bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of GWAS‐linked loci with late‐onset Alzheimer's disease in a northern Han Chinese population
Authors: Tan Lan , Yu Jin‐Tai , Zhang Wei , Wu Zhong‐Chen , Zhang Qun , Liu Qiu‐Yan , Wang Wei , Wang Hui‐Fu , Ma Xiao‐Ying , Cui Wei‐Zhen 
Published: December 2012

AbstractObjectiveFive genomewide association studies (GWAS) in white populations have recently identified and confirmed 9 novel Alzheimer's disease (AD) susceptibility loci (CLU, CR1, PICALM, BIN1, ABCA7, MS4A gene cluster, CD2AP, CD33, and EPHA1). These studies have been conducted almost exclusively in white populations and it is unclear whether these observations generalize to populations with different ethnicities.MethodsWe recruited 1224 unrelated northern Han Chinese subjects comprising 612 patients with a clinical diagnosis of late‐onset AD (LOAD) according to the criteria of the National Institute of Neurological and Communicative Diseases and Stroke/Alzheimer's Disease and Related Disorders Association and 612 healthy age‐ and sex‐matched control subjects. Because of our previous study investigating CLU, CR1, and PICALM in the Han population, we limited the current analysis to BIN1, ABCA7, MS4A gene cluster, CD2AP, CD33, and EPHA1.ResultsIn a multivariate analysis, associations of MS4A6A (rs610932; odds ratio = 0.632, Bonferroni corrected P = .019) and CD33 (rs3865444; odds ratio = 1.492, Bonferroni corrected P = .017) with LOAD were replicated successfully. When these data were stratified by apolipoprotein E (APOE) ε4 status, both rs610932 and rs610932 were evident only among subjects without the APOE ε4 allele. For BIN1, assuming a dominant model of inheritance, a positive association for rs7561528 in APOE ε4 carriers was observed. This association, however, did not remain significant after Bonferroni correction. As for ABCA7, CD2AP, and EPHA1 single nucleotide polymorphisms from recent GWAS, despite the similar directional effects, no significant differences in genotype and estimated allele frequency distribution between patients and control subjects were observed.ConclusionsThis study provides the first independent evidence that MS4A and CD33 loci are associated with the risk of LOAD in northern Han Chinese population. Genotypes at the two loci confer risk predominantly in APOE ε4‐negative subjects.
Polypharmacy in nursing home residents with severe cognitive impairment: Results from the SHELTER Study
Authors: Vetrano Davide L. , Tosato Matteo , Colloca Giuseppe , Topinkova Eva , Fialova Daniela , Gindin Jacob , van der Roest Henriëtte G. , Landi Francesco , Liperoti Rosa , Bernabei Roberto , Onder Graziano ,   SHELTER Study
Published: December 2012

