraham , Mierzwa Michelle L. , Spector Matthew E. , Wolf Gregory T. , Shuman Andrew G. , Taylor Jeremy M. G. 
Published: October 2018

AbstractBackgroundAccurate, individualized prognostication in patients with oropharyngeal squamous cell carcinoma (OPSCC) is vital for patient counseling and treatment decision making. With the emergence of human papillomavirus (HPV) as an important biomarker in OPSCC, calculators incorporating this variable have been developed. However, it is critical to characterize their accuracy prior to implementation.MethodsFour OPSCC calculators were identified that integrate HPV into their estimation of 5‐year overall survival. Treatment outcomes for 856 patients with OPSCC who were evaluated at a single institution from 2003 through 2016 were analyzed. Predicted survival probabilities were generated for each patient using each calculator. Calculator performance was assessed and compared using Kaplan‐Meier plots, receiver operating characteristic curves, concordance statistics, and calibration plots.ResultsCorrelation between pairs of calculators varied, with coefficients ranging from 0.63 to 0.90. Only 3 of 6 pairs of calculators yielded predictions within 10% of each other for at least 50% of patients. Kaplan‐Meier curves of calculator‐defined risk groups demonstrated reasonable stratification. Areas under the receiver operating characteristic curve ranged from 0.74 to 0.80, and concordance statistics ranged from 0.71 to 0.78. Each calculator demonstrated superior discriminatory ability compared with clinical staging according to the seventh and eighth editions of the American Joint Committee on Cancer staging manual. Among models, the Denmark calculator was found to be best calibrated to observed outcomes.ConclusionsExisting calculators exhibited reasonable estimation of survival in patients with OPSCC, but there was considerable variability in predictions for individual patients, which limits the clinical usefulness of these calculators. Given the increasing role of personalized treatment in patients with OPSCC, further work is needed to improve accuracy and precision, possibly through the identification and incorporation of additional biomarkers.
A taxonomy of various attacks on smart card–based applications and countermeasures
Authors: Gupta B.B. , Quamara Megha 
Published: October 2018

SummaryDeployment of smart card–based applications is becoming prevalent these days. Security of these applications depends upon the nature of underlying hardware and software platforms, cryptographic algorithms, along with a number of other security mechanisms. To develop a secure smart card–based application, preliminary evaluation of the security of embedded software as well as how that software will work in real time is required. Over the past few years, significant improvements have been made in smart card technology for its large‐scale acceptance. However, attackers are in continuous search for exploiting the unknown issues related to this technology. This survey discusses smart card technology in detail and provides a comprehensive taxonomy of security attacks on smart card–based applications and their countermeasures. In addition, it covers some of the open source tools available for its development. Finally, it provides a brief outline of some of the major open challenges and future research directions that are yet to be explored.
Explaining the Different Geometries of the Water Oxidising Complex in the Nominal S3 State Crystal Structures of Photosystem II at 2.25 Å and 2.35 Å
Authors: Petrie Simon , Stranger Robert , Pace Ron J. 
Published: October 2018

AbstractRecently two atomic resolution crystal structures of Photosystem II, in the double flashed, nominal S3 intermediate state of its Mn4Ca water oxidising complex (WOC), have been presented (Young et al., Nature 2016, 540, 453; Suga et al., Nature 2017, 543, 131). These structures are at 2.25 Å and 2.35 Å resolution, respectively. Although highly similar in most respects, the structures differ in a key region within the WOC catalytic site. In the 2.25 Å structure, one oxy species (O5) is observed within the WOC cavity, weakly associated with the Mn centres, similar to that seen earlier in the 1.95 Å XRD structure of the S1 intermediate (Suga et al., Nature, 2015, 517, 99). In the 2.35 Å structure, two such species are seen (O5, O6), with the Mn centres and O5 positioned as in the 2.25 Å structure and an O5–O6 separation of ∼1.5 Å, consistent with peroxo formation. This suggests O5 and O6 are substrate water derived species in this double flashed form. Recently we have presented (Petrie, et al., Chem. Phys. Chem., 2017) a large scale (220 atom) quantum chemical model of the Young et al. 2.25 Å structure, which quantitatively explains all significant features within the WOC region of that structure, particularly the positions of the metal centres and O5 group. Critical to this was our assumption of a ‘low’ Mn oxidation paradigm (mean S1 Mn oxidation level of +3.0, Petrie et al., Angew. Chem. Int. Ed., 2015), rather than a ‘high’ oxidation model (mean S1 oxidation level of +3.5), widely assumed in the literature. Here we show that our same oxidation state model predicts two classes of energetically close S3 structural forms, analogous to the S1 state, one with the metal centres and O5 positioned as in the 2.25 Å structure, and the other with the metals similarly placed, but with O5 located in the O6 position of the 2.35 Å structure. We show that the Suga et al. 2.35 Å structure is likely a superposition of two such forms, one from each class, which is consistent with reported atomic occupancies for that structure and the relative total energies we calculate for the two structural forms.
Effect of Substitution Pattern of tert‐Butyl Groups in a Bisbenzofuropyrazine Core π‐System on Optical Properties: Unique Mechanochromic Fluorescence Behavior
Authors: Nakamura Shotaro , Tohnai Norimitsu , Nishii Yuji , Hinoue Tomoaki , Miura Masahiro 
Published: October 2018

