bluuebunny/crossref_metadata_2025 huggingface dataset:
Relationship Between Hepatitis C Clinical Testing Site and Linkage to Care
Authors: Assoumou Sabrina A. , Huang Wei , Horsburgh C. Robert , Drainoni Mari-Lynn , Linas Benjamin P.
Published: May 2014

Background.  The Centers for Disease Control and Prevention recommends one-time hepatitis C virus (HCV) testing of the population born between 1945 and 1965 with follow-up RNA testing for those with reactive serology. To increase the rate of diagnosis, testing may be considered in settings other than outpatient clinics (OC), such as inpatient wards (IP) or emergency department (ED).

Methods.  We used electronic medical records to create a retrospective cohort with reactive HCV serology between 2005 and 2010 at an urban safety net hospital. We determined factors associated with linkage to HCV care as measured by HCV RNA testing, and we evaluated the rate of linkage to care according to diagnosis location (OC, IP, or ED).

Results.  Individuals, 37 828, were tested and 5885 (16%) were reactive. Seropositivity was similar across all sites. Of the 4466 patients who met inclusion criteria, 3400 (76%) were diagnosed in the OC, whereas 967 (22%) and 99 (2%) were tested in the IP and the ED, respectively. A total of 2135 (48%) underwent HCV RNA testing. Using multivariable regression modeling, the following factors were independently associated with HCV RNA testing: diagnosis in the OC (odds ratio [OR], 1.64; 95% confidence interval [CI], 1.42–1.90); age at diagnosis in decades (OR, 0.98; 95% CI, 0.98–0.99); private insurance (OR, 1.17; 95% CI, 1.01–1.34); and ≥10 visits after diagnosis (OR, 2.15; 95% CI, 1.89–2.44).

Conclusion.  There is an opportunity to increase HCV diagnosis by testing in sites other than the OC, but this opportunity needs to be coupled with robust initiatives to improve linkage to care.
Observation and Measurement of Residual Bran on Milled Rice Using Hyperspectral Imaging
Authors: Chen Wei‐Tung , Kuo Yan‐Fu
Published: May 2014

Residual bran on milled rice is directly related to its quality. This study proposes a method to measure the residual bran patterns on a single rice grain by using hyperspectral imaging (HSI). HSI is a sensing technique that combines both spatial and spectral information and may be used for chemical compound identification and quantification. In this study, HSI was applied to assess rice bran residue nondestructively. In the experiment, rice samples were milled and scanned with an HSI system. Afterward, the rice samples were dyed to enable the residual bran to be identified with optical microscopy and image processing algorithms. Classifiers were then developed to predict the rice bran residue by using the HSI measurements as inputs. The predicted images were compared with the micrograph images for classifier performance evaluation. The proposed approach can estimate the residual bran distribution on milled rice surface with an accuracy of 93.5%.
Tomato ringspot virusCoat Protein Binds to ARGONAUTE 1 and Suppresses the Translation Repression of a Reporter Gene
Authors: Karran Rajita A. , Sanfaçon Hélène
Published: May 2014

RNA silencing regulates plant gene expression and antiviral defenses and functions by cleaving target RNAs or repressing translation. As a counter defense, many plant viruses encode suppressor proteins that sequester small RNAs or inactivate Argonaute (AGO) proteins. All known plant virus silencing suppressor activities eventually inhibit the degradation of target mRNAs. Using a transiently expressed green fluorescent protein (GFP) reporter gene, we show that Tomato ringspot virus (ToRSV) coat protein (CP) is a suppressor of RNA silencing that enhances GFP expression but does not prevent the degradation of the GFP mRNA or the accumulation of GFP small interfering RNAs (siRNAs). Coexpression of the CP with GFP resulted in increased association of residual GFP mRNAs with polysome fractions and reduced association of GFP siRNAs with monosome fractions. AGO1 was co-immunoprecipitated with the CP and CP expression destabilized AGO1. A WG motif within the CP was critical for the enhanced GFP expression, AGO1 interaction, and AGO1 destabilization, suggesting that the ToRSV CP acts as an AGO-hook protein and competes for AGO binding with a plant cellular GW/WG protein involved in translation repression.
First Report of Powdery Mildew Caused by Erysiphe betae on Swiss Chard in China
Authors: Zhang Y. , Zhang F. L. , Cao P. , Liu Y. , Liu K. , Xu K. D. , Liu K. , Zhang J. , Tan G. X. , Li C. W.
Published: May 2014