AbstractObjectivePharmacological treatment of older adults with cognitive impairment represents a challenge for prescribing physicians, and polypharmacy is common in these complex patients. The aim of the current study is to assess prevalence and factors related to polypharmacy in a sample of nursing home (nursing home) residents with advanced cognitive impairment.MethodsWe conducted a cross‐sectional analysis of 1449 nursing home residents with advanced cognitive impairment participating to the Services and Health for Elderly in Long Term Care (SHELTER) project, a study collecting information on residents admitted to 57 nursing home in eight countries. Data were collected using the International Resident Assessment Instrument (InterRAI) for long‐term care facilities. Polypharmacy status was categorized into three groups: nonpolypharmacy (zero to four drugs), polypharmacy (five to nine drugs), and excessive polypharmacy (≥10 drugs).ResultsPolypharmacy was observed in 735 residents (50.7%) and excessive polypharmacy was seen in 245 (16.9%). Compared with nonpolypharmacy, excessive polypharmacy was associated directly with ischemic heart disease (odds ratio [OR], 3.68; 95% confidence interval [CI], 2.01–6.74), diabetes mellitus (OR, 2.66; 95% CI; 1.46–4.84), Parkinson's disease (OR, 2.84; 95% CI, 1.36–5.85), gastrointestinal symptoms (OR, 1.20; 95% CI, 1.43–3.39), pain (OR, 3.12; 95% CI, 1.99–4.89), dyspnea (OR, 2.57; 95% CI, 1.31–5.07), and recent hospitalization (OR, 2.56; 95% CI, 1.36–5.85). An inverse relation with excessive polypharmacy was shown for age (OR, 0.74; 95% CI, 0.59–0.93), activities of daily living disability (OR, 0.79; 95% CI, 0.63–0.99) and presence of a geriatrician on the nursing home staff (OR, 0.36; 95% CI, 0.20–0.64).ConclusionPolypharmacy and excessive polypharmacy are common among nursing home residents with advanced cognitive impairment. Determinants of polypharmacy status includes not only comorbidities, but also specific symptoms, age, and functional status. A geriatrician in the facility is associated with lower prevalence of excessive polypharmacy.
Deep Hooking and Angling Success When Passively and Actively Fishing for Stream-Dwelling Trout with Baited J and Circle Hooks
Authors: Sullivan Christopher L. , Meyer Kevin A. , Schill Daniel J. 
Published: December 2012

Abstract
Circle hooks are becoming commonplace in recreational fisheries because they often reduce deep hooking, but there has been little evaluation of their effectiveness in trout fisheries. To compare the occurrence of deep hooking and angling success rates for stream-dwelling trout, we used three baited hook types (i.e., inline circle hooks, inline J hooks, and 4°-offset J hooks) fished with two angling methods (i.e., active fishing, using a traditional bait fishing hook set; and passive fishing, with no sharp hook set). Of the 583 wild trout caught by anglers, 20% were deep hooked. The deep hooking rate varied by hook type and angling method, but the interaction term hook type × angling method was statistically significant, indicating that the effect of hook type could not be interpreted separately from fishing method. Accordingly, the occurrence of deep hooking was significantly greater for offset J hooks fished passively (28 ± 9% [95% CI about the mean]) and inline J hooks fished actively (27 ± 9%) than for offset J hooks fished actively (9 ± 6%) and inline circle hooks fished actively (10 ± 6%). Fish length affected deep-hooking rates, such that trout smaller than 250 mm were less likely to be deeply hooked than trout 250–350 mm in length. Hooking success (i.e., successful hook-ups divided by strikes) was greatest for actively fished inline J hooks (75 ± 7%), lowest for passively fished inline circle hooks (45 ± 6%) and passively fished offset J hooks (48 ± 8%), and always greater for actively fished hooks than for passively fished hooks of the same type. We found deep hooking was nearly twice as likely for inline circle hooks when fished according to manufacturers’ recommendations (i.e., passively) than when fished actively. These results and those of others suggest that fishing circle hooks actively when bait fishing for stream-dwelling trout will result in less deep hooking than fishing circle hooks passively.
Received May 25, 2012; accepted September 17, 2012
Evaluation of Hydrolyzed Poultry Feathers as a Dietary Ingredient for Pond-Raised Channel Catfish
Authors: Li Menghe H , Robinson Edwin H , Bosworth Brian G , Oberle Daniel F , Lucas Penelope M 
Published: December 2012

