bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enzymatic generation of peptides flanked by basic amino acids to obtain MS/MS spectra with 2× sequence coverage
Authors: Ebhardt H. Alexander , Nan Jie , Chaulk Steven G. , Fahlman Richard P. , Aebersold Ruedi 
Published: November 2014

RATIONALETandem mass (MS/MS) spectra generated by collision‐induced dissociation (CID) typically lack redundant peptide sequence information in the form of e.g. b‐ and y‐ion series due to frequent use of sequence‐specific endopeptidases cleaving C‐ or N‐terminal to Arg or Lys residues.METHODSHere we introduce arginyl‐tRNA protein transferase (ATE, EC 2.3.2.8) for proteomics. ATE recognizes acidic amino acids or oxidized Cys at the N‐terminus of a substrate peptide and conjugates an arginine from an aminoacylated tRNAArg onto the N‐terminus of the substrate peptide. This enzymatic reaction is carried out under physiological conditions and, in combination with Lys‐C/Asp‐N double digest, results in arginylated peptides with basic amino acids on both termini.RESULTSWe demonstrate that in vitro arginylation of peptides using yeast arginyl tRNA protein transferase 1 (yATE1) is a robust enzymatic reaction, specific to only modifying N‐terminal acidic amino acids. Precursors originating from arginylated peptides generally have an increased protonation state compared with their non‐arginylated forms. Furthermore, the product ion spectra of arginylated peptides show near complete 2× fragment ladders within the same MS/MS spectrum using commonly available electrospray ionization peptide fragmentation modes. Unexpectedly, arginylated peptides generate complete y‐ and c‐ion series using electron transfer dissociation (ETD) despite having an internal proline residue.CONCLUSIONSWe introduce a rapid enzymatic method to generate peptides flanked on either terminus by basic amino acids, resulting in a rich, redundant MS/MS fragment pattern. © 2014 The Authors. Rapid Communications in Mass Spectrometry published by John Wiley & Sons Ltd.
Generation of new AgmTen clusters via laser ablation synthesis using Ag‐Te nano‐composite as precursor. Quadrupole ion trap time‐of‐flight mass spectrometry
Authors: Mawale Ravi Madhukar , Amato Filippo , Alberti Milan , Havel Josef 
Published: November 2014

RATIONALESilver tellurides find applications in the development of infrared detection, imaging, magnetics, sensors, memory devices, and optic materials. However, only a limited number of silver tellurides have been described to date. Laser ablation synthesis (LAS) was selected to generate new Ag‐Te clusters.METHODSIsothermal adsorption was used to study the formation of silver nano‐particles‐tellurium aggregates. Laser desorption ionization quadrupole ion trap time‐of‐flight mass spectrometry (LDI‐QIT‐TOFMS) was used for the generation and analysis of AgmTen clusters. Scanning electron microscopy and energy‐dispersive X‐ray spectroscopy were used to visualize the structure of materials. The stoichiometry of the generated clusters was determined by computer modeling of isotopic patterns.RESULTSA simple, one‐pot method for the preparation of Ag‐Te nano‐composite was developed and found suitable for LAS of silver tellurides. The LDI of Ag‐Te nano‐composite leads to the formation of 11 unary and 52 binary clusters. The stoichiometry of the 34 novel AgmTen clusters is reported here for the first time.CONCLUSIONSLAS with TOFMS detection was proven to be a powerful technique for the generation of silver telluride clusters. Knowledge of the stoichiometry of the generated clusters might facilitate the further development of novel high‐tech silver tellurium nano‐materials. Copyright © 2014 John Wiley & Sons, Ltd.
Effects of decalcification on bulk and compound‐specific nitrogen and carbon isotope analyses of dentin
Authors: Brault Emily K. , Koch Paul L. , Gier Elizabeth , Ruiz‐Cooley R. I. , Zupcic Jessica , Gilbert Kwasi N. , McCarthy Matthew D. 
Published: November 2014