Swiss chard (Beta vulgaris L. subsp. cicla) is a widely planted vegetable in China. From May to June 2013, an outbreak of powdery mildew on Swiss chard cultivar Fangzheng was observed in the commercial fields in Zhoukou city of Henan Province, located in central China. More than 80% of the plants exhibited symptoms of the disease. At the beginning of infection, circular, white, dust-like colonies of powdery mildew occurred mainly on adaxial surfaces of leaves. As the disease progressed, white mycelia covered the foliar parts of plant. No cleistothecia were found on or in collected samples. Upon microscopic evaluation, conidiophores were unbranched with the length of 63 to 126 and width of 7 to 10 μm (n = 50), produced conidia singly, and composed of a cylindrical foot cell followed by one to three short cells. Conidia were colorless, hyaline, ovoid, measured 29 to 40 × 12 to 18 μm (n = 100), lacked fibrosin bodies, and produced germ tubes on the ends of the conidia. The fungus was identified as Erysiphe betae according to the morphological features (1). To verify the identity, the internal transcribed spacer (ITS) region was amplified with the universal primers ITS1 and ITS4 (2) and sequenced. The ITS sequence obtained was assigned as Accession No. KF268348 in GenBank, which showed 100% homogeneity with two ITS sequences of E. betae isolates from UK (DQ164432 and DQ164436). Koch's postulates were conducted by inoculating 15 healthy 5-week-old plants (cv. Fangzheng) with detached infected leaves, which grew in a growth chamber under 22/16°C (day/night), 50% relative humidity, 120 μmol/m2/s light and a 16-h photoperiod. Fifteen non-inoculated plants grew in another growth chamber with the same conditions as control. Symptoms consistent with the infected field plants were observed on the inoculated plants, while no symptoms were found on the control plants. Microscopic observation revealed that the pathogen growing on the inoculated plants was consistent with the morphology of the original fungus. To our knowledge, this is the first report of E. betae infection on Swiss chard in China (3).

References: (1) S. Francis. Mol. Plant Pathol. 3:119, 2002. (2) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications. M. A. Innis et al., eds. Academic Press, San Diego, CA, 1990. (3) R. Y. Zheng et al. Page 63 in: Flora Fungorum Sinicorum, Vol. 1, Erysiphales. Science Press, Beijing, 1987.
First Report of Ageratum enation virus, Betasatellite and Alphasatellite Causing Leaf Curl and Enation Disease of Amaranthus hypochondriacus in India
Authors: Srivastava A. , Kumar S. , Raj S. K.
Published: May 2014

During a survey in February 2011, severe symptoms of upward leaf curling, vein enation on lower side of the leaves, and shortening of internodes were observed on 20 out of 117 Amaranthus hypochondriacus plants (17% disease incidence) examined at breeding plots of CSIR-NBRI, Lucknow. These symptoms are typical of begomovirus infection. PCR with begomovirus-specific primers (3) produced the expected ~1.1-kb product from DNA extracts of 20 symptomatic plants but not from a non-symptomatic plant, suggesting the association of a begomovirus. The full-length begomoviral genome from a representative sample was amplified by rolling circle amplification using Ø-29 DNA polymerase and digested by BamHI, which resulted in a ~2.7 kb product when electrophoresed in 1.0% agarose gel. The product obtained was cloned, sequenced, and sequence data of 2,753 nucleotides was deposited in GenBank (Accession No. JF682242). BLASTn analysis revealed 97 to 98% nucleotide identity and forms a distinct clade with Ageratum enation virus (AEV) isolates. This shows the virus in A. hypochondriacus to be an isolate of AEV. The separate PCRs were also performed with betasatellite and alphasatellite specific primers (1,2) that resulted in ~1.3-kb amplicons from all samples, suggesting their association. The amplification products were cloned and sequenced. An analysis of betasatellite (JX512904) revealed highest 98% nucleotide identity and close phylogenetic relationship with Ageratum leaf curl betasatellite (ALCB, JQ710745). The alphasatellite (JX512905) showed highest 95% identity and close relationship with Hibiscus leaf curl alphasatellite (HLCA, FN794199). This shows the betasatellite and alphasatellite in A. hypochondriacus to be isolates of ALCB and HLCA, respectively. The partial direct repeat clones of the begomovirus (pCAM-AEV), betasatellite (pCAM-ALCB), alphasatellite (pCAM-HLCA) were generated and mobilized into Agrobacterium tumefaciens strain GV3101 and infiltrated in A. hypochondriacus seedlings. The plants inoculated with pCAM-AEV, pCAM-ALCB, and pCAM-HLCA; pCAM-AEV and pCAM-ALCB developed severe leaf curl and enation symptoms on 5/5 plant at 35 days post inoculation, which were similar to those of naturally infected plants, satisfying Koch's postulates. On the other hand, plants inoculated with pCAM-AEV alone or in combination with pCAM-HLCA developed mild symptoms. Plants inoculated with pCAM-ALCB and pCAM-HLCA did not develop symptoms. The results here show that leaf curl and enation disease of A. hypochondriacus in India is caused by AEV and ALCB and that an alphasatellite may be associated with symptomatic plants.

References: (1) R. W. Briddon et al. Mol. Biotechnol. 20:315, 2002. (2) S. E. Bull et al. Mol. Biotechnol. 23:83, 2003. (3) M. R. Rojas et al. Plant Dis. 77:340, 1993.
Paludibacterium
paludis sp. nov., isolated from a marsh
Authors: Sheu Shih-Yi , Chen Zih-Han , Young Chiu-Chung , Chen Wen-Ming
Published: May 2014

A bacterial strain, designated KBP-21T, was isolated from a water sample taken from the Banping Lake Wetland Park in Taiwan and characterized in a taxonomic study using a polyphasic approach. Cells of strain KBP-21T were Gram-stain-negative, facultatively anaerobic, poly-β-hydroxybutyrate-accumulating, motile rods that formed yellow colonies. Growth occurred at 15–40 °C (optimum, 30 °C), at pH 5.0–8.0 (optimum, pH 8.0) and with 0–2 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KBP-21T belonged to the genus