Abstract
The present study examined the use of hydrolyzed poultry feathers (HPF) as a replacement for soybean meal in diets for pond raised Channel Catfish Ictalurus punctatus. Four isonitrogenous (28% crude protein) diets were evaluated that contained 0, 5, 10, or 15% HPF. Fingerling Channel Catfish (mean ± SD initial weight was 47.5 ± 2.2 g) were stocked into twenty 0.04-ha earthen ponds at a rate of 14,830 fish/ha. Fish were fed once daily to apparent satiation for 140 d. No significant differences were observed for weight gain, feed conversion ratio (FCR), and survival among fish fed various levels of HPF. There were also no significant differences in net yield of fish fed diets containing 0, 5, and 10% HPF, but net yield of fish fed a diet containing 15% HPF was significantly lower than that of fish fed the control diet. Fish on diets containing 5% HPF and above were fed significantly less feed than fish fed the control diet. Regression analysis showed that total amount of diet fed, net yield, and weight gain decreased linearly as dietary HPF levels increased. Based on weight gain and net yield data, 5% HPF with supplemental lysine may be used in Channel Catfish diets without marked impact on fish growth performance. However, carcass and fillet yield were significantly reduced in fish fed diets containing 5% HPF and higher. Fillet protein generally decreased and fillet fat increased with increasing dietary HPF levels.
Sulfite Reductase Protects Plants against Sulfite Toxicity
Authors: Yarmolinsky Dmitry , Brychkova Galina , Fluhr Robert , Sagi Moshe 
Published: December 2012

Abstract
Plant sulfite reductase (SiR; Enzyme Commission 1.8.7.1) catalyzes the reduction of sulfite to sulfide in the reductive sulfate assimilation pathway. Comparison of SiR expression in tomato (Solanum lycopersicum ‘Rheinlands Ruhm’) and Arabidopsis (Arabidopsis thaliana) plants revealed that SiR is expressed in a different tissue-dependent manner that likely reflects dissimilarity in sulfur metabolism between the plant species. Using Arabidopsis and tomato SiR mutants with modified SiR expression, we show here that resistance to ectopically applied sulfur dioxide/sulfite is a function of SiR expression levels and that plants with reduced SiR expression exhibit higher sensitivity than the wild type, as manifested in pronounced leaf necrosis and chlorophyll bleaching. The sulfite-sensitive mutants accumulate applied sulfite and show a decline in glutathione levels. In contrast, mutants that overexpress SiR are more tolerant to sulfite toxicity, exhibiting little or no damage. Resistance to high sulfite application is manifested by fast sulfite disappearance and an increase in glutathione levels. The notion that SiR plays a role in the protection of plants against sulfite is supported by the rapid up-regulation of SiR transcript and activity within 30 min of sulfite injection into Arabidopsis and tomato leaves. Peroxisomal sulfite oxidase transcripts and activity levels are likewise promoted by sulfite application as compared with water injection controls. These results indicate that, in addition to participating in the sulfate assimilation reductive pathway, SiR also plays a role in protecting leaves against the toxicity of sulfite accumulation.
A Triple Helix-Loop-Helix/Basic Helix-Loop-Helix Cascade Controls Cell Elongation Downstream of Multiple Hormonal and Environmental Signaling Pathways inArabidopsis
Authors: Bai Ming-Yi , Fan Min , Oh Eunkyoo , Wang Zhi-Yong 
Published: December 2012

AbstractEnvironmental and endogenous signals, including light, temperature, brassinosteroid (BR), and gibberellin (GA), regulate cell elongation largely by influencing the expression of the paclobutrazol-resistant (PRE) family helix-loop-helix (HLH) factors, which promote cell elongation by interacting antagonistically with another HLH factor, IBH1. However, the molecular mechanism by which PREs and IBH1 regulate gene expression has remained unknown. Here, we show that IBH1 interacts with and inhibits a DNA binding basic helix-loop-helix (bHLH) protein, HBI1, in Arabidopsis thaliana. Overexpression of HBI1 increased hypocotyl and petiole elongation, whereas dominant inactivation of HBI1 and its homologs caused a dwarf phenotype, indicating that HBI1 is a positive regulator of cell elongation. In vitro and in vivo experiments showed that HBI1 directly bound to the promoters and activated two EXPANSIN genes encoding cell wall–loosening enzymes; HBI1's DNA binding and transcriptional activities were inhibited by IBH1, but the inhibitory effects of IBH1 were abolished by PRE1. The results indicate that PREs activate the DNA binding bHLH factor HBI1 by sequestering its inhibitor IBH1. Altering each of the three factors affected plant sensitivities to BR, GA, temperature, and light. Our study demonstrates that PREs, IBH1, and HBI1 form a chain of antagonistic switches that regulates cell elongation downstream of multiple external and endogenous signals.
Comparative Quantitative Analysis of Gene Expression Profiles of Glycoside Hydrolase Family 10 Xylanases in the Sheep Rumen during a Feeding Cycle
Authors: Li Zhongyuan , Zhao Heng , Yang Peilong , Zhao Junqi , Huang Huoqing , Xue Xianli , Zhang Xinshang , Diao Qiyu , Yao Bin 
Published: December 2012

