bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epstein-barr virus infected gastric adenocarcinoma expresses latent and lytic viral transcripts and has a distinct human gene expression profile
Authors: Tang Weihua , Morgan Douglas R , Meyers Michael O , Dominguez Ricardo L , Martinez Enrique , Kakudo Kennichi , Kuan Pei Fen , Banet Natalie , Muallem Hind , Woodward Kimberly , Speck Olga , Gulley Margaret L 
Published: August 2012

AbstractBackgroundEBV DNA is found within the malignant cells of 10% of gastric cancers. Modern molecular technology facilitates identification of virus-related biochemical effects that could assist in early diagnosis and disease management.MethodsIn this study, RNA expression profiling was performed on 326 macrodissected paraffin-embedded tissues including 204 cancers and, when available, adjacent non-malignant mucosa. Nanostring nCounter probes targeted 96 RNAs (20 viral, 73 human, and 3 spiked RNAs).ResultsIn 182 tissues with adequate housekeeper RNAs, distinct profiles were found in infectedversusuninfected cancers, and in malignantversusadjacent benign mucosa. EBV-infected gastric cancers expressed nearly all of the 18 latent and lytic EBV RNAs in the test panel. Levels ofEBER1andEBER2RNA were highest and were proportional to the quantity of EBV genomes as measured by Q-PCR. Among protein coding EBV RNAs,EBNA1from the Q promoter andBRLF1were highly expressed whileEBNA2levels were low positive in only 6/14 infected cancers. Concomitant upregulation of cellular factors implies that virus is not an innocent bystander but rather is linked to NFKB signaling (FCER2, TRAF1) and immune response(TNFSF9, CXCL11, IFITM1, FCRL3, MS4A1 and PLUNC), withPPARGexpression implicating altered cellular metabolism. Compared to adjacent non-malignant mucosa, gastric cancers consistently expressedINHBA, SPP1, THY1, SERPINH1, CXCL1, FSCN1, PTGS2 (COX2), BBC3, ICAM1, TNFSF9, SULF1, SLC2A1, TYMS, three collagens, the cell proliferation markersMYCandPCNA, and EBVBLLF1while they lackedCDH1 (E-cadherin), CLDN18,PTEN, SDC1(CD138),GAST(gastrin) and its downstream effectorCHGA(chromogranin). Compared to lymphoepithelioma-like carcinoma of the uterine cervix, gastric cancers expressedCLDN18, EPCAM, REG4, BBC3, OLFM4, PPARG, andCDH17while they had diminished levels ofIFITM1andHIF1A. The druggable targets ERBB2 (Her2), MET, and the HIF pathway, as well as several other potential pharmacogenetic indicators (including EBV infection itself, as well asSPARC, TYMS, FCGR2BandREG4) were identified in some tumor specimens.ConclusionThis study shows how modern molecular technology applied to archival fixed tissues yields novel insights into viral oncogenesis that could be useful in managing affected patients.
CADLIVE optimizer: web-based parameter estimation for dynamic models
Authors: Inoue Kentaro , Maeda Kazuhiro , Kato Yuki , Tonami Shinpei , Takagi Shogo , Kurata Hiroyuki 
Published: August 2012

Abstract
Computer simulation has been an important technique to capture the dynamics of biochemical networks. In most networks, however, few kinetic parameters have been measured in vivo because of experimental complexity. We develop a kinetic parameter estimation system, named the CADLIVE Optimizer, which comprises genetic algorithms-based solvers with a graphical user interface. This optimizer is integrated into the CADLIVE Dynamic Simulator to attain efficient simulation for dynamic models.
New bactericide derived from Isatin for treating oilfield reinjection water
Authors: Chen Gang , Su Hui-jun , Zhang Min , Huo Fang , Zhang Jie , Hao Xiao-jiang , Zhao Jing-rui 
Published: August 2012

Abstract
Isatin, an extract from Strobilanthes cusia (Nees) Kuntze, was the base for synthesizing derivatives that were screened for antibacterial activity against oilfield water-borne bacteria. The bacterial groups are sulfate reducing, iron and total. The derivatives were characterized by spectrums and they showed good to moderate activity against sulfate reducing bacteria.
Portable bacterial identification system based on elastic light scatter patterns
Authors: Bae Euiwon , Ying Dawei , Kramer Donald , Patsekin Valery , Rajwa Bartek , Holdman Cheryl , Sturgis Jennifer , Davisson V Jo , Robinson J Paul 
Published: August 2012

Abstract

Background
Conventional diagnosis and identification of bacteria requires shipment of samples to a laboratory for genetic and biochemical analysis. This process can take days and imposes significant delay to action in situations where timely intervention can save lives and reduce associated costs. To enable faster response to an outbreak, a low-cost, small-footprint, portable microbial-identification instrument using forward scatterometry has been developed.

