bluuebunny/crossref_metadata_2025_split huggingface dataset:
Directing positional specificity in enzymatic synthesis of bioactive 1‐phosphatidylinositol by protein engineering of a phospholipase D
Authors: Damnjanović Jasmina , Kuroiwa Chisato , Tanaka Hidetoshi , Ishida Ken , Nakano Hideo , Iwasaki Yugo 
Published: July 2015

ABSTRACTPhosphatidylinositol (PI) holds a potential of becoming an important dietary supplement due to its effects on lipid metabolism in animals and humans manifested as a decrease of the blood cholesterol and lipids, and relief of the metabolic syndrome. To establish an efficient, enzymatic system for PI production from phosphatidylcholine and myo‐inositol as an alcohol acceptor, our previous study started with the wild‐type Streptomyces antibioticus phospholipase D (SaPLD) as a template for generation of PI‐synthesizing variants by saturation mutagenesis targeting positions involved in acceptor accommodation, W187, Y191, and Y385. The isolated variants generated PI as a mixture of positional isomers, among which only 1‐PI exists in nature. Thus, the current study has focused to improve positional specificity of W187N/Y191Y/Y385R SaPLD (NYR) which generates PI as a mixture of 1‐PI and 3‐PI in the ratio of 76/24, by subjecting four residues of its acceptor‐binding site to saturation mutagenesis. Subsequent screening pointed at NYR‐186T and NYR‐186L as the most improved variants producing PI with a ratio of 1‐/3‐PI = 93/7 and 87/13, respectively, at 37°C. Lowering the reaction temperature further improved the specificity of both variants to 1‐/3‐PI > 97/3 at 20°C with no change in total PI yield. Structure model analyses imply that G186T and G186L mutations increased rigidity of the acceptor‐binding site, thus limiting the possible orientations of myo‐inositol. The two newly isolated PLDs are promising for future application in large‐scale 1‐PI production. Biotechnol. Bioeng. 2016;113: 62–71. © 2015 Wiley Periodicals, Inc.
Limitation of thiamine pyrophosphate supply to growing Escherichia coli switches metabolism to efficient d‐lactate formation
Authors: Tian Kangming , Niu Dandan , Liu Xiaoguang , Prior Bernard A. , Zhou Li , Lu Fuping , Singh Suren , Wang Zhengxiang 
Published: July 2015

ABSTRACTEfficient production of d‐lactate by engineered Escherichia coli entails balancing cell growth and product synthesis. To develop a metabolic switch to implement a desirable transition from cell growth to product fermentation, a thiamine auxotroph B0013‐080A was constructed in a highly efficient d‐lactate producer E. coli strain B0013‐070. This was achieved by inactivation of thiE, a gene encoding a thiamine phosphate synthase for biosynthesis of thiamine monophosphate. The resultant mutant B0013‐080A failed to grow on the medium in the absence of thiamine yet growth was restored when exogenous thiamine was provided. A linear relationship between cell mass formation and amount of thiamine supplemented was mathematically determined in a shake flask experiment and confirmed in a 7‐L bioreactor system. This calculation revealed that ∼95–96 thiamine molecules per cell were required to satisfy cell growth. This relationship was employed to develop a novel fermentation process for d‐lactate production by using thiamine as a limiting condition. A d‐lactate productivity of 4.11 g · L−1 · h−1 from glycerol under microaerobic condition and 3.66 g · L−1 · h−1 from glucose under anaerobic condition was achieved which is 19.1% and 10.2% higher respectively than the parental strain. These results revealed a convenient and reliable method to control cell growth and improve d‐lactate fermentation. This control strategy could be applied to other biotechnological processes that require optimal allocation of carbon between cell growth and product formation. Biotechnol. Bioeng. 2016;113: 182–188. © 2015 Wiley Periodicals, Inc.
How many object colors can we distinguish?
Authors: Kuehni Rolf G. 
Published: July 2015