ABSTRACT
Xylanase is a crucial hydrolytic enzyme that degrades plant polysaccharides in the rumen. To date, there is no information on the genetic composition and expression characteristics of ruminal xylanase during feeding cycles of ruminants. Here, the major xylanase of the glycoside hydrolase family 10 (GH 10) from the rumen of small-tail Han sheep was investigated during a feeding cycle. We identified 44 distinct GH 10 xylanase gene fragments at both the genomic and transcriptional levels. Comparison of their relative abundance showed that results from the evaluation of functional genes at the transcriptional level are more reliable indicators for understanding fluctuations in xylanase levels. The expression patterns of six xylanase genes, detected at all time points of the feeding cycle, were investigated; we observed a complex trend of gene expression over 24 h, revealing the dynamic expression of xylanases in the rumen. Further correlation analysis indicated that the rumen is a dynamic ecosystem where the transcript profiles of xylanase genes are closely related to ruminal conditions, especially rumen pH and bacterial population. Given the huge diversity and changing composition of enzymes over the entire rumen, this research provides valuable information for understanding the role of functional genes in the digestion of plant material.
Evidence for Niche Partitioning Revealed by the Distribution of Sulfur Oxidation Genes Collected from Areas of a Terrestrial Sulfidic Spring with Differing Geochemical Conditions
Authors: Headd Brendan , Engel Annette Summers 
Published: December 2012

ABSTRACT

The diversity and phylogenetic significance of bacterial genes in the environment has been well studied, but comparatively little attention has been devoted to understanding the functional significance of different variations of the same metabolic gene that occur in the same environment. We analyzed the geographic distribution of 16S rRNA pyrosequences and
soxB
genes along a geochemical gradient in a terrestrial sulfidic spring to identify how different taxonomic variations of the
soxB
gene were naturally distributed within the spring outflow channel and to identify possible evidence for altered SoxB enzyme function in nature. Distinct compositional differences between bacteria that utilize their SoxB enzyme in the
Paracoccus
sulfide oxidation pathway (e.g.,
Bradyrhizobium
,
Paracoccus
, and
Rhodovulum
) and bacteria that utilize their SoxB enzyme in the branched pathway (e.g.,
Chlorobium
,
Thiothrix
,
Thiobacillus
,
Halothiobacillus
, and
Thiomonas
) were identified. Different variations of the
soxB
genes were present at different locations within the spring outflow channel in a manner that significantly corresponded to geochemical conditions. The distribution of the different
soxB
gene sequence variations suggests that the enzymes encoded by these genes are functionally different and could be optimized to specific geochemical conditions that define niche space for bacteria capable of oxidizing reduced sulfur compounds.
New Insights into Sulfur Metabolism in Yeasts as Revealed by Studies of Yarrowia lipolytica
Authors: Hébert Agnès , Forquin-Gomez Marie-Pierre , Roux Aurélie , Aubert Julie , Junot Christophe , Heilier Jean-François , Landaud Sophie , Bonnarme Pascal , Beckerich Jean-Marie 
Published: December 2012

