gebhart/patrepeval huggingface dataset:
Regulated expression of Wnt family members during proliferation of C57mg mammary cells. (1994)

At least six members of the Wnt gene family are expressed in the murine mammary gland during growth and differentiation, whereas several other Wnt family members participate in malignant transformation of this tissue. We have used the C57mg mammary cell line, which naturally expresses the Wnt-4 and Wnt-5a genes, to examine Wnt gene expression during proliferation. The data show that the growth factors basic fibroblast growth factor, transforming growth factor beta 1, and epidermal growth factor are mitogenic for C57mg cells, and partial transformation by Wnt-1 can substitute for the proliferative signal provided by these factors. Several different mitogenic stimuli selectively down-modulate the levels of endogenous Wnt-4 and Wnt-5a RNA in C57mg cells. Partial transformation by either Wnt-1 or Wnt-2 is accompanied by a dramatic decrease in Wnt-4 RNA and a small decrease in Wnt-5a RNA. Mitogenic stimulation by basic fibroblast growth factor or partial transformation by Int-2, a fibroblast growth factor family member, also leads to a selective decrease in the levels of endogenous Wnt RNA. No expression of the Wnt-4 and Wnt-5a genes is detectable in C57mg cells that are fully transformed by the activated tyrosine kinase oncogene Neu. In contrast, overexpression of Wnt-5a in C57mg cells does not lead to a transformed phenotype and is not accompanied by a decrease in endogenous Wnt-4 RNA levels. Overexpression of Wnt-5a does lead to a small decrease in endogenous Wnt-5a levels, perhaps through autoregulation. These data indicate that Wnt-4 and Wnt-5a expression in mammary cells is responsive to growth regulatory signals, and the down-modulation of expression of either or both genes correlates with cell proliferation. The inverse correlation between expression of the endogenous Wnt genes and cell proliferation suggests that Wnt-4 and Wnt-5a may participate in restricting the proliferation of C57mg cells.
Isolation enhanced principal component analysis (1999)

Abstract Principal component analysis (PCA) may reduce the dimensionality of plant models significantly by exposing linear dependences among the variables. While PCA is a popular tool in detecting faults in complex plants, it offers little support in its original form for fault isolation. However, by utilizing the equivalence between PCA and parity relations, all the powerful concepts of analytical redundancy may be transferred to PCA. Following this path, it is shown how structured residuals, which have the same isolation properties as analytical redundancy residuals, are obtained by PCA. The existence conditions of such residuals are demonstrated, as well as how disturbance decoupling is implied in the method. The effect of the presence of control constraints in the training data is analyzed. Statistical testing methods for structured PCA residuals are also outlined. The theoretical findings are fully supported by simulation studies performed on the Tennessee Eastman process.
How to Design Practical Client Honeypots Based on Virtual Environment (2016)

Honeypot is known as the most famous and widely deployed tool for collecting malwares on the Internet. Conventional honeypots lure attackers into them by simulating vulnerable applications, programs and services, and are able to collect malwares by monitoring malicious activities of attackers. While client honeypots visit websites linked to URLs which are previously provided by users and collect malwares by analyzing the websites. Since attackers mainly use websites for spreading their well-crafted malwares or compromising their target systems, client honeypots have a remarkable attention for the purpose of collecting malwares effectively. However, most existing approaches focus on only collecting malwares by using open source client honeypots such as Capture-HPC, HoneyClient, HoneyMonkey, etc and analyzing them. In this paper, we present how to design practical client honeypots based on virtual environment. The proposed client honeypots are able to help users who want to develop their own client honeypots and deploy them. The experimental results show that the proposed client honeypots visited 2,276,733 URLs, identified 28,831 malicious URLs and succeeded in collecting 2,115 malwares.
A comparative laboratory trial evaluating the immediate efficacy of fluralaner, afoxolaner, sarolaner and imidacloprid + permethrin against adult Rhipicephalus sanguineus (sensu lato) ticks attached to dogs (2016)

The systemically distributed isoxazolines performed much better than cutaneously distributed imidacloprid + permethrin and are optimal treatment choices against attached ticks based on the combination of earlier onset of activity and speed of kill. Fluralaner had a 4 h onset of activity, an 8 h speed of kill and achieved 100% efficacy at 12 h.
Cell-cycle kinetics and VSV-G pseudotyped retrovirus-mediated gene transfer in blood-derived CD34+ cells. (1996)

