bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing the Dimensions of Product Variety on Performance: The Value of Product Line and Pack Size
Authors: Wan Xiang , Dresner Martin E. , Evers Philip T.
Published: August 2014

This article studies the impacts of product variety along two dimensions: product‐line variety and pack‐size variety. Previous research has often found that increased product variety is associated with increased sales. Interestingly, we find that this is not always the case, once the negative impact of product variety on fill rates is introduced. Specifically, product‐line variety has a positive total effect on sales, but pack‐size variety has a negative total effect on sales. We also investigate potential nonlinear impacts (with decreasing marginal effects) of product‐line and pack‐size variety, and find the result to be one of diminishing returns.
The Phylogenetic Position of Kofoidia loriculata (Parabasalia) and its Implications for the Evolution of the Cristamonadea
Authors: Tai Vera , Gile Gillian H. , Pan Jingwen , James Erick R. , Carpenter Kevin J. , Scheffrahn Rudolf H. , Keeling Patrick J.
Published: August 2014

Kofoidia loriculata is a parabasalid symbiont inhabiting the hindgut of the lower termite Paraneotermes simplicicornis. It was initially described as a lophomonad due to its apical tuft of multiple flagella that disintegrate during cell division, but its phylogenetic relationships have not been investigated using molecular evidence. From single cell isolations, we sequenced the small subunit rRNA gene and determined that K. loriculata falls within the Cristamonadea, but is unrelated to other lophomonads. This analysis further demonstrates the polyphyly of the lophomonads and the necessity to re‐assess the morphological and cellular evolution of the Cristamonadea.
IL‐18 Cytokine Levels Modulate Innate Immune Responses and Cryptosporidiosis in Mice
Authors: Bedi Brahmchetna , McNair Nina N. , Förster Irmgard , Mead Jan R.
Published: August 2014

IL‐18 is known to play a key role limiting Cryptosporidium parvum infection. In this study, we show that IL‐18 depletion in SCID mice significantly exacerbates C. parvum infection, whereas, treatment with recombinant IL‐18 (rIL‐18), significantly decreases the parasite load, as compared to controls. Increases in serum IFN‐γ levels as well as the up‐regulation of the antimicrobial peptides, cathelicidin antimicrobial peptide and beta defensin 3 (Defb3) were observed in the intestinal mucosa of mice treated with rIL‐18. In addition, C. parvum infection significantly increased mRNA expression levels (> 50 fold) of the alpha defensins, Defa3 and 5, respectively. Interestingly, we also found a decrease in mRNA expression of IL‐33 (a recently identified cytokine in the same family as IL‐18) in the small intestinal tissue from mice treated with rIL‐18. In comparison, the respective genes were induced by IL‐18 depletion. Our findings suggest that IL‐18 can mediate its protective effects via different routes such as IFN‐γ induction or by directly stimulating intestinal epithelial cells to increase antimicrobial activity.
Does the Introduction of Nursing Home Culture Change Practices Improve Quality?
Authors: Miller Susan C. , Lepore Michael , Lima Julie C. , Shield Renee , Tyler Denise A.
Published: August 2014

Objectives

To understand whether nursing home (NH) introduction of culture change practices is associated with improved quality.

Design

NH‐level panel study using multivariate fixed‐effects statistical modeling to estimate the effect of culture change introduction on quality outcomes.

Setting

Eight hundred twenty‐four U.S. NHs with culture change practice involvement beginning between 2005 and 2010.

Participants

Directors of nursing and nursing home administrators.

Measurements

A culture change practice score (derived from a 2009/10 national NH survey) was used to stratify NHs according to practice implementation (high (scores in the top quartile; n = 217) vs other (n = 607)). NH‐level outcomes included prevalence of seven care practices and three resident outcomes, health‐related and quality‐of‐life weighted survey deficiencies, and average number of hospitalizations per resident year.

Results

For NHs with high practice implementation, introduction of culture change was associated with a significant decrease in prevalence of restraints, tube feeding, and pressure ulcers; an increase in the proportion of residents on bladder training programs; and a small decrease in the average number of hospitalizations per resident year (coefficient −0.04, standard error (SE) 0.02, P = .06). For NHs with lower practice implementation (practice scores in lower three quartiles), introduction was associated with fewer health‐related (coefficient −5.26, SE 3.05; P = .09) and quality‐of‐life (coefficient −0.10, SE 0.05; P = .04) survey deficiencies, although these NHs also had small statistically significant increases in the prevalence of residents with urinary tract infections and in average hospitalizations per resident year (coefficient 0.03, SE 0.01, P = .02).

Conclusion

The introduction of NH culture change appears to result in significant improvements in some care processes and outcomes in NHs with high practice implementation. For other NHs, culture change introduction results in fewer survey deficiencies.
Clonality of bacterial consortia in root canals and subjacent gingival crevices
Authors: Parahitiyawa Nipuna B. , Chu Frederick C. S. , Leung Wai K. , Yam Wing C. , Jin Li Jian , Samaranayake Lakshman P.
Published: August 2014

Aim

No oral niche can be considered to be segregated from the subjacent milieu because of the complex community behavior and nature of the oral biofilms. The aim of this study was to address the paucity of information on how these species are clonally related to the subjacent gingival crevice bacteria.

Methods

We utilized a metagenomic approach of amplifying 16S rDNA from genomic DNA, cloning, sequencing and analysis using LIBSHUFF software to assess the genetic homogeneity of the bacterial species from two infected root canals and subjacent gingival crevices.

