bluuebunny/crossref_metadata_2025_split huggingface dataset:
A flexible toolbox to study protein‐assisted metalloenzyme assembly in vitro
Authors: Schiffels Johannes , Selmer Thorsten 
Published: May 2015

ABSTRACTA number of metalloenzymes harbor unique cofactors, which are incorporated into the apo‐enzymes via protein‐assisted maturation. In the case of [NiFe]‐hydrogenases, minimally seven maturation factors (HypABCDEF and a specific endopeptidase) are involved, making these enzymes an excellent example for studying metallocenter assembly in general. Here, we describe an innovative toolbox to study maturation involving multiple putative gene products. The two core elements of the system are a modular, combinatorial cloning system and a cell‐free maturation system, which is based on recombinant Escherichia coli extracts and/or purified maturases. Taking maturation of the soluble, oxygen‐tolerant [NiFe]‐hydrogenase (SH) from Cupriavidus necator as an example, the capacities of the toolbox are illustrated. In total 18 genes from C. necator were analyzed, including four SH‐structural genes, the SH‐dedicated hyp‐genes and a second set of hyp‐genes putatively involved in maturation of the Actinobacterium‐like hydrogenase (AH). The two hyp‐sets were either expressed in their entirety from single vectors or split into functional modules, which enabled flexible approaches to investigate limitations, specificities and the capabilities of individual constituents to functionally substitute each other. Affinity‐tagged Hyp‐Proteins were used in pull‐down experiments to demonstrate direct interactions between dedicated or non‐related constituents. The dedicated Hyp‐set from C. necator exhibited the highest maturation efficiency in vitro. Constituents of non‐related maturation machineries were found to interact with and to accomplish partial activation of SH. In contrast to homologues of the Hyp‐family, omission of the SH‐specific endopeptidase HoxW completely abolished in vitro maturation. We detected stoichiometric imbalances inside the recombinant production system, which point to limitations by the cyanylation complex HypEF and the premature subunit HoxH. Purification of HoxW revealed strong indications for the presence of a putative [4Fe‐4S]‐cluster, which is unique among this class of maturases. Results are discussed in the context of [NiFe]‐hydrogenase maturation, and in light of the capacity of the novel toolbox. Biotechnol. Bioeng. 2015;112: 2360–2372. © 2015 Wiley Periodicals, Inc.
Lipophilicity study of eight cephalosporins by reversed‐phase thin‐layer chromatographic method
Authors: Dąbrowska Monika , Komsta Łukasz , Krzek Jan , Kokoszka Kinga 
Published: May 2015

AbstractThe lipophilicity (RM0) and specific hydrophobic surface area for the representatives of four generation cephalosporins have been determined by reversed‐phase thin‐layer chromatography, and the effect of different mobile‐phase modifiers (such as methanol, acetonitrile, acetone, 1,4‐dioxane and 2‐propanol) on the retention has been studied. The compounds studied showed typical retention behavior; their RM values decreased linearly with increasing concentration of the organic modifier in the eluent. The linear correlations between the volume fraction of the organic solvent and the RM values over a limited range were established for each solute, resulting in high values of correlation coefficients (>0.95 in most cases). RM values were determined by various concentrations of organic modifier, and the correlation obtained was extrapolated to 0% of organic modifier. Chromatographically established logP (RM0) parameters were compared with computationally calculated partition coefficients values (AClogP, ALOGP, KOWWIN, ALOGPs, XLOGP2, MLOGP and XLOGP3) and experimental octanol–water logP values (measured by the shake flask method). The received results demonstrate that RP‐TLC may be a good alternative technique for analytics in describing the lipophilic nature of investigated cephalosporins as well as the activity. Copyright © 2015 John Wiley & Sons, Ltd.
Adsorption of cinnabarinic acid from culture fluid with magnetic microbeads
Authors: Göçenoğlu Sarıkaya Aslı , Osman Bilgen , Kara Ali , Pazarlioglu Nurdan , Beşirli Necati 
Published: May 2015