Paludibacterium

within the family

Neisseriaceae

of the class

Betaproteobacteria

and the closest related neighbour was

Paludibacterium yongneupense

5YN8-15T with a 16S rRNA gene sequence similarity value of 96.4 %. Strain KBP-21T contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c as the predominant fatty acids. The major respiratory quinone was Q-8. The DNA G+C content of the genomic DNA was 62.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one uncharacterized aminophospholipid and several uncharacterized phospholipids. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain KBP-21T represents a novel species in the genus

Paludibacterium

, for which the name Paludibacterium
paludis sp. nov. is proposed. The type strain is KBP-21T ( = BCRC 80514T = LMG 27230T = KCTC 32182T).
Nonomuraea
muscovyensis sp. nov., isolated from soil
Authors: Ozdemir-Kocak Fadime , Isik Kamil , Veyisoglu Aysel , Tatar Demet , Sahin Nevzat
Published: May 2014

A novel actinomycete, strain FMN03T, was isolated from a soil sample collected from Yuga Zapadnaya South-West Forest Park, Moscow, Russia. The isolate had chemical and morphological properties typical of members of the genus

Nonomuraea

and formed a distinct 16S rRNA gene subclade with the type strains

Nonomuraea roseoviolacea subsp. carminata

NBRC 15903T and

Nonomuraea roseoviolacea subsp. roseoviolacea

NBRC 14098T. The organism formed extensively branched substrate and aerial hyphae, which generated spiral chains of spores with smooth surfaces. The cell wall contained meso-diaminopimelic acid and the whole cell sugars were glucose, galactose and trace amounts of madurose, mannose and xylose. The polar lipids were phosphatidylethanolamine, hydroxyphosphatidylethanolamine, four unidentified phospholipids, four unidentified glycolipids and one unidentified lipid. The predominant menaquinone was MK-9(H4). The major fatty acids were iso-C16 : 0 2-OH, C17 : 0 10-methyl, C17 : 1
cis9 and iso-C16 : 0. Analyses of its morphological, physiological and biochemical characteristics, together with DNA–DNA relatedness data, confirmed that strain FMN03T is a representative of a novel species of the genus
Nonomuraea
, which is distinct from closely related reference strains. Strain FMN03T ( = DSM 45913T = KCTC 29233T) is proposed as the type strain of a novel species, for which the name Nonomuraea muscovyensis sp. nov. is proposed.
Nocardioides
zeae sp. nov., isolated from the stem of Zea mays
Authors: Glaeser Stefanie P. , McInroy John A. , Busse Hans-Jürgen , Kämpfer Peter
Published: May 2014

A Gram-stain-positive aerobic organism, isolated from the healthy stem of a Zea mays plant was studied for its taxonomic position. Based on 16S rRNA gene sequence analysis strain JM-1068T was most closely related to

Nocardioides alkalitolerans

(97.2 %). The 16S rRNA gene sequence similarity to all other species of the genus
Nocardioides
was ≤96.1 %. The quinone system of strain JM-1068T contained the major menaquinone MK-8(H4). The diagnostic diamino acid of the peptidoglycan was ll-diaminopimelic acid. In the polar lipid profile, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and two unidentified phospholipids were predominant. The polyamine pattern contained predominantly spermidine and spermine. The fatty acid profile was composed of iso-C16 : 0 and C18 : 1ω9c in addition to C16 : 0, C17 : 0 and C17 : 1ω8c and low amounts of C16 : 0 2-OH and C17 : 0 2-OH. This supported the allocation of the strain to the genus

Nocardioides

. In addition, the results of physiological and biochemical tests also allowed phenotypic differentiation of strain JM-1068T from

N. alkalitolerans

. It is concluded that JM-1068T represents a novel species of the genus

Nocardioides

, for which we propose the name Nocardioides zeae sp. nov., with JM-1068T ( = CIP 110696T = LMG 28079T) as the type strain.
Bacillus qingshengii sp. nov., a rock-weathering bacterium isolated from weathered rock surface
Authors: Xi Jun , He Lin-Yan , Huang Zhi , Sheng Xia-Fang
Published: May 2014

A novel type of rock-weathering bacterium was isolated from weathered rock (tuff) surface collected from Dongxiang (Jiangxi, eastern China). Cells of strain G19Twere Gram-reaction-positive, rod-shaped, endospore-forming and non-motile. The strain was aerobic, catalase- and oxidase-positive, and grew optimally at 30 °C and pH 7.0. On the basis of 16S rRNA gene sequence analysis, strain G19Twas shown to belong to the genusBacillusand the closest phylogenetic relatives wereBacillus aryabhattaiB8W22T(97.4 %) andBacillus megateriumIAM 13418T(97.1 %). The DNA G+C content was 36.7 mol% and the predominant respiratory quinone was MK-7. The major fatty acids were iso-C14 : 0, iso-C15 : 0and anteiso-C15 : 0. The polar lipid profile of strain G19Tcontained phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and an unidentified lipid. Based on the low level of DNA–DNA relatedness (ranging from 49.4 % to 55.0 %) to these type strains of species of the genusBacillusand unique phenotypic characteristics, strain G19Trepresents a novel species of the genusBacillus, for which the nameBacillusqingshengiisp. nov. is proposed. The type strain is G19T( = CCTCC AB 2013273T = JCM 19454T).
Reyranella
graminifolii sp. nov., isolated from bamboo (Phyllostachys bambusoides) litter
Authors: Lee Jae-Chan , Whang Kyung-Sook
Published: May 2014