Results

The four niches studied yielded 186 clones representing 54 phylotypes. Clone library comparisons using LIBSHUFF software indicated that each niche was inhabited by a unique flora. Further, 42% of the clones were of hitherto unknown phylotypes indicating the extent of bacterial diversity, especially in infected root canals and subjacent gingival crevices.

Conclusions

We believe data generated through this novel analytical tool shed new light on understanding oral microbial ecosystems.
Characterization of long‐term in vitro culture‐related alterations of human tonsil‐derived mesenchymal stem cells: role for CCN1 in replicative senescence‐associated increase in osteogenic differentiation
Authors: Yu Yeonsil , Park Yoon Shin , Kim Han Su , Kim Ha Yeong , Jin Yoon Mi , Jung Sung‐Chul , Ryu Kyung‐Ha , Jo Inho
Published: August 2014

Although mesenchymal stem cells (MSC) isolated from bone marrow and adipose tissues are known to be subjected to in vitro culture‐related alterations in their stem cell properties, such data have not been reported in human tonsil‐derived MSC (T‐MSC). Here, we investigated the culture‐related changes of phenotypes, the senescence, and the differentiation potential of T‐MSC. T‐MSC were serially passaged by a standard protocol, and their characteristics were assessed, including MSC‐specific surface antigen profiles, the senescence, and the differentiation potentials into adipocytes, chondrocytes and osteocytes. Up to at least passage 15, we found no alterations in either MSC‐specific surface marker, CD14, CD34, CD45, CD73 and CD90, or the mRNA expression of embryonic stem cell gene markers, Nanog, Oct4‐A and Sox‐2. However, the expression of CD146, recently identified another MSC marker, dramatically decreased with increasing passages from ~ 23% at passage 3 to ~ 1% at passage 15. The average doubling time increased significantly from ~ 38 h at passage 10 to ~ 46 h at passage 15. From passage 10, the cell size increased slightly and SA‐β‐gal staining was evident. Both Alizarin Red S staining and osteocalcin expression showed that the osteogenic differentiation potential increased up to passage 10 and decreased thereafter. However, the adipogenic and chondrogenic differentiation potential decreased passage‐dependently from the start, as evidenced by staining of Oil Red O and Alcian Blue, respectively. Consistent with a passage‐dependent osteogenic differentiation, the expression of CCN1, an angiogenic protein known to be related to both senescence and osteogenesis, also increased up to passage 10. Furthermore, ectopic expression of small interfering RNA against CCN1 at passage 10 significantly reversed Alizarin Red S staining and osteocalcin expression. Altogether, our study demonstrates the characterization of long‐term in vitro cultured T‐MSC and that CCN1 may be involved in mediating a passage‐dependent increase in osteogenic potential of T‐MSC.
The influence of fixed orthodontic appliances on masticatory and swallowing threshold performances
Authors: Magalhães I. B. , Pereira L. J. , Andrade A. S. , Gouvea D. B. , Gameiro G. H.
Published: August 2014

To test the hypothesis that treatment with orthodontic appliances disturbs masticatory and swallowing performances. Twenty‐seven subjects with malocclusions requiring orthodontic treatment were included in this prospective study. The masticatory and swallowing performances were evaluated at five different times: before bracket placement (T0), immediately after archwire placement (T1), 48 h after archwire placement (T2), 30 days after archwire placement (T3) and 3 months after the initial appointment (T4). Masticatory performance was determined by the median particle sizes for the Optocal test food after 15 chewing strokes, and the swallowing thresholds were registered for both the test food and a natural food (peanuts). Pain during mastication was evaluated using a 100‐mm visual analogue scale. Masticatory performance was significantly reduced at T2, at which time patients reported the highest pain values. The time spent to the first swallow was increased at T2 for the natural food but not for the test food. The values for pain, masticatory and swallowing performances at T3 and T4 were similar to those at T0. Orthodontic patient masticatory function is only reduced during the period of higher pain experience, which could also disrupt the deglutition of harder foods. However, neither mastication nor deglutition processes were disturbed by orthodontic appliances in long‐term treatment.
Stability of Recalled Parental Rearing Behavior in a Community Sample of Adolescents and Young Adults
Authors: Asselmann Eva , Knappe Susanne , Wittchen Hans‐Ulrich , Lieb Roselind , Beesdo‐Baum Katja
Published: August 2014

This study examined the temporal stability of recalled parental rearing behavior (RPRB) in a community sample of adolescents and young adults (aged 15–19 at first assessment, N = 945) over a period of nearly two years. RPRB (overprotection/control, rejection/punishment, and emotional warmth, separately for mother and father) was assessed at two assessment waves (time interval: M = 21.18 months, SD = 0.09 months) using the Questionnaire of Recalled Parental Rearing Behavior. Intraclass correlations (ICCs) between both assessments were examined. ICCs were similar for maternal and paternal RPRB and slightly higher for emotional warmth (mother: .70; father: .70) than for rejection/punishment (mother: .69; father: .68) and overprotection/control (mother: .66; father: .62). These findings suggest an at least moderate temporal stability of RPRB in adolescents of the community.
The microRNA‐146a/b attenuates acute small‐for‐size liver graft injury in rats
Authors: Jiang Weiwei , Ni Qingfeng , Tan Longwei , Kong Liangliang , Lu Yeting , Xu Xiaoqun , Kong Lianbao
Published: August 2014

Background & Aims

A critical role of the Toll‐like receptor (TLR)‐4 and its downstream mediators in the pathogenesis of small‐for‐size liver graft injury has been documented. Recently, the microRNA‐146 (miR‐146) was identified as a potent negative regulator of the TLR4 signalling pathway. In this study, the role of miR‐146a and miR‐146b in the attenuation of TLR‐4 signalling and small‐for‐size liver graft injury was investigated.

