bluuebunny/crossref_metadata_2025 huggingface dataset:
Cachexia in children with chronic kidney disease: challenges in diagnosis and treatment
Authors: Mak Robert H.
Published: June 2016

Purpose of review

Although cachexia is highly prevalent in adult patients with chronic kidney disease (CKD), it is understudied and less well characterized in children. Recent evidence suggests that cachexia is also prevalent in children with CKD but presents challenges in diagnosis and treatment.

Recent findings

A study from the CKD in children cohort showed that CKD cachexia or protein-energy wasting, using modified pediatric diagnostic criteria, such as lack of expected weight gain instead of weight loss and BMI for height age, had a prevalence of 7–20%. When growth indices such as height SD score (SDS)/height velocity SDS was included in the criteria, cachexia or PEW correlated with the morbidity outcome of increased hospitalization risk in children with CKD. Conversely, aggressive nutritional supplementation in children with advanced CKD, with nasogastric or gastric tube feeding, led to prevalence of obesity over that of cachexia. Body habitus of underweight and obesity have been shown to be associated with the worst clinical outcomes in both adults and children with CKD.

Optimal nutritional therapy remains the mainstay of treatment of cachexia in CKD children with therapeutic goals of maintaining BMI as well as linear growth within the normal range.
The essential tremor syndromes
Authors: Elble Rodger J.
Published: June 2016

Purpose of review

Essential tremor has not been defined or used consistently in clinical diagnosis and research. Other monosymptomatic disorders are often referred to as essential tremor variants.

Recent findings

There is now solid evidence that essential tremor, however defined, is a syndrome with multiple causes.

A new tremor classification scheme is being developed by the International Parkinson and Movement Disorder Society Task Force on Tremor. In this scheme, tremor in the absence of other neurological signs is called isolated tremor, and tremor in combination with other signs is called combined tremor. Many isolated and combined tremor syndromes can be defined on the basis of commonly recurring or unique clinical symptoms and signs, including historical features (age at onset, family history, and temporal evolution) and tremor characteristics (body distribution, activation condition, associated features). Essential tremor, however defined, is simply a syndrome and not a specific disease. Essential tremor should be defined and used consistently, or this term should be abandoned. As essential tremor is an arbitrarily defined syndrome, it makes no sense to refer to other tremors as variants of essential tremor or essential tremor syndromes.
Quality characteristics of tangerine peel Soksungjang prepared from different koji strains
Authors: Youn Young , Jeon Sung-Hee , Yoo Jeong-Hee , Jeong Do-Yeon , Kim Young-Soo
Published: June 2016

This study was performed to provide information for improving the quality characteristics of tangerine peel Soksungjang. Tangerine peel Soksungjangs were prepared with 10% tangerine peel powder by addition of different koji such as Rhizopus oligosporus (RS, RTS) and Aspergillus oryzae (AS, ATS). As a result, the moisture content was not changed and crude protein content decreased during fermentation in all samples. The pH of RS (Soksungjang manufactured with Rhizopus oligosporus koji) and RTS (Soksungjang manufactured with Rhizopus oligosporus koji and 10% tangerine peel powder) was not changed, whereas pH of AS (Soksungjang manufactured with Aspergillus oryzae) and ATS (Soksungjang manufactured with Aspergillus oryzae koji and 10% tangerine peel powder) decreased rapidly after 10 days of fermentation. The acidity values of all the samples increased during fermentation. The major free sugars were glucose, fructose, and maltose; while, the major organic acids were citric acid, succinic acid, acetic acid, and lactic acid in all the samples. The amino nitrogen content and protease activity were highest in the AS and ATS. Conversely, the reducing sugar content and α-amylase activity were highest in the RS and RTS. The major free amino acids in all samples were glutamic acid, lysine, leucine, and arginine. Sixty kinds of volatile flavor compounds were identified from all samples; the majority of which were 21 alcohols, 14 hydrocarbons, 5 esters, and others identifies as acids, ketones, and aldehydes.
Characteristics and nutritional compositions of two jujube varieties cultivated in Korea
Authors: Choi Sang Yoon , Yoon Bo-Ra , Kim Sung Soo
Published: June 2016

The appearance and physicochemical characteristics of a native jujube (called Yak jujube) and Bokjo jujube were compared in this study. Our results revealed that the native jujube had smaller size, lower hardness, and higher contents of sugar, crude protein, crude fat, crude ash, dietary fiber, and calcium contents, when compared to that of Bokjo jujube. Therefore, native jujube is softer and sweeter, with higher general nutrient content, despite being smaller than that of Bokjo jujube.
Physicochemical components of Astragalus membranaceus fermented with mushroom mycelia
Authors: Jang Yeon-Jeong , Lee Yun-Hye , Lee Chan-Jung , Kim Jae-Hyeon , Kim Eun-Ju , Ji Soo-Jeong , Park Shin-Young
Published: June 2016