AbstractThe question of how many different colors humans can perceive has been of interest to philosophers, psychologists and color scientists for centuries. In recent years the question of the number of distinguishable object color stimuli has been addressed by color scientists by defining a distinguishable color as a given stimulus surrounded by the contour of stimuli just noticeably different from the central stimulus. For a particular set of conditions the number of distinguishable object color stimuli assessed in this manner has recently been found to be slightly larger than 2 million. In this article an argument is made that the related rules are arbitrary and unnecessarily limiting. Based on logical arguments and experimental just noticeable difference data it is shown that, for the conditions involved, a more realistic if conservative number of distinguishable object color stimuli is ∼40 million. © 2015 Wiley Periodicals, Inc. Col Res Appl, 41, 439–444, 2016
Detection of BRAF c.1799T > A (p.V600E) mutation using residual routine fine‐needle aspiration specimens of papillary thyroid carcinoma
Authors: Zhao Huan , Zhang Zhi‐hui , Zhou Bin , Xiao Ting , Pan Qin‐jing , Guo Hui‐qin 
Published: July 2015

BackgroundBRAF p.V600E mutation is the most common genetic alteration in papillary thyroid cancer (PTC) and has been used as a diagnostic and prognostic marker in PTC. The aim of this study was to investigate the utility of preoperative BRAF p.V600E mutation analysis as an adjunctive diagnostic and prognostic tool to routine fine‐needle aspiration (FNA).MethodsSpecimens were collected from thyroid nodules by FNA. Cytology diagnosis and BRAF p.V600E testing were performed on these specimens. Molecular and cytological results were correlated with histology outcomes.ResultsA total of 195 patients with thyroid nodules were enrolled, including 25 benign lesions and 170 PTCs. BRAF p.V600E testing was successfully performed in all specimens. The combination of BRAF p.V600E testing and cytology improved the sensitivity of cytology from 70% to 85.3% (P = 0.001). This significant increase in sensitivity was due to the detection of PTC by BRAF p.V600E testing in the nodules with atypical or suspicious PTC cytology results. Patients with BRAF p.V600E‐positive tumors were significantly older than those who did not harbor mutations (45.6 years vs. 39.8 years, P = 0.002). No correlations between BRAF p.V600E mutation and other clinical‐pathology parameters were observed.ConclusionsDetection of BRAF p.V600E mutation can be successfully carried out using residual liquid‐based materials. It can be performed as a diagnostic tool to supplement traditional thyroid FNA, especially in cases with atypical or suspicious PTC. However, the role of BRAF p.V600E in guidance of the extent of thyroidectomy and nodal clearance requires further study. Diagn. Cytopathol. 2015;43:786–790. © 2015 Wiley Periodicals, Inc.
Interobserver reproducibility and agreement with original diagnosis in the categories “atypical” and “suspicious for malignancy” for bile and pancreatic duct brushings
Authors: Layfield Lester J. , Schmidt Robert L. , Chadwick Barbara E. , Esebua Magda , Witt Benjamin L. 
Published: July 2015

BackgroundThe Papanicolaou Society of Cytopathology has developed a set of guidelines which include a diagnostic scheme with the categories “atypical” and “suspicious for malignancy.” These intermediate categories may help stratify risk of malignancy for samples obtained from the bile and pancreatic ducts. However, the reproducibility of these intermediate categories is currently unknown.MethodsTwenty sequential brushing specimens of bile or pancreatic ducts from each of the categories “atypical” and “suspicious for malignancy” were identified and the slides retrieved. All 40 cases were reviewed independently by four cytopathologists blinded to the original diagnoses. Resulting review diagnoses were statistically analyzed for agreement and the Kappa statistic calculated. Agreement of the observers’ diagnoses with original diagnoses was also evaluated.ResultsInterobserver agreement was graded as slight to fair with observers agreeing in about 50% of cases. The corresponding kappa statistic for the category “atypical” was 0.21 and 0.18 for the category “suspicious for malignancy.” Reviewer agreement with the original reference diagnosis occurred in approximately one half of review diagnoses.ConclusionAnalysis of agreement shows that interobserver agreement was only slight to fair. Despite the categories “atypical” and “suspicious for malignancy” having distinct risks of malignancy (62% versus 74%), the reproducibility of these categories is relatively poor. A single intermediate category may improve reproducibility over the scheme proposed by the Papanicolaou Society of Cytopathology while maintaining an ability to stratify risk of malignancy. Diagn. Cytopathol. 2015;43:797–801. © 2015 Wiley Periodicals, Inc.
ALK and ROS1 rearrangements tested by fluorescence in situ hybridization in cytological smears from advanced non‐small cell lung cancer patients
Authors: Bozzetti Cecilia , Nizzoli Rita , Tiseo Marcello , Squadrilli Anna , Lagrasta Costanza , Buti Sebastiano , Gasparro Donatello , Zanoni Daniele , Majori Maria , De Filippo Massimo , Mazzoni Francesca , Maddau Cristina , Naldi Nadia , Sammarelli Gabriella , Frati Caterina , Pinto Carmine , Ardizzoni Andrea 
Published: July 2015