Methods

The expression levels of miR‐146a and miR‐146b during small‐for‐size liver graft injury were studied in vivo. In addition, the effects of miR‐146a and miR‐146b on the expression of IRAK1 and TRAF6 in the rat macrophage cell line NR8383 and rat liver kupffer cells were studied in vitro. The in vivo effect of miR‐146a and miR‐146b on small‐for‐size liver graft injury was studied by the tail vein injection of miR‐146a mimics and miR‐146b mimics.

Results

The levels of miR‐146a and miR‐146b decreased with a small‐for‐size liver graft. MiR‐146a and miR‐146b inhibited IRAK1 and TRAF6 expression by binding to the 3′UTR of IRAK1 or TRAF6, respectively, in the rat macrophage cell line NR8383. The administration of miR‐146a mimics and miR‐146b mimics prevented liver graft injury in small‐for‐size liver graft injury via the inactivation of IRAK1 and TRAF6 in vivo.

Conclusions

miR‐146a and miR‐146b prevent liver injury in small‐for‐size liver graft injury via the inactivation of IRAK1 and TRAF6.
Branched‐chain amino acids reduce hepatic iron accumulation and oxidative stress in hepatitis C virus polyprotein‐expressing mice
Authors: Korenaga Masaaki , Nishina Sohji , Korenaga Keiko , Tomiyama Yasuyuki , Yoshioka Naoko , Hara Yuichi , Sasaki Yusuke , Shimonaka Yasushi , Hino Keisuke
Published: August 2014

Background & Aims

Branched‐chain amino acids (BCAA) reduce the incidence of hepatocellular carcinoma (HCC) in patients with cirrhosis. However, the mechanisms that underlie these effects remain unknown. Previously, we reported that oxidative stress in male transgenic mice that expressed hepatitis C virus polyprotein (HCVTgM) caused hepatic iron accumulation by reducing hepcidin transcription, thereby leading to HCC development. This study investigated whether long‐term treatment with BCAA reduced hepatic iron accumulation and oxidative stress in iron‐overloaded HCVTgM and in patients with HCV‐related advanced fibrosis.

Methods

Male HCVTgM were fed an excess‐iron diet that comprised either casein or 3.0% BCAA, or a control diet, for 6 months.

Results

For HCVTgM, BCAA supplementation increased the serum hepcidin‐25 levels and antioxidant status [ratio of biological antioxidant potential (BAP) relative to derivatives of reactive oxygen metabolites (dROM)], decreased the hepatic iron contents, attenuated reactive oxygen species generation, and restored mitochondrial superoxide dismutase expression and mitochondrial complex I activity in the liver compared with mice fed the control diet. After 48 weeks of BCAA supplementation in patients with HCV‐related advanced fibrosis, BAP/dROM and serum hepcidin‐25 increased and serum ferritin decreased compared with the pretreatment levels.

Conclusions

BCAA supplementation reduced oxidative stress by restoring mitochondrial function and improved iron metabolism by increasing hepcidin‐25 in both iron‐overloaded HCVTgM and patients with HCV‐related advanced fibrosis. These activities of BCAA may partially account for their inhibitory effects on HCC development in cirrhosis patients.
Liver inflammation is a risk factor for prediabetes in at‐risk latinos with and without hepatitis C infection
Authors: Burman Blaire E. , Bacchetti Peter , Ayala Claudia E. , Gelman Nicholas , Melgar Jennifer , Khalili Mandana
Published: August 2014

Background & Aims

Early recognition of prediabetes can lead to timely clinical interventions to prevent type 2 diabetes. Both Latino ethnicity and chronic hepatitis C (HCV) have been identified as diabetic risk factors. We aimed to investigate predictors of impaired fasting glucose (IFG), a common prediabetic state, among Latinos with and without HCV.

Methods

One hundred Latino adults with no history of diabetes or cirrhosis underwent clinical, laboratory, and metabolic evaluation, including oral glucose tolerance testing (OGTT) and insulin suppression testing to quantify directly measured insulin resistance (IR). Isolated IFG was defined as fasting glucose ≥100 mg/dl and <140 mg/dl at 2 h during normal glucose tolerance during OGTT.

Results

Overall subject characteristics included median age 44 years, 64% male, 40% HCV‐positive and 32% with isolated IFG. Factors associated with isolated IFG included subject age (OR 2.42 per decade, 95%CI 1.40–3.90, P = 0.001), HCV infection (OR 4.0, 95%CI 1.71–9.72, P = 0.002) and alanine aminotransferase (ALT) (OR 2.35 per doubling, 95%CI 1.46–3.77, P < 0.0001). Multipredictor logistic regression analysis identified ALT (OR 2.05 per doubling, P = 0.005, 95% CI 1.24–3.40) and age (OR 2.20 per 10 years, P = 0.005, 95%CI 1.27–3.80) as factors independently associated with IFG. While HCV was associated with 4‐fold higher odds of IFG, this entire effect was mediated by ALT.