Results
This device, weighing 9 lb and measuring 12 × 6 × 10.5 in., utilizes elastic light scatter (ELS) patterns to accurately capture bacterial colony characteristics and delivers the classification results via wireless access. The overall system consists of two CCD cameras, one rotational and one translational stage, and a 635-nm laser diode. Various software algorithms such as Hough transform, 2-D geometric moments, and the traveling salesman problem (TSP) have been implemented to provide colony count and circularity, centering process, and minimized travel time among colonies.

Conclusions
Experiments were conducted with four bacteria genera using pure and mixed plate and as proof of principle a field test was conducted in four different locations where the average classification rate ranged between 95 and 100%.
Rapid phylogenetic and functional classification of short genomic fragments with signature peptides
Authors: Berendzen Joel , Bruno William J , Cohn Judith D , Hengartner Nicolas W , Kuske Cheryl R , McMahon Benjamin H , Wolinsky Murray A , Xie Gary 
Published: August 2012

Abstract

Background
Classification is difficult for shotgun metagenomics data from environments such as soils, where the diversity of sequences is high and where reference sequences from close relatives may not exist. Approaches based on sequence-similarity scores must deal with the confounding effects that inheritance and functional pressures exert on the relation between scores and phylogenetic distance, while approaches based on sequence alignment and tree-building are typically limited to a small fraction of gene families. We describe an approach based on finding one or more exact matches between a read and a precomputed set of peptide 10-mers.

Results
At even the largest phylogenetic distances, thousands of 10-mer peptide exact matches can be found between pairs of bacterial genomes. Genes that share one or more peptide 10-mers typically have high reciprocal BLAST scores. Among a set of 403 representative bacterial genomes, some 20 million 10-mer peptides were found to be shared. We assign each of these peptides as a signature of a particular node in a phylogenetic reference tree based on the RNA polymerase genes. We classify the phylogeny of a genomic fragment (e.g., read) at the most specific node on the reference tree that is consistent with the phylogeny of observed signature peptides it contains. Using both synthetic data from four newly-sequenced soil-bacterium genomes and ten real soil metagenomics data sets, we demonstrate a sensitivity and specificity comparable to that of the MEGAN metagenomics analysis package using BLASTX against the NR database. Phylogenetic and functional similarity metrics applied to real metagenomics data indicates a signal-to-noise ratio of approximately 400 for distinguishing among environments. Our method assigns ~6.6 Gbp/hr on a single CPU, compared with 25 kbp/hr for methods based on BLASTX against the NR database.

Conclusions
Classification by exact matching against a precomputed list of signature peptides provides comparable results to existing techniques for reads longer than about 300 bp and does not degrade severely with shorter reads. Orders of magnitude faster than existing methods, the approach is suitable now for inclusion in analysis pipelines and appears to be extensible in several different directions.
Epidemiology of anti-tuberculosis drug resistance patterns and trends in tuberculosis referral hospital in Addis Ababa, Ethiopia
Authors: Abate Dereje , Taye Bineyam , Abseno Mohammed , Biadgilign Sibhatu 
Published: August 2012

Abstract

Background
Drug-resistant TB has emerged as a major challenge facing TB prevention and control efforts. In Ethiopia, the extent/trend of drug resistance TB is not well known. The aim of this study was to determine the pattern and trend of resistance to first line anti-TB drugs among culture positive retreatment cases at St.Peter’s TB Specialized Hospital.

Findings
A hospital based retrospective study was used to assess the pattern of anti-TB drug resistance among previously treated TB patients referred to St.Peter’s TB Specialized Hospital from January 2004-December 2008 Gregorian calendar(GC) for better diagnosis and treatment.
Among 376 culture positive for M. tuberculosis one hundred and two (27.1%) were susceptible to all of the four first line anti-TB drugs -Isoniazid (INH), Rifampicin (RIF), Ethambutol (ETB) & Streptomycin (STM). While 274 (72.9%) were resistant to at least one drug. Any resistance to STM (67.3%) was found to be the most common and the prevalence of MDR-TB was 174 (46.3%). Trend in resistance rate among re-treatment cases from 2004 to 2008 showed a significant increase for any drug as well as for INH, RIF, and MDR resistance (P <0.05 for trend).