As hematopoietic stem and progenitor cells have a low mitotic index, we have quantitated the impact of cytokine combinations on cell cycling of CD34+ cells and, using VSV-G pseudotyped retroviral vectors, correlated our findings with ex vivo gene transfer. We tested nine different combinations of cytokines for induction of human peripheral blood CD34+ cells into cell cycle over 72 hours. Using the 5-bromodeoxyuridine-Hoechst 33258 (BrdU-Hoechst) assay, we measured the cell-cycle kinetics. The combinations of cytokines tested that were most efficient in inducing the CD34+ cells into cycle were stem cell factor (SCF) plus one of the following: interleukin-1 (IL-1), IL-3, granulocyte colony-stimulating factor (G-CSF). The maximum numbers of cells in S+G2M phase were observed after 48 hours of culture. At least 35 +/- 5% of the CD34+ cells remained quiescent in the first G0/G1 phase, however, no matter which cytokine combination was used. Cell-cycle analysis of the CD34+CD38- subset by 7-amino actinomycin D staining did not detect cycling cells during 72 hours of culture with any of the cytokines tested. To investigate whether the cells could be infected by the VSV-G pseudotyped virus containing the neomycin phospho-transferase gene (neo), we exposed CD34+ cells to the virus for 7-8 hours after 0, 36, and 48 hours of cytokine stimulation. Total CD34+ cells and the CD34+CD38- subset were analyzed by polymerase chain reaction (PCR) for reverse-transcribed viral DNA of the neomycin resistance gene (RT-neoDNA). Immediately after exposure to the virus, RT-neoDNA was detectable in CD34+ cells that have been cultured with or without cytokines for 36 to 48 hours. Forty-eight hours postinfection, however, RT-neoDNA could be detected only with cytokine combinations that induced mitosis of the CD34+ cells, consistent with the requirement for mitotic activity for retroviral integration. Similar experiments performed with the 34+CD38- subset showed that RT-reoDNA could not be detected at any time point. Thus, postinfection RT-neoDNA could be immediately detected in noncycling CD34+ cells but not in CD34+CD38- cells. These results suggest during short-term liquid culture, there may be blocks for reverse transcription of retroviral RNA in CD34+CD38-cells in addition to the lack of mitotic activity.
Is cross-validation valid for small-sample microarray classification? (2004)

An extensive simulation study has been performed comparing cross-validation, resubstitution and bootstrap estimation for three popular classification rules-linear discriminant analysis, 3-nearest-neighbor and decision trees (CART)-using both synthetic and real breast-cancer patient data. Comparison is via the distribution of differences between the estimated and true errors. Various statistics for the deviation distribution have been computed: mean (for estimator bias), variance (for estimator precision), root-mean square error (for composition of bias and variance) and quartile ranges, including outlier behavior. In general, while cross-validation error estimation is much less biased than resubstitution, it displays excessive variance, which makes individual estimates unreliable for small samples. Bootstrap methods provide improved performance relative to variance, but at a high computational cost and often with increased bias (albeit, much less than with resubstitution).
Evaluation of clinical phenotype, survival, and circulating tumor cell (CTC) enumeration in men with metastatic castration-resistant prostate cancer (mCRPC). (2013)

5031 Background: The presence of ≥ 5 CTCs is prognostic for shorter survival in mCRPC men. However, many men have low CTCs despite widespread metastatic disease, suggesting heterogeneity in CTC phenotype or detection. We evaluated the association of baseline CTC enumeration with clinical characteristics and survival in mCRPC men at our institution. Methods: CTCs were enumerated with the standard CellSearch method in mCRPC men in a prospective correlative clinical study. The association between baseline CTC count and prostate-specific antigen (PSA), alkaline phosphatase (AP), lactate dehydrogenase (LDH) was explored using the Spearman correlation (r), and the relationship with Gleason sum, sites of metastasis (mets), and prior docetaxel exposure was explored using summary statistics. The overall survival probability (OS) was estimated by the Kaplan-Meier method. Results: In our cohort, 59/82 men had prior docetaxel exposure, and the median CTC count was 16.5. There were 25 men with visceral mets, 55 with bone-predominant mets, and 2 with lymph node only mets. We found a weak relationship between CTCs and PSA (r=0.20), but a more moderate and significant association with AP (r=0.48) and LDH (r= 0.50). We found no relationship between CTCs and Gleason sum, site of mets, or prior docetaxel. 66 men died, and the median OS was 11.2 months (95% CI: 9.2, 12.7). OS was improved in patients with &lt;5 CTCs at baseline compared to ≥ 5 (8.9 vs. 16.6 months, HR=0.47 (95% CI: 0.27, 0.80)). CTC enumeration may further stratify outcomes in men with mCRPC and either visceral or bone metastasis as shown in the table below. Conclusions: The prognostic significance of CTCs is distinct from other established biomarkers and may reflect a unique biology of metastasis, dissociated in part from androgen receptor activity (as reflected by PSA values) but related in part to bone microenvironment, hypoxia, and tumor burden (as reflected by AP and LDH values). These associations need to be validated in larger trials. [Table: see text]
신디케이션 모델(Syndication Model)을 적용한 지적정보 활용 비즈니스 모델 수립 (2005)