This study analyzed the physicochemical characteristics of Astragalus membranaceus (AM) fermented with seven different mushroom mycelia. Physicochemical characteristics, such as contents of moisture, pH, total reducing sugars, free sugar, and isoflavonoid, were investigated. The moisture content was increased in most of the samples. The pH values of AM fermented with Phellinus linteus and Flammulina velutipes were increased, while the pH of other samples were similar to that of non-fermented AM. The reducing sugar content was in the range of 211.69~391.74 mg/100 g. The extraction yield using water was higher than that when extracted with 80% ethanol. The free sugar content was increased through fermentation with mushroom mycelia. However, the glucose contents of the 80% ethanol and water extracts were decreased. Finally, the calycosin and formononetin contents in 80% ethanol and water extracts of AM fermented with Phellinus linteus were 2,549.24 mg/g, and 827.66 mg/g for calycosin, and 1,366.69 mg/g and 221.28 mg/g for formononetin, respectively. These results suggest that fermentation with mushroom mycelia could be used to increase the bioactivity of AM. The mycelium-fermented AM might be a valuable source of functional material and edible resource for industry.
The effect of decylcyclopropene derivative on the softening of ‘Fuyu’persimmon fruits
Authors: Choi Seong-Jin , Ahn Gwang-Hwan
Published: June 2016

In order to develop a sprayable ethylene antagonist, unlike 1-methylcyclopropene (MCP), we synthesized 2-decylcyclopropene-1-carboxylic acid ethyl ester (DCPE) as a derivative of cyclopropene and tested its effect on the flesh softening of ‘Fuyu’ persimmon fruits. The fruits on trees were sprayed with 4·10-4 M DCPE solution before harvest. After harvest, the persimmon fruits were stored at a low temperature for 1.5 months. The ripening progress of the fruits was then evaluated during storage at ambient temperature (20℃). Flesh softening, a measure of ethylene response, was considerably delayed up to 7 days after DCPE treatment. However control fruits was rapidly softened after 3-day storage. The treatment effect of DCPE at 4·10-4 M was also compared to that of 1-MCP at 1 ppm. DCPE was storable at refrigerated conditions for at least one month without any loss. The results show that DCPE could be a potential sprayable agent for the prevention of flesh softening of persimmon fruit.
Chemical compositions and antioxidant activities of Cheonnyuncho (Opuntia humifusa) stems and fruit
Authors: Shin Dong-Sun , Han Gwi-Jung
Published: June 2016

The purpose of this study was to investigate the chemical composition of the freeze-dried stems and fruit of the cactus Cheonnyuncho. The analysis showed that powdered stems have the highest fat content (1.91%) and the powdered fruits have he highest protein content (2.62%). The K content of the fruits higher than that of the stems, while the Ca, Mg, Na and P contents of the stems were higher than those of the fruits. Both the stems and fruits powders contained high levels of the amino acids glutamic acid and aspartic acid. The free sugars such as sucrose, fructose, and glucose were detected in both the stems and fruits. The 75% ethanol (EtOH) extract showed a relatively high antioxidative activity compared to those of the water and 75% methanol (MeOH) extracts. Furthermore, the 75% EtOH extract of the stem powder exhibited a total polyphenol content of 3.60 g/100 g, and a total flavonoid content of 2.00 g/100 g. The antioxidant activities of the stem and fruit powder extracts, measured in DPPH radical scavenging experiments, were higher than that of the control group.
Antioxidant and digestive enzyme inhibitory effects of Eisenia bicyclis extracted by different methods
Authors: Kim Jin-Hak , Park La Young , Lee Shin-Ho
Published: June 2016

The antioxidant and digestive enzyme inhibitory effects of Eisenia bicyclis extracted by various extraction methods (RE, reflux extraction; SE, ultrasonification extraction; AE, autoclave extraction; LE, low-temperature high-pressure extraction) were investigated. The extraction yield (55.21%) and the laminarin (39.03%), fucoidan (24.75%), total polyphenol (115.68 mg GAE/g) and flavonoid (36.67 mg RHE/g) contents of AE were higher than those in other methods. The DPPH radical (86.60%, 500 mg%), ABTS radical (58.56%, 25 mg%), nitrite (86.38%, 100 mg%) scavenging activities of the Eisenia bicyclis extracted by AE were higher than those of Eisenia bicyclis extracted by other methods. The ABTS radical and nitrite scavenging activities were above 98% in all tested Eisenia bicyclis extracts and these activities were dependent on its concentration. The inhibitory effects of AE against amylase (50 mg%) and α-glucosidase (5 mg%) were 64.76% and 86.71%, respectively. The AE showed the best inhibitory effect of Eisenia bicyclis extracts (50 mg%) against trypsin (24.37%) and α-chymotrypsin (49.05%), respectively. These results suggest that Eisenia bicyclis extracted by AE can be used as a bioactive and functional material in the food industry.
Survey on packaging status and changes in quality oftomato and paprika using different packaging types
Authors: Chang Min-Sun , Lim Byung Sun , Kim Ji Gang , Kim Gun-Hee
Published: June 2016

This study aimed to evaluate the commercialized packaging status of tomato and paprika, and to investigate theeffect of different packaging materials on the quality of tomato and paprika during storage. Packaging statuses were surveyed at a department store, wholesale market, and supermarket in Seoul, Korea. Materials used for packaging tomato and paprika were cartons, polypropylene (PP), low-density polyethylene (LDPE), polystyrene (PS), and polyvinyl chloride (PVC). Tomato and paprika were packaged by using corrugated boxes, Styrofoam trays, PP film, and PVC film. The weight loss and hardness of non-packaged tomato and paprika were significantly different after 48 hr to the initial values (p<0.05). Box-packaged tomatoes had the lowest pH values and showed significantly higher soluble solid contents (p<0.05). However, there were no significant differences in among other packaging materials. For paprika, the ΔE values of PVC wrapping were higher than those of other packagings. Hence, the results demonstrated that a corrugated box with PP film and PP film bags with four holes plus wire-tying were most able to maintain the overall qualities of tomato and paprika, respectively, during storage.
Quality characteristics of Yakju containing pretreated lotus leaves
Authors: Choi Jeong-Sil , Yeo Soo-Hwan , Choi Han-Seok , Jeong Seok-Tae
Published: June 2016

