bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serum microRNA‐124 is a novel biomarker for liver necroinflammation in patients with chronic hepatitis B virus infection
Authors: Wang J.‐Y , Mao R.‐C , Zhang Y.‐M , Zhang Y.‐J , Liu H.‐Y , Qin Y.‐L , Lu M.‐J , Zhang J.‐M 
Published: August 2014

SummaryPatients with chronic hepatitis B virus (HBV) infection and normal or mildly increased transaminases may have sustained significant liver damage, as verified by liver biopsy. However, no suitable noninvasive method exists for identifying liver necroinflammation in such patients. We aimed to investigate the power of microRNA‐124 as a novel biomarker for liver necroinflammation. A total of 131 recruited patients with chronic HBV infection underwent liver biopsy for grading of necroinflammation (G) and staging of fibrosis (S). Thirty healthy individuals were included as controls (HCs). Serum microRNA‐124 and microRNA‐122 levels were measured using qRT‐PCR. Forty‐five patients from the study population receiving entecavir therapy were monitored for changes in serum microRNA‐124 levels in association with improved liver histology. The capacity of serum microRNA‐124 levels in discriminating the grade of liver necroinflammation was compared with alanine aminotransferase (ALT) with liver biopsy validation. Serum microRNA‐124 levels were significantly higher in patients with chronic HBV infection than in HCs (P < 0.0001). Patients with considerable liver necroinflammation (G ≥ 2) had significantly higher serum miRNA‐124 levels than those without or with mild necroinflammation (P < 0.0001). After 48 weeks of antiviral therapy, serum microRNA‐124 levels considerably declined in 45 patients (P < 0.0001), which were associated with histological improvement. In patients with normal ALT and a serum HBV DNA load >104 copies/mL, receiver operating characteristic (ROC) curve of serum microRNA‐124 levels yielded an area under ROC curve (AUC) of 0.840, with 58.3% sensitivity and 91.7% specificity in discriminating between moderate‐to‐severe liver necroinflammation (G ≥ 2).
HBV preS2 transactivates FOXP3 expression in malignant hepatocytes
Authors: Zhang Xiaoning , Gao Lifen , Liang Xiaohong , Guo Min , Wang Rong , Pan Yingfang , Liu Peng , Zhang Feng , Guo Chun , Zhu Faliang , Qu Chunfeng , Ma Chunhong 
Published: August 2014

AbstractBackground & AimsRecent data reported the increased expression of forkhead box protein 3 (FOXP3), the well known master regulator of CD4+C25+ regulatory T cells, in hepatocellular carcinoma (HCC) cells. However, the mechanisms remain unknown. We previously showed that preS2, one of important regulatory proteins encoded by HBV, triggers transactivation of hTERT in malignant hepatocytes. Here, we aimed to explore the role of preS2 in regulating FOXP3 expression in HCC.MethodsFOXP3 expression was detected by RT‐PCR, Western blot and immunohistochemical staining. Cotransfection and siRNA knockdown were involved to study the regulation effects of preS2 on FOXP3 expression in cultured HCC cell lines. Luciferase reporter assay and EMSA assay were performed to explore the mechanism of preS2‐mediated FOXP3 upregulation.ResultsImmunohistochemical staining detected significant increased FOXP3 expression in malignant hepatocytes from sections of HCC patients. The total FOXP3 expression in hepatocytes from patients with HBsAg‐positive HCC was significantly increased compared to that of HBV‐negative HCCs (P = 0.002). In accordance, preS2 overexpression enhanced FOXP3 expression in HCC cell lines, while preS2 knockdown significantly reduced FOXP3 expression in HBV‐integrated HepG2.2.15 cells. Results of cotransfection and luciferase report assay showed that preS2 transactivated FOXP3 promoter in a dose‐dependent manner. Further study identified the AP‐1 binding site at 20 bp region from −465 bp to −445 bp of FOXP3 promoter was responsible for preS2‐induced FOXP3 transcriptional activation.ConclusionsOur data here, for the first time, provided direct evidence to demonstrate that preS2 oncoprotein encoded by HBV transactivated FOXP3 transcription in HCC cells.
CINCINNATA in Antirrhinum majus directly modulates genes involved in cytokinin and auxin signaling
Authors: Das Gupta Mainak , Aggarwal Pooja , Nath Utpal 
Published: August 2014

Summary

Mutations in the CINCINNATA (CIN) gene in Antirrhinum majus and its orthologs in Arabidopsis result in crinkly leaves as a result of excess growth towards the leaf margin. CIN homologs code for TCP (TEOSINTE‐BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTOR 1 AND 2) transcription factors and are expressed in a broad zone in a growing leaf distal to the proliferation zone where they accelerate cell maturation. Although a few TCP targets are known, the functional basis of CIN‐mediated leaf morphogenesis remains unclear.