Conclusions
There has been an increasing trend in drug resistance in recent years, particularly in retreatment cases. Therefore, establishing advanced diagnostic facilities for early detection of MDR-TB and expanding second line treatment center to treat MDR-TB patients and to prevent its transmission is recommended.
Specific-mutational patterns of p53 gene in bladder transitional cell carcinoma among a group of Iraqi patients exposed to war environmental hazards
Authors: Al-Kashwan Thekra A , Houshmand Massoud , Al-Janabi Asaad , Melconian Alice K , Al-Abbasi Dhafir , Al-Musawi Muhammad N , Rostami Maryam , Yasseen Akeel A 
Published: August 2012

Abstract

Background
To unfold specific-mutational patterns in TP53 gene due to exposures to war environmental hazards and to detect the association of TP53 gene alteration with the depth of bladder cancer.

Methods
Twenty-nine bladder carcinomas were analyzed for TP53 alterations. PCR-single strand conformational polymorphism analysis, DNA sequencing and immunohistochemical analysis using monoclonal mouse anti-human p53 antibody (Clone DO-7) were employed.

Results
TP53 gene mutations occurred in 37.9% of the cases while TP53 overexpression occurred in 58.6%. Both of them were associated with deep invasive-tumors. Single mutations were seen in 63.6%, whereas only 27.3% have shown double mutations. Four mutations were frameshifted (30.8%); two of them showed insertion A after codon 244. There was no significant association between TP53 mutations and protein overexpression (P>0.05), while a significant association was observed between TP53 alterations and tumors progression (P ≤ 0.01).

Conclusion
The infrequent TP53mutations, especially insertion A and 196 hotspot codon, may represent the specific-mutational patterns in bladder carcinoma among the Iraqi patients who were exposed to war environmental hazards. TP53 alteration associated with bladder cancer progression should be analyzed by both mutational and protein expression analysis.
Selected imprinting of INS in the marsupial
Authors: Stringer Jessica M , Suzuki Shunsuke , Pask Andrew J , Shaw Geoff , Renfree Marilyn B 
Published: August 2012

Abstract

Background
In marsupials, growth and development of the young occur postnatally, regulated by milk that changes in composition throughout the long lactation. To initiate lactation in mammals, there is an absolute requirement for insulin (INS), a gene known to be imprinted in the placenta. We therefore examined whether INS is imprinted in the mammary gland of the marsupial tammar wallaby (Macropus eugenii) and compared its expression with that of insulin-like growth factor 2 (IGF2).

Results

INS was expressed in the mammary gland and significantly increased, while IGF2 decreased, during established milk production. Insulin and IGF2 were both detected in the mammary gland macrophage cells during early lactation and in the alveolar cells later in lactation. Surprisingly, INS, which was thought only to be imprinted in the therian yolk sac, was imprinted and paternally expressed in the liver of the developing young, monoallelically expressed in the tammar mammary gland and biallelic in the stomach and intestine. The INS transcription start site used in the liver and mammary gland was differentially methylated.

Conclusions
This is the first study to identify tissue-specific INS imprinting outside the yolk sac. These data suggest that there may be an advantage of selective monoallelic expression in the mammary gland and that this may influence the growth of the postnatal young. These results are not consistent with the parental conflict hypothesis, but instead provide support for the maternal–infant co-adaptation hypothesis. Thus, imprinting in the mammary gland maybe as critical for postnatal growth and development in mammals as genomic imprinting in the placenta is prenatally.
GC-MS analysis of insecticidal essential oil of flowering aerial parts of Saussurea nivea Turcz
Authors: Chu Sha Sha , Jiang Guo Hua , Liu Zhi Long 
Published: August 2012

Abstract

Background
Several species from Saussurea have been used in the traditional medicine, such as S. lappa, S. involucrate, and S. obvallata. There is no report on medicinal use of S. nivea. The aim of this research was to determine chemical composition and insecticidal activity of the essential oil of S. nivea Turcz (Asteraceae) aerial parts against maize weevils (Sitophilus zeamais Motschulsky) for the first time.