RATIONALEFor bulk carbon and nitrogen isotope analysis of dentin, samples are typically decalcified. Since the non‐protein carbon in dentin is low, whole sample analysis may produce reliable data. Compound‐specific isotope analysis (CSIA) of bone and tooth dentin protein is a powerful tool for reconstructing the flow of carbon and nitrogen in modern and past food webs. Decalcification has also been used to prepare bone and dentin samples for CSIA, but the effects of this process on bulk dentin, amino acid composition, and their specific isotope values are not known.METHODSThe bulk isotope values of raw and decalcified dentin from a sperm whale tooth were measured to determine the effects of decalcification and the accuracy of untreated dentin results. CSIA was also performed on decalcified and raw dentin to examine differences in the amino acid isotope values and molar composition between these two approaches.RESULTSAnalysis of raw dentin yields precise and accurate bulk isotope measurements for this animal. The isotopic values of decalcified samples and raw dentin for individual amino acids were similar, but the average of the isotope value offsets between the two sample types was significant. The presence of inorganic material complicated raw sample processing for individual amino acid isotope values, and may have contributed to the isotopic differences between decalcified and raw samples.CONCLUSIONSDecalcification is not needed to measure bulk isotope values in dentin from this modern odontocete, probably because the lipid and carbonate concentrations are low and the carbon isotope values of dentin protein and carbonate are similar. This method should not be applied in some cases (e.g., with fossil dentin and modern bone). Decalcification should still be used prior to CSIA since significant matrix issues occur with raw dentin processing and decalcification does not alter the amino acid molar composition or isotopic values of dentin. Copyright © 2014 John Wiley & Sons, Ltd.
RNAi in the mouse: rapid and affordable gene function studies in a vertebrate system
Authors: Rytlewski Julie A. , Beronja Slobodan 
Published: November 2014

The addition of RNA interference (RNAi) to the mammalian genomic toolbox has significantly expanded our ability to use higher‐order models in studies of development and disease. The mouse, in particular, has benefited most from RNAi technology. Unique combinations of RNAi vectors and delivery methods now offer a broad platform for gene silencing in transgenic mice, enabling the design of new physiologically relevant models. The era of RNAi mice has accelerated the pace of genetic study and made high‐throughput screens not only feasible but also affordable. WIREs Dev Biol 2015, 4:45–57. doi: 10.1002/wdev.164This article is categorized under:

Technologies > Perturbing Genes and Generating Modified Animals
Paternal care behaviors of Japanese giant salamander Andrias japonicus in natural populations
Authors: Okada Sumio , Fukuda Yukihiro , Takahashi Mizuki K. 
Published: November 2014

Abstract
Parental care among salamanders is typically provided by females. A rare case of parental care by male salamanders appears to occur in Cryptobranchidae. Yet, paternal behaviors have rarely been reported from natural populations of any Cryptobranchid salamanders, and their adaptive significance is poorly understood. The present study aimed to examine paternal care behaviors in a fully aquatic Japanese giant salamander (Andrias japonicus) in situ. At the beginning of the summer breeding season, large males, called den-masters, occupy burrows along stream banks for breeding and nesting. We videotaped post-breeding behaviors of two den-masters that stayed with the eggs, one in a natural and the other in an artificial nest in natural streams. We identified three behaviors, tail fanning, agitating and egg eating, to be parental care. Tail fanning provides oxygenated water for the eggs. We found that the den-master in the artificial nest, where dissolved oxygen level was lower, displayed tail fanning more frequently. Agitating the eggs with its head and body likely prevents yolk adhesions. The den-masters selectively ate whiter eggs that appeared to be dead or infected with water mold. This behavior, which we termed hygienic filial cannibalism, likely prevents water mold from spreading over healthy eggs. Digital video images relating to this article are available at http://www.momo-p.com/showdetail-e.php?movieid=momo140906aj01a, http://www.momo-p.com/showdetail-e.php?movieid=momo140906aj02a, http://www.momo-p.com/showdetail-e.php?movieid=momo140906aj03a and http://www.momo-p.com/showdetail-e.php?movieid=momo140906aj04a.
A phase I study of farletuzumab, a humanized anti-folate receptor α monoclonal antibody, in patients with solid tumors
Authors: Sasaki Yasutsuna , Miwa Keisuke , Yamashita Keishi , Sunakawa Yu , Shimada Ken , Ishida Hiroo , Hasegawa Kosei , Fujiwara Keiichi , Kodaira Makoto , Fujiwara Yasuhiro , Namiki Masayuki , Matsuda Minami , Takeuchi Yutaka , Katsumata Noriyuki 
Published: November 2014

