bluuebunny/crossref_metadata_2025_split huggingface dataset:
Studies of the extracytoplasmic function sigma factor PG0162 in Porphyromonas gingivalis
Authors: Dou Y. , Aruni W. , Muthiah A. , Roy F. , Wang C. , Fletcher H.M. 
Published: July 2015

SummaryPG0162, annotated as an extracytoplasmic function (ECF) sigma factor in Porphyromonas gingivalis, is composed of 193 amino acids. As previously reported, the PG0162‐deficient mutant, P. gingivalis FLL350 showed significant reduction in gingipain activity compared with the parental strain. Because this ECF sigma factor could be involved in the virulence regulation in P. gingivalis, its genetic properties were further characterized. A 5’‐RACE analysis showed that the start of transcription of the PG0162 gene occurred from a guanine (G) residue 69 nucleotides upstream of the ATG translation initiation codon. The function of PG0162 as a sigma factor was confirmed in a run‐off in vitro transcription assay using the purified rPG0162 and RNAP core enzyme from Escherichia coli with the PG0162 promoter as template. As an appropriate PG0162 inducing environmental signal is unknown, a strain overexpressing the PG0162 gene designated P. gingivalis FLL391 was created. Compared with the wild‐type strain, transcriptome analysis of P. gingivalis FLL391 showed that approximately 24% of the genome displayed altered gene expression (260 upregulated genes; 286 downregulated genes). Two other ECF sigma factors (PG0985 and PG1660) were upregulated more than two‐fold. The autoregulation of PG0162 was confirmed with the binding of the rPG0162 protein to the PG0162 promoter in electrophoretic mobility shift assay. In addition, the rPG0162 protein also showed the ability to bind to the promoter region of two genes (PG0521 and PG1167) that were most upregulated in P. gingivalis FLL391. Taken together, our data suggest that PG0162 is a sigma factor that may play an important role in the virulence regulatory network in P. gingivalis.
Enhanced resistance in Theobroma cacao against oomycete and fungal pathogens by secretion of phosphatidylinositol‐3‐phosphate‐binding proteins
Authors: Helliwell Emily E. , Vega‐Arreguín Julio , Shi Zi , Bailey Bryan , Xiao Shunyuan , Maximova Siela N. , Tyler Brett M. , Guiltinan Mark J. 
Published: July 2015

SummaryThe internalization of some oomycete and fungal pathogen effectors into host plant cells has been reported to be blocked by proteins that bind to the effectors' cell entry receptor, phosphatidylinositol‐3‐phosphate (PI3P). This finding suggested a novel strategy for disease control by engineering plants to secrete PI3P‐binding proteins. In this study, we tested this strategy using the chocolate tree Theobroma cacao. Transient expression and secretion of four different PI3P‐binding proteins in detached leaves of T. cacao greatly reduced infection by two oomycete pathogens, Phytophthora tropicalis and Phytophthora palmivora, which cause black pod disease. Lesion size and pathogen growth were reduced by up to 85%. Resistance was not conferred by proteins lacking a secretory leader, by proteins with mutations in their PI3P‐binding site, or by a secreted PI4P‐binding protein. Stably transformed, transgenic T. cacao plants expressing two different PI3P‐binding proteins showed substantially enhanced resistance to both P. tropicalis and P. palmivora, as well as to the fungal pathogen Colletotrichum theobromicola. These results demonstrate that secretion of PI3P‐binding proteins is an effective way to increase disease resistance in T. cacao, and potentially in other plants, against a broad spectrum of pathogens.
Transcriptional coordination of physiological responses in Nannochloropsis oceanicaCCMP1779 under light/dark cycles
Authors: Poliner Eric , Panchy Nicholas , Newton Linsey , Wu Guangxi , Lapinsky Andrew , Bullard Blair , Zienkiewicz Agnieszka , Benning Christoph , Shiu Shin‐Han , Farré Eva M. 
Published: July 2015