A novel strain designated Wo-34T was isolated from bamboo (Phyllostachys bambusoides) litter. Cells were Gram-stain-negative, non-motile, catalase-negative and oxidase-positive rods. The isolate grew aerobically at 15–35 °C (optimum 28 °C), pH 4.0–9.0 (optimum pH 7.0) and in the presence of 0–1.0 % (w/v) NaCl (optimum 0.1 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain Wo-34T belonged to the genus
Reyranella
with the sequence similarities of 97.9 % and 97.3 % to the other species of the genus

Reyranella

,

Reyranella massiliensis

521T and

Reyranella soli

KIS14-15T, respectively. The predominant ubiquinone was Q-10. Major fatty acids were C18 : 1ω7c, C18 : 1 2-OH and C19 : 0 cyclo ω8c. The polar lipids contained phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown aminolipid, unidentified phospholipids and unknown lipids. DNA–DNA relatedness values between strain Wo-34T and

R. massiliensis

DSM 23428T and

R. soli

KACC 13034T were 35 % and 29 %, respectively. On the basis of polyphasic analysis from this study, strain Wo-34T represents a novel species of the genus

Reyranella

for which the name Reyranella graminifolii sp. nov. is proposed. The type strain is Wo-34T ( = KACC 17605T = NBRC 109813T).
Pseudogracilibacillus auburnensis gen. nov., sp. nov., isolated from the rhizosphere of Zea mays
Authors: Glaeser Stefanie P. , McInroy John A. , Busse Hans-Jürgen , Kämpfer Peter
Published: May 2014

A Gram-positive-staining, aerobic, endospore-forming bacterium, strain P-207T, was isolated from a rhizosphere soil sample in Auburn, AL, USA. On the basis of 16S rRNA gene sequence comparisons, strain P-207T was grouped in the vicinity of representatives of the genera

Virgibacillus

,

Ornithinibacillus

,

Cerasibacillus

,

Lentibacillus

and

Oceanobacillus

, but could not be assigned clearly to any of these genera. The highest similarity was found to the sequence of

Virgibacillus carmonensis

LMG 20964T (94.4 %); however, the 16S rRNA gene sequence similarity to the type strain of the type species of

Virgibacillus

,

Virgibacillus pantothenticus

, was only 92.9 %. The quinone system of strain P-207T consisted predominantly of menaquinone MK-7. The polar lipid profile exhibited the major lipids diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine and moderate to minor amounts of several unidentified phospholipids, glycolipids and phosphoglycolipids, an aminophospholipid and an aminolipid. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid and the polyamine pattern contained predominantly spermidine and spermine. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0. The G+C content of the genomic DNA was 34 mol%. Because of the low sequence similarity of strain P-207T to all representatives of

Virgibacillus

,

Ornithinibacillus

,

Cerasibacillus

,

Lentibacillus

and

Oceanobacillus

, which was always <95 %, and its unique lipid pattern, we propose that strain P-207T represents a novel species in a new genus, for which the name Pseudogracilibacillus auburnensis gen. nov., sp. nov. is proposed. The type strain of Pseudogracilibacillus auburnensis is P-207T ( = CCM 8509T = LMG 28212T = CIP 110797T).
Preparation and characteristics of Haliotis Discus Hannai Ino (abalone) viscera Jeotgal, a Korean fermented seafood
Authors: Li Jinglei , Kim Bo-Sub , Kang Seong-Gook
Published: May 2014

We prepared Jeotgal with Haliotis Discus Hannai Ino (abalone) viscera and the studied the physicochemical properties. Abalone viscus was fermented with varying amounts of salt for 60 days in order to prepare for the Jeotgal. During the fermentation, we measured the change of pH, volatile basic nitrogen (VBN), amino nitrogen (AN) and protease activity. After the fermentation, we examined the composition of free amino acids and sensory evaluation. The pH decreased with the fermentation, which was not significant (from 5.5 to 6.5). After the fermentation, the highest VBN was 96.7 mg/g, while the highest AN value was 406.3 mg/g. Unlike VBN and AN, the protease activity increased and reached the highest activity at the 30th day, and then decreased afterward. Based on the results, it was deduced that higher salinity restrained the fermentation and lowered the VBN, AN and protease activity. The total free amino acids of abalone Jeotgal, which were analyzed after the fermentation, (62.75 mg/g) was more than twice the amount in the abalone viscera before the fermentation (30.37 mg/g). We prepared abalone viscera Jeotgal and studied the characteristics for the first time. This will provide us with useful information for future related researches.
Effect of the supplementation of Coconopsis lanceolata extract on lipid metabolism amelioration in type 2 diabetes mouse model induced by high fat diet
Authors: Yun Won-Kap , Bae Hyun-Ji , Kim You-Jeong , Kwon O Jun , Im Moo Hyeog , Cho Hyun Duk , Kim Taewan
Published: May 2014