Conclusions

We found strong evidence that liver inflammation is a risk factor for prediabetes among Latinos with and without HCV. Among HCV‐infected individuals, early antiviral therapy could mitigate the effect of inflammation and represent an important intervention to prevent diabetes in this at‐risk population.
Reduced Flow‐and Acetylcholine‐Induced Dilations in Visceral Compared to Subcutaneous Adipose Arterioles in Human Morbid Obesity
Authors: Grizelj Ivana , Cavka Ana , Bian Jing‐Tan , Szczurek Mary , Robinson Austin , Shinde Shruti , Nguyen Van , Braunschweig Carol , Wang Edward , Drenjancevic Ines , Phillips Shane A.
Published: August 2014

Background and Aims

The hypothesis of this study was that microvascular FID and AChID is impaired in visceral (VAT) compared to SAT arterioles in morbidly obese women. An Additional aim was to determine the mechanisms contributing to FID and AChID in VAT and SAT arterioles.

Methods and Results

Arterioles were obtained from SAT and VAT biopsies from women (BMI > 35 kg/m2) undergoing bariatric surgery. Microvessels were cannulated for reactivity measurements in response to flow (pressure gradients of 10–100 cmH2O) and to ACh (10−9–10−4 M) with and without l‐NAME, INDO, and PEG‐catalase. NO and H2O2 generation were detected in arterioles by fluorescence microscopy. FID and AChID of arterioles from VAT were reduced compared to SAT arterioles. In SAT arterioles, l‐NAME, INDO, and PEG‐catalase significantly reduced FID and AChID but had no effect individually on VAT arterioles' vasodilator reactivity. INDO +l‐NAME reduced FID in VAT arterioles. NO‐fluorescence was greater in arterioles from SAT compared to VAT arterioles. Vascular H2O2 generation during flow was similar in both VAT and SAT.

Conclusion

Our results suggest that VAT arterioles display reduced vasodilator reactivity to flow and ACh compared to SAT arterioles, mediated by different regulatory mechanisms in human obesity.
Changes in dermal papilla structures due to aging in the facial cheek region
Authors: Mizukoshi K. , Yonekura K. , Futagawa M. , Nakamura T. , Hirayama K. , Takahashi K.
Published: August 2014

Background/purpose

In the past, it has been possible to measure the dermal papilla structures which are undulations between the epidermis and dermis by noninvasive method. However, almost all of previous studies were not intended to measure facial skin but another site of body. Here, we investigated age‐dependent alterations for dermal papilla structures in the facial cheek region after elucidating the difference of characteristics between the body site.

Methods

The surface of the dermis was observed under scanning electron microscope (SEM) using face and abdominal skin biopsy samples. A total of 90 Japanese women were investigated by in vivo confocal laser microscope (CLSM). The number and the shape in the horizontal cross‐sectional images of the dermal papilla were analyzed.

Results

The facial skin had different characteristics in comparison to the abdominal skin by SEM observation. Under CLSM observation, we found abnormal dermal papilla structures which were accompanied by spots or enlarged pore areas and eliminated these structures from our analysis. We revealed a decrease in the number of normal dermal papilla structures with age and large individual differences at younger ages.

Conclusion

We found abnormal dermal papilla structures and differences in the dermal papilla structures between face and other body site. With these taken into consideration, we could precisely investigate the aging alteration of normal dermal papilla structures in the face.
A stearoyl‐acyl carrier protein desaturase, NbSACPD‐C, is critical for ovule development in Nicotiana benthamiana
Authors: Zhang Jiantao , Li Jianhui , Garcia‐Ruiz Hernan , Bates Philip D. , Mirkov Theodore Erik , Wang Xiaofeng
Published: August 2014

Stearoyl‐acyl carrier protein desaturase (SACPD) activity is essential for production of the major unsaturated fatty acids (UFAs) in plant lipids. We report here the characterization of three SACPD genes from Nicotiana benthamiana, NbSACPD‐A, ‐B, and ‐C. All three genes share high similarity to AtSSI2/FAB2 (Suppressor of Salicylic acid‐Insensitivity2/Fatty Acid Biosynthesis2), the primary SACPD isoform in Arabidopsis. Knocking down the expression of individual or combinations of NbSACPDs by an artificial microRNA approach resulted in significantly reduced accumulation of 18C UFAs and elevated levels of 18:0‐FA (Fatty acids) in leaves, indicating that all three genes participated in fatty acid desaturation. The triple knockdown (KD) plants displayed severe growth phenotypes, including spontaneous cell death and dwarfing. While no vegetative morphologic abnormality was observed in NbSACPD‐A, ‐B, or ‐C KD plants, strikingly, NbSACPD‐C KD plants produced small fruits with aborted ovules. Reciprocal crosses with wild‐type and NbSACPD‐C KD plants revealed that knocking down NbSACPD‐C expression caused female, but not male, sterility. Furthermore, arrested ovule development and significantly altered lipid composition in ovaries were observed in NbSACPD‐C KD plants, consistent with the predominant NbSACPD‐C expression in ovules. The ovule development defect was fully complemented by coexpressing an amiRNA‐resistant NbSACPD‐C variant in the NbSACPD‐C KD background, further supporting a specific requirement for NbSACPD‐C in female fertility. Our results thus indicated that NbSACPD‐C plays a critical role maintaining membrane lipid composition in ovule development for female fertility in N. benthamiana, complementing and extending prior understanding on the well‐demonstrated roles of SACPDs in biotic and abiotic stresses.
Arabidopsis inositol pentakisphosphate 2‐kinase, AtIPK1, is required for growth and modulates phosphate homeostasis at the transcriptional level
Authors: Kuo Hui‐Fen , Chang Tzu‐Yun , Chiang Su‐Fen , Wang Wei‐Di , Charng Yee‐yung , Chiou Tzyy‐Jen
Published: August 2014