SummaryFarletuzumab is a humanized monoclonal antibody against folate receptor α (FRA). The purpose of the study is to assess safety and tolerability, the pharmacokinetic (PK) profile, and preliminary antitumor effect. Patients with ovarian cancer (OC) or FRA-expressing solid tumors who are resistant to standard treatments were eligible for the study. After single-dose administration for PK assessment, farletuzumab was administered by intravenous injection, repeating every week until disease progression. Dose-limiting toxicities (DLTs) were defined as grade 4 hematological and grade 3/4 nonhematological toxicities. Dose escalation was planned in 4 cohorts (50, 100, 200, and 400 mg/m2). Fourteen patients with OC and two patients with gastric cancer (GC) received farletuzumab infusion. Neither DLTs nor grade 3/4 toxicities were reported in all cohorts. Major adverse events, including grade 1/2 infusion related reaction (15 patients, 93.8 %), headache (seven patients, 43.8 %), and nausea and decreased appetite (five patients each, 31.3 %), were observed and medically managed. AUC and Cmax increased dose-dependently and linear PK profiles were observed. No tumor shrinkage was recorded, but long-term disease stabilization for 25 and 20 months was observed in one patient with clear cell OC (100 mg/m2) and one patient with GC (400 mg/m2), respectively. No cumulative toxicity occurred in any patient. Farletuzumab was well tolerated in Japanese patients with a similar PK profile as compared with the US population. Long-term disease stabilization was observed in a subpopulation of clear cell OC and GC; both of them were resistant and progressive after standard chemotherapies (ClinicalTrials.gov Identifier: NCT01049061).
Estimation of annual spatial variations in forest production and crop yields at landscape scale in temperate climate regions
Authors: Ruidisch M. , Nguyen T. T. , Li Y. L. , Geyer R. , Tenhunen J. 
Published: November 2014

AbstractSimulating regional variations in gross primary production (GPP) and yields of major land cover types is complex due to differences in plant physiological properties, landscape topography, and climate gradients. In our study, we analyzed the inter‐annual and inter‐regional variation, as well as the effect of summer drought, on gross primary production and crop yields of 9 major land uses within the state‐funded Bioenergy Region Bayreuth in Germany. We developed a simulation framework using a process based model which accounts for variations in both CO2 gas exchange, and in the case of crops, growth processes. The results indicated a severe impact of summer drought on GPP, particularly of forests and grasslands. Yields of winter crops, early planted summer grain crops as well as the perennial 2nd generation biofuel crop Silphium perfoliatum, on the other hand, were buffered despite drought by comparatively mild winter and spring temperatures. We estimated regional yield increases from SW to NE, suggesting a comparative advantage for these crops in the cooler and upland part of the region. In contrast, grasslands and annual summer crops such as maize and potato did not exhibit any apparent regional pattern in the simulations. The 2nd generation bioenergy crop exhibited significantly higher GPP and yields compared to the conventional bioenergy crop maize, suggesting that cultivation of S. perfoliatum should be increased for economic and environmental reasons, but additional study of the growth of S. perfoliatum is still required.
Soil microbial response to experimental warming in cool temperate semi‐natural grassland in Japan
Authors: Yoshitake Shinpei , Tabei Nozomi , Mizuno Yu , Yoshida Hitomi , Sekine Yuya , Tatsumura Makoto , Koizumi Hiroshi 
Published: November 2014