AbstractIn this study, antimicrobial pigment cinnabarinic acid (CA) was produced from Pycnoporus cinnabarinus in laboratory‐scale batch cultures. Magnetic poly(ethylene glycol dimethacrylate‐N‐methacryloyl‐l‐tryptophan methyl ester) [m‐poly(EGDMA‐MATrp)] beads (average diameter = 53–103 µm) were synthesized by copolymerizing of N‐methacryloyl‐l‐tryptophan methyl ester (MATrp) with ethylene glycol dimethacrylate (EGDMA) in the presence of magnetite (Fe3O4) and used for the adsorption of CA. The m‐poly(EGDMA‐MATrp) beads were characterized by N2 adsorption/desorption isotherms (Brunauer Emmet Teller), X‐ray photoelecron spectroscopy, scanning electron microscopy, infrared spectroscopy, thermal gravimetric analysis, electron spin resonance and swelling studies. The efficiency of m‐poly(EGDMA‐MATrp) beads for separation of CA from culture fluid was evaluated. The effects of pH, initial concentration, contact time and temperature on adsorption were analyzed. The maximum CA adsorption capacity of the m‐poly(EGDMA‐MATrp) beads was 272.9 mg g−1 at pH 7.0, 25 °C. All the isotherm data can be fitted with the Langmuir, Freundlich and Dubinin–Radushkevich isotherm models. The adsorption process obeyed pseudo‐second‐order kinetic model. Thermodynamic parameters ΔH = 5.056 kJ mol−1, ΔS = 52.44 J K−1 mol−1 and ΔG = −9.424 kJ mol−1 to ‐11.27 kJ mol−1 with the rise in temperature from 4 to 40 °C indicated that the adsorption process was endothermic and spontaneous. Copyright © 2015 John Wiley & Sons, Ltd.
The long‐term outcomes of alternating chemoradiotherapy for locoregionally advanced nasopharyngeal carcinoma: a multiinstitutional phase II study
Authors: Fuwa Nobukazu , Kodaira Takeshi , Daimon Takashi , Yoshizaki Tomokazu 
Published: May 2015

AbstractTo examine the long‐term outcomes of alternating chemoradiotherapy (ALCRT) for patients with locoregionally advanced nasopharyngeal carcinoma (NPC) and to assess the efficacy of ALCRT for NPC. Patients with stage IIB to IVB, ECOG PS 0–2, 18–70 years‐old, and sufficient organ function were eligible for this study. First, chemotherapy, consisting of 5‐fluorouracil (800 mg/m2 per 24 h on days 1–5) and cisplatin (100 mg/m2 per 24 h on day 6), was administered, then a wide field of radiotherapy (36 Gy/20 fraction), chemotherapy, a shrinking field of radiotherapy (34 Gy/17 fraction), and chemotherapy were performed alternately. Between December 2003 and March 2006, 90 patients in 25 facilities were enrolled in this study, 87 patients were finally evaluated. A total of 67 patients (76.1%) completed the course of treatment. The overall survival and the progression‐free survival rates at 5 years were 78.04% (95% CI: 69.1~87.0%), and 68.74% (95% CI: 58.8~78.7%), respectively. The long‐term outcomes of ALCRT for NPC were thought to be promising. ALCRT will be considered to be a controlled trial to compare therapeutic results with those of concurrent chemoradiotherapy for NPC.
Genomic characterization of chromosome 8 pericentric trisomy
Authors: Vander Pluym Juliana H. , O'Sullivan Julia , Andrew Gail , Bolduc Francois V. 
Published: May 2015

Key Clinical MessageWe present a patient with trisomy 8p11.21q11.21 associated with language, gross motor, fine motor, and cognitive delay. Furthermore, using array‐based comparative genomic hybridization, we identify the specific genes duplicated in our patient.
The impact of the new proposed Papanicolaou Society of Cytopathology terminology for pancreaticobiliary cytology in endoscopic US‐FNA: A single‐Institutional experience
Authors: Saieg Mauro Ajaj , Munson Valerie , Colletti Shanna , Nassar Aziza 
Published: May 2015