Inositol hexakisphosphate (IP6) provides a phosphorous reservoir in plant seeds; in addition, along with its biosynthesis intermediates and derivatives, IP6 also plays important roles in diverse developmental and physiological processes. Disruption of the Arabidopsis inositol pentakisphosphate 2‐kinase coding gene AtIPK1 was previously shown to reduce IP6 content in vegetative tissues and affect phosphate (Pi) sensing. Here we show that AtIPK1 is required for sustaining plant growth, as null mutants are non‐viable. An incomplete loss‐of‐function mutant, atipk1‐1, exhibited disturbed Pi homeostasis and overaccumulated Pi as a consequence of increased Pi uptake activity and root‐to‐shoot Pi translocation. The atipk1‐1 mutants also showed a Pi deficiency‐like root system architecture with reduced primary root and enhanced lateral root growth. Transcriptome analysis indicated that a subset of Pi starvation‐responsive genes was transcriptionally perturbed in the atipk1‐1 mutants and the expression of multiple genes involved in Pi uptake, allocation, and remobilization was increased. Genetic and transcriptional analyses suggest that disturbance of Pi homeostasis caused by atipk1 mutation involved components in addition to PHR1(‐like) transcription factors. Notably, the transcriptional increase of a number of Pi starvation‐responsive genes in the atipk1‐1 mutants is correlated with the reduction of histone variant H2A.Z occupation in chromatin. The myo‐inositol‐1‐phosphate synthase mutants, atmips1 and atmips2 with comparable reduction in vegetative IP6 to that in the atipk1‐1 mutants did not overaccumulate Pi, suggesting that Pi homeostasis modulated by AtIPK1 is not solely attributable to IP6 level. This study reveals that AtIPK1 has important roles in growth and Pi homeostasis.
Arhodomonas sp. Strain Seminole and Its Genetic Potential To Degrade Aromatic Compounds under High-Salinity Conditions
Authors: Dalvi Sonal , Nicholson Carla , Najar Fares , Roe Bruce A. , Canaan Patricia , Hartson Steven D. , Fathepure Babu Z.
Published: August 2014

Arhodomonas
sp. strain Seminole was isolated from a crude oil-impacted brine soil and shown to degrade benzene, toluene, phenol, 4-hydroxybenzoic acid (4-HBA), protocatechuic acid (PCA), and phenylacetic acid (PAA) as the sole sources of carbon at high salinity. Seminole is a member of the genus
Arhodomonas
in the class
Gammaproteobacteria
, sharing 96% 16S rRNA gene sequence similarity with
Arhodomonas aquaeolei
HA-1. Analysis of the genome predicted a number of catabolic genes for the metabolism of benzene, toluene, 4-HBA, and PAA. The predicted pathways were corroborated by identification of enzymes present in the cytosolic proteomes of cells grown on aromatic compounds using liquid chromatography-mass spectrometry. Genome analysis predicted a cluster of 19 genes necessary for the breakdown of benzene or toluene to acetyl coenzyme A (acetyl-CoA) and pyruvate. Of these, 12 enzymes were identified in the proteome of toluene-grown cells compared to lactate-grown cells. Genomic analysis predicted 11 genes required for 4-HBA degradation to form the tricarboxylic acid (TCA) cycle intermediates. Of these, proteomic analysis of 4-HBA-grown cells identified 6 key enzymes involved in the 4-HBA degradation pathway. Similarly, 15 genes needed for the degradation of PAA to the TCA cycle intermediates were predicted. Of these, 9 enzymes of the PAA degradation pathway were identified only in PAA-grown cells and not in lactate-grown cells. Overall, we were able to reconstruct catabolic steps for the breakdown of a variety of aromatic compounds in an extreme halophile, strain Seminole. Such knowledge is important for understanding the role of
Arhodomonas
spp. in the natural attenuation of hydrocarbon-impacted hypersaline environments.
Combined Use of Bacteriophage K and a Novel Bacteriophage To Reduce Staphylococcus aureus Biofilm Formation
Authors: Alves D. R. , Gaudion A. , Bean J. E. , Perez Esteban P. , Arnot T. C. , Harper D. R. , Kot W. , Hansen L. H. , Enright M. C. , Jenkins A. Tobias A.
Published: August 2014

Biofilms are major causes of impairment of wound healing and patient morbidity. One of the most common and aggressive wound pathogens isStaphylococcus aureus, displaying a large repertoire of virulence factors and commonly reduced susceptibility to antibiotics, such as the spread of methicillin-resistantS. aureus(MRSA). Bacteriophages are obligate parasites of bacteria. They multiply intracellularly and lyse their bacterial host, releasing their progeny. We isolated a novel phage, DRA88, which has a broad host range amongS. aureusbacteria. Morphologically, the phage belongs to theMyoviridaefamily and comprises a large double-stranded DNA (dsDNA) genome of 141,907 bp. DRA88 was mixed with phage K to produce a high-titer mixture that showed strong lytic activity against a wide range ofS. aureusisolates, including representatives of the major international MRSA clones and coagulase-negativeStaphylococcus. Its efficacy was assessed both in planktonic cultures and when treating established biofilms produced by three different biofilm-producingS. aureusisolates. A significant reduction of biofilm biomass over 48 h of treatment was recorded in all cases. The phage mixture may form the basis of an effective treatment for infections caused byS. aureusbiofilms.
Collagen-Like Glycoprotein BclS Is Involved in the Formation of Filamentous Structures of the Lysinibacillus sphaericus Exosporium
Authors: Zhao Ni , Ge Yong , Shi Tingyu , Hu Xiaomin , Yuan Zhiming
Published: August 2014