The present study was designed to investigate the antihyperlipidemic effect of Coconopsis lanceolata extract in C57BL/6J mice. The mice were divided into four groups: normal diet group (ND), high fat diet group (HFD), positive control group with 0.05% metformin (PC), Coconopsis lanceolata extract group (UCL). After 5 weeks of feeding, average body weight of the UCL group mice was slightly decreased, while that of the HFD group significantly increased) Also, liver and adipose tissue weights in the UCL group significantly increased. The levels of trigliceride (TG) and total in the plasma of UCL-supplemented group were significantly lower than those of high fat diet group. On the other hand, HDL-cholesterol level was increased. Expression level of proteins related with adipogenesis such as SREBP-1c, ACC, and FAS in the liver of the UCL group mice was much lower comparing with the HFD group mice. In conclusion, the results showed that the Coconopsis lanceolata extract possesses significant antihyperlipidemic effects in C57BL/6J mice.
Inflammatory mediator regulation of the Zizyphus jujube leaf fractions in the LPS-stimulated Raw264.7 mouse machrophage
Authors: Kim Ye Jin , Son Dae-Yeul
Published: May 2014

Zizyphus jujube leaf fractions (ZLFs) showed no cytotoxic effects of up to 100 μg/mL, while the anti-inflammatory effects of ZLFs were analyzed by checking the productions of nitric oxide (NO), prostaglandin E2 (PGE2), cyclooxygenase-2 (COX-2), and inflammatory cytokines TNF-α, IL-1β, and IL-6 in the lipopolysaccharide (LPS)-stimulated Raw264.7 macrophage up to the concentration of 100 μg/mL. ZLFs (100 μg/mL) demonstrated a strong anti-inflammatory activity that reduced 61~85% of NO and 71~100% of PGE2 production in the LPS-stimulated Raw264.7 macrophage. Even the low ZLFs concentration of 1 μg/mL have reduced NO and PGE2 production by 34~64%. Expressions of COX-2 protein were also effectively inhibited by the ZLFs. Furthermore, the TNF-α, IL-1β, and IL-6 production were significantly suppressed through the treatment of ZLFs at concentrations of 1, 10, and 100 μg/mL. In the order of the Zizyphus jujube leaf water fraction (ZLWF) < buthanol fraction (ZLBF) < ethyl acetate fraction (ZLEF) showed anti-inflammatory activity. In particular, the ethyl acetate fraction ZLEF at 100 μg/mL showed an excellent anti-inflammatory activity by reducing the production of NO, PGE2, COX-2, and inflammatory cytokines (TNF-α, IL-1β, IL-6) in the level of Raw264.7 macrophage without LPS-stimulation or even better. The results of our study suggest the potential of ZLEF for use as an excellent ant-inflammatory inhibiting mediator and may be used as a therapeutic approach to various inflammatory diseases.
Sensory quality, antioxidant, and inhibitory activities of XO and AO of Smilax china leaf tea fermented by Aspergillus oryzae
Authors: Lee Sang-Il , Lee Ye-Kyung , Kim Soon-Dong , Yang Seung Hwan , Suh Joo-Won
Published: May 2014

This study was conducted in order to investigate the optimal fermentation periods of the Smilax china L. leaves as a fermented tea via Aspergillus oryzae for 0 (non-fermented), and 10, 20, and 30 days (NF, F10, F20, F30). It was also observed for its quality characteristics. In the color and spectrum (400~700nm) of 1% tea water extract, NF was light yellow, whereas fermented tea (F10~F30) was light red color, and the F10 among F10~F30 has the clearest color and spectrum. Furthermore, acceptabilities of aroma and brightness were insignificantly different between NF and F10~30, while the mouth feel and overall acceptabilities were insignificantly distinct among all of the fermented teas. Therefore, these results suggest that the appropriate fermentation period for tea fermentation is 10 days. On the other hand, the total polyphenol and flavonoid content in the NF was the highest among all of the fermented teas. In the antioxidant parameters, EDA (electron donating ability), FRAP (ferric reducing antioxidant power), and LPOIA (lipid peroxidation inhibitory activity) in the NF were the highest among all fermented teas. Meanwhile, the XOI (xanthine oxidase inhibitory activity) was low, as well as insignificantly different from NF and F10~F30, whereas the AOI (aldehyde oxidase inhibitory activity) was markedly higher (38.09~41.70%) by the hot water tea extract (with or without fermentation), particularly the AOI that has increased via fermentation. In conclusion, the overall antioxidant activity tended to be reduced by fermentation; however, the EDA, FRAP and LPOIA in the fermented tea for 10 days was higher than the activities during 20~30 days of fermentation. There was a similar result in the color and acceptability of fermented tea for 10 days, which was remarkably better than those of 20-30 days. Therefore, fermented tea from the leaves of Smilax china L. could be expected to be used as a functional tea without the loss of inhibitory activity of both the XO and AO via fermentation.
Quality characteristics of cookies added with jujube powder
Authors: Kim Min Jung , Choi Ji Eun , Lee Jun Ho
Published: May 2014

The feasibility of incorporating jujube powder as a value-added food ingredient in cookies was investigated. The amount of jujube powder added (0~20%) was found to have significantly affected the cookie quality (p<0.05). Furthermore, the pH ranged from 6.16 to 6.69, and moisture content gradually increased from 4.11% to 4.76%, while the spread ratio and loss rate have significantly decreased with the increasing levels of the powder added (p<0.05). Lightness decreased; however, the redness and yellowness, as well as hardness, have significantly increased with the higher amount of jujube powder in the formulation (p<0.05). In addition, 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity was significantly increased (p<0.05) without remarkable differences between the control and 5% sample, and 15% and 20% sample (p>0.05). The consumer acceptance test indicated that the addition of jujube powder of up to 10% had a favorable effect on the consumer preferences in general. Based on the overall observation, the cookies with 5~10% jujube powder is recommended for taking advantage of the functional properties of jujube powder without sacrificing the sensory quality.
Effect of the ice pack treatment in the corrugated box for improving the storage quality of the oriental melon (Cucumis melo var. makuwa) at high temperature conditions during summer
Authors: Choi Woo Suk , Chung Dae-Sung , Lee Youn Suk
Published: May 2014