BACKGROUNDThe Papanicolaou Society of Cytopathology has recently published a new proposal for pancreaticobiliary cytology terminology. For the current study, the authors applied this new classification for pancreaticobiliary cytology to a set of previously diagnosed endoscopic ultrasound (EUS)‐guided fine‐needle aspiration (EUS‐FNA) samples and correlated the results with those from the corresponding available final surgical specimens.METHODSPancreatic FNA specimens were retrospectively collected from a 12‐month period at the Mayo Clinic in Jacksonville, Florida. Cases with cytohistologic disagreement were reviewed to assess the reasons for discrepancies. The sensitivity and specificity of EUS‐FNA specimens were assessed using the Pearson chi‐square test.RESULTSOne hundred fifty‐five pancreatic FNA specimens were retrieved. The median patient age was 70 years (range, 25‐93 years). Eleven specimens previously classified as negative and 3 previously classified as non‐diagnostic were reclassified as neoplastic:other, as well as all specimens primarily classified as atypical or positive for neoplasm and half the specimens primarily classified as suspicious. All positive specimens remained within their same categories in the revised classification. Sixteen patients (10.3%) had surgical resection specimens available, and complete or partial agreement with FNA results was achieved in 13 of those surgical specimens (81.2%). Reasons for discrepancy comprised sampling errors in 5 specimens and an interpretation error in 1 specimen. Overall, sensitivity was 66.7%, specificity was 66.7%, the positive predictive value was 88.9%, and the negative predictive value was 33.3%.CONCLUSIONSThe application of the new proposed terminology for pancreaticobiliary cytology had a greater impact among specimens that were previously classified as atypical and suspicious. EUS‐FNA of the pancreas is a highly accurate method, and its use, allied with the new proposed terminology, may ultimately contribute to better outcomes. Cancer (Cancer Cytopathol) 2015;123:488–94. © 2015 American Cancer Society.
User accessible reply capabilities in invoking and servicing operations
Authors: Olsson Ronald A. , Keen Aaron W. 
Published: May 2015

SummaryMany message passing languages and packages include some form of synchronous invocation. In a synchronous invocation, the invoker waits for the invocation's servicer to pass back results. A synchronous invocation can be viewed as a pair of asynchronous invocations: one—initiating the computation—with parameter values from the invoker to the servicer and the other—once the requested computation has completed—with the ‘go‐ahead’ and return value from the servicer to the invoker. The target of the latter invocation is known as the reply operation, and a reference to it is known as a reply capability. This paper addresses the issues of making such reply capabilities directly accessible to user code. It presents the design and prototype implementation of a new version of the JR concurrent programming language, called xJR, in which the reply capability can be explicit. This paper gives xJR examples, including realistic ones, to highlight the additional flexibility the new features offer (such as a non‐lexical reply). These additional features do not impact the run‐time performance of existing JR features and can even lead to more efficient code in some programming scenarios. Our experience with the prototype implementation indicates that an actual implementation would be fruitful and would preserve the prototype's performance advantages. Copyright © 2015 John Wiley & Sons, Ltd.
Population genetics of four heavily exploited shark species around the Arabian Peninsula
Authors: Spaet Julia L. Y. , Jabado Rima W. , Henderson Aaron C. , Moore Alec B. M. , Berumen Michael L. 
Published: May 2015

AbstractThe northwestern Indian Ocean harbors a number of larger marine vertebrate taxa that warrant the investigation of genetic population structure given remarkable spatial heterogeneity in biological characteristics such as distribution, behavior, and morphology. Here, we investigate the genetic population structure of four commercially exploited shark species with different biological characteristics (Carcharhinus limbatus, Carcharhinus sorrah, Rhizoprionodon acutus, and Sphyrna lewini) between the Red Sea and all other water bodies surrounding the Arabian Peninsula. To assess intraspecific patterns of connectivity, we constructed statistical parsimony networks among haplotypes and estimated (1) population structure; and (2) time of most recent population expansion, based on mitochondrial control region DNA and a total of 20 microsatellites. Our analysis indicates that, even in smaller, less vagile shark species, there are no contemporary barriers to gene flow across the study region, while historical events, for example, Pleistocene glacial cycles, may have affected connectivity in C. sorrah and R. acutus. A parsimony network analysis provided evidence that Arabian S. lewini may represent a population segment that is distinct from other known stocks in the Indian Ocean, raising a new layer of conservation concern. Our results call for urgent regional cooperation to ensure the sustainable exploitation of sharks in the Arabian region.
Toxicity in relation to mode of action for the nematode Caenorhabditis elegans: Acute-to-chronic ratios and quantitative structure–activity relationships
Authors: Ristau Kai , Akgül Yeliz , Bartel Anna Sophie , Fremming Jana , Müller Marie-Theres , Reiher Luise , Stapela Frederike , Splett Jan-Paul , Spann Nicole 
Published: May 2015