Lysinibacillus sphaericus
produces mosquitocidal binary toxins (Bin toxins) deposited within a balloon-like exosporium during sporulation. Unlike
Bacillus cereus
group strains, the exosporium of
L. sphaericus
is usually devoid of the hair-like nap, an external filamentous structure formed by a collagen-like protein, BclA. In this study, a new collagen-like exosporium protein encoded by Bsph_0411 (BclS) from
L. sphaericus
C3-41 was characterized. Thin-section electron microscopy revealed that deletion of
bclS
resulted in the loss of the filamentous structures that attach to the exosporium basal layer and spread through the interspace of spores.
In vivo
visualization of BclS-green fluorescent protein (GFP)/mCherry fusion proteins revealed a dynamic pattern of fluorescence that encased the spore from the mother cell-distal (MCD) pole of the forespore, and the BclS-GFP fusions were found to be located in the interspace of the spore, as confirmed by three-dimensional (3D) superresolution fluorescence microscopy. Further studies demonstrated that the
bclS
mutant spores were more sensitive to wet-heat treatment and germinated at a lower rate than wild-type spores and that these phenotypes were significantly restored in the
bclS
-complemented strain. These results suggested novel roles of collagen-like protein in exosporium assembly and spore germination, providing a hint for a further understanding of the genetic basis of the high level of persistence of Bin toxins in nature.
Erythrocyte Lysis and Xenopus laevis Oocyte Rupture by Recombinant Plasmodium falciparum Hemolysin III
Authors: Moonah Shannon , Sanders Natalie G. , Persichetti Jason K. , Sullivan David J.
Published: August 2014

Malaria kills more than 1 million people per year worldwide, with severe malaria anemia accounting for the majority of the deaths. Malaria anemia is multifactorial in etiology, including infected erythrocyte destruction and decrease in erythrocyte production, as well as destruction or clearance of noninfected erythrocytes. We identified a panspecies
Plasmodium
hemolysin type III related to bacterial hemolysins. The identification of a hemolysin III homologue in
Plasmodium
suggests a potential role in host erythrocyte lysis. Here, we report the first characterization of
Plasmodium falciparum
hemolysin III, showing that the soluble recombinant
P. falciparum
hemolysin III is a pore-forming protein capable of lysing human erythrocytes in a dose-, time-, and temperature-dependent fashion. The recombinant
P. falciparum
hemolysin III-induced hemolysis was partially inhibited by glibenclamide, a known channel antagonist. Studies with polyethylene glycol molecules of different molecular weights indicated a pore size of approximately 3.2 nm. Heterologous expression of recombinant
P. falciparum
hemolysin III in
Xenopus
oocytes demonstrated early hypotonic lysis similar to that of the pore-forming aquaporin control. Live fluorescence microscopy localized transfected recombinant green fluorescent protein (GFP)-tagged
P. falciparum
hemolysin III to the essential digestive vacuole of the
P. falciparum
parasite. These transfected trophozoites also possessed a swollen digestive vacuole phenotype. Native
Plasmodium
hemolysin III in the digestive vacuole may contribute to lysis of the parasitophorous vacuole membrane derived from the host erythrocyte. After merozoite egress from infected erythrocytes, remnant
P. falciparum
hemolysin III released from digestive vacuoles could potentially contribute to lysis of uninfected erythrocytes to contribute to severe life-threatening anemia.
Factors that are associated with the risk of acquiringPlasmodium knowlesimalaria in Sabah, Malaysia: a case-control study protocol
Authors: Grigg M J , William T , Drakeley C J , Jelip J , von Seidlein L , Barber B E , Fornace K M , Anstey N M , Yeo T W , Cox J
Published: August 2014

Introduction

Plasmodium knowlesihas long been present in Malaysia, and is now an emerging cause of zoonotic human malaria. Cases have been confirmed throughout South-East Asia where the ranges of its natural macaque hosts andAnopheles leucosphyrusgroup vectors overlap. The majority of cases are from Eastern Malaysia, with increasing total public health notifications despite a concurrent reduction inPlasmodium falciparumandP. vivaxmalaria. The public health implications are concerning givenP. knowlesihas the highest risk of severe and fatal disease of allPlasmodiumspp in Malaysia. Current patterns of risk and disease vary based on vector type and competence, with individual exposure risks related to forest and forest-edge activities still poorly defined. Clustering of cases has not yet been systematically evaluated despite reports of peri-domestic transmission and known vector competence for human-to-human transmission.

Methods and analysis

A population-based case–control study will be conducted over a 2-year period at two adjacent districts in north-west Sabah, Malaysia. Confirmed malaria cases presenting to the district hospital sites meeting relevant inclusion criteria will be requested to enrol. Three community controls matched to the same village as the case will be selected randomly. Study procedures will include blood sampling and administration of household and individual questionnaires to evaluate potential exposure risks associated with acquisition ofP. knowlesimalaria. Secondary outcomes will include differences in exposure variables betweenP. knowlesiand otherPlasmodiumspp, risk of severeP. knowlesimalaria, and evaluation ofP. knowlesicase clustering. Primary analysis will be per protocol, with adjusted ORs for exposure risks between cases and controls calculated using conditional multiple logistic regression models.

