bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nomogram of the Barcelona Clinic Liver Cancer system for individual prognostic prediction in hepatocellular carcinoma
Authors: Hsu Chia‐Yang , Liu Po‐Hong , Hsia Cheng‐Yuan , Lee Yun‐Hsuan , Al Juboori Alhareth , Lee Rheun‐Chuan , Lin Han‐Chieh , Huo Teh‐Ia 
Published: March 2016

AbstractBackground & AimsThe predictive accuracy of the Barcelona Clinic Liver Cancer (BCLC) staging system on a single patient is not clear. This study aimed to develop a nomogram to predict individualized survival of patients with hepatocellular carcinoma (HCC) based on the BCLC system.MethodsA total of 3179 patients were randomly grouped into derivation (n = 2119) and validation (n = 1060) sets. The multivariate Cox proportional hazards model was used to generate the nomogram from tumour burden, cirrhosis and performance status (PS). The performance of the nomogram was evaluated by concordance indices and calibration tests.ResultsBeta coefficients from the Cox model were used to assign nomogram points to different degrees of tumour burden, Child‐Turcotte‐Pugh classification and PS. A nomogram with a scale of 0–26 was developed and the predicted survival rates at 3 and 5 years were calculated. The derivation set had a concordance index of 0.766 (95% confidence interval [CI]: 0.686–0.838); and the validation set showed a concordance index of 0.775 (95% CI: 0.607–0.909). The calibration plots were close to the 45‐degree line for 3‐ and 5‐year survival prediction of BCLC stages 0–C patients in both derivation and validation groups. For BCLC stage D patients, calibration plots in both groups showed deviation from the 45‐degree line for 3‐ and 5‐year prediction.ConclusionsThis study provides quantitative evidence to support the prognostic ability of BCLC system. This straightforward and easy‐to‐use nomogram may accurately predict the survival at 3 and 5 years for individual HCC patient except for BCLC stage D patients.
Diabetes mellitus in patients with cirrhosis: clinical implications and management
Authors: Elkrief Laure , Rautou Pierre‐Emmanuel , Sarin Shiv , Valla Dominique , Paradis Valérie , Moreau Richard 
Published: March 2016

AbstractDisorders of glucose metabolism, namely glucose intolerance and diabetes, are frequent in patients with chronic liver diseases. In patients with cirrhosis, diabetes can be either a classical type 2 diabetes mellitus or the so‐called hepatogenous diabetes, i.e. a consequence of liver insufficiency and portal hypertension. This review article provides an overview of the possible pathophysiological mechanisms explaining diabetes in patients with cirrhosis. Cirrhosis is associated with portosystemic shunts as well as reduced hepatic mass, which can both impair insulin clearance by the liver, contributing to peripheral insulin resistance through insulin receptors down‐regulation. Moreover, cirrhosis is associated with increased levels of advanced‐glycation‐end products and hypoxia‐inducible‐factors, which may play a role in the development of diabetes. This review also focuses on the clinical implications of diabetes in patients with cirrhosis. First, diabetes is an independent factor for poor prognosis in patients with cirrhosis. Specifically, diabetes is associated with the occurrence of major complications of cirrhosis, including ascites and renal dysfunction, hepatic encephalopathy and bacterial infections. Diabetes is also associated with an increased risk of hepatocellular carcinoma in patients with chronic liver diseases. Last, the management of patients with concurrent diabetes and liver disease is also addressed. Recent findings suggest a beneficial impact of metformin in patients with chronic liver diseases. Insulin is often required in patients with advanced cirrhosis. However, the favourable impact of controlling diabetes in patients with cirrhosis has not been demonstrated yet.
Deciphering the regulon of a GntR family regulator via transcriptome and ChIP‐exo analyses and its contribution to virulence in Xanthomonas citri
Authors: Zhou Xiaofeng , Yan Qing , Wang Nian 
Published: March 2016