SummaryNannochloropsis oceanica CCMP1779 is a marine unicellular stramenopile and an emerging reference species for basic research on oleogenic microalgae with biotechnological relevance. We investigated its physiology and transcriptome under light/dark cycles. We observed oscillations in lipid content and a predominance of cell division in the first half of the dark phase. Globally, more than 60% of the genes cycled in N. oceanica CCMP1779, with gene expression peaking at different times of the day. Interestingly, the phase of expression of genes involved in certain biological processes was conserved across photosynthetic lineages. Furthermore, in agreement with our physiological studies we found the processes of lipid metabolism and cell division enriched in cycling genes. For example, there was tight coordination of genes involved in the lower part of glycolysis, fatty acid synthesis and lipid production at dawn preceding lipid accumulation during the day. Our results suggest that diel lipid storage plays a key role for N. oceanica CCMP1779 growth under natural conditions making this alga a promising model to gain a basic mechanistic understanding of triacylglycerol production in photosynthetic cells. Our data will help the formulation of new hypotheses on the role of cyclic gene expression in cell growth and metabolism in Nannochloropsis.
Towards pathway‐centric cancer therapies via pharmacogenomic profiling analysis of ERK signalling pathway
Authors: Wang Haiyun , Zheng Xiaoqi , Fei Teng , Wang Jinzeng , Li Xujuan , Liu Yin , Zhang Fan 
Published: July 2015

AbstractBackgroundGenomic heterogeneity in human cancers complicates gene‐centric personalized medicine. Malignant tumors often share a core group of pathways that are perturbed by diverse genetic mutations. Therefore, one possible solution to overcome the heterogeneity challenge is a shift from gene‐centric to pathway‐centric therapies. Pathway‐centric perspectives, which underscore the need to understand key pathways and their critical properties, could address the complexity of cancer heterogeneity better than gene‐centric approaches to aid cancer drug discovery and therapy.MethodsWe used large‐scale pharmacogenomic profiling data provided by the Cancer Genome Project of the Wellcome Trust Sanger Institute and the Cancer Cell Line Encyclopedia. In a systematic in silico investigation of ERK signalling pathway components and topological structures determines their influences on pathway activity and targeted therapies. Mann–Whitney U test was used to identify gene alterations associated with drug sensitivity withpvalues and Benjamini–Hochberg correction for multiple hypotheses testing.ResultsThe analysis demonstrated that genetic alterations were crucial to activation of effector pathway and subsequent tumorigenesis, however drug sensitivity suffered from both drug effector and non‐effector pathways, which were determined by not only underlying genomic alterations, but also interplay and topological relationship of components in pathway, suggesting that the combinatorial targets of key nodes in perturbed pathways may yield better treatment outcome. Furthermore, we proposed a model to provide a more comprehensive insight and understanding of pathway‐centric cancer therapies.ConclusionsOur study provides a holistic view of factors influencing drug sensitivity and sheds light on pathway‐centric cancer therapies.
Prevalence of depression among subjects with and without gestational diabetes mellitus in Bangladesh: a hospital based study
Authors: Natasha Khurshid , Hussain Akhtar , Khan A. K. Azad 
Published: July 2015

Abstract
Background
Data on association between depression and diabetes during the pregnancy period in Asia, specifically in Bangladesh are scarce. The study was designed to measure the prevalence of depression during pregnancy with or without Gestational Diabetes Mellitus (GDM).

Methods
Seven hundred and forty eight pregnant women (382 with GDM, 366 without-GDM) attending at the Bangladesh Institute of Research and Rehabilitation in Diabetes, Endocrine and Metabolic Disorders, participated in the study. Blood glucose was measured following both WHO and ACOG criteria; GDM was diagnosed within 24–28 weeks. Depressive symptoms were assessed following MADRS scale. Semi-structured questionnaire was used to record their socio-demographic status and clinical and family history. Blood pressure, height, weight were also measured.

Results
Overall prevalence of depression was 18.32 %. Depression was higher in GDM subjects (25.92 %) compared to without-GDM subjects (10.38 %) with mean age of of 28.34 and 27.17 years respectively. Prevalence of depression was alarming in both the extreme of age. Dwelling place (P < 0.009) and past history of GDM (P < 0.018) had strong association with Depression. Higher prevalence of depression was found in Primipara whereas the risk of GDM increased with parity. Other obstetrical factors did not show any significant association with depression and GDM. Income (self and total family), physical exercise, sedentary lifestyle and workload had no significant statistical association with depression or GDM.