This study aimed to find an effective preservation method of lotus leaves for the preparation of lotus-leaf Yakjuthroughout the year. The characteristics of Yakju containing lotus leaves pretreated by blanching, steaming, roasting, and drying were investigated in this study. The chemical properties of Yakju (pH, amino acidity, alcohol content, and volatile acid content) were significantly different for all treatments, except for the total acid content. The polyphenol content ranging from 315.89 to 462.63 ppm (p<0.05) was significantly different depending on pretreatment method L color value for Yakju was not significantly different all treatments, while a value was significantly different in Yakju containing frozen stored leaves after pretreatment. The b value was lowest for the blanching treatment, and was significantly different for all treatments. Among the organic acids present in Yakju, the oxalic, citric, and malic acid contents were significantly different for all treatments. In sensory evaluation, lotus-leaf Yakjus containing fresh leaves and dried leaves were preferred to the others in color and flavor among Yakjus prepared with lotus leaves before cold storage. However, among the Yakjus prepared with lotus leaves after cold storage, that containing blanched leaves was preferred to the others in terms of flavor, taste, and overall acceptability.
Evaluation of quality characteristics of Korean and Chinesebuckwheats
Authors: Cho MyoungLae , Choi Sun-il , Lee Jin-Ha , Cho Bong-Jae , Lee Hyo-ku , Rhee Seong-Kap , Lim Jeong-Ho , Lee Ok-Hwan
Published: June 2016

This study investigated the quality characteristics (chemical composition, amino acid content, lipid content, andrutin content) of common and tartary buckwheats cultivated from Korea and China. The moisture, crude protein, crude fat, crude ash, and carbohydrate contents of various common and tartary buckwheats were 8.78~13.37%, 11.00~12.11%, 2.87~3.18%, 1.80~2.58%, and 70.2~73.8%, respectively. The major amino acids in Korean and Chinese buckwheats were aspartic acid (1,105.1~1,403.5 mg/100 g), glutamine (2,250.9~2,996.1 mg/100 g), and arginine (932.5~1,388.6 mg/100 g). The major minerals were K (423.7~569.4 mg/100 g), Mg (181.8~255.9 mg/100 g), and P (328.6~555.0 mg/100 g). Palmitic acid (14.2~16.1%) was the major saturated fatty acid, and oleic (37.0~40.8%) and linoleic (31.7~38.6%) acids were the major unsaturated fatty acids. Tartary buckwheats (261.0~265.0 mg/g) had significantly higher rutin contents than that of common buckwheats (4.39~5.68 mg/g). These results suggested that common and tartary buckwheats cultivated in Korea and China contain naturally occurringnutrients in an abundance.
Antioxidant abilities and physiological properties ofdried Haw extracts prepared using different drying methods
Authors: Nam San , Kwon Yu-ri , Chung Hun-Sik , Youn Kwang-Sup
Published: June 2016

This study was performed to determine the effects of drying methods (HD, hot air drying; FD, freeze-drying) onthe antioxidant and physiological abilities of Haw (Crataegus pinnatifida Bunge). Powder color values of dried Haw, L and b, were higher for HD, while the chroma values were higher for FD. The total polyphenol, and flavonoid contents of HD Haw and FD Haw were found to be 9.29±0.50 mg GAE/mL and 15.48±0.38 mg GAE/mL, and 9.41±0.26 mg RHE/mL and 26.46±0.34 mg RHE/mL, respectively. DPPH radical scavenging abilities at 100 mg/mL concentration were higher for FD (64.90%) than HD (28.66%), as were the reducing power, ABTS radical scavenging ability, and nitrite scavenging ability. However, the HMG-COA reductase of HD (74.67%) was higher than that of FD (72.10%). The α-glucosidase inhibitory abilities of HD and FD at a concentration of 0.1 mg/mL were 24.69% and 97.38%, respectively. These results indicate that Haw is a potential functional material and that freeze-drying Haw is better than hot air drying.
Antioxidant activities and physiological properties ofEuphorbia humifusa extracts prepared using different solvents
Authors: Kwon Yu-Ri , Lee Hyun Ryung , Hwang So-Hyun , Kwon O-Jun , Youn Kwang-Sup
Published: June 2016