We compared the global transcription profiles of wild‐type and the cin mutant of A. majus to identify the targets of CIN. We cloned and studied the direct targets using RNA in situ hybridization, DNA–protein interaction, chromatin immunoprecipitation and reporter gene analysis.

Many of the genes involved in the auxin and cytokinin signaling pathways showed altered expression in the cin mutant. Further, we showed that CIN binds to genomic regions and directly promotes the transcription of a cytokinin receptor homolog HISTIDINE KINASE 4 (AmHK4) and an IAA3/SHY2 (INDOLE‐3‐ACETIC ACID INDUCIBLE 3/SHORT HYPOCOTYL 2) homolog in A. majus.

Our results suggest that CIN limits excess cell proliferation and maintains the flatness of the leaf surface by directly modulating the hormone pathways involved in patterning cell proliferation and differentiation during leaf growth.
Cartesian Modes and The Simplicity of Mind
Authors: Barry Galen 
Published: August 2014

AbstractMalebranche argues that we lack a clear idea of the mind because we cannot, even in principle, derive all the possible modes of mind solely from the idea of thought. But we can, in principle, derive all the possible modes of body from the idea of extension. Therefore, there is epistemic asymmetry between our ideas of mind and body. I offer a defense ofDescartes whereby he can assert that we have a clear idea of mind despite this asymmetry. I argue that he can do this by distinguishing the simplicity of mind from the divisibility of body.
Skin as a living coloring book: how epithelial cells create patterns of pigmentation
Authors: Weiner Lorin , Fu Wenyu , Chirico William J. , Brissette Janice L. 
Published: August 2014

SummaryThe pigmentation of mammalian skin and hair develops through the interaction of two basic cell types — pigment donors and recipients. The pigment donors are melanocytes, which produce and distribute melanin through specialized structures. The pigment recipients are epithelial cells, which acquire melanin and put it to use, collectively yielding the pigmentation visible to the eye. This review will focus on the pigment recipients, the historically less understood cell type. These end‐users of pigment are now known to exert a specialized control over the patterning of pigmentation, as they identify themselves as melanocyte targets, recruit pigment donors, and stimulate the transfer of melanin. As such, this review will discuss the evidence that the skin is like a coloring book: the pigment recipients create a ‘picture,’ a blueprint for pigmentation, which is colorless initially but outlines where pigment should be placed. Melanocytes then melanize the recipients and ‘color in’ the picture.
Directed Improvement of Luciferin Regenerating Enzyme Binding Properties: Implication of Some Conserved Residues in Luciferin‐Binding Domain
Authors: Hemmati Roohullah , Sajedi Reza H. , Bakhtiari Nuredin , Hosseinkhani Saman 
Published: August 2014

AbstractLuciferin regenerating enzyme (LRE) contributes to in vitro recycling of d‐luciferin to produce persistent and longer light emission by luciferase. Luciferin binding domains I and II among LREs regarded as potential candidates for luciferin‐binding sites. In this study, for the first time, amino acids T69, G75 and K77 located at luciferin binding domain I of LRE from L. turkestanicus (T‐LRE) substituted by using site‐directed mutagenesis. Single mutant T69R increased luciferase light output more than two‐fold over a longer time in comparison with a wild‐type and other mutants of T‐LRE. Nevertheless, double mutant (K77E/T69R) increased the amount of bioluminescent signal more than two‐fold over a short time. In addition, G75E, K77E and G75E/T69R mutants did not improve luciferin–luciferase in vitro bioluminescence. Based on our results, addition of K77E/G75E and K77E/G75E/T69R mutants caused intermediate changes in bioluminescence from in vitro luciferin–luciferase reaction. These findings indicated that the amino acids in question are possible to be located within T‐LRE active site. It may also be suggested that substituted Arg69 (Arg218) plays an important role in luciferin binding and the existence of Gly75 as well as Lys77 is essential for T‐LRE which has already evolved to have different functions in nature.
Forward Simulation Markov Chain Monte Carlo with Applications to Stochastic Epidemic Models
Authors: Neal Peter , Terry Huang Chien Lin 
Published: August 2014