Conclusion
Higher rate of depression in pregnancy deserves medical attention especially women diagnosed with GDM. Further studies should estimate adverse pregnancy outcome for untreated depression especially in GDM cases.
Using Akaike's information theoretic criterion in mixed-effects modeling of pharmacokinetic data: a simulation study
Authors: Olofsen Erik , Dahan Albert 
Published: July 2015

Akaike's information theoretic criterion for model discrimination (AIC) is often stated to "overfit", i.e., it selects models with a higher dimension than the dimension of the model that generated the data. However, with experimental pharmacokinetic data it may not be possible to identify the correct model, because of the complexity of the processes governing drug disposition. Instead of trying to find the correct model, a more useful objective might be to minimize the prediction error of drug concentrations in subjects with unknown disposition characteristics. In that case, the AIC might be the selection criterion of choice.We performed Monte Carlo simulations using a model of pharmacokinetic data (a power function of time) with the property that fits with common multi-exponential models can never be perfect - thus resembling the situation with real data. Prespecified models were fitted to simulated data sets, and AIC and AICc (the criterion with a correction for small sample sizes) values were calculated and averaged. The average predictive performances of the models, quantified using simulated validation sets, were compared to the means of the AICs. The data for fits and validation consisted of 11 concentration measurements each obtained in 5 individuals, with three degrees of interindividual variability in the pharmacokinetic volume of distribution.Mean AICc corresponded very well, and better than mean AIC, with mean predictive performance. With increasing interindividual variability, there was a trend towards larger optimal models, but with respect to both lowest AICc and best predictive performance. Furthermore, it was observed that the mean square prediction error itself became less suitable as a validation criterion, and that a predictive performance measure should incorporate interindividual variability.This simulation study showed that, at least in a relatively simple mixed-effects modelling context with a set of prespecified models, minimal mean AICc corresponded to best predictive performance even in the presence of relatively large interindividual variability.
The Negative Effects of Public Benefits on Individual Employment: A Multilevel Analysis of Work Hours
Authors: Nord Derek , Nye-Lengerman Kelly 
Published: July 2015

AbstractPublic benefits are widely used by people with intellectual and development disabilities (IDD) as crucial financial supports. Using Rehabilitation Service Administration 911 and Annual Review Report datasets to account for individual and state vocational rehabilitation (VR) agency variables, a sample of 21,869 people with IDD were analyzed using hierarchical linear modeling to model the effects of public benefits on hours worked per week. Findings point to associations that indicate that public benefits not only limit access to employment participation, they also have a restricting effect on growth of weekly hours that typically come with higher wage positions, compared those that do not access benefits. The article also lays out important implications and recommendations to increase the inclusion of people with IDD in the workplace.
Quantification of some secondary metabolites in selected Cornaceae species / Stanovenie vybraných sekundárnych metabolitov v niektorých druhoch čeľade Cornaceae
Authors: Forman V. , Haladová M. , Grančai D. 
Published: July 2015

Abstract
Leaves of selected species of the Cornaceae family (Swida alba, Swida australis, Swida controversa, Swida coreana, Swida baileyi, Cornus kousa, Cornus mas) were investigated in this study. These shrubs or small trees with hard wood are cultivated in Slovakia (Tesarske Mlyňany Arboretum). Some species (C. mas and C. kousa) have edible fruits. Cornels find broad ethnopharmacological use, for example, in Traditional Chinese Medicine (TCM), where fruits of C. officinalis are used for the treatment of several disorders, such as organ hypersecretion or diabetes. They are also used as tonics and for astringent effects. Leaves and fruits of C. kousa have been reported to possess antioxidative, anti-inflammatory and antidiabetic properties. The aim of our study is to compare the content of selected secondary metabolites groups in the leaves of above-mentioned species. The plant material was collected in the Tesarske Mlyňany Arboretum, Slovakia, in September 2010. Modified spectrophotometric methods of the European Pharmacopoeia, 8th edition (Ph. Eur. 8) were used for all assays. Results show that the total hydroxycinnamic derivatives (THD) content varied from 1.14 (S. alba) to 2.86% (S. coreana) when expressed as rosmarinic acid, and from 1.01 (S. alba) to 2.55% (S. coreana) when expressed as caffeic acid. The flavonoids content ranged from 0.21 (C. mas) to 1.37% (S. coreana), total polyphenols content from 9.6 (C. kousa) to 7.27% (S. coreana), and tannins content from 7.17 (C. kousa) to 4.04% (S. coreana). Leaves of Korean dogwood (S. coreana) were observed to show the highest content of THD expressed as rosmarinic acid (2.86%) and caffeic acid (2.55%), as well as of flavonoids (1.37%). Kousa dogwood (C. kousa) contained the highest amounts of tannins (7.17%) and total polyphenols (9.6%) on the other hand.
Polyphenolic compounds and essential oil analysis of selected species of the genus Thymus / Analýza fenolových zložiek a analýza silice vybraných druhov rodu Thymus
Authors: Kameníková M. , Fialová S. , Ťažký A. , Čičová I. 
Published: July 2015