AbstractTo assess soil microbial response to global warming in cool temperate semi‐natural grassland, we conducted an in situ warming experiment in grassland located in the mountains of central Japan. Five pairs of plots (control and warmed) of Zoysia japonica were established. For each pair of plots, one was warmed by ca. 2 °C using infrared heaters during the growing seasons of 2009–2011. Above‐ground biomass of Z.japonica was estimated using the modified point‐frame method. Soil organic matter contents, soil total carbon and nitrogen contents, as well as inorganic nitrogen (ammonium and nitrate) contents were determined from soil samples. Total phospholipid fatty acid (PLFA) contents and PLFA compositions were determined and used as indices for total microbial biomass and community structure, respectively. Analyses showed that the warming increased the above‐ground biomass of Z. japonica significantly. Soil organic matter and soil total nitrogen contents were significantly decreased, while soil ammonium content was significantly increased in the warmed plots. Soil microbial biomass (especially fungal biomass) was lower in the warmed plots, probably reflecting higher temperature, lower soil water content, and/or depletion in available nutrients. The significant decrease in fungal biomass, in combination with our PLFA composition data, suggests that the soil microbial community structure shifted from a fungal‐dominated to a bacteria‐dominated one, causing changes in community‐level physiological activity.
Separation and Detection of Plasmalogen in Marine Invertebrates by High‐Performance Liquid Chromatography with Evaporative Light‐Scattering Detection
Authors: Yamashita Shinji , Abe Akihiro , Nakagawa Kiyotaka , Kinoshita Mikio , Miyazawa Teruo 
Published: November 2014

AbstractWe have developed a new method for determining ethanolamine plasmalogen contents in marine invertebrates. This quantification method involves derivatization of ethanolamine glycerophospholipid (EtnGpl) subclasses, alkenylacyl (plasmalogen), diacyl, and alkylacyl subclasses, by enzyme treatment and acetylation, followed by separation and detection by high‐performance liquid chromatography (HPLC) with evaporative light‐scattering detection (ELSD). This method enabled complete separation of the subclasses, and the limit of detection for plasmalogen was 200 ng (260 pmol). The peak area of plasmalogen by ELSD was unaffected by the degree of unsaturated fatty acids in EtnGpl, in contrast to ultraviolet (UV) detection. Thus, this method enables accurate determination of plasmalogen contents in various species containing marine products possessing abundant polyunsaturated fatty acids (PUFA). The method developed here was applied to marine invertebrates available in Japan. The examined marine invertebrates showed a wide range of plasmalogen contents ranging from 19 to 504 μmol/100 g wet wt. The plasmalogen levels in samples except those of class Cephalopoda and Crustacea were more than 60 mol% of EtnGpl.
Health-related quality of life in children with flexible flatfeet: A cross-sectional study
Authors: Kothari Alpesh , Stebbins Julie , Zavatsky Amy Beth , Theologis Tim 
Published: November 2014

Purpose The effect of paediatric flexible flatfeet (PFF) on health-related quality of life (HRQOL) has not been investigated. In this prospective cross-sectional study, the HRQOL of children with PFF was compared to those with typically developing feet (TDF) using two validated measures. We hypothesised that reduced HRQOL would be observed in children with PFF. The reliability of parents’ perceptions of their child's symptoms was also investigated. Methods 48 children with PFF and 47 with TDF between the ages of 8 and 15 completed The Oxford Ankle Foot Questionnaire for Children (OxAFQ-C) and Pediatric Quality of Life Inventory (PedsQL™ 4.0). Proxy questionnaires were also completed. Reliability of parent and child questionnaire scores was assessed using the intraclass correlation coefficient (ICC) and Student's t test. Differences between HRQOL between PFF and TDF were assessed using the Student's t test. Results ICCs overall demonstrated good reliability between parent and child questionnaire domain scores. There was a tendency for parents to overestimate the impairment of the child in the PFF group. PFF children demonstrated clinically significant decreased HRQOL than TDF children. This was most marked in the physical domain scores. Conclusion Although parents may overestimate their child's impairment, children with PFF still have significantly impaired HRQOL when compared to TDF children. The impairment can be as severe, or worse, than published HRQOL for acutely and chronically unwell children. As such, PFF cannot be regarded as just a benign normal variant. The management of PFF should involve consideration of the symptom profile and HRQOL. Level of evidence II.
Cabergoline administration prevents development of moderate to severe ovarian hyperstimulation syndrome and it contributes to reduction in ovarian volume
Authors: Inoue Tomoko , Hashimoto Shu , Iwahata Hideyuki , Ito Keijiro , Nakaoka Yoshiharu , Morimoto Yoshiharu 
Published: November 2014