AbstractBisbenzofuro[2,3‐b : 2′,3′‐e]pyrazine (BBFPy) and its 2,8‐ and 3,9‐di(tert‐butyl)‐substituted derivatives (2 a and 2 b) were synthesized by palladium‐catalyzed intramolecular direct arylation as the key step. The effect of introduction of two tert‐butyl groups to the BBFPy core at the different positions on the fluorescent properties was then investigated. The tert‐butyl groups not only enhance the tractability with increasing solubility, but also induce different crystal‐packing patterns as anticipated. The compounds 2 a and 2 b show relatively strong blue fluorescence in both the solution and solid state. The 2,8‐isomer 2 a specifically exhibits a unique mechanochromism in the solid state; 2 a exhibits two crystalline forms, both of which show green fluorescence by grinding, while different self‐recovering fluorescence patterns between them are observed by standing. The intriguing mechanochromism is rationally interpreted in terms of molecular arrangements determined by X‐ray crystallography.
C@TiO2/MoO3 Composite Nanofibers with 1T‐Phase MoS2 Nanograin Dopant and Stabilized Interfaces as Anodes for Li‐ and Na‐Ion Batteries
Authors: Zhou Huimin , Xia Xin , Lv Pengfei , Zhang Jin , Hou Xuebin , Zhao Min , Ao Kelong , Wang Di , Lu Keyu , Qiao Hui , Zimniewska Malgorzata , Wei Qufu 
Published: October 2018

AbstractIntegrating layered nanostructured MoS2 with a structurally stable TiO2 backbone to construct reciprocal MoS2/TiO2‐based nanocomposites is an effective strategy. C@TiO2/MoO3 composite nanofibers doped with 1T‐phase MoS2 nanograins were fabricated by partially sulfurizing MoOx/TiO2 precursors. By controlling a suitable preoxidation temperature before severe thermolysis of polyvinylpyrrolidone (PVP), the MoOx/TiO2 precursors formed a polymer‐embedded array through coordination of the Mo source and pyrrolidyl groups of PVP. Sulfidation under water/solvent hydrothermal conditions led to partial formation of metallic 1T‐phase MoS2 from the MoOx precursor with preoxidation at 200 °C. After carbonization, the TiO2/MoO3/MoS2 nanograins were encapsulated in a carbon backbone in a vertical pattern, providing both chemical contact for confined electron transport and sufficient space to adapt to volume changes. The obtained carbon‐based platform not only has the advantages of an integral structure, but also exhibited ultrastable specific capacities of 540 and 251 mAh g−1 for Li‐ion batteries and Na‐ion batteries, respectively, after 100 cycles.
Investigation of the Reaction Pathways of Biomass‐Derived Oxygenate Conversion into Monoalcohols in Supercritical Methanol with CuMgAl‐Mixed‐Metal Oxide
Authors: Galebach Peter H. , Thompson Sean , Wittrig Ashley M. , Buchanan J. Scott , Huber George W. 
Published: October 2018

AbstractReaction pathways for the conversion of cellulose into C2–C6 monoalcohols by supercritical methanol depolymerization and hydrodeoxygenation (SCM‐DHDO) over a CuMgAl oxide catalyst have been elucidated using a range of model compounds. SCM‐DHDO of intermediate oxygenates including glycerol, methyl lactate, and 1,2‐ethanediol produces similar products as those produced from the SCM‐DHDO of cellulose. The pathway to C2–C6 monoalcohols occurs through rapid C−C coupling reactions between methanol and diols followed by C−C scission between vicinal alcohol groups to produce two monoalcohols. Methyl‐branched monoalcohols are produced through a methyl shift in a secondary diol followed by dehydration. Esters are produced by dehydrogenative coupling between an adsorbed methoxy and a primary alcohol. Both dehydrogenation to a ketone and esterification to a methyl ester are in equilibrium with the corresponding alcohol and were reversible. Dehydration of diols is the slowest observed reaction and not a main pathway to monoalcohols. SCM‐DHDO of glucose, dihydroxyacetone, and cellulose all produced similar high molecular weight species indicating that condensation of intermediates can produce undesired side products.
In‐house chemical library repurposing: A case example for Pseudomonas aeruginosa antibiofilm activity and quorum sensing inhibition
Authors: Ravithej Singh L , Tripathi Vikash C. , Raj Sneha , Kumar Anoop , Gupta Sampa , Horam Soyar , Upadhyay Akanksha , Kushwaha Pragati , Arockiaraj Jesu , Sashidhara Koneni V. , Pasupuleti Mukesh 
Published: October 2018

Abstract

Hit, Lead & Candidate Discovery

Drug repurposing has become a recent trend in drug development programs, where previously developed drugs are explored for hit and redeveloped into potential therapeutic agents for new diseases. Globally, in any drug development program, a series of molecules are synthesized and evaluated for the hypothesized activity. Hits are developed into lead molecules or drugs, whereas the negative ones are shelved in the lab with no immediate use. We in this project took the previously sidelined small chemical molecules to the next level of utility, where previously developed in‐house small molecules library are tested for the unexplored biological relevant activity. As biofilm formation and quorum sensing play a vital role in bacterial pathogenesis, we believe that they could be one of the most effective targets for antimicrobial agents. In this study, we report the evaluation of 50 different compounds for anti‐biofilm and anti‐quorum sensing activity against Pseudomonas aeruginosa. Out of the screened compounds, three hydrazine‐carboxamide hybrid derivatives showed promising anti‐biofilm property and inhibition of pyocyanin production without any direct antimicrobial activity and cytotoxicity issues. Hydrazine‐carboxamide hybrids can be a new class and promising leads for further anti‐biofilm and anti‐virulence development against microbial infections.