SummaryXanthomonas contains a large group of plant‐associated species, many of which cause severe diseases on important crops worldwide. Six gluconate‐operon repressor (GntR) family transcriptional regulators are predicted in Xanthomonas, one of which, belonging to the YtrA subfamily, plays a prominent role in bacterial virulence. However, the direct targets and comprehensive regulatory profile of YtrA remain unknown. Here, we performed microarray and high‐resolution chromatin immunoprecipitation‐exonuclease (ChIP‐exo) experiments to identify YtrA direct targets and its DNA binding motif in X. citri ssp. citri (Xac), the causal agent of citrus canker. Integrative microarray and ChIP‐exo data analysis revealed that YtrA directly regulates three operons by binding to a palindromic motif GGTG‐N16‐CACC at the promoter region. A similar palindromic motif and YtrA homologues were also identified in many other bacteria, including Stenotrophomonas, Pseudoxanthomonas and Frateuria, indicating a widespread phenomenon. Deletion of ytrA in Xac abolishes bacterial virulence and induction of the hypersensitive response (HR). We found that YtrA regulates the expression of hrp/hrc genes encoding the bacterial type III secretion system (T3SS) and controls multiple biological processes, including motility and adhesion, oxidative stress, extracellular enzyme production and iron uptake. YtrA represses the expression of its direct targets in artificial medium or in planta. Importantly, over‐expression of yro3, one of the YtrA directly regulated operons which contains trmL and XAC0231, induced weaker canker symptoms and down‐regulation of hrp/hrc gene expression, suggesting a negative regulation in Xac virulence and T3SS. Our study has significantly advanced the mechanistic understanding of YtrA regulation and its contribution to bacterial virulence.
An Approach to Breast Cancer Immunotherapy: The Apoptotic Activity of Recombinant Anti‐Interleukin‐6 Monoclonal Antibodies in Intact Tumour Microenvironment of Breast Carcinoma
Authors: Abou‐Shousha S. , Moaaz M. , Sheta M. , Motawea M. A. 
Published: March 2016

AbstractCurrent work is one of our comprehensive preclinical studies, a new approach to breast cancer (BC) immunotherapy through induction of tumour cell apoptosis. Tumour growth is not just a result of uncontrolled cell proliferation but also of reduced apoptosis. High levels of interleukin‐6 (IL‐6) are associated with metastatic BC and correlated with poor survival as it promotes growth of tumour‐initiating cells during early tumorigenesis protecting these cells from apoptosis. Therefore, this study aims at investigating the potential of anti‐IL‐6 monoclonal antibodies to suppress IL‐6 proliferative/anti‐apoptotic activities in intact tumour microenvironment of BC. Fresh sterile tumour and normal breast tissue specimens were taken from 50 female Egyptian patients with BC undergoing radical mastectomy. A unique tissue culture system designed to provide cells of each intact tumour/normal tissue sample with its proper microenvironment either supplemented or not with anti‐IL‐6 monoclonal antibodies. To evaluate the apoptotic activity of anti‐IL‐6 as a novel candidate for BC treatment strategy, we compared its effects with those obtained using tumour necrosis‐related apoptosis‐inducing ligand TRAIL as an established apoptotic agent. Our results revealed that levels of either anti‐IL‐6‐ or TRAIL‐induced apoptosis in the tumour or normal tissue cultures were significantly higher than those in their corresponding untreated ones (P < 0.001). No statistically significant differences have been found between apoptosis levels induced by anti‐IL‐6 monoclonal antibodies and those induced by TRAIL. Recombinant anti‐IL‐6 monoclonal antibodies could represent a novel effective element of immunotherapeutic treatment strategy for BC. The selectivity and anti‐apoptotic potential of anti‐IL‐6 is highly hopeful in IL‐6‐ abundant BC tumour microenvironment.
Clinical Significance of Myeloid‐Derived Suppressor Cells in Human Immunodeficiency Virus‐1/ Hepatitis C Virus‐coinfected Patients
Authors: Lei A. H. , Yang Q. , Cai W. P. , Liu Y. F. , Lan Y. , Qin A. P. , Hu F. Y. , Zhou J. 
Published: March 2016