Abstract

Acute-to-chronic ratios (ACRs) and quantitative structure–activity relationships (QSARs) are of particular interest in chemical risk assessment. Previous studies focusing on the relationship between the size or variation of ACRs to substance classes and QSAR models were often based on data for standard test organisms, such as daphnids and fish. In the present study, acute and chronic toxicity tests were performed with the nematode Caenorhabditis elegans for a total of 11 chemicals covering 3 substance classes (nonpolar narcotics: 1-propanol, ethanol, methanol, 2-butoxyethanol; metals: copper, cadmium, zinc; and carbamates: methomyl, oxamyl, aldicarb, dioxacarb). The ACRs were variable, especially for the carbamates and metals, although there was a trend toward small and less variable ACRs for nonpolar narcotic substances. The octanol–water partition coefficient was a good predictor for explaining acute and chronic toxicity of nonpolar narcotic substances to C. elegans, but not for carbamates. Metal toxicity could be related to the covalent index χm2r. Overall, the results support earlier results from ACR and QSAR studies with standard freshwater test animals. As such C. elegans as a representative of small soil/sediment invertebrates would probably be protected by risk assessment strategies already in use. To increase the predictive power of ACRs and QSARs, further research should be expanded to other species and compounds and should also consider the target sites and toxicokinetics of chemicals. Environ Toxicol Chem 2015;34:2347–2353. © 2015 SETAC
Microencapsulation of vanillin by spray drying using soy protein isolate–maltodextrin as wall material
Authors: Noshad Mohammad , Mohebbi Mohebbat , Koocheki Arash , Shahidi Fakhri 
Published: May 2015

AbstractIn this study, the application of a response surface methodology (RSM) to optimize the microencapsulation of vanillin as a nutraceutical was studied. Soy protein isolate and maltodextrin were used as a wall material. Microencapsulate of vanillin using spray drying with maltodextrin solutions at different concentration (5–15% wt), vanillin concentrations (0.1–0.4 %wt) and inlet temperature (180–200 °C) were the factors investigated with respect to moisture content, particle size and encapsulation efficiency. RSM was used to determine the optimum processing conditions that yielded maximum encapsulation efficiency and minimum moisture content and particle size during drying of vanillin microencapsulate. The results revealed that microencapsulated powder obtained at 184 °C with a 8.5% maltodextrin concentration and 0.36% vanillin concentration was optimum among investigated samples in terms of its encapsulation efficiency, particle size and moisture content. The scanning electron microscopy (SEM) of the powders produced at the selected optimal conditions showed a spherical shape with no apparent cracks or fissures, which promotes better protection and retention of the core material. Copyright © 2015 John Wiley & Sons, Ltd.
Prevalence and risk factors of sialocele formation after partial superficial parotidectomy: A multi‐institutional analysis of 357 consecutive patients
Authors: Lee Young Chan , Park Gi Cheol , Lee Jung‐Woo , Eun Young Gyu , Kim Seung Woo 
Published: May 2015

ABSTRACTBackgroundThe purpose of this study was to identify the prevalence of sialoceles and the risk factors associated with their formation after parotidectomy.MethodsWe performed a retrospective analysis of the data from consecutive patients who underwent partial superficial parotidectomy of parotid tumors. Demographic data, preoperative imaging results, operative variables, including tumor type, incision type, tumor size, and method of parenchymal disruption were assessed.ResultsTwenty‐three of 357 patients (6.4%) undergoing partial superficial parotidectomy developed sialoceles during the postoperative period. Sialoceles occurred more often in patients who had tumors in the anterior portion of the parotid gland. Multivariate analysis showed that an anterior tumor location was a significant risk factor for sialocele formation.ConclusionThe incidence of sialocele development was 6.4% in patients undergoing partial superficial parotidectomy. An anterior tumor location may increase the risk of sialocele formation. © 2015 Wiley Periodicals, Inc. Head Neck 38: E941–E944, 2016
Short‐term donor site morbidity: A comparison of the anterolateral thigh and radial forearm fasciocutaneous free flaps
Authors: Knott P. Daniel , Seth Rahul , Waters Heather H. , Revenaugh Peter C. , Alam Daniel , Scharpf Joseph , Meltzer Noah E. , Fritz Michael A. 
Published: May 2015

ABSTRACTBackgroundDonor site morbidity is an important consideration in the overall decision‐making algorithm for fasciocutaneous free flap reconstruction of the head and neck.MethodsA retrospective case series was conducted of donor site complications occurring within 30 days of surgery among 226 consecutive anterolateral thigh (ALT) or radial forearm free flap (RFFF) microvascular free tissue transfers performed by multiple reconstructive surgeons between 2005 and 2010.ResultsA greater number of donor site complications occurred among patients undergoing RFFF versus ALT free flaps (40; 35.4%; vs 14; 12.4%; p < .001). Wound dehiscence occurred significantly more frequently among patients undergoing RFFF versus ALT free flap reconstruction (34; 30%; vs 6; 5%; p < .001). Tendon exposure occurred in 16 of the 113 RFFFs (14.1%). Seromas occurred more commonly in the ALT group (6; 5%; vs 2; 1.7%; p = .280).ConclusionAlthough short‐term donor site morbidity was low in both groups, the ALT was associated with a significantly lower incidence of wound dehiscence with or without tendon exposure. © 2015 Wiley Periodicals, Inc. Head Neck 38: E945–E948, 2016
Concomitant chemoradiotherapy for advanced squamous cell carcinoma of the temporal bone
Authors: Shinomiya Hirotaka , Hasegawa Shingo , Yamashita Daisuke , Ejima Yasuo , Kenji Yoshida , Otsuki Naoki , Kiyota Naomi , Sakakibara Shunsuke , Nomura Tadashi , Hashikawa Kazunobu , Kohmura Eiji , Sasaki Ryohei , Nibu Ken‐ichi 
Published: May 2015