This study was conducted to investigate the antioxidant activities and physiological properties of Euphorbia humifusaextracts prepared using three different solvents (water, ethanol, and methanol). The highest total polyphenol content (293.25 mg/100 g) and total flavonoid content (21.05 mg/100 g) were observed in the methanol extract. The content of substances related to proanthocyanidin were highest in the water extract (8.42 mg/100 g), followed by methanol (5.70 mg/100 g) and ethanol (5.39 mg/100 g) extracts. The DPPH and ABTS radical scavenging activities of the methanol extract were 91.72% and 85.83%, respectively, at 50 mg% concentrations, which were higher than those of the other extracts. The extract reducing power decreased in the following order: ethanol > methanol > water. The methanol extract had relatively high antioxidant activity. The α-glucosidase and xanthine oxidase inhibitory activities of the methanol extract at a concentration of 10 mg% were somewhat higher than the other extracts. HMG-CoA reductase inhibitory activity in the water extract was slightly higher than in the methanol and water extracts. These results indicated that Euphorbia humifusa extracts were a high-value food ingredient due to their antioxidant activities and nutritional value.
Physicochemical properties and antioxidant activities of hot waterextracts from medicinal fruit mixture
Authors: Gu Yul-Ri , Park Hye-Mi , Jeong Yoo Seok , Jung Hee Kyoung , Yun Jeong Hyun , Hong Joo-Heon
Published: June 2016

This study was conducted to examine the physicochemical properties and antioxidant activities of medicinal fruitextracts (Corni fructus, Schizandra chinensis, Rubus coreanus Miquel and Lycii folium) with different extraction mixing ratios (MS, an equal ratio of the medicinal fruit = 1.25:1.25:1.25:1.25; M1, 2:1:1:1; M2, 1:2:1:1; M3, 1:1:2:1 and M4, 1:1:1:2) from medicinal fruit. pH, sugar content and acidity of the extracts were 3.22~3.52, 3.20~4.20 °Brix and 3.60~5.85%, respectively. The extraction yield of M2 (42.33%) was higher than those of MS (36.03%), M1 (40.40%), M3 (32.53%) and M4 (35.90%). The total polyphenol and flavonoid contents of M3 were 14.54 g/100 g and 5.65 g/100 g, respectively. The DPPH and ABTS radical scavenging activities of M3 at 1,000 μg/mL were 86.09% and 90.49%, respectively. The ferric-reducing antioxidant power and the reducing power of M3 at 250~1,000 μg/mL were 0.36~0.86 μM and 0.21~0.96, respectively. The antioxidant activities of M3 were significantly higher than those of the other extracts. In conclusion, this study demonstrated that medicinal fruit extracts had potential as a functional material.
Inhibitory effects of advanced glycation end products formation andfree radical scavenging activity of Cirsium setidens
Authors: Kim Taewan , Lee Jaemin , Jeong Gyeong Han , Kim Tae Hoon
Published: June 2016

Naturally occurring antioxidants, such as polyphenols are widely found in fruits, vegetables, wines, juices, andother plant-based dietary sources and are divided into several sub classes, including phenylpropanoids, flavonoids, stilbenoids, and lignans. As part of the our ongoing search for bioactive food ingredients, the antioxidant and advanced glycation end products (AGEs) formation inhibitory activities of the methanolic extract of the aerial parts of Cirsium setidens were investigated in vitro bioassay system. The antioxidant properties were evaluated through radical scavenging assays using 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) (ABTS+) radicals. In addition, the activity of C. setidens against diabetes complications was also tested via AGEs formation inhibition assay. The total phenolic contents were determined using a UV-VIS spectrophotometric method. All tested samples showed a dose-dependent radical scavenging and AGEs inhibitory activities. In particular, the n-butanol (BuOH)-soluble portion showed the most potent radical scavenging activities against DPPH and ABTS+ radicals with IC50 values of 24.3±1.7 and 25.0±3.3 μg/mL, respectively. Futhermore, the inhibition of AGEs formation by the n-BuOH-soluble portion (IC50 value; 46.0±1.5 μg/mL) was higher than that those of the soluble portions for the other solvent. The results showed that C. setidens could be considered as an effective source of natural antioxidants and other ingredients.
Genotyping of Inversions and Tandem Duplications
Authors: Ebler Jana , Schönhuth Alexander , Marschall Tobias
Published: June 2016

Motivation

Next Generation Sequencing (NGS) has enabled studying structural genomic variants (SVs) such as duplications and inversions in large cohorts. SVs have been shown to play important roles in multiple diseases, including cancer. As costs for NGS continue to decline and variant databases become ever more complete, the relevance of genotyping also SVs from NGS data increases steadily, which is in stark contrast to the lack of tools to do so.

Results

We introduce a novel statistical approach, called DIGTYPER (Duplication and Inversion GenoTYPER), which computes genotype likelihoods for a given inversion or duplication and reports the maximum likelihood genotype. In contrast to purely coverage-based approaches, DIGTYPER uses breakpoint-spanning read pairs as well as split alignments for genotyping, enabling typing also of small events. We tested our approach on simulated and on real data and compared the genotype predictions to those made byDELLY, which discovers SVs and computes genotypes. DIGTYPER compares favorable especially for duplications (of all lengths) and for shorter inversions (up to 300 bp). In contrast to DELLY, our approach can genotype SVs from data bases without having to rediscover them.