Abstract
The content of phenolic compounds (total phenolic compounds, tannins, flavonoids and anthocyanidins) of three species of thyme (Thymus pulegioides, Thymus pannonicus, Thymus praecox) of different origin (Bohemian-Moravian highlands, Křivoklat and Považsky Inovec) was determined using spectrophotometric methods of European Pharmacopoeia 8th edition. Furthermore, the determination of the content of essential oil and analysis of its constituents was realised. The amount of total phenolics was determined by a spectrophotometric method using the Folin-Ciocalteu reagent. Their content ranged from 3.87 to 8.86%. The content of tannins was established on a preliminary determination of the total phenolics, followed by adsorption of tannins on hide powder. The amount of tannins in our samples varied from 1.96 to 5.65%. The content of total flavonoids was determined by a spectrophotometric method using aluminium chloride. Quantitative analysis of flavonoids has shown that content in our samples ranged from 0.59 to 1.52% expressed as luteolin-7-O-glucoside (λ = 392 nm) and from 0.41 to 1.12% expressed as rutin (λ = 420 nm). Anthocyanins represent a small amount of total polyphenol content in Thymus species. In our samples, the content of anthocyanins expressed as cyanidin-3-O-glucoside varied from 0.02 to 0.1%. The determination of essential oil was realised by method of European Pharmacopoeia 8th edition. Its contents in our samples ranged from 0.2 to 0.75%. Gas chromatography-mass spectrometry was used for essential oil analysis. According to the presence of main monoterpene in Thymus essential oil, we can distinguish three chemotypes: thymol, carvacrol and linalool. Due to variations of chemical constituents of thyme essential oil, it was possible to observe a relationship between occurrence of certain chemotype and origin of sample. Differences in content of flavonoids have not shown a significant relationship to locality of origin.
Phenolic compounds variation in Mentha L. Species in the course of a four-years period / Kolísanie fenolových látok v rôznych druhoch Mentha L. Počas 4 ročného obdobia
Authors: Fialová S. , Tekeľová D. , Rendeková K. , Klinčok J. , Kolárik M. , Kurucová K. , Grančai D. 
Published: July 2015

Abstract
Mints rank among the most important Lamiaceae plants. In addition to essential oil, they contain many valuable phenolic compounds, including flavonoids and phenolic acids that participate in mints’ pharmacological properties. In this work, we examined the contents of phenolic compounds variation in the course of 4 years of vegetation. We compared the contents of total hydroxycinnamic derivatives expressed as rosmarinic acid (λ = 505 nm), total polyphenols and tannins expressed as rosmarinic acid (λ = 760 nm), and flavonoids expressed as luteolin-7-O-glucoside (λ = 392 nm) and quercetin (λ = 420 nm) in 1-, 2-, 3-, and 4-year-old plants’ dry leaves, respectively. Spectrophotometric methods of the European Pharmacopoeia were employed. Our results show high levels of active phenolic compounds, particularly in 3- and 4-year-old plants.
Dependence Of SO2 Of Immissions Measurement Methods For Selected Areas Power Plant Vojany
Authors: Pokrývková Jozefína , Micáková Emília 
Published: July 2015