AbstractMyeloid‐derived suppressor cells (MDSCs) are known to accumulate during chronic viral infection, including human immunodeficiency virus‐1 (HIV‐1) and hepatitis C virus (HCV) infection, and play a critical role in suppressing immune responses. However, the role of MDSCs in HIV/HCV coinfection is unclear. Here, we observed a dramatic increase in monocytic MDSCs (M‐MDSCs) level in the peripheral blood of HIV/HCV‐coinfected patients compared to that of healthy controls; the level of M‐MDSCs proportion in coinfection was not higher than that in HIV or HCV monoinfection. Interestingly, we found the M‐MDSCs level in coinfected patients correlated well with CD4+ T cell loss (r = −0.5680; P = 0.0058), HIV‐1 load (r = 0.6011; P = 0.0031), HCV load (r = 0.6288; P = 0.0017) and activated CD38+ T cells (r = 0.5139; P = 0.0144). Initiation of highly active antiretroviral therapy considerably reduced both M‐MDSCs and CD8+CD38+‐activated T cell proportion in coinfected patients, and they showed a parallel course of decline. Thus, our results suggest that HIV‐1 infection and high chronic immune activation may contribute to the expansion of M‐MDSCs and accelerate the disease progression in HIV/HCV‐coinfected patients.
Clinical impact and prevalence of IgG1 and IgG3 subclasses in antenatal alloimmunized women: experience from a tertiary medical centre in South India
Authors: Choudhuri J. , Chacko M. P. , Kuruvilla A. K. , Jose R. , Mathews J. , Regi A. , Daniel D. 
Published: March 2016

BackgroundHaemolytic disease of the foetus and newborn (HDFN) occurs due to maternal sensitization to paternal antigens. According to literature, IgG1 and IgG3 have a greater impact when compared to IgG2 and IgG4. To date, there is limited literature available from India. The current study was therefore executed using the column agglutination technique (CAT) for subclass identification (IgG1 and IgG3). The findings might be important to facilitate early referral, to centers where appropriate care is possible.MethodologyEighty‐five alloimmunized antenatal women were included in the study. IgG subclass (IgG1/IgG3) was determined using the ‘DAT IgG1/IgG3 ID’ card (Bio‐Rad). Pregnancies were followed up and categorized into ‘no/mild/moderate’ or ‘severe’ HDFN. Prevalence was calculated and severity of HDFN was correlated with subclass.ResultIn alloimmunized women (2·18%), the prevalence of IgG subclass was 20% for IgG1, 3·53% for IgG3, 24·71% for IgG1 + IgG3 and 51·76% had neither IgG1 nor IgG3. There was a highly significant difference between disease severity and the absence/presence of IgG1/IgG3 – either singly or in combination (P < 0·001) in newborns at risk. The risk of severe HDFN increased a sevenfold: it was lowest in patients with neither IgG1 nor IgG3, when compared to having either one of them or both (P < 0·05, CI between 1·5–31·89).ConclusionThe presence of IgG1/IgG3 subclass has a significant impact on the severity of HDFN. Therefore, these mothers require close antenatal monitoring to provide appropriate and timely intervention for newborns. CAT is a feasible option to identify high‐risk pregnancies and facilitate early referral.
Role of annexin gene and its regulation during zebrafish caudal fin regeneration
Authors: Saxena Sandeep , Purushothaman Sruthi , Meghah Vuppalapaty , Bhatti Bhawna , Poruri Akhila , Meena Lakshmi Mula G. , Sarath Babu Nukala , Narasimha Murthy Ch. Lakshmi , Mandal Komal K. , Kumar Arvind , Idris Mohammed M. 
Published: March 2016

AbstractThe molecular mechanism of epimorphic regeneration is elusive due to its complexity and limitation in mammals. Epigenetic regulatory mechanisms play a crucial role in development and regeneration. This investigation attempted to reveal the role of epigenetic regulatory mechanisms, such as histone H3 and H4 lysine acetylation and methylation during zebrafish caudal fin regeneration. It was intriguing to observe that H3K9,14 acetylation, H4K20 trimethylation, H3K4 trimethylation and H3K9 dimethylation along with their respective regulatory genes, such asGCN5, SETd8b,SETD7/9, andSUV39h1, were differentially regulated in the regenerating fin at various time points of post‐amputation. Annexin genes have been associated with regeneration; this study reveals the significant up‐regulation ofANXA2aandANXA2btranscripts and their protein products during the regeneration process. Chromatin immunoprecipitation and PCR analysis of the regulatory regions of theANXA2aandANXA2bgenes demonstrated the ability to repress two histone methylations, H3K27me3 and H4K20me3, in transcriptional regulation during regeneration. It is hypothesized that this novel insight into the diverse epigenetic mechanisms that play a critical role during the regeneration process may help to strategize the translational efforts, in addition to identifying the molecules involved in vertebrate regeneration.
DNA barcodes, cryptic diversity and phylogeography of a W Mediterranean assemblage of thermosbaenacean crustaceans
Authors: Cánovas Fernando , Jurado‐Rivera José A. , Cerro‐Gálvez Elena , Juan Carlos , Jaume Damià , Pons Joan 
Published: March 2016