AbstractFor many stochastic models, it is difficult to make inference about the model parameters because it is impossible to write down a tractable likelihood given the observed data. A common solution is data augmentation in a Markov chain Monte Carlo (MCMC) framework. However, there are statistical problems where this approach has proved infeasible but where simulation from the model is straightforward leading to the popularity of the approximate Bayesian computation algorithm. We introduce a forward simulation MCMC (fsMCMC) algorithm, which is primarily based upon simulation from the model. The fsMCMC algorithm formulates the simulation of the process explicitly as a data augmentation problem. By exploiting non‐centred parameterizations, an efficient MCMC updating schema for the parameters and augmented data is introduced, whilst maintaining straightforward simulation from the model. The fsMCMC algorithm is successfully applied to two distinct epidemic models including a birth–death–mutation model that has only previously been analysed using approximate Bayesian computation methods.
Estimating Mean Survival Time: When is it Possible?
Authors: Ding Ying , Nan Bin 
Published: August 2014

ABSTRACTFor right‐censored survival data, it is well‐known that the mean survival time can be consistently estimated when the support of the censoring time contains the support of the survival time. In practice, however, this condition can be easily violated because the follow‐up of a study is usually within a finite window. In this article, we show that the mean survival time is still estimable from a linear model when the support of some covariate(s) with non‐zero coefficient(s) is unbounded regardless of the length of follow‐up. This implies that the mean survival time can be well estimated when the support of linear predictor is wide in practice. The theoretical finding is further verified for finite samples by simulation studies. Simulations also show that, when both models are correctly specified, the linear model yields reasonable mean square prediction errors and outperforms the Cox model, particularly with heavy censoring and short follow‐up time.
Scarcity of protective items against HIV and other bloodborne infections in 13 low‐ and middle‐income countries
Authors: Gupta Shailvi , Wong Evan G. , Kushner Adam L. 
Published: August 2014

AbstractObjectiveTo assess protection of surgical healthcare workers against HIV and other bloodborne infections in low‐ and middle‐income countries (LMICs).MethodsLiterature review based on recent studies assessing baseline surgical capacity in LMICs using the WHO Situational Analysis of Access to Emergency and Essential Surgical Care, the Surgeons OverSeas (SOS) Personnel, Infrastructure, Procedures, Equipment and Supplies (PIPES) survey and the Harvard Humanitarian Initiative survey tools. The availability of protective eyewear, sterile gloves and sterilisers was assessed.ResultsThirteen individual country studies with relevant data were identified documenting items from 399 hospitals. The countries included Afghanistan, Bolivia, Gambia, Ghana, Liberia, Mongolia, Nigeria, Sierra Leone, Solomon Islands, Somalia, Sri Lanka, Tanzania and Zambia. Overall, only 29% (79/270) of hospitals always had eye protection. Sterilisers were only available at 64% (244/383) of facilities. Sterile gloves were the most available item, available at 75% of facilities (256/340).ConclusionSurgical healthcare worker protection for bloodborne infections continues to be deficient in LMICs. Improved documentation of these items should be incorporated into future surgical capacity studies. Policy makers and clinicians should work together to secure resources and interventions that will protect this vital workforce.
The phylogenetic relationships of the Early Miocene storkGrallavis edwardsi, with comments on the interrelationships of living Ciconiidae (Aves)
Authors: De Pietri Vanesa L. , Mayr Gerald 
Published: August 2014

The fossil record of storks (Aves, Ciconiidae) includes a relatively large number of specimens from the Middle Eocene onwards, but no taxon is as well represented asGrallavis edwardsiform the Early Miocene of the Allier region in central France. Despite this, the phylogenetic placement ofG. edwardsiamong other storks has remained elusive not least because of the lack of a robust phylogenetic framework for living storks. To find out howG. edwardsirelates to recent Ciconiidae, we performed a phylogenetic analysis based on osteological features including all living genus‐level taxa of the Ciconiidae. We show that the previously reported similarities to the extant taxaEphippiorhynchusandJabiruare based on plesiomorphic features, and our analysis supports a sister group relationship betweenGrallavis edwardsiandLeptoptilos. Our results are also consistent with a basal divergence within Ciconiidae betweenMycteriaandAnastomus, which are among the smallest storks, and all other storks. A sister group relationship between storks of the genusCiconiaand all large storks (Leptoptilini) is recovered albeit with weak support, which may be due to homoplastic features linked to their large size.Grallavis edwardsipossessed several osteological adaptations suited for scavenging, and despite lacking some derived traits characteristic ofLeptoptilos, it is likely to have been a precursor of large marabou and adjutant storks.
Measurement of time delays in gated radiotherapy for realistic respiratory motions
Authors: Chugh Brige P. , Quirk Sarah , Conroy Leigh , Smith Wendy L. 
Published: August 2014