ABSTRACTBackgroundThe purpose of this study was to analyze outcomes for the treatment of locally advanced temporal bone cancer by means of concomitant chemoradiotherapy (CCRT) with a combination of cisplatin (CDDP), 5‐fluorouracil (5‐FU), and docetaxel (TPF).MethodsBetween 2006 and 2011, 34 patients with squamous cell carcinoma of the temporal bone were treated at Kobe University Hospital. Medical records were retrospectively reviewed to obtain information concerning patient characteristics, extent of disease, treatment, adverse events, and oncologic results.ResultsTen patients were treated with CCRT using TPF regimen. The 5‐year overall survival rate and disease‐free survival rate were both 60%. Of special interest is that even for patients with unresectable T4 disease, the 5‐year overall survival rate was 56%.ConclusionThe results of our study indicate that CCRT with TPF for locally advanced temporal bone cancer is an effective and promising regimen. © 2015 Wiley Periodicals, Inc. Head Neck 38: E949–E953, 2016
Writing Instruction for Adolescents in the Shadow of the Common Core State Standards
Authors: Sundeen Todd H. 
Published: May 2015

AbstractCurrent research on instructional practices for secondary student writing reveals little emphasis on compositions requiring analysis, interpretation, and argumentation. Indeed, written expression in English language arts classes is generally confined to writing assignments of very limited length. Additionally, recent efforts for educational reform have led the United States to adopt national academic standards. This article examines the current focus on composition instruction for secondary students as girded by recent influences of the Common Core State Standards and within the context of four teacher surveys that investigated secondary instructional practices for writing. Questions are addressed regarding what and how often students write, influences of standardized testing, instruction for struggling writers, and teacher preparation. Opportunities are described for improving secondary writing instruction while building on the potential effects of the Common Core.
In vitro and in vivo antioxidant, cytotoxic, and anti‐chronic inflammatory arthritic effect of selenium nanoparticles
Authors: Malhotra Sonam , Welling M. N. , Mantri S. B. , Desai Krutika 
Published: May 2015

AbstractThe toxicity of selenium (Se) as an antioxidant supplement in the treatment of arthritis is debatable. In this study, Dextrin stabilized Se nanoparticles (SeNP) of size 64 nm ± 0.158 were used to explore its effects as a potent antioxidant with reduced toxicity in both in vitro and in vivo. In vitro toxicity of SeNP was determined using cytotoxicity assay. In vitro interactions of SeNP with DNA and protein was established. Subacute toxicity of SeNP was studied. Wistar rats with complete freunds adjuvant induced arthritis were used. Various concentrations of SeNP per kg body weight were fed orally daily upto to 21 days. Arthritic profile based on paw swelling, histopathological changes in joints, blood indices, and antioxidant enzymes level in organs such as liver, kidney, and spleen were investigated. Dextrin‐SeNP when interacted with NIH‐3T3 cells showed 15% cytotoxicity at 100 µg/mL whereas, bulk Se showed 95% at the same concentration. SeNP at 250 µg/mL showed protective effect on DNA. Interaction of SeNP with BSA showed increase in quenching of BSA fluorescence. SeNP did not show any subacute toxicity at concentration as high as 5 mg/kg b.w. in Wistar rats. SeNP at a concentration of 250 µg/kg b.w. acted as potent anti‐inflammatory agent and significantly reduced (p < 0.05) arthritis induced parameters. The enzymatic antioxidant levels in liver, kidney, and spleen were restored significantly (p < 0.05) at 500 µg/kg b.w. while CRP was regained to normal at concentration of 100 µg/kg b.w. concluding SeNP at 500 µg/kg b.w. can be a potential antiarthritic drug supplement. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 104B: 993–1003, 2016.