We assess the occurrence of crypticism and analyse the phylogeography of a thermosbaenacean crustacean, the monodellid Tethysbaena scabra, endemic to the Balearic Islands (W Mediterranean). This species occurs only in mixohaline waters of coastal wells and caves adjacent to the seashore. We have used the mitochondrial DNA barcode region to assess its genetic population structure throughout the anchialine environment of the islands. Maximum likelihood phylogenetic analyses showed that the Balearic Tethysbaena and those from the NW Italian Peninsula form a monophyletic assemblage subdivided into several lineages. Cytochrome c oxidase subunit 1 (cox1) p‐distances among the more divergent Mallorcan lineages are remarkably high and on par with those established between the formally described species T. scabra from Menorca and T. argentarii from Italy. This result and the application of the generalised mixed Yule coalescence model (GMYC) suggest that at least some of the Mallorcan lineages represent cryptic species. A clear‐cut phylogeographic pattern is displayed by this anchialine assemblage: six of its seven lineages appear in allopatry, with the exception of a Mallorcan lineage limited to a single cave nested within the geographic range of another lineage. All lineages show a distribution reduced to a single cave or to short portions of coast not exceeding 60 km in length. Our coalescence estimations suggest an early Tortonian (10.7 Ma) origin for the Balearic + Italy Tethysbaena clade, an age that is largely prior to the onset of the eustatic oscillations associated with the Quaternary glaciations. Only the diversification that took place within some of the Mallorcan lineages could be coeval with the broad glacio‐eustatic oscillations of the Quaternary.
USING Z-SCAN TECHNIQUE TO MEASURE THE NONLINEAR OPTICAL PROPERTIES OF PMMA/ZNO NANOCOMPOSITES
Authors: Mohammed Shanshool Haider , Yahaya Muhammad , Mat Yunus Wan Mahmood , Abdullah Ibtisam Yahya 
Published: March 2016

The study of nonlinear optical properties of polymer nanocomposites has been given increasing attention due its application in laser, communication and data storage technology. There is a need to enhance the understanding of all photonics technologies. In the current work, PMMA-ZnO nanocomposites as foils and as thin films have been successfully prepared. Casting method and spin coating were used to prepare them respectively. Nanocomposites were prepared by mixing ZnO nanoparticles with polymethyl methacrylate (PMMA) as the polymer matrix. Different contents of ZnO nanoparticles were used as the filler in the nanocomposites. The absorbance spectra of the samples were obtained. The linear absorption coefficient was calculated. The nonlinear refractive index and nonlinear absorption coefficient were investigated using a single beam Z-scan technique. A Q-switched Nd-YAG pulsed laser (532 nm, 7 ns, 5 Hz) was used as a light source. Both thin film’s and foil’s samples showed peak absorption at 375 nm and increasing absorption with ZnO nanoparticles concentration. The nonlinear refractive index was in the order of 10-11 cm2/W for thin film samples and 10-12 cm2 /W for foil’s samples with a negative sign. In contrast, the nonlinear absorption coefficient is in the order of 10-6 cm/W and 10-7 cm /W for thin film and foil respectively. The figures of merit W and T were calculated in order to evaluate the suitability of the samples as optical switching device .However; they unsatisfied the requirements of optical switching devices but they can be considered as an excellent candidate for optical limiting.
FIBRE BRAGG GRATING SENSOR SYSTEM FOR TEMPERATURE APPLICATION
Authors: Daud Suzairi , Ahmad Noorden Ahmad Fakhrurrazi 
Published: March 2016

A practical pass-through type fibre Bragg grating (FBG) temperature sensor system have been designed and experimentally investigated. The performance of FBG was evaluated with the varying of focusing elements in harsh environments, under direct sunlight. The sensor head of FBG was designed to be focused with convex and hand lens. Results shows that the Bragg wavelength shift, increase proportionally with the temperature for both systems. The sensitivities of FBG were recorded to be 0.0107 and 0.0122 nm °C-1 for the system where convex and hand lens applied to the FBG’s sensor head respectively.
THEORETICAL STUDY ON SLOW-LIGHT GENERATED BY INTEGRATED MICRORING RESONATOR WITH WIDE BANDWIDTH AND HIGH GAIN
Authors: Aziz M. S. , Affandi M. S. , Daud S. , Bahadoran M. , Chaudhary K. T. , Ali J. 
Published: March 2016