Purpose:Gated radiotherapy is used to reduce internal motion margins, escalate target dose, and limit normal tissue dose; however, its temporal accuracy is limited. Beam‐on and beam‐off time delays can lead to treatment inefficiencies and/or geographic misses; therefore, AAPM Task Group 142 recommends verifying the temporal accuracy of gating systems. Many groups use sinusoidal phantom motion for this, under the tacit assumption that use of sinusoidal motion for determining time delays produces negligible error. The authors test this assumption by measuring gating time delays for several realistic motion shapes with increasing degrees of irregularity.Methods:Time delays were measured on a linear accelerator with a real‐time position management system (Varian TrueBeam with RPM system version 1.7.5) for seven motion shapes: regular sinusoidal; regular realistic‐shape; large (40%) and small (10%) variations in amplitude; large (40%) variations in period; small (10%) variations in both amplitude and period; and baseline drift (30%). Film streaks of radiation exposure were generated for each motion shape using a programmable motion phantom. Beam‐on and beam‐off time delays were determined from the difference between the expected and observed streak length.Results:For the system investigated, all sine, regular realistic‐shape, and slightly irregular amplitude variation motions had beam‐off and beam‐on time delays within the AAPM recommended limit of less than 100 ms. In phase‐based gating, even small variations in period resulted in some time delays greater than 100 ms. Considerable time delays over 1 s were observed with highly irregular motion.Conclusions:Sinusoidal motion shapes can be considered a reasonable approximation to the more complex and slightly irregular shapes of realistic motion. When using phase‐based gating with predictive filters even small variations in period can result in time delays over 100 ms. Clinical use of these systems for patients with highly irregular patterns of motion is not advised due to large beam‐on and beam‐off time delays.
Genome Sequences of 228 Shiga Toxin-Producing Escherichia coli Isolates and 12 Isolates Representing Other Diarrheagenic E. coli Pathotypes
Authors: Trees Eija , Strockbine Nancy , Changayil Shankar , Ranganathan Satishkumar , Zhao Kun , Weil Ryan , MacCannell Duncan , Sabol Ashley , Schmidtke Amber , Martin Haley , Stripling Devon , Ribot Efrain M. , Gerner-Smidt Peter 
Published: August 2014

ABSTRACT

Shiga toxin-producing
Escherichia coli
(STEC) are a common cause for food-borne diarrheal illness outbreaks and sporadic cases. Here, we report the availability of the draft genome sequences of 228 STEC strains representing 32 serotypes with known pulsed-field gel electrophoresis (PFGE) types and epidemiological relationships, as well as 12 strains representing other diarrheagenic
E. coli
pathotypes.
Draft Genome Sequence of the Dye-Decolorizing and Nanowire-Producing Bacterium Shewanella xiamenensis BC01
Authors: Li Yuzhe , Ng I-Son , Zhang Xia , Wang Nan 
Published: August 2014

ABSTRACT

Shewanella xiamenensis
BC01 is an important biodecolorizing and nanowire-producing bacterium which was found in Xiamen, China. Here, we present the draft genome sequence consisting of 4,677,169 bp (GC content, 46.21%) and 3,999 coded proteins. This information boosts insight into and understanding of the genetic evolution of
Shewanella
species.
Draft Genome Sequence of the Rodent Opportunistic Pathogen Pasteurella pneumotropica ATCC 35149
T
Authors: Sasaki Hiraku , Ishikawa Hiroki , Asano Ryoki , Ueshiba Hidehiro , Matsumoto Tetsuya , Boot Ron , Kawamoto Eiichi 
Published: August 2014