The effects of the ice pack and aluminum coated board in the corrugated boxes for maintaining the quality of fresh oriental melons (Cucumis melo var. makuwa) were investigated. The harvested oriental melons were stored at a temperature of 30°C for 21 days after placing them in the corrugated boxes treated with control, including ice pack and aluminum coated board. The treatment with the ice pack and aluminum coated board was identified to have maintained the relative low temperature in the corrugated box against the high temperature from the environment. For the storage study of the oriental melon, the treatments with the ice pack and aluminum coated board reduced the respiration rate, the development of external color, and total weight loss. All treatments were also effective in maintaining the firmness and decreasing the decay ratio of the oriental melon as compared to those that were controlled. However, the value of total soluble solids regarding the fruit was insignificantly affected by the ice pack treatment. The results indicated that the application of the ice pack and aluminum coated board in the corrugated box played an important role in maintaining the quality of oriental melons during storage. The combination with the ice pack and aluminum coated board had more effective values on the storage qualities for oriental melons than that with the ice pack only. Based on the results of this study, the ice pack and aluminum coated board were the useful treatments for reducing the loss of quality of the fresh oriental melons in high temperature storage conditions.
Quality characteristics of noodles added with Houttuynia cordata Thunb. powder
Authors: Park Woo-Po
Published: May 2014

The purpose of this study was to evaluate appropriate concentrations of Houttuynia cordata Thunb. powder, which has various functions, to dried wheat flour noodles. The viscosity of the composite flour and cooking quality of the noodle samples were measured, and sensory evaluations were conducted in this study. When measured by the amylograph, the composite flour had lower viscosity in the gelatinization points, maximum viscosity, and viscosity at a temperature of 95°C than those of control. However, the gap between the maximum viscosity and viscosity after 15 minutes at a temperature of 95°C was not great among all of the samples. While cooked noodles containing H. cordata Thunb. powder had lower weight and lower volume than those of control, the weight of two cooked noodle samples with 0.5% and 1.5% of H. cordata Thunb. powder was insignificantly different. Cooked noodles had higher concentrations of H. cordata Thunb. powder; therefore, the L value of cooked noodles decreased, while a and b color values of the noodles increased. Color, flavor, taste, and overall acceptability of the samples with H. cordata Thunb. powder were lower than those of wheat flour noodles via sensory evaluation. In the overall acceptability, however, samples with 0.5% and 1.5% of H. cordata Thunb. powder were insignificantly different from control. As a result, it was finally suggested that optimum level of the H. cordata Thunb. powder in the product was below 0.5%.
Quality characteristics of brown rice boiled with medicinal herbs extract for diabetes prevention
Authors: Yang Kyung-Mi , Park Jung-Ran , Hwang Su-Jung
Published: May 2014

This study was to investigate the quality characteristics of brown rice mixed with white rice and boiled in hydrothermal extract of the medicinal herbs which was effective for diabetes in order to suggest a way of taking the rice everyday in Korean dietary life. The moisture content of the cooked rice was decreased with an increase of brown rice addition. The moisture content was same at Herbs extract (H2). The physical properties of Herbs extract (H1)and Herbs extract (H2) showed a similar tendency. The hardness of the control, 100% of white rice, was lowest. The hardness was increased with increase of brown rice addition. The springiness, cohesiveness and gumminess tended to be decreased with increase of brown rice addition, while the chewiness was increased with increase of brown rice addition. In chromaticity, H1 and H2 revealed a similar trend. The color value L was decreased with increase of brown rice addition. The value a was decreased with increase of brown rice amount. On the contrary, the value b was increased with increase of brown rice amount. In the sensory test result of the cooked rice by using H2, the appearance, taste, texture and the overall preference exhibited a tendency to decreased with increase of brown rice addition. The incase was similar to the rice cooked with H1 and the overall preference showed a similar tendency, being highest at the sample added with 30% of brown rice.
Antioxidant activities of hot water extract of Syneilesis palmata root and aerial part
Authors: Lee Yang-Suk , Kim Nam-Woo
Published: May 2014

This study was performed in order to investigate the antioxidant properties of hot water extract from the root and aerial part of the Syneilesis palmata in respect to its potential use as food, cosmetics material, or medicinal resource. The results showed that the S. palmata root hot water extract (RHW) possessed a higher content of total flavonoid compounds (4.58 mg/g) and total polyphenol compounds (59.11 mg/g). The SOD-like activities of the RHW and APHW were 23.74% and 21.61%, respectively, at a concentration 2,000 ug/mL. In the nitrite scavenging ability of a 2,000 μg/mL concentration, the RHW showed 63.06% (pH 1.2) and 47.16% (pH 3.0). The IC50 values of the nitrite scavenging abilities were 99.93 μg/mL (ascorbic acid), 1,150.85 μg/mL (RHW), and 1,610.25 μg/mL (APHW). The IC50 values of DPPH free radical scavenging abilities were 99.87 μg/mL (RHW) and 118.29 μg/mL (APHW). The inhibition values (IC50) of xanthine oxidase were 139.62 μg/mL (RHW) and 111.11 μg/mL (APHW). In all of the experiments, the S. palmata root hot water extracts have higher activities than the aerial hot water extract, except for the xanthine oxidase inhibitory activity. These results suggest that the S. palmata is a potentially useful antioxidant source for the development of functional nutraceuticals, cosmetics and medicine.
A gene expression atlas of abicoid-depleted Drosophila embryo reveals early canalization of cell fate
Authors: Staller Max V , Fowlkes Charless C , Bragdon Meghan D.J. , Wunderlich Zeba B. , DePace Angela
Published: May 2014