BackgroundThe identification of ALK and ROS1 rearrangements and the availability of an effective target therapy, such as crizotinib, represent a new option in the treatment of advanced non‐small cell lung cancer (NSCLC) patients. In light of recent advances in non‐invasive diagnostic procedures, we aimed to demonstrate that direct cytological smears are suitable for assessing ALK and ROS1 rearrangements in patients with NSCLC.MethodsFifty‐five patients with a cytological diagnosis of lung adenocarcinoma (ADC) were evaluated for ALK rearrangements by fluorescence in situ hybridization (FISH) and 12 patients for ROS1 FISH rearrangements. Seventeen of the 55 cytological samples tested for ALK were obtained from the primary tumor and 38 from metastatic lesions. Ten of 12 samples evaluated for ROS1 were obtained from metastatic sites and two from the primary tumor.ResultsALK FISH was successful in 49/55 (89%) cytological ADC samples and ROS1 FISH in all 12 cytological samples. ALK rearrangements were found in 3/13 (23%) primary tumors and 7/36 (19%) metastatic sites. ROS1 rearrangements were found in one of the two primary tumors and in two of the 10 metastases. Two of the three rearranged cases were tested on cytology after knowing that they were rearranged on histology in order to increase representativeness of ROS1 rearranged cases in this study.ConclusionWhenever cytology represents the only available material for diagnosis and biological characterization of NSCLC, minimally invasive procedures may provide an additional important source of cellular material for FISH assessment of ALK and ROS1 rearrangements.//// Diagn. Cytopathol. 2015;43:941–946. © 2015 Wiley Periodicals, Inc.
High quality lard with low cholesterol content produced by aqueous enzymatic extraction and β‐cyclodextrin treatment
Authors: Wang Qing‐Ling , Jiang Jiang , Li Jin‐Wei , Qiu Mei‐Bin , Lin Chuan‐Zhou , Shi Xu‐Hao , Cao Pei‐Rang , Liu Yuan‐Fa 
Published: July 2015

New food processing technology is required for food production with high quality and healthfulness. In this study, a novel application was developed to extract lard from pig fatback, a by‐product of the slaughter plant, by an aqueous enzymatic extraction method (AEE). Various proteases with different properties including Alcalase 2.4 L, Neutrase 1.5 MG, Flavourzyme 1000 L, and Protamex were evaluated for their efficiency in oil release and lard qualities. Alcalase 2.4 L was more effective for oil extraction with a yield of 95.19%. A high quality of lard was produced by AEE in comparison with lards produced by conventional extraction methods in aspects of color, acid value, peroxide value, phospholipids, cholesterol, and oxidation stability. A further refinement to reduce cholesterol from lard by β‐cyclodextrin (β‐CD) was developed and the optimal conditions were established. The optimal conditions were 7% β‐CD addition (w/w) to a mixture of equal amount of lard and distilled water at reaction temperature 50°C for about 60 min. The cholesterol content of lard from this refinement process was about 3.2 mg/100 g which was about 93.7% reduction from 51.2 mg/100 g. This simple process by AEE and cholesterol reduction did not affect the composition of fatty acids and construction of triglyceride. Factors that were components of lard or produced during the lard extraction processes were evaluated for their influence on the cholesterol removal. Phospholipids could slightly enhance cholesterol removal, while free fatty acids with saturated or unsaturated aliphatic chains would have inhibitory effects because of their competition with cholesterol for β‐CD.Practical applications: An excellent quality of lard was produced by a novel application of an aqueous enzymatic extraction method (AEE). This lard could be further refined by β‐cyclodextrin for cholesterol reduction. This procedure would be a promising technology to obtain healthy lard and explore animal by‐products for the food industry. This lard with high nutrients could have very broad applications such as in baking, cooking, deep fat frying in food industry.Lard obtained by combination of aqueous enzymatic extraction and β‐cyclodextrin treatment presented high quality and very low cholesterol.
Fate of contaminants during the refining process of vegetable oils and fats: A calculation model
Authors: van Duijn Gerrit 
Published: July 2015