Abstract
The results of imperfect knowledge of the natural environment’s basic laws show that the negative effects of our actions are manifested in most cases only belatedly, in forms such as: the loss of arable land, the extinction of rare species of plants and animals, the depletion of the ozone layer, the climate change, the deterioration of air quality, the acid rain, the worsening quality of surface and ground water, the surface loss of rainforests and many other negative aspects of our thoughtless actions. For the measurement of sulphur concentration, we chose locality surrounding the power plant Vojany, where we identified two locations for mounting our stands. The first place was the village Tušice, and the second one the area of AMS Leles. This is where we planted in alkaline strips in stands used for this purpose and by the sorption – cumulative method we evaluated concentrations of sulphur amount collected on the strips. In the period 2012–2014, we conducted experiments in regular 30-day intervals; we performed 104 analyses of filter plates using the sorption-cumulative method. The current position of some habitats infestation causes damage to various parts of environment. Therefore, we consider it relevant to continue in monitoring this affliction and quantifying the extent of its negative effects. The proposed procedure with the possibility of a retrospective determination of concentrations of SO2 using mathematical modelling can also be used for the determination of old burdens.
Virulence factors and antimicrobial resistance of
coagulase-negative staphylococci isolated from
drinking water
Authors: Čuvalová Zuzana , Pipová Monika , Kantíková Miriam , Brtková Andrea , Fajber Jozef 
Published: July 2015

Abstract
Little has been published about the occurrence,
speciesidentification, andpathogenicpotentialofcoagulasenegative
staphylococci (CoNS) present in drinking water. In
this study, ten species were identified among 57 isolates
of staphylococci from 756 samples of chlorinated drinking
water taken from public distribution networks in the Slovak
Republic. S. warneri (37%), S. haemolyticus (23%), and S.
saprophyticus ssp. saprophyticus (14%) were identified
most frequently. Isolates did not produce coagulase,
DNase, or hyaluronidase; production of gelatinase and
lecithinase was observed in 28 and 22 isolates, respectively.
Genetically encoded ability for production of enterotoxin
SED was revealed in two isolates. Among ten antibiotics
tested, resistance to ampicillin (66.7%), penicillin (64.9%),
and erythromycin (57.9%) were observed most frequently.
Resistance to gentamicin, vancomycin, or clindamycin was
not confirmed. Production of β-lactamase was observed
in 64.9% of isolates. Fourty-two isolates were resistant to
two or more antibiotics tested, and eight isolates showed
multiresistance. The presence of mecA gene was confirmed
in 8 isolates, while PBP2a was revealed in 7. Two isolates of S.
epidermidis were identified as methicillin-resistant (MRSE).
The results demonstrate that CoNS in chlorinated drinking
water may possess virulence factors and show resistance to
various antibiotics. Therefore, their pathogenic potential
should not be ignored.
The first report on periphytic diatoms on artificial and natural substrate in the karstic spring Bunica, Bosnia and Herzegovina
Authors: Dedić Anita , Plenković-Moraj Anđelka , Borojević Koraljka Kralj , Hafner Dubravka 
Published: July 2015

Abstract
This study presents investigations of the periphytic diatoms on artificial (glass slides) and natural substrates in the karstic, limnocrene spring of Bunica situated in the south of Bosnia and Herzegovina. Investigations were performed in summer 2010. Samples were collected every seven days for eight weeks. Physical and chemical characteristics of water, temperature, oxygen saturation, dissolved oxygen, electric conductivity and nutrients as well as fl ow velocity at sample site, were measured simultaneously with each sampling. Physical and chemical characteristics showed low temperature oscillations, good aeration and oligotrophic conditions. In general, greater diatom diversity was noted on natural substrate. A total of 104 diatom species were found on natural substrate and 82 on glass slides. The best represented genera on both types of substrate were Gomphonema and Navicula (each with eight species), Nitzschia (with six species), and Cocconeis (with five species). Achnanthidium exiguum, Achnanthidium minutissimum, Amphora pediculus, Cymbopleura amphicephala and Surirella minuta were recorded in all samples of natural substrate and Gomphonema minutum in artificial substrate samples.