In developing embryos, gene regulatory networks canalize cells towards discrete terminal fates. We studied the behavior of the anterior-posterior segmentation network in Drosophila melanogaster embryos depleted of a key maternal input, bicoid (bcd), by building a cellular- resolution gene expression atlas containing measurements of 12 core patterning genes over 6 time points in early development. With this atlas, we determine the precise perturbation each cell experiences, relative to wild type, and observe how these cells assume cell fates in the perturbed embryo. The first zygotic layer of the network, consisting of the gap and terminal genes, is highly robust to perturbation: all combinations of transcription factor expression found in bcd depleted embryos were also found in wild type embryos, suggesting that no new cell fates were created even at this very early stage. All of the gap gene expression patterns in the trunk expand by different amounts, a feature that we were unable to explain using two simple models of the effect of bcd depletion. In the second layer of the network, depletion of bcd led to an excess of cells expressing both even skipped and fushi tarazu early in the blastoderm stage, but by gastrulation this overlap resolved into mutually exclusive stripes. Thus, following depletion of bcd, individual cells rapidly canalize towards normal cell fates in both layers of this gene regulatory network. Our gene expression atlas provides a high resolution picture of a classic perturbation and will enable further modeling of canalization in this transcriptional network.
Some plants dont play games: An ideal free distribution explains the root production of plants that do not engage in a tragedy of the commons game.
Authors: McNickle Gordon , Brown Joel S
Published: May 2014

1. Game theoretic models that seek to predict the most competitive strategy plants use for competition in soil are clear; they generally predict that over-proliferation of roots is the only evolutionarily stable strategy. However, empirical studies are equally clear that not all plants employ this strategy of over-proliferation of roots. Here, our goal was to develop and test an alternative non-game theoretic model that can be used to develop alternative hypotheses for plants that do not appear to play games. 2. The model is similar to previous models, but does not use a game theoretic optimization criterion. Instead, plants use only nutrient availability to select a root allocation strategy, ignoring neighbours. To test the model we compare root allocation and seed yield of plants grown either alone or with neighbours. 3. The model predicted plants that do not sense neighbours (or ignore neighbours) should allocate roots relative to resource availability following an ideal free distribution. This means that if a soil volume of quality R contains x roots, then a soil volume of quality R/n will contain x/n roots. The experimental data were consistent with this prediction. That is, plants grown with 1.2g of slow release fertilizer resources produced 0.043 g of roots, while plants grown with neighbours, or plants grown with half as much fertilizer produced half as much root mass (0.026g, and 0.24g respectively). Seed yield followed a similar pattern. 4. This model presents an alternative predictive framework for those plant species that do not seem to play a tragedy of the commons game for belowground competition. 5. Synthesis: It remains unclear why some plants do not engage in belowground games for competition. Models suggest over-proliferation is an unbeatable evolutionary stable strategy, yet plants that do not play the game apparently coexist with plants that do. We suggest that a greater understanding of trade-offs among traits that are important for other biotic interactions (above-ground competition, enemy defence, mutualisms) will lead to a greater understanding of why some species over-proliferate roots when in competition but other species do not.
Missing kinaesthesia challenges precise naturalistic cortical prosthetic control
Authors: Galán Ferran , Baker Mark R , Alter Kai , Baker Stuart N
Published: May 2014

A major assumption of brain-machine interface (BMI) research is that patients with disconnected neural pathways can still volitionally recall precise motor commands that could be decoded for naturalistic prosthetic control. However, the disconnected condition of these patients also blocks kinaesthetic feedback from the periphery, which has been shown to regulate centrally generated output responsible for accurate motor control. Here we tested how well motor commands are generated in the absence of kinaesthetic feedback by decoding hand movements from human scalp electroencephalography (EEG) in three conditions: unimpaired movement, imagined movement, and movement attempted during temporary disconnection of peripheral afferent and efferent nerves by ischemic nerve block. Our results suggest that the recall of cortical motor commands is impoverished in absence of kinaesthetic feedback, challenging the possibility of precise naturalistic cortical prosthetic control.
Epistasis analysis for quantitative traits by functional regression model
Authors: Zhang Futao , Boerwinkle Eric , Xiong Momiao
Published: May 2014