Crude vegetable oils and fats after oil extraction may contain contaminants introduced in the supply chain. Many of these contaminants are largely removed from the oil by the refining process. However, these contaminants will concentrate in the refinery by‐products; acid oil from soapsplitting and filter blowing, spent bleaching earth, and deodorizer distillate. The contaminant levels in these by‐products are calculated by determining the lipids balance of the refinery and the fate of the contaminants in the refining process. Calculations of some example oils with characteristic contaminant levels show that deodorizer distillate from chemical refining has a high‐contamination risk, deodorizer distillate from physical refining and spent bleaching earth has a medium risk, whereas acid oil from soapsplitting and filter blowing have a low‐contamination risk.Extracted oils and fats contain impurities like free fatty acids, phospholipids, etc., and may contain contaminants like polycyclic aromatic hydrocarbons and pesticides. The impurities and some entrained oil form the refinery by‐products; acid oil, spent earth, and deodorizer distillate. The contaminants will concentrate in these by‐products. For application in animal feed, acid oil is relatively safe (green), oil from spent bleaching earth requires contaminant analysis (orange), whereas contaminant levels in deodorizer distillate are often too high for use in feed (red).
Simulation of masonry out‐of‐plane failure modes by multi‐body dynamics
Authors: Costa Alexandre A. , Penna Andrea , Arêde António , Costa Aníbal 
Published: July 2015

SummaryThe seismic assessment of the local failure modes in existing masonry buildings is currently based on the identification of the so‐called local mechanisms, often associated with the out‐of‐plane wall behavior, whose stability is evaluated by static force‐based approaches and, more recently, by some displacement‐based proposals. Local mechanisms consist of kinematic chains of masonry portions, often regarded as rigid bodies, with geometric nonlinearity and concentrated nonlinearity in predefined contact regions (unilateral no‐tension behavior, possible sliding with friction). In this work, the dynamic behavior of local mechanisms is simulated through multi‐body dynamics, to obtain the nonlinear response with efficient time history analyses that directly take into account the characteristics of the ground motion. The amplification/filtering effects of the structure are considered within the input motion.The proposed approach is validated with experimental results of two full‐scale shaking‐table tests on stone masonry buildings: a sacco‐stone masonry façade tested at Laboratório Nacional de Engenharia Civil and a two‐storey double‐leaf masonry building tested at European Centre for Training and Research in Earthquake Engineering (EUCENTRE). Copyright © 2015 John Wiley & Sons, Ltd.
Candor about Adverse Events: Physicians versus the Data Bank
Authors: Morreim Haavi 
Published: July 2015

AbstractMany major medical institutions have now embraced the idea that it is best to be honest with patients and families when an error causes harm that could have been avoided. This kind of disclosure improves patient safety and quality of care; enhances satisfaction for patients, families, and providers; and reduces malpractice litigation costs. The University of Michigan has perhaps the best‐known program. Since 2001, that institution has seen more than a 55 percent drop in the number of new malpractice claims filed, a comparable reduction in lawsuits, and a dramatic drop in both defense costs and malpractice payouts—money then redirected toward quality improvement. A few states have also embraced this approach, sometimes known as “Candor” (for “communication and optimal resolution”). Yet all of these efforts face a major challenge. Although many physicians would like very much to achieve insight, reconciliation, and quality improvement in just this way, many fear that money paid to resolve an incident in which they were involved can result in a lifelong black mark in the National Practitioner Data Bank.
The Bitter Pill of Name‐Brand Drugs
Authors: Gorin Moti 
Published: July 2015

AbstractImagine a drug—let's call it Curebitt—that is safe, cheap, and very effective: take a pill once a day and you will be healthier. Curebitt's taste is so unpleasant, so bitter, however, that a significant proportion of patients cannot bring themselves to ingest the pill regularly. Now suppose that after some time, another drug, Curesweet, hits the market. This drug is clinically equivalent to Curebitt and costs the same, but it is much more palatable, so adherence rates for it are significantly higher than for Curebitt. Should physicians continue prescribing Curebitt, now that Curesweet is available? No, prescribing the bitter pill puts patients at a greater risk of nonadherence and ultimately results in reduced clinical benefit for a significant proportion of patients, whereas prescribing Curesweet benefits more patients and increases the probability that any given patient's health will improve. The Curebitt versus Curesweet scenario draws our attention to how a physician can fail her patients by prescribing drugs with lower adherence rates when equivalent drugs with higher adherence rates are available. What does this fictional case tell us about the real world? A lot. We know that adherence rates vary with out‐of‐pocket costs. Name‐brand drugs carry higher out‐of‐pocket costs than their generic counterparts; as a result, when name‐brand drugs are prescribed rather than their generic counterparts, fewer patients receive health benefits. If prescribing Curebitt is unethical, then so is prescribing the name‐brand drug.
Training in Research Ethics and Standards for Community Health Workers and Promotores Engaged in Latino Health Research
Authors: Nebeker Camille , Kalichman Michael , Talavera Ana , Elder John 
Published: July 2015