Availability

https://bitbucket.org/jana_ebler/digtyper.git
Massively parallel clonal analysis using CRISPR/Cas9 induced genetic scars
Authors: Junker Jan Philipp , Spanjaard Bastiaan , Peterson-Maduro Josi , Alemany Anna , Hu Bo , Florescu Maria , van Oudenaarden Alexander
Published: June 2016

A key goal of developmental biology is to understand how a single cell transforms into a full-grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches, analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scartrace, a strategy for massively parallel clonal analysis based on Cas9 induced genetic scars in the zebrafish.
Parallel, independent reversions to an embryonic expressionphenotype in multiple types of cancer
Authors: Hudson Corey M. , Conant Gavin C.
Published: June 2016

Changes in gene expression provide a valuable frame of reference for explaining the development and progression of cancer. Many tissue types radically alter their gene expression profile after becoming oncogenic. We evaluate this change in gene expression in 8 different cancer lines by comparing their expression profiles to that of their associated differentiated tissues as well as profiles for proliferative human embryonic stem cells. We find that, for non-proliferative tissues, the alterations in expression after oncogenesis result in a profile that is significantly more similar to the embryonic expression profile than to the original tissue profile. Wealso find that the lists of co-similar genes among embryonic and tumor cells are clustered within gene regulatory, protein interaction and metabolicnetworks. There is however little overlap in these lists between cancer lines and no pattern shared among all cancers in this analysis. We conclude that the manner in which cancers instantiate a proliferative pattern of expression following oncogenesis is diverse and we find no uniform proliferative program among the cancers in this analysis.
The Wnt segment polarity pathway and TMED2 protein may interact via a lectin- and decoy-type mechanism
Authors: Fiedler Klaus
Published: June 2016

The Secl4-like protein (280-385 GOLD-domain) in this study scores highly with the carbohydrate-binding module (CBM) of the RetS domain fromPseudomonas aeruginosa.The thereupon modeledCricetulus griseusp24-GOLD domain of p24, a member of intra-Golgi cargo receptors, is shown to interact with Wnt8 (wingless 8) ofXenopus laeviswith a ΔG=-18.3 kcal/mol. Lower ranked models listed a smaller ΔG (PDBePISA) and energy of Del Phi interaction. Complex/hybrid N-glycans provide increasing energy of binding up to −7.1 kcal/mol to simulated p24-GOLD-ligand interaction. It is likely, that Wnt proteins and p24 cargo-receptors interact analogously to Wnt-Frizzled and that Wnt transport may involve early lectin binding. The possibly promiscuous interaction of p24-GOLD with ligands, including collagen, may shed light on cargo-receptor mediated traffic.

Highlights

p24s are usually described as type I transmembrane proteins containing a GOLD domain

p24-GOLD can be modeled based on the Sec14-like protein with X-ray structure quality

A concave patch on the p24 surface binds to diverse ligands

N-glycans may provide increased binding energy in p24-cargo interaction

Wnt binding to TMED2 may quench signaling similar to a decoy-type mechanism
iSUMO - integrative prediction of functionally relevant SUMOylation events
Authors: Yao Xiaotong , Maity Shuvadeep , Gandhi Shashank , Imielenski Marcin , Vogel Christine
Published: June 2016

Post-translational modifications by the Small Ubiquitin-like Modifier (SUMO) are essential for diverse cellular functions. Large-scale experiment and sequence-based predictions have identified thousands of SUMOylated proteins. However, the overlap between the datasets is small, suggesting many false positives with low functional relevance. Therefore, we integrated ~800 sequence features and protein characteristics such as cellular function and protein-protein interactions in a machine learning approach to score likely functional SUMOylation events (iSUMO). iSUMO is trained on a total of 24 large-scale datasets, and it predicts 2,291 and 706 SUMO targets in human and yeast, respectively. These estimates are five times higher than what existing sequence-based tools predict at the same 5% false positive rate. Protein-protein and protein-nucleic acid interactions are highly predictive of protein SUMOylation, supporting a role of the modification in protein complex formation. We note the marked prevalence of SUMOylation amongst RNA-binding proteins. We validate iSUMO predictions by experimental or other evidence. iSUMO therefore represents a comprehensive tool to identify high-confidence, functional SUMOylation events for human and yeast.
TransRate: reference-free quality assessment of de novo transcriptome assemblies
Authors: Smith-Unna Richard , Boursnell Chris , Patro Rob , Hibberd Julian M. , Kelly Steven
Published: June 2016

TransRate is a tool for reference-free quality assessment of de novo transcriptome assemblies. Using only the sequenced reads and the assembly as input, we show that multiple common artifacts of de novo transcriptome assembly can be readily detected. These include chimeras, structural errors, incomplete assembly, and base errors. TransRate evaluates these errors to produce a diagnostic quality score for each contig, and these contig scores are integrated to evaluate whole assemblies. Thus, TransRate can be used for de novo assembly filtering and optimization as well as comparison of assemblies generated using different methods from the same input reads. Applying the method to a data set of 155 published de novo transcriptome assemblies, we deconstruct the contribution that assembly method, read length, read quantity, and read quality make to the accuracy of de novo transcriptome assemblies and reveal that variance in the quality of the input data explains 43% of the variance in the quality of published de novo transcriptome assemblies. Because TransRate is reference-free, it is suitable for assessment of assemblies of all types of RNA, including assemblies of long noncoding RNA, rRNA, mRNA, and mixed RNA samples.
Changing image of the ideal manager
Authors: Beal Brian
Published: June 2016

Purpose

The purpose of this paper is to extend the “think manager, think male” research paradigm by examining managerial stereotypes as a function of both gender and sexual orientation, thus comparing the similarity of managerial stereotypes against the stereotypes of male (heterosexual and gay) and female (heterosexual and lesbian) managers.