Results
Essential oil of S. nivea flowering aerial parts was obtained by hydrodistillation and analyzed by gas chromatography–mass spectrometry (GC-MS). A total of 43 components of the essential oil of S. nivea were identified. The principal compounds in the essential oil were (+)-limonene (15.46%), caryophyllene oxide (7.62%), linalool (7.20%), α-pinene (6.43%), β-pinene (5.66%) and spathulenol (5.02%) followed by β-eudesmoll (4.64%) and eudesma-4,11-dien-2-ol (3.76%). The essential oil of S. nivea exhibited strong contact toxicity against S. zeamais with an LD50 value of 10.56 μg/adult. The essential oil also possessed fumigant toxicity against S. zeamais with an LC50 value of 8.89 mg/L.

Conclusion
The study indicates that the essential oil of S. nivea flowering aerial parts has a potential for development into a natural insecticide/fumigant for control of insects in stored grains.
Concomitant production of lipase, protease and enterocin by Enterococcus faecium NCIM5363 and Enterococcus durans NCIM5427 isolated from fish processing waste
Authors: Ramakrishnan Vrinda , Balakrishnan Bijinu , Rai Amit Kumar , Narayan Bhaskar , Halami Prakash M 
Published: August 2012

Abstract
Enterococci are widely distributed in the environment ranging from foods to humans and are gaining industrial importance due to their technological traits. In the present study, enterococci (Enterococcus faecium NCIM5363 (EF-63) and Enterococcus durans NCIM5427 (ED-27)) which are native to fish processing waste with an ability to produce lipase, protease and enterocin concomitantly were characterised. Lipase assay was performed by titrimetry and protease activity and was estimated using haemoglobin and casein as substrates in the presence of buffers at acidic, basic and neutral pH. Furthermore, enterocin produced by the isolates was characterised. Enterocin was also checked for its stability at different pH, temperature and proteolytic enzymes. Lipase production was found to be 22 and 10 U/ml in the absence of tributryin and increased to 40 and 24 U/ml in its presence for EF-63 and ED-27, respectively, indicating that the lipase produced is substrate dependent. Protease production was confirmed by protease assay, and the protease produced showed more affinity towards the acidic substrate. Enterocin produced was stable at low pH (2 to 3) and high temperature (121°C, 15 min) and had a molecular weight of approximately 6 kDa. It exhibited antibacterial activity against both Gram-positive and Gram-negative food-borne pathogens. Proteinase K inactivated enterocin completely, whereas trypsin did not. Novelty of this work lies in the immense industrial importance these cultures hold as they are capable of producing lipase, protease and enterocin apart from being useful in recovering proteins and lipids from fish processing wastes.
Tumor Stage Affects Risk and Prognosis of Contralateral Breast Cancer: Results From a Large Swedish-Population–Based Study
Authors: Vichapat Voralak , Garmo Hans , Holmqvist Marit , Liljegren Göran , Wärnberg Fredrik , Lambe Mats , Fornander Tommy , Adolfsson Jan , Lüchtenborg Margreet , Holmberg Lars 
Published: August 2012

Purpose The number of breast cancer survivors at risk of developing contralateral breast cancer (CBC) is increasing. However, ambiguity remains regarding risk factors and prognosis for women with CBC. Patients and Methods In a cohort of 42,670 women with breast cancer in the Uppsala/Örebro and Stockholm regions in Sweden in 1992 to 2008, we assessed risk factors for and prognosis of metachronous CBC by using survival analysis. Breast cancer–specific survival for women with CBC was evaluated and compared with results for women with unilateral breast cancer (UBC) by using time-dependent Cox-regression modeling. Results An increased risk for CBC was observed among women who had primary breast cancer with ≥ 10 involved lymph nodes compared with node-negative women (adjusted hazard ratio [HR], 1.8; 95% CI, 1.2 to 2.7). The prognosis was poorer in women with CBC than with UBC. The hazard of dying from breast cancer was especially high for women with a short interval time to CBC (adjusted HR, 2.3; 95% CI, 1.8 to 2.8 for CBC diagnosed ≤ 5 years v UBC) and gradually decreased with longer follow-up time but remained higher than the hazard originating from the primary tumor for ≥ 10 years. Conclusion Women with advanced-stage primary breast cancer had an increased risk of developing CBC. CBC is associated with an increased risk of dying from breast cancer throughout a long period of follow-up after the primary tumor. Our findings suggest that the event of CBC marks a new clinical situation in terms of investigations for metastases, treatment considerations, and follow-up strategy.
Clinical Significance of Tumor-Associated Inflammatory Cells in Metastatic Neuroblastoma
Authors: Asgharzadeh Shahab , Salo Jill A. , Ji Lingyun , Oberthuer André , Fischer Matthias , Berthold Frank , Hadjidaniel Michael , Liu Cathy Wei-Yao , Metelitsa Leonid S. , Pique-Regi Roger , Wakamatsu Peter , Villablanca Judith G. , Kreissman Susan G. , Matthay Katherine K. , Shimada Hiroyuki , London Wendy B. , Sposto Richard , Seeger Robert C. 
Published: August 2012