AbstractA model frequently used to implement community‐based research involves engaging local community health workers who are trusted members of the community and familiar with local customs, language, and culture. In Spanish‐speaking communities, the CHWs are also known as promotores de salud (“health promoters”). Depending on the study design and nature of the research, promotores facilitate research through community outreach, instrument design, participant recruitment, intervention delivery, data collection, and other research‐related tasks. In 2000, the National Institutes of Health published a regulation requiring training of “key personnel” named on NIH‐supported research involving human subjects. Regardless of whether promotores are technically designated as key personnel on a particular study, they may benefit from training in research ethics. Unfortunately, the educational programs designed for academic researchers in response to the NIH mandate were poorly aligned with the needs of promotores and not suited for learning about human research ethics applied to the community health setting. For example, many promotores in our California‐Mexico border region are monolingual Spanish speakers who have no formal academic research training. Therefore, we set out to develop a training alternative appropriate to our local CHWs. In this essay, we provide overviews of the relevant instructional design principles and our formative research process, including examples of key findings.
Beyond Harms and Benefits: Rethinking Duties to Disclose Misattributed Parentage
Authors: Garrett Jeremy R. 
Published: July 2015

AbstractIn this issue of the Hastings Center Report, Amulya Mandava, Joseph Millum, and Benjamin E. Berkman revisit an old conundrum—whether to disclose incidental findings of misattributed parentage—in light of new developments in genomic sequencing that will make that conundrum both more complex and more common. While the authors’ defense of nondisclosure as the appropriate default action in genomic research aligns with prior thinking and practice, their exploration of philosophical foundations is refreshingly rigorous and developed. The final product of their analysis—an applied taxonomy of the types of harms and benefits that can result from disclosure of misattributed parentage—is an important contribution to the literature on this subject and worthy of serious consideration by genomic researchers and bioethicists alike. Despite these virtues, I am struck by the authors’ deference to the traditional assumption that disclosure ethics can be adequately understood and appreciated within a purely consequentialist framework.
Tissue performance of bladder following stretched electrospun silk fibroin matrix and bladder acellular matrix implantation in a rabbit model
Authors: Huang Jian‐Wen , Xu Yue‐Min , Li Zhao‐Bo , Murphy Sean V. , Zhao Weixin , Liu Qiang‐Qiang , Zhu Wei‐Dong , Fu Qiang , Zhang Yao‐Peng , Song Lu‐Jie 
Published: July 2015

AbstractThe goal of this study was to investigate the tissue performance of bladder following stretched electrospun silk fibroin matrix (SESFM) implantation compared with bladder acellular matrix (BAM). We compared SESFM with BAM based on porosity and pore size. Scaffolds were separately transplanted into opposite walls of the bladder of 30 rabbits after stripping the bladder mucosa and smooth muscle (1.5 × 2.0 cm2). Gross anatomical observation, histological analysis and muscle contractility studies were performed at 2, 4, and 8 weeks post‐op. SESFM has higher porosity and larger pore size compared with BAM (p < 0.05). At 2 weeks, the presence of vesical calculus was evident in 7/10 rabbits. Histological analysis showed that SESFM and BAM promoted similar degree of urothelium regeneration (p > 0.05). However, SESFM promoted a higher degree of smooth muscle and vessel regeneration compared to BAM (p < 0.05). In addition, muscle strips supported by SESFM displayed higher contractile responses to carbachol, KCl, and phenylephrine compared with BAM. At 8 weeks, both matrices elicited similar mild acute and chronic inflammatory reactions. Our results demonstrated that SESFM has greater ability to promote bladder tissue regeneration with structural and functional properties compared to BAM, and with similar biocompatibility. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 9–16, 2016.