ABSTRACT

Yarrowia lipolytica
, located at the frontier of hemiascomycetous yeasts and fungi, is an excellent candidate for studies of metabolism evolution. This yeast, widely recognized for its technological applications, in particular produces volatile sulfur compounds (VSCs) that fully contribute to the flavor of smear cheese. We report here a relevant global vision of sulfur metabolism in
Y. lipolytica
based on a comparison between high- and low-sulfur source supplies (sulfate, methionine, or cystine) by combined approaches (transcriptomics, metabolite profiling, and VSC analysis). The strongest repression of the sulfate assimilation pathway was observed in the case of high methionine supply, together with a large accumulation of sulfur intermediates. A high sulfate supply seems to provoke considerable cellular stress via sulfite production, resulting in a decrease of the availability of the glutathione pathway's sulfur intermediates. The most limited effect was observed for the cystine supply, suggesting that the intracellular cysteine level is more controlled than that of methionine and sulfate. Using a combination of metabolomic profiling and genetic experiments, we revealed taurine and hypotaurine metabolism in yeast for the first time. On the basis of a phylogenetic study, we then demonstrated that this pathway was lost by some of the hemiascomycetous yeasts during evolution.
Expression of
UME6
, a Key Regulator of Candida albicans Hyphal Development, Enhances Biofilm Formation via Hgc1- and Sun41-Dependent Mechanisms
Authors: Banerjee Mohua , Uppuluri Priya , Zhao Xiang R. , Carlisle Patricia L. , Vipulanandan Geethanjali , Villar Cristina C. , López-Ribot José L. , Kadosh David 
Published: December 2012

ABSTRACT

Biofilm formation is associated with the ability of
Candida albicans
, the major human fungal pathogen, to resist antifungal therapies and grow on tissues, catheters, and medical devices. In order to better understand the relationship between
C. albicans
morphology and biofilm formation, we examined biofilms generated in response to expression of
UME6
, a key filament-specific transcriptional regulator. As
UME6
levels rise,
C. albicans
cells are known to transition from yeast to hyphae, and we also observed a corresponding increase in the level of biofilm formation
in vitro
. In addition to forming a biofilm, we observed that a
C. albicans
strain expressing constitutive high levels of
UME6
promoted tissue invasion in a reconstituted human three-dimensional model of oropharyngeal candidiasis. Confocal microscopy indicated that both the top and bottom layers of the biofilm generated upon high-level constitutive
UME6
expression consist primarily of hyphal cells.
UME6
-driven biofilm formation was reduced upon deletion of Hgc1, a cyclin-related protein important for hyphal development, as well as Sun41, a putative cell wall glycosidase. Constitutive high-level
UME6
expression was also able to completely bypass both the filamentation and biofilm defects of a strain deleted for Efg1, a key transcriptional regulator of these processes. Finally, we show that both Sun41 and Efg1 affect the ability of
UME6
to induce certain filament-specific transcripts. Overall, these findings indicate a strong correlation between increased
C. albicans
hyphal growth and enhanced biofilm formation and also suggest functional relationships between
UME6
and other regulators of biofilm development.
The Zinc Cluster Protein Sut1 Contributes to Filamentation in Saccharomyces cerevisiae
Authors: Foster Helen A. , Cui Mingfei , Naveenathayalan Angel , Unden Heike , Schwanbeck Ralf , Höfken Thomas 
Published: December 2012