Ethics

This study has been approved by the human research ethics committees of Malaysia, the Menzies School of Health Research, Australia, and the London School of Hygiene and Tropical Medicine, UK.
Official lay basic life support courses in Germany: is delivered content up to date with the guidelines? An observational study
Authors: Wagner Patrick , Lingemann Christian , Arntz Hans-Richard , Breckwoldt Jan
Published: August 2014

Background and objectives

Educating the lay public in basic life support (BLS) is a cornerstone to improving bystander cardiopulmonary resuscitation (CPR) rates. In Germany, the official rescue organisations deliver accredited courses based on International Liaison Committee on Resuscitation (ILCOR) guidelines to up to 1 million participants every year. However, it is unknown how these courses are delivered in reality. We hypothesised that delivered content might not follow the proposed curriculum, and miss recent guideline updates.

Methods

We analysed 20 official lay BLS courses of 240 min (which in Germany are always embedded into either a 1-day or a 2-day first aid course). One expert rated all courses as a participating observer, remaining incognito throughout the course. Teaching times for specific BLS elements were recorded on a standardised checklist. Quality of content was rated by 5-point Likert scales, ranging from −2 (not mentioned) to +2 (well explained).

Results

Median total course time was 101 min (range 48–138) for BLS courses if part of a 1-day first aid course, and 123 min (53–244) if part of a 2-day course. Median teaching time for CPR was 51 min (range 20–70) and 60 min (16–138), respectively. Teaching times for recovery position were 44 min (range 24–66) and 55 min (24–114). Quality of content was rated worst for ‘agonal gasping’ (−1.35) and ‘minimising chest compression interruptions’ (−1.70).

Conclusions

Observed lay BLS courses lasted only half of the assigned curricular time. Substantial teaching time was spent on non-evidence-based interventions (eg, recovery position), and several important elements of BLS were not included. The findings call for curriculum revision, improved instructor training and systematic quality management.
A theoretical investigation of the S2+ cation in the gas phase
Authors: Yu Wei , Zhu Zunlue , Cheng Chuncai , Shi Deheng
Published: August 2014

The potential energy curves (PECs) of 18 lowest energy Λ-S states of the S2+ cation have been calculated using the complete active space self-consistent field method followed by the internally contracted multireference configuration interaction approach with the Davidson modification. When spin−orbit coupling is computed using the Breit−Pauli Hamiltonian with the cc-pCVTZ basis set, the 18 Λ-S states split into 56 Ω components. To improve the quality of the PECs, core−valence correlation and scalar relativistic corrections are included. All PECs are extrapolated to the complete basis set limit. Based on the PECs obtained by the icMRCI+CV+DK+Q/(CBS-56) calculations, the spectroscopic parameters of 17 Λ-S bound states and 50 Ω bound states are obtained. The transitions (including the Franck−Condon factors and radiative lifetimes) from two low-lying states to the ground state are calculated for several low vibrational levels. Analyses show that the spectroscopic parameters reported here can be expected to be reliably predicted.
Protein Sorting at thetrans-Golgi Network
Authors: Guo Yusong , Sirkis Daniel W. , Schekman Randy
Published: August 2014

The trans-Golgi network (TGN) is an important cargo sorting station within the cell where newly synthesized proteins are packaged into distinct transport carriers that are targeted to various destinations. To maintain the fidelity of protein transport, elaborate protein sorting machinery is employed to mediate sorting of specific cargo proteins into distinct transport carriers. Protein sorting requires assembly of the cytosolic sorting machinery onto the TGN membrane and capture of cargo proteins. We review the cytosolic and transmembrane sorting machinery that function at the TGN and describe molecular interactions and regulatory mechanisms that enable accurate protein sorting. In addition, we highlight the importance of TGN sorting in physiology and disease.
Regulated Cell Death: Signaling and Mechanisms
Authors: Ashkenazi Avi , Salvesen Guy
Published: August 2014

Cell turnover is a fundamental feature in metazoans. Cells can die passively, as a consequence of severe damage to their structural integrity, or actively, owing to a more confined biological disruption such as DNA damage. Passive cell death is uncontrolled and often harmful to the organism. In contrast, active cell death is tightly regulated and serves to support the organism's life. Apoptosis—the primary form of regulated cell death—is relatively well defined. Necroptosis—an alternative, distinct kind of regulated cell death discovered more recently—is less well understood. Apoptosis and necroptosis can be triggered either from within the cell or by extracellular stimuli. Certain signaling components, including several death ligands and receptors, can regulate both processes. Whereas apoptosis is triggered and executed via intracellular proteases called caspases, necroptosis is suppressed by caspase activity. Here we highlight current understanding of the key signaling mechanisms that control regulated cell death.
Determinants and Functions of Mitochondrial Behavior
Authors: Labbé Katherine , Murley Andrew , Nunnari Jodi
Published: August 2014

Mitochondria are ancient organelles evolved from bacteria. Over the course of evolution, the behavior of mitochondria inside eukaryotic cells has changed dramatically, and the corresponding machineries that control it are in most cases new inventions. The evolution of mitochondrial behavior reflects the necessity to create a dynamic compartment to integrate the myriad mitochondrial functions with the status of other endomembrane compartments, such as the endoplasmic reticulum, and with signaling pathways that monitor cellular homeostasis and respond to stress. Here we review what has been discovered about the molecular machineries that work together to control the collective behavior of mitochondria in cells, as well as their physiological roles in healthy and disease states.
Biogenesis, Secretion, and Intercellular Interactions of Exosomes and Other Extracellular Vesicles
Authors: Colombo Marina , Raposo Graça , Théry Clotilde
Published: August 2014