AbstractPurposeThe aim of this study was to determine the prophylactic effects of cabergoline on ovarian hyperstimulation syndrome (OHSS) after oocyte retrieval.MethodsA total of 187 women underwent controlled ovarian stimulation using gonadotropin releasing hormone (GnRH) agonist long protocol or flexible GnRH antagonist protocol for in vitro fertilization. They responded excessively to ovulation induction, and fresh embryo transfers were canceled. Sixty‐one patients in the intervention group were administered oral cabergoline (0.5 mg) three times after oocyte retrieval (day 0, 2, and 4 following the oocyte retrieval). Ultrasonography and blood examination were performed on the seventh day following oocyte retrieval. The main outcomes measured were the incidence of OHSS, estimated ovarian volumes, ascites, hematocrits, and white blood cell counts.ResultsThe incidence of moderate to severe OHSS was lower after cabergoline administration (9.8 vs. 23.0 %, p = 0.03). The ovarian volumes reduced after intervention (96.2 vs. 145.5 cm3, p = 0.008). The reduction was evident in the patients with agonist long protocol (92.1 vs. 167.5 cm3, p = 0.0005). No significant differences were observed for other factors.ConclusionsCabergoline has a favorable effect on the prevention of moderate to severe OHSS affiliated with ovarian volume reduction.
Effect of boron addition on the microstructure and stress-rupture properties of directionally solidified superalloys
Authors: Wu Bao-ping , Li Lin-han , Wu Jian-tao , Wang Zhen , Wang Yan-bin , Chen Xing-fu , Dong Jian-xin , Li Jun-tao 
Published: November 2014

Abstract
This study is focused on the effect of boron addition, in the range of 0.0007wt% to 0.03wt%, on the microstructure and stress-rupture properties of a directionally solidified superalloy. With increasing boron content in the as-cast alloys, there is an increase in the fraction of the γ′/γ eutectic and block borides precipitate around the γ′/γ eutectic. At a high boron content of 0.03wt%, there is precipitation of lamellar borides. Upon heat treatment, fine block borides tend to precipitate at grain boundaries with increasing boron content. Overall, the rupture life of the directionally solidified superalloy is significantly improved with the addition of nominal content of boron. However, the rupture life decreases when the boron content exceeds 0.03wt%.
Why Lifespans Are More Variable Among Blacks Than Among Whites in the United States
Authors: Firebaugh Glenn , Acciai Francesco , Noah Aggie J. , Prather Christopher , Nau Claudia 
Published: November 2014

Abstract
Lifespans are both shorter and more variable for blacks than for whites in the United States. Because their lifespans are more variable, there is greater inequality in length of life—and thus greater uncertainty about the future—among blacks. This study is the first to decompose the black-white difference in lifespan variability in America. Are lifespans more variable for blacks because they are more likely to die of causes that disproportionately strike the young and middle-aged, or because age at death varies more for blacks than for whites among those who succumb to the same cause? We find that it is primarily the latter. For almost all causes of death, age at death is more variable for blacks than it is for whites, especially among women. Although some youthful causes of death, such as homicide and HIV/AIDS, contribute to the black-white disparity in variance, those contributions are largely offset by the higher rates of suicide and drug poisoning deaths for whites. As a result, differences in the causes of death for blacks and whites account, on net, for only about one-eighth of the difference in lifespan variance.
Tape casting of a YAG/Yb:YAG/YAG transparent ceramic for a broadband tunable laser
Authors: Wang Chao , Li Wenxue , Yang Xianghui , Bai Dongbi , Yang Kangwen , Ba Xuewei , Li Jiang , Pan Yubai , Zeng Heping 
Published: November 2014

Abstract
A composite transparent YAG/Yb:YAG/YAG ceramic was prepared by a non-aqueous tape-casting method. An optical transmittance of 82% was obtained at visible wavelength and around 1100 nm. A low-threshold, broadband tunable continuous-wave (CW) laser at 1031 nm was further demonstrated from the ceramic sample, which was pumped by a 974 nm fiber-pigtailed laser diode. The threshold pump power was 0.45 W and the maximum output power was 3.2 W, corresponding to a slope efficiency of 20.4%. By inserting an SF57 prism in the laser cavity, the output wavelength could be tuned continuously from 1021 to 1058 nm.