ABSTRACT

Sut1 is a transcriptional regulator of the Zn(II)
2
Cys
6
family in the budding yeast
Saccharomyces cerevisiae
. The only function that has been attributed to Sut1 is sterol uptake under anaerobic conditions. Here, we show that Sut1 is also expressed in the presence of oxygen, and we identify a novel function for Sut1.
SUT1
overexpression blocks filamentous growth, a response to nutrient limitation, in both haploid and diploid cells. This inhibition by Sut1 is independent of its function in sterol uptake. Sut1 downregulates the expression of
GAT2
,
HAP4
,
MGA1
,
MSN4
,
NCE102
,
PRR2
,
RHO3
, and
RHO5
. Several of these Sut1 targets (
GAT2
,
HAP4
,
MGA1
,
RHO3
, and
RHO5
) are essential for filamentation in haploids and/or diploids. Furthermore, the expression of the Sut1 target genes, with the exception of
MGA1
, is induced during filamentous growth. We also show that
SUT1
expression is autoregulated and inhibited by Ste12, a key transcriptional regulator of filamentation. We propose that Sut1 partially represses the expression of
GAT2
,
HAP4
,
MGA1
,
MSN4
,
NCE102
,
PRR2
,
RHO3
, and
RHO5
when nutrients are plentiful. Filamentation-inducing conditions relieve this repression by Sut1, and the increased expression of Sut1 targets triggers filamentous growth.
A Novel
dnaJ
Family Gene,
sflA
, Encodes an Inhibitor of Flagellation in Marine Vibrio Species
Authors: Kitaoka Maya , Nishigaki Takehiko , Ihara Kunio , Nishioka Noriko , Kojima Seiji , Homma Michio 
Published: December 2012

ABSTRACT

The marine bacterium
Vibrio alginolyticus
has a single polar flagellum. Formation of that flagellum is regulated positively and negatively by FlhF and by FlhG, respectively. The Δ
flhF
mutant makes no flagellum, whereas the Δ
flhFG
double-deletion mutant usually lacks a flagellum. However, the Δ
flhFG
mutant occasionally reverts to become motile by forming peritrichous flagella. We have isolated a suppressor pseudorevertant from the Δ
flhFG
strain (Δ
flhFG
-sup). The suppressor strain forms peritrichous flagella in the majority of cells. We identified candidate suppressor mutations by comparing the genome sequence of the parental strain, VIO5, with the genome sequences of the suppressor strains. Two mutations were mapped to a gene, named
sflA
(
s
uppressor of Δ

fl
hFG

), at the VEA003730 locus of the
Vibrio
sp. strain EX25 genome. This gene is specific for
Vibrio
species and is predicted to encode a transmembrane protein with a DnaJ domain. When the wild-type gene was introduced into the suppressor strain, motility was impaired. Introducing a mutant version of the
sflA
gene into the Δ
flhFG
strain conferred the suppressor phenotype. Thus, we conclude that loss of the
sflA
gene is responsible for the suppressor phenotype and that the wild-type SflA protein plays a role in preventing polar-type flagella from forming on the lateral cell wall.
Impact of errors in age estimates on the classification of proper child occupant restraint use: an observational survey
Authors: Nie Carrie , Colunga Isabel , McCoy Mary , Stephens-Stidham Shelli , Istre Gregory R 
Published: December 2012

BackgroundProper classification of child occupant restraint use is dependent on the age of the child occupant. Observations of vehicle restraint use involve estimating child age. If estimates of age are incorrect, then a potential for misclassification of restraint use exists.ObjectiveTo compare estimated and confirmed child occupant age and calculate the impact of errors in age estimates on the proportion of children classified as properly restrained.MethodsObservations of restraint use were completed for occupants 0–8 years of age at two health clinics. After initial observation, we approached the driver to confirm the child's age. Each child's restraint use was classified as either compliant or not compliant with state law, based on type of restraint used and based on the child's estimated and confirmed ages.ResultsClassification of age categories for child occupants (n=218) was correct in 86.3% of observations. For 48.6%, the confirmed and estimated age matched exactly, and for 98.1%, age matched within ±1 year. Overall, compliant restraint use based on estimated age was 39.4%, and based on confirmed age was 38.5%. In paired comparisons, restraint use based on estimated age versus confirmed age was concordant for more than 95% of children.ConclusionsThe level of accuracy for age estimates was sufficient for making estimates of compliant restraint use. Errors in estimated age resulted in a less than 1 percentage point difference in overall proper restraint use calculations. The results suggest that such observations can be a reliable measure of proper child occupant restraint use.