Design/methodology/approach

In total, 163 heterosexual participants used the 92-item “Descriptive Index” attribute inventory to rate one of five target groups: successful managers, heterosexual male managers, heterosexual female managers, gay male managers and lesbian female managers. Intraclass correlation coefficients were calculated to assess the degree of correspondence between ratings of the target groups.

Findings

The findings showed a higher correspondence between the descriptions of heterosexual male or female managers and the successful manager prototype than between the descriptions of gay male managers and the successful manager prototype. Additionally, results showed that the stereotypes of lesbian female managers were seen as having a moderate level of fit with the successful manager prototype.

Originality/value

This study it is the first empirical investigation to assess whether the “think manager, think male” phenomenon holds for managers who are members of sexual minority groups.
Is it time to do away with Annual Performance Appraisal System?
Authors: Sarkar Anita
Published: June 2016

Purpose

The purpose of this paper is to describe factors that determine scrapping of traditional performance appraisal system.

Design/methodology/approach

The study explains how the new system of feedback giving is aligned with the requirement of performance management system.

Findings

Traditional performance appraisal often created employee dissatisfaction, stalled employee creativity and team work, and increased employee attrition and missed out on performance improvement of employees. New check-in system promises to develop employees on the basis of continuous feedback mechanism.

Originality/value

This paper aims to provides insights on how the new system of performance management is connected to overall needs of the organization and the employees.
Following a ‘standstill’: An ethnographic approach to financialization
Authors: Sarmadi Behzad
Published: June 2016

This article addresses Dubai's recent financial crisis, bringing an ethnographic approach to ‘financialization’. It does so by repurposing the financial concept of ‘standstill’. Focusing on the consequences of the Dubai government's infamous ‘standstill announcement’, in late 2009, it argues that unpacking the literal and figurative registers of this concept offers insights into the political economy and lived experiences of financial crises.
TRANSLATING MIERES
Authors: Robertson A.F. , Cardús i Font Laura
Published: June 2016

Unlike journalists, anthropologists will tend to mostly anonymize the places they visit. However, as van der Geest has pointed out in these pages before, anonymity is not always what the people we research want from us. In this narrative, A.F. Robertson and Laura Cardús i Font show how our writing can become an asset to the communities we study, who, like us, are seeking to confirm their identities and improve their reputation in the overall scheme of things. In this narrative, the authors dwell on the nature of writing for both academic and vernacular audiences.
Diversification Benefits of REIT Preferred and Common Stock: New Evidence from a Utility‐based Framework
Authors: Boudry Walter I. , deRoos Jan A. , Ukhov Andrey D.
Published: June 2016

We study the diversification benefits of REIT preferred and common stock using a utility‐based framework in which investors segment based on risk aversion. We examine optimal mean‐variance portfolios of investors with different levels of risk aversion given access to different classes of assets and establish three main results. First, REIT common stock helps low risk aversion investors attain portfolios with higher returns, while REIT preferred stock helps high risk aversion investors by providing a venue for risk reduction. Second, REIT preferred stock has a risk‐return profile not easily replicated by other asset classes. Finally, conclusions drawn from the empirical analysis are markedly different under these constraints compared to the classical unconstrained setting.
Review of therapeutic agents employed by an Australian aeromedical prehospital and retrieval service
Authors: Hayward Marcus D , Regan Luke , Glasheen John , Burns Brian
Published: June 2016

Objective

There is little current evidence regarding which therapeutic agents are actually used within existing aeromedical services. The Greater Sydney Area Helicopter Emergency Medical Service operates a large, physician‐staffed, multimodal, prehospital and interhospital retrieval service. The aim of the present study was to identify the range and frequency of drug, fluid and blood product use within our service.

Methods

This was a retrospective cross‐sectional study. Case sheets relating to a 12 month period were inspected to identify the therapeutic agents used by retrieval teams during each mission. Corresponding case notes, demographic data (age, sex) and case data (prehospital vs interhospital, trauma vs medical) were extracted from an electronic database.

Results

Of 2566 missions, 848 were prehospital, 1662 interhospital and 56 mixed. Prehospital missions were associated with fewer agents per case (median, 2 vs 3) and a narrower range of agents overall (45 vs 117) compared to interhospital missions. In both mission types, the most frequently used agents included morphine, fentanyl, Hartmann's solution, ketamine, rocuronium, ondansetron and midazolam. Noradrenaline, propofol and metaraminol were used frequently in interhospital missions only. A number of stocked and unstocked agents were used less commonly, or not at all, over the study period.

Conclusions

The results of the present study form a practical guide to aid prehospital and retrieval services in establishing or reviewing their medical agent formularies. Key practice points illuminated by the data provide insights into current practice in critical care. There remains a clear need for similar studies from other services worldwide.
Extraction of chitin and chitosan from housefly, Musca domestica, pupa shells
Authors: Kim Min‐Woo , Han Yeon Soo , Jo Yong Hun , Choi Myung Hyo , Kang Seung Ho , Kim Sun‐Am , Jung Woo‐Jin
Published: June 2016