ABSTRACT

Pasteurella pneumotropica
is an opportunistic pathogen in rodents that is commonly isolated from upper respiratory tracts in laboratory rodents. Here, we report the draft genome sequence of the
P. pneumotropica
type strain ATCC 35149, which was first isolated and characterized as biotype Jawetz.
Draft Genome Sequence of a Hypersensitive Reaction-Inducing Pantoea agglomerans Strain Isolated from Olive Knots Caused by Pseudomonas savastanoi pv. savastanoi
Authors: Moretti Chiaraluce , Cortese Chiara , Passos da Silva Daniel , Venturi Vittorio , Torelli Emanuela , Firrao Giuseppe , Buonaurio Roberto 
Published: August 2014

ABSTRACT

Pantoea agglomerans
strains inducing a hypersensitive reaction in tobacco leaves are frequently isolated inside olive knots caused by
Pseudomonas savastanoi
pv. savastanoi. Here, we report the draft genome sequence of the Italian
P. agglomerans
strain, which is able to increase olive knot disease severity when coinoculated with
P. savastanoi
pv. savastanoi.
Draft Genome Sequences of Clinical Vibrio parahaemolyticus Strains Isolated in Maryland (2010 to 2013)
Authors: Haendiges Julie , Timme Ruth , Allard Marc , Myers Robert A. , Payne Justin , Brown Eric W. , Evans Peter , Gonzalez-Escalona Narjol 
Published: August 2014

ABSTRACT

Vibrio parahaemolyticus
is the leading cause of food-borne illnesses associated with the consumption of raw shellfish worldwide. Here, we report 45 draft genomes of
V. parahaemolyticus
. Thirty-five of them are strains that were isolated from clinical cases in the state of Maryland from 2010 to 2013. The remaining 10 strains were historical isolates, isolated mostly from the West Coast of the United States during the period of 1988 to 2004. The availability of these genomes will allow for future phylogenetic analyses with other
V. parahaemolyticus
strains.
Leukocyte Telomere Length in Relation to Pancreatic Cancer Risk: A Prospective Study
Authors: Campa Daniele , Mergarten Björn , De Vivo Immaculata , Boutron-Ruault Marie-Christine , Racine Antoine , Severi Gianluca , Nieters Alexandra , Katzke Verena A. , Trichopoulou Antonia , Yiannakouris Nikos , Trichopoulos Dimitrios , Boeing Heiner , Quirós J. Ramón , Duell Eric J. , Molina-Montes Esther , Huerta José María , Ardanaz Eva , Dorronsoro Miren , Khaw Kay-Tee , Wareham Nicholas , Travis Ruth C. , Palli Domenico , Pala Valeria , Tumino Rosario , Naccarati Alessio , Panico Salvatore , Vineis Paolo , Riboli Elio , Siddiq Afshan , Bueno-de-Mesquita H.B. , Peeters Petra H. , Nilsson Peter M. , Sund Malin , Ye Weimin , Lund Eiliv , Jareid Mie , Weiderpass Elisabete , Duarte-Salles Talita , Kong So Yeon , Stepien Magdalena , Canzian Federico , Kaaks Rudolf 
Published: August 2014

Abstract
Background: Several studies have examined leukocyte telomere length (LTL) as a possible predictor for cancer at various organ sites. The hypothesis originally motivating many of these studies was that shorter telomeres would be associated with an increase in cancer risk; the results of epidemiologic studies have been inconsistent, however, and suggested positive, negative, or null associations. Two studies have addressed the association of LTL in relation to pancreatic cancer risk and the results are contrasting.
Methods: We measured LTL in a prospective study of 331 pancreatic cancer cases and 331 controls in the context of the European Prospective Investigation into Cancer and Nutrition (EPIC).
Results: We observed that the mean LTL was higher in cases (0.59 ± 0.20) than in controls (0.57 ± 0.17), although this difference was not statistically significant (P = 0.07), and a basic logistic regression model showed no association of LTL with pancreas cancer risk. When adjusting for levels of HbA1c and C-peptide, however, there was a weakly positive association between longer LTL and pancreatic cancer risk [OR, 1.13; 95% confidence interval (CI), 1.01–1.27]. Additional analyses by cubic spline regression suggested a possible nonlinear relationship between LTL and pancreatic cancer risk (P = 0.022), with a statistically nonsignificant increase in risk at very low LTL, as well as a significant increase at high LTL.
Conclusion: Taken together, the results from our study do not support LTL as a uniform and strong predictor of pancreatic cancer.
Impact: The results of this article can provide insights into telomere dynamics and highlight the complex relationship between LTL and pancreatic cancer risk. Cancer Epidemiol Biomarkers Prev; 23(11); 2447–54. ©2014 AACR.