Purpose Children diagnosed at age ≥ 18 months with metastatic MYCN-nonamplified neuroblastoma (NBL-NA) are at high risk for disease relapse, whereas those diagnosed at age < 18 months are nearly always cured. In this study, we investigated the hypothesis that expression of genes related to tumor-associated inflammatory cells correlates with the observed differences in survival by age at diagnosis and contributes to a prognostic signature. Methods Tumor-associated macrophages (TAMs) in localized and metastatic neuroblastomas (n = 71) were assessed by immunohistochemistry. Expression of 44 genes representing tumor and inflammatory cells was quantified in 133 metastatic NBL-NAs to assess age-dependent expression and to develop a logistic regression model to provide low- and high-risk scores for predicting progression-free survival (PFS). Tumors from high-risk patients enrolled onto two additional studies (n = 91) served as independent validation cohorts. Results Metastatic neuroblastomas had higher infiltration of TAMs than locoregional tumors, and metastatic tumors diagnosed in patients at age ≥ 18 months had higher expression of inflammation-related genes than those in patients diagnosed at age < 18 months. Expression of genes representing TAMs (CD33/CD16/IL6R/IL10/FCGR3) contributed to 25% of the accuracy of a novel 14-gene tumor classification score. PFS at 5 years for children diagnosed at age ≥ 18 months with NBL-NA with a low- versus high-risk score was 47% versus 12%, 57% versus 8%, and 50% versus 20% in three independent clinical trials, respectively. Conclusion These data suggest that interactions between tumor and inflammatory cells may contribute to the clinical metastatic neuroblastoma phenotype, improve prognostication, and reveal novel therapeutic targets.
Prognostic Significance of Signet Ring Gastric Cancer
Authors: Taghavi Sharven , Jayarajan Senthil N. , Davey Adam , Willis Alliric I. 
Published: August 2012

PurposeStudies in Asia have questioned the dictum that signet ring cell carcinoma (SRC) has a worse prognosis than other forms of gastric cancer. Our study determined differences in presentation and outcomes between SRC and gastric adenocarcinoma (AC) in the United States.Patients and MethodsThe National Cancer Institute Surveillance, Epidemiology, and End Results database was reviewed for SRC and AC from 2004 to 2007.ResultsWe reviewed 10,246 cases of patients with gastric cancer, including 2,666 of SRC and 7,580 of AC. SRC presented in younger patients (61.9 v 68.7 years; P < .001) and less often in men (52.7% v 68.7%; P < .001). SRC patients were more frequently black (11.3% v 10.9%), Asian (16.4% v 13.2%), American Indian/Alaska Native (0.9% v 0.8%), or Hispanic (23.3% v 14.0%; P < .001). SRC was more likely to be stage T3-4 (45.8% v 33.3%), have lymph node spread (59.7% v 51.8%), and distant metastases (40.2% v 37.6%; P < .001). SRC was more likely to be found in the lower (30.7% v 24.2%) and middle stomach (30.6% v 20.7%; P < .001). Median survival was not different between the two (AC, 14.0 months v SRC, 13.0 months; P = .073). Multivariable analyses demonstrated SRC was not associated with mortality (hazard ratio [HR], 1.05; 95% CI, 0.96 to 1.11; P = .150). Mortality was associated with age (HR, 1.01; 95% CI, 1.01 to 1.02; P < .001), black race (HR, 1.10; 95% CI, 1.01 to 1.20; P = .026), and tumor grade. Variables associated with lower mortality risk included Asian race (HR, 0.83; 95% CI, 0.77 to 0.91; P < .001) and surgery (HR, 0.37; 95% CI, 0.34 to 0.39; P < .001).ConclusionIn the United States, SRC significantly differs from AC in extent of disease at presentation. However, when adjusted for stage, SRC does not portend a worse prognosis.