We proposed a new approach to generate slow light transmission with large bandwidth and high buildup factor by using a soliton pulse propagating within integrated ring resonator circuit. The system consisted series of micron-size ring resonator fabricated by using nonlinear InGaAsP/InP material that are laterally coupled together. For convenience of analysis, optical transfer function for this model is obtained by using z-transform method. Slow light performances were modeled and discuss in this paper. Intensity buildup induced within the series of rings located at left and right sides of the system while strong nonlinear Kerr effect and mutual coupling leads to the spreading frequency bands within the device. Numerical simulation verifies that signal pulse with 45 ps relative delay time and bandwidth of 5.9 GHz (47 pm) are obtained at the communication wavelength around 1550 nm for a 100 ps signal pulse.
DETERMINATION SOUND SPEED OF METAL IN AQUEOUS SOLUTION VIA LASER INDUCED ACOUSTIC WAVE TECHNIQUE
Authors: Duralim Maisarah , Bidin Noriah , Nugroho Waskito , Zainal Jasman 
Published: March 2016

Laser induced breakdown and shock wave propagation are nonlinear phenomena. The high temperature and high pressure associated with plasma formation offering a lot advantages in industrial and scientific research. However not many realized that the end product of nonlinear effect such as the generation of acoustic wave will also attribute to significant impact. Thus the intention of this study is to materialize the usefulness of such acoustic wave for determination the sound speed of metal element like Pb, Hg and K in aqueous solution. In this attempt a Q-switched Nd:YAG laser was focused to induce optical breakdown and its associated shock wave generation which later follow by the generation of acoustic wave. The phenomenon is observed in conjunction with high speed photography based shadowgraph technique. The experimental results of sound speed for K, Hg and Pb is found in good agreement with the standard value from references. This confirmed that laser induced acoustic wave will be other alternative method for measuring sound speed for metal element in periodic table.
Reducing false positives of microcalcification detection systems by removal of breast arterial calcifications
Authors: Mordang Jan‐Jurre , Gubern‐Mérida Albert , den Heeten Gerard , Karssemeijer Nico 
Published: March 2016

Purpose:In the past decades, computer‐aided detection (CADe) systems have been developed to aid screening radiologists in the detection of malignant microcalcifications. These systems are useful to avoid perceptual oversights and can increase the radiologists’ detection rate. However, due to the high number of false positives marked by these CADe systems, they are not yet suitable as an independent reader. Breast arterial calcifications (BACs) are one of the most frequent false positives marked by CADe systems. In this study, a method is proposed for the elimination of BACs as positive findings. Removal of these false positives will increase the performance of the CADe system in finding malignant microcalcifications.Methods:A multistage method is proposed for the removal of BAC findings. The first stage consists of a microcalcification candidate selection, segmentation and grouping of the microcalcifications, and classification to remove obvious false positives. In the second stage, a case‐based selection is applied where cases are selected which contain BACs. In the final stage, BACs are removed from the selected cases. The BACs removal stage consists of a GentleBoost classifier trained on microcalcification features describing their shape, topology, and texture. Additionally, novel features are introduced to discriminate BACs from other positive findings.Results:The CADe system was evaluated with and without BACs removal. Here, both systems were applied on a validation set containing 1088 cases of which 95 cases contained malignant microcalcifications. After bootstrapping, free‐response receiver operating characteristics and receiver operating characteristics analyses were carried out. Performance between the two systems was compared at 0.98 and 0.95 specificity. At a specificity of 0.98, the sensitivity increased from 37% to 52% and the sensitivity increased from 62% up to 76% at a specificity of 0.95. Partial areas under the curve in the specificity range of 0.8–1.0 were significantly different between the system without BACs removal and the system with BACs removal, 0.129 ± 0.009 versus 0.144 ± 0.008 (p<0.05), respectively. Additionally, the sensitivity at one false positive per 50 cases and one false positive per 25 cases increased as well, 37% versus 51% (p<0.05) and 58% versus 67% (p<0.05) sensitivity, respectively. Additionally, the CADe system with BACs removal reduces the number of false positives per case by 29% on average. The same sensitivity at one false positive per 50 cases in the CADe system without BACs removal can be achieved at one false positive per 80 cases in the CADe system with BACs removal.Conclusions:By using dedicated algorithms to detect and remove breast arterial calcifications, the performance of CADe systems can be improved, in particular, at false positive rates representative for operating points used in screening.