In the 1980s, exosomes were described as vesicles of endosomal origin secreted from reticulocytes. Interest increased around these extracellular vesicles, as they appeared to participate in several cellular processes. Exosomes bear proteins, lipids, and RNAs, mediating intercellular communication between different cell types in the body, and thus affecting normal and pathological conditions. Only recently, scientists acknowledged the difficulty of separating exosomes from other types of extracellular vesicles, which precludes a clear attribution of a particular function to the different types of secreted vesicles. To shed light into this complex but expanding field of science, this review focuses on the definition of exosomes and other secreted extracellular vesicles. Their biogenesis, their secretion, and their subsequent fate are discussed, as their functions rely on these important processes.
Modeling the Rheology of Polymer Melts and Solutions
Authors: Larson R.G. , Desai Priyanka S.
Published: August 2014

We review constitutive modeling of solutions and melts of linear polymers, focusing on changes in rheological behavior in shear and extensional flow as the concentration increases from unentangled dilute, to entangled, to dense melt. The rheological changes are captured by constitutive equations, prototypes of which are the FENE-P model for unentangled solutions and the DEMG model for entangled solutions and melts. From these equations, and supporting experimental data, for dilute solutions, the extensional viscosity increases with the strain rate from the low–strain rate to the high–strain rate asymptote, but in the densely entangled state, the high–strain rate viscosity is lower than the low–shear rate value, especially when orientation-dependent friction is accounted for. In shearing flow, shear thinning increases dramatically as the entanglement density increases, which can eventually lead to a shear-banding inhomogeneity. Recent improvements in constitutive modeling are paving the way for robust and accurate numerical simulations of polymer fluid mechanics and industrial processing of polymers.
Liquid Transfer in Printing Processes: Liquid Bridges with Moving Contact Lines
Authors: Kumar Satish
Published: August 2014

High-speed printing processes are a leading technology for the large-scale manufacture of a new generation of nanoscale and microscale devices. Central to all printing processes is the transfer of liquid from one surface to another, a seemingly simple operation that is still not well understood. A useful idealization of liquid transfer is a liquid bridge with moving contact lines being deformed between two separating surfaces. The fluid mechanics of such bridges are relevant not only to printing, but also to other important applications, such as adhesion, tribology, biology, oil recovery, and microfluidics.
pENCODE: A Plant Encyclopedia of DNA Elements
Authors: Lane Amanda K. , Niederhuth Chad E. , Ji Lexiang , Schmitz Robert J.
Published: August 2014

ENCODE projects exist for many eukaryotes, including humans, but as of yet no defined project exists for plants. A plant ENCODE would be invaluable to the research community and could be more readily produced than its metazoan equivalents by capitalizing on the preexisting infrastructure provided from similar projects. Collecting and normalizing plant epigenomic data for a range of species will facilitate hypothesis generation, cross-species comparisons, annotation of genomes, and an understanding of epigenomic functions throughout plant evolution. Here, we discuss the need for such a project, outline the challenges it faces, and suggest ways forward to build a plant ENCODE.
In Praise of Tents: Regulatory Studies and Transformative Social Science
Authors: Braithwaite John
Published: August 2014

What are the virtues of institutions we take for granted—universities, the study of the social sciences and humanities, and scholarship on professions such as law? What are the vices of the disciplinary structure of the social sciences, even in the law and society movement and criminology that started as interdisciplinary projects? Research on regulation within an interdisciplinary structure, the Regulatory Institutions Network, is used to illustrate the difficulties of attempts to change direction in the social sciences. The article advocates the creative destruction of disciplinary structures by organizing in tents that study institutionalization (rather than buildings that study categories of institutions). To keep pace with social change, pulling tents down and endlessly pegging out new ones is a path forward. A politics of defending universities and opposing the disciplines that have captured them does not mean advocacy of restructuring. If more interesting work issues from poorly funded tents than from disciplinary edifices, reformers can advance creative destruction.
Bilingualism, Mind, and Brain
Authors: Kroll Judith F. , Dussias Paola E. , Bice Kinsey , Perrotti Lauren
Published: August 2014

The use of two or more languages is common in most of the world. Yet, until recently, bilingualism was considered to be a complicating factor for language processing, cognition, and the brain. The past 20 years have witnessed an upsurge of research on bilingualism to examine language acquisition and processing, their cognitive and neural bases, and the consequences that bilingualism holds for cognition and the brain over the life span. Contrary to the view that bilingualism complicates the language system, this new research demonstrates that all of the languages that are known and used become part of the same language system. The interactions that arise when two languages are in play have consequences for the mind and the brain and, indeed, for language processing itself, but those consequences are not additive. Thus, bilingualism helps reveal the fundamental architecture and mechanisms of language processing that are otherwise hidden in monolingual speakers.
Sign Language Typology: The Contribution of Rural Sign Languages
Authors: de Vos Connie , Pfau Roland
Published: August 2014

Since the 1990s, the field of sign language typology has shown that sign languages exhibit typological variation at all relevant levels of linguistic description. These initial typological comparisons were heavily skewed toward the urban sign languages of developed countries, mostly in the Western world. This review reports on the recent contributions made by rural signing varieties, that is, sign languages that have evolved in village communities, often in developing countries, due to a high incidence of deafness. With respect to a number of structural properties, rural sign languages fit into previously established typological classifications. However, they also exhibit unique and typologically marked features that challenge received views on possible sign languages. At the same time, the shared features of geographically dispersed rural signing varieties provide a unique window into the social dynamics that may shape the structures of modern human languages.