Chitins and chitosans are some of the most abundant natural polysaccharide materials, and are used to increase innate immune response and disease resistance in humans and animals. In this work, chitin and chitosan from housefly, Musca domestica, pupa shells were obtained by treatment with HCl and NaOH. For chitin extraction, 2 N HCl and 1.25 N NaOH solutions were used to achieve decalcification and deproteinization, respectively. For chitosan extraction, 50% NaOH solution was used to achieve deacetylation. The yields of chitin and chitosan from pupa shells of M. domestica were 8.02% and 5.87%, respectively. The deacetylations of chitosan (from chitin C1 and C2) were 89.76% and 92.39%, respectively, after the first alkali treatment with 50% NaOH (w/w) solution at 105 °C for 3 h and 5 h, respectively. The viscosities of the chitosans (from chitin C1 and C2) were 33.6 and 19.2 cP, respectively.
Napping‐Ultra Flash Profile as a Tool for Category Identification and Subsequent Model System Formulation of Caramel Corn Products
Authors: Mayhew Emily , Schmidt Shelly , Lee Soo‐Yeun
Published: June 2016

In a novel approach to formulation, the flash descriptive profiling technique Napping‐Ultra Flash Profile (Napping‐UFP) was used to characterize a wide range of commercial caramel corn products. The objectives were to identify product categories, develop model systems based on product categories, and correlate analytical parameters with sensory terms generated through the Napping‐UFP exercise. In one 2 h session, 12 panelists participated in 4 Napping‐UFP exercises, describing and grouping, on a 43×56 cm paper sheet, 12 commercial caramel corn samples by degree of similarity, globally and in terms of aroma‐by‐mouth, texture, and taste. The coordinates of each sample's placement on the paper sheet and descriptive terms generated by the panelists were used to conduct Multiple Factor Analysis (MFA) and hierarchical clustering of the samples. Strong trends in the clustering of samples across the 4 Napping‐UFP exercises resulted in the determination of 3 overarching types of commercial caramel corn: “small‐scale dark” (typified by burnt, rich caramel corn), “large‐scale light” (typified by light and buttery caramel corn), and “large‐scale dark” (typified by sweet and molasses‐like caramel corn). Representative samples that best exemplified the properties of each category were used as guides in the formulation of 3 model systems that represent the spread of commercial caramel corn products. Analytical testing of the commercial products, including aw measurement, moisture content determination, and thermal characterization via differential scanning calorimetry, were conducted and results related to sensory descriptors using Spearman's correlation.
Development of an Emergency Medicine Simulation Fellowship Consensus Curriculum: Initiative of the Society for Academic Emergency Medicine Simulation Academy
Authors: Frallicciardi Alise , Vora Samreen , Bentley Suzanne , Nadir Nur‐Ain , Cassara Michael , Hart Danielle , Park Chan , Cheng Adam , Aghera Amish , Moadel Tiffany , Dobiesz Valerie
Published: June 2016

Objectives

There is currently no consolidated list of existing simulation fellowship programs in emergency medicine (EM). In addition, there are no universally accepted or expected standards for core curricular content. The objective of this project is to develop consensus‐based core content for EM simulation fellowships to help frame the critical components of such training programs.

Methods

This paper delineates the process used to develop consensus curriculum content for EM simulation fellowships. EM simulation fellowship curricula were collected. Curricular content was reviewed and compiled by simulation experts and validated utilizing survey methodology, and consensus was obtained using a modified Delphi methodology.

Results

Fifteen EM simulation fellowship curricula were obtained and analyzed. Two rounds of a modified Delphi survey were conducted. The final proposed core curriculum content contains 47 elements in nine domains with 14 optional elements.

Conclusion

The proposed consensus content will provide current and future fellowships a foundation on which to build their own specific and detailed fellowship curricula. Such standardization will ultimately increase the transparency of training programs for future trainees and potential employers.
The recent fall in postperinatal mortality in New Zealand and the Safe Sleep programme
Authors: Mitchell Edwin A. , Cowan Stephanie , Tipene‐Leach David
Published: June 2016

Aim

Postneonatal mortality rates changed very little from 2000 until recently. There has been a decrease in mortality in New Zealand from 2009 to 2015. This study describes an infant Safe Sleep programme and postulates it is the cause for the recent decrease in deaths.

Methods

The Safe Sleep programme involved as follows: a focus on preventing accidental suffocation, a ‘blitz’ approach to SUDI education, the targeted provision of portable infant Safe Sleep devices (ISSD) and the development of Safe Sleep policy across all district health boards (DHBs).

Results

Participation in the education ‘blitz’ by health professionals exceeded one in 23 live births, distribution of Safe Sleep leaflets exceeded two for every live birth, and over 16 500 ISSDs have been distributed to vulnerable infants. Postperinatal mortality fell 29% from 2009 to 2015 (2.8 to 2.0/1000 live births). The fall has been greatest for Māori and in regions with the most intensive programmes.