The critical barrier in interaction analysis for rare variants is that most traditional statistical methods for testing interactions were originally designed for testing the interaction between common variants and are difficult to apply to rare variants because of their prohibitive computational time and poor ability. The great challenges for successful detection of interactions with next-generation sequencing (NGS) data are (1) lack of methods for interaction analysis with rare variants, (2) severe multiple testing, and (3) time-consuming computations. To meet these challenges, we shift the paradigm of interaction analysis between two loci to interaction analysis between two sets of loci or genomic regions and collectively test interactions between all possible pairs of SNPs within two genomic regions. In other words, we take a genome region as a basic unit of interaction analysis and use high-dimensional data reduction and functional data analysis techniques to develop a novel functional regression model to collectively test interactions between all possible pairs of single nucleotide polymorphisms (SNPs) within two genome regions. By intensive simulations, we demonstrate that the functional regression models for interaction analysis of the quantitative trait have the correct type 1 error rates and a much better ability to detect interactions than the current pairwise interaction analysis. The proposed method was applied to exome sequence data from the NHLBI’s Exome Sequencing Project (ESP) and CHARGE-S study. We discovered 27 pairs of genes showing significant interactions after applying the Bonferroni correction (P-values < 4.58 × 10−10) in the ESP, and 11 were replicated in the CHARGE-S study.
Three cases of reconstruction with a simply designed bilobed flap after excision of squamous cell carcinomas of the lateral eyebrow areas
Authors: Hikage Satoko , Ono Ichiro , Yamashita Toshiharu , Kimura Tetsunori
Published: May 2014

Squamous cell carcinoma is frequently observed on the lateral eyebrow, one of the most difficult sites for one‐stage reconstruction because of its location close to the eyelids. The reconstruction of defects by the single‐stage flap is advantageous for elderly patients because of its good functional and aesthetic outcome. We surgically treated three cases of squamous cell carcinoma on this area and performed reconstruction with a simply designed bilobed flap, all of which resulted in favorable outcomes. We therefore report on the usefulness of this reconstructive method for the lateral eyebrow defects.
Growth trajectory influences temperature preference in fish through an effect on metabolic rate
Authors: Killen Shaun S.
Published: May 2014

Most animals experience temperature variations as they move through the environment. For ectotherms, in particular, temperature has a strong influence on habitat choice. While well studied at the species level, less is known about factors affecting the preferred temperature of individuals; especially lacking is information on how physiological traits are linked to thermal preference and whether such relationships are affected by factors such feeding history and growth trajectory.

This study examined these issues in the common minnow Phoxinus phoxinus, to determine the extent to which feeding history, standard metabolic rate (SMR) and aerobic scope (AS), interact to affect temperature preference.

Individuals were either: 1) food deprived (FD) for 21 days, then fed ad libitum for the next 74 days; or 2) fed ad libitum throughout the entire period. All animals were then allowed to select preferred temperatures using a shuttle‐box, and then measured for SMR and AS at 10 °C, estimated by rates of oxygen uptake. Activity within the shuttle‐box under a constant temperature regime was also measured.

In both FD and control fish, SMR was negatively correlated with preferred temperature. The SMR of the FD fish was increased compared with the controls, probably due to the effects of compensatory growth, and so these growth‐compensated fish preferred temperatures that were on average 2·85 °C cooler than controls fed a maintenance ration throughout the study. Fish experiencing compensatory growth also displayed a large reduction in activity. In growth‐compensated fish and controls, activity measured at 10 °C was positively correlated with preferred temperature.

Individual fish prefer temperatures that vary predictably with SMR and activity level, which are both plastic in response to feeding history and growth trajectories. Cooler temperatures probably allow individuals to reduce maintenance costs and divert more energy towards growth. A reduction in SMR at cooler temperatures, coupled with a decrease in spontaneous activity, could also allow individuals to increase surplus AS for coping with environmental stressors. In warming climates, however, aquatic ectotherms could experience frequent fluctuations in food supply with long‐lasting effects on metabolic rate due to compensatory growth, while simultaneously having limited access to preferred cooler habitats.
Species distribution models of an endangered rodent offer conflicting measures of habitat quality at multiple scales
Authors: Bean William T. , Prugh Laura R. , Stafford Robert , Butterfield H. Scott , Westphal Michael , Brashares Justin S.
Published: May 2014

The high cost of directly measuring habitat quality has led ecologists to test alternate methods for estimating and predicting this critically important ecological variable. In particular, it is frequently assumed but rarely tested that models of habitat suitability (‘species distribution models’, SDMs) may provide useful indices of habitat quality, either from an individual animal or manager's perspective. Critically, SDMs are increasingly used to estimate species’ ranges, with an implicit assumption that areas of high suitability will result in higher probability of persistence. This assumption underlies efforts to use SDMs to design protected areas, assess the status of cryptic species or manage responses to climate change. Recent tests of this relationship have provided mixed results, suggesting SDMs may predict abundance but not other measures of high‐quality habitat (e.g. survival, persistence).

In this study, we created a suite of SDMs for the endangered giant kangaroo rat Dipodomys ingens at three distinct scales using the machine‐learning method Maxent. We compared these models with three measures of habitat quality: survival, abundance and body condition.

Species distribution models were not correlated with survival, while models at all scales were positively correlated with abundance. Finer‐scale models were more closely correlated with abundance than the largest scale. Body condition was not correlated with habitat suitability at any scale. The inability of models to predict survival may be due to a lack of information in environmental covariates; unmeasured community processes or stochastic events; or the inadequacy of using models that predict species presence to also predict demography.

Synthesis and applications. Species distribution models (SDMs), especially fine scale ones, may be useful for longer‐term management goals, such as identifying high‐quality habitat for protection. However, short‐term management decisions should be based only on models that use covariates appropriate for the necessary temporal and spatial scales. Assumptions about the relationship between habitat suitability and habitat quality must be made explicit. Even then, care should be taken in inferring multiple types of habitat quality from SDMs.