Conclusion

The recent fall in postperinatal mortality has not happened by chance. It is likely that the components of end‐stage prevention strategy, a focus on preventing accidental suffocation, the education ‘blitz’, the targeted supply of ISSDs and strengthened health policy, have all contributed to varying degrees.
Exome sequencing identifies a novel nonsense mutation of HOXD13 in a Chinese family with synpolydactyly
Authors: Wang Bo , Li Niu , Geng Juan , Wang Zhigang , Fu Qihua , Wang Jian , Xu Yunlan
Published: June 2016

Synpolydactyly (SPD) is an autosomal dominant limb malformation with a distinctive combination of syndactyly and polydactyly. SPD is clinically heterogeneous and could be genetically classified into three types. The clinical phenotype of SPD is complicated by its variable expressivity. In the present study, whole exome sequencing (WES) was used to identify the affected gene(s) in a Chinese family with atypical SPD phenotype. Our results showed that a novel heterogenous nonsense mutation (c.556C > T, p.R186X) in HOXD13 was associated with this SPD case. Due to variable expressivity, the diagnosis of a clinical heterogenous disease such as SPD is usually difficult. Our results also suggested that WES is an efficient tool to assist with these diagnoses.
Sequential morphometric evaluation at UnicCa® and DCD® implant surfaces. An experimental study in the dog
Authors: Favero Vittorio , Lang Niklaus P. , Favero Riccardo , Antunes Antonio A. , Salata Luiz A. , Botticelli Daniele
Published: June 2016

Aim

To study tissue components adjacent to implants with nanotechnologically modified surfaces at different periods of healing.

Material & methods

In 12 beagle dogs, two different implant systems with different surface configurations were randomly installed in the edentulous premolar regions of the mandible.

One surface was first acid‐etched and subsequently, nanotechnologically modified with calcium ions (UnicCa®), while the other was first sandblasted and acid‐etched, and then additionally treated with a nanometer calcium phosphate deposition (discrete crystalline deposition; DCD®). The implants were fully submerged; surgeries and sacrifices were planned to harvest biopsies after 1, 2, 4 and 8 weeks of healing (n = 6 per period).

A morphometric evaluation of percentages of new and old bone, bone debris/particles and clot, new soft tissues (provisional matrix and immature marrow), mature bone marrow and vessels was performed in the spongiosa compartment adjacent to the implant surface up to a distance of about 0.4 mm from the surface.

Results

After 2 weeks of healing, the soft tissues were represented by 41.0% at the UnicCa® and 37.9% at the DCD® surfaces, in both cases mainly being composed of provisional matrix. These percentages decreased over time, being composed of greater amounts of immature bone marrow, and disappeared after 8 weeks. New bone increased progressively between 1 and 8 weeks of healing from 9.7 ± 6.3% to 70.0 ± 8.4% and from 8.2 ± 3.5% to 67.0 ± 6.1% at the UnicCa® and DCD® surfaces, respectively. Pristine bone was progressively resorbed.

Conclusions

Throughout the periods of healing observed, the formation of a provisional matrix followed by the formation of new bone and marrow was revealed in a similar fashion as for other modified surface configurations.
Adverse reaction after hyaluronan injection for minimally invasive papilla volume augmentation. A report on two cases
Authors: Bertl Kristina , Gotfredsen Klaus , Jensen Simon S. , Bruckmann Corinna , Stavropoulos Andreas
Published: June 2016

Objectives

To report two cases of adverse reaction after mucosal hyaluronan (HY) injection around implant‐supported crowns, with the aim to augment the missing interdental papilla.

Material and Methods

Two patients with single, non‐neighbouring, implants in the anterior maxilla, who were treated within the frames of a randomized controlled clinical trial testing the effectiveness of HY gel injection to reconstruct missing papilla volume at single implants, presented an adverse reaction. Injection of HY was performed bilaterally using a 3‐step technique: (i) creation of a reservoir in the mucosa directly above the mucogingival junction, (ii) injection into the attached gingiva/mucosa below the missing papilla, and (iii) injection 2–3 mm apically to the papilla tip. The whole‐injection session was repeated once after approximately 4 weeks.

Results

Both patients presented with swelling and extreme tenderness with a burning sensation on the lip next to the injection area, after the second injection session. In one of the cases, a net‐like skin discoloration (livedo reticularis) was also noted. The symptoms lasted for up to 7 days, and in both cases, symptoms resolved without any signs of skin or mucosal necrosis or any permanent damage.

Conclusion

Most likely, water attraction over time by the highly hygroscopic HY, exerted progressively an external vascular compression and at least partial occlusion of neighbouring blood vessels. An infection or an allergic reaction seems unlikely, since all symptoms gradually disappeared within a week irrespective use of antimicrobials, while an allergic reaction most likely would not have been restricted to one side.
A systematic review of motivational values and conservation success in and around protected areas
Authors: Cetas Elijah R. , Yasué Maï
Published: June 2016

In conservation projects in and around protected areas (PAs), a suite of policy instruments are used to promote conservation behavior in local people. Few studies have related psychological research on motivational values to conservation in PAs. We conducted a systematic review of 120 peer‐reviewed articles to assess the relative frequencies of policy instruments that aimed to foster intrinsic versus extrinsic motivations to conserve. We examined how the type of motivation engendered by the instrument (i.e., intrinsic or extrinsic motivation and based on the description of how the project was designed and implemented) influenced the ecological, economic, and social success of the project. We assessed the success of the project in only the case studies that included a quantitative or qualitative analysis of success. Projects designed to foster at least one intrinsically motivating instrument were 3 times more likely to meet socioeconomic or ecological goals. Although certain types of instruments such as payments or fines tended to be based on extrinsic motivators more often than education or monitoring programs, several successful projects involving payments or fines were linked to intrinsic motivation in the local community. Thus, our results suggest that rather than debating the relative merits of specific types of policy instruments, conservationists may have more success by focusing on how different motivators, suited to specific contexts, can better empower local communities to conserve. Broadly, our results suggest the current emphasis on social justice and well‐being of local communities is a positive step toward protecting the world's remaining biodiversity.