최근 지적 및 토지 관련 정보화사업의 지속적 추진과 토지 가격의 안정 그리고 부동산 증권화 제도 도입 등 지적정보를 둘러싼 환경 변화에 부응하는 새로운 형태의 지적정보를 활용한 사업의 중요성이 부각되고 있고, 지적정보에 대한 사회적 수요가 증대하고 있다. 본 연구의 목적은 상기한 환경변화에 대한지적공사가 효과적으로 대처하기 위해 지적정보를 활용한 위치정보 제공에 관한 특화된 사업화 전략을 수립하여 제시하는 것이다. 본 연구에서는 현재 또는 향후 지적정보를 사용하고 있는 고객에 대하여 충족되지 않고 있는 요구들을 조사하였다. 또한 대한지적공사의 핵심 역량과 자원시스템을 분석하여 고객 중심의 서비스 강화 및 수익성 향상을 도모하는 신디케이션 비즈니스 모델을 설계하고 구체적인 실행계획을 제시하였다. 연구 결과물들은 향후 GIS, ITS, 텔레매틱스 등의 유사분야에서도 학문적으로나 실증적으로 접목되어 활용될 수 있을 것이다.
Sperm storage and antioxidative enzyme expression in the honey bee, Apis mellifera (2004)

Honey bee (Apis mellifera) sperm remains viable in the spermatheca of mated female honey bees for several years. During this time, the sperm retains respiratory activity, placing it at risk of the damaging effects of reactive oxygen species common to many biological processes. Antioxidative enzymes might help reduce this damage. Here we use quantitative real-time RT-PCR to establish gene-expression profiles in male and female honey bee reproductive tissues for three antioxidative enzymes: catalase, glutathione-S-transferase (GST) and superoxide dismutase (SOD1, cytosolic). Catalase and GST showed ten- to twenty-fold transcript increases in the sperm storage organs of mated queens vs. unmated queens, whereas SOD1 levels are high in both mated and unmated queens. Male reproductive and somatic tissues showed relatively high levels of all three antioxidant-encoding transcripts. All three enzymes screened were higher in mature males vs. young males, although this effect did not appear to be confined to reproductive tissues and, hence, need not reflect a role in sperm longevity. Furthermore, antioxidative enzyme transcripts remained present, and apparently increased, in male tissues long after sperm had matured and seminal fluid was produced. We also found measurable levels of catalase transcripts in honey bee semen. The presence of catalase transcripts in both reproductive tissues and semen in bees suggests that this enzyme might play a key role in antioxidative protection.
Dual analyte flow injection fluorescence immunoassays using thiophilic gel reactors and synchronous scanning detection (2000)

Heterogeneous fluorescence immunoassays have been automated using flow injection manifolds incorporating thiophilic gel solid phase reactors to separate antibody-bound and unbound analyte molecules. Antibody elution is achieved by changes in ionic strength, thus allowing the use of pH sensitive fluorescent labels. This facilitates the development of dual analyte systems, in which two competitive immunoassays with separate labels are monitored in parallel. Detection of the fluorophores by high speed synchronous fluorescence scanning while the flow is briefly stopped utilises either one synchronous interval which detects both fluorophores, or two separate scans at different wavelength intervals, one for each fluorophore. Simultaneous analyses of serum albumin and transferrin exemplify these novel approaches. Spectroscopic interferences are very small, analyte recoveries are close to 100%, with a relative standard deviation of 5-6% and a sampling rate of 20 h-1.
Improved Detection of Quantitative Differences Using a Combination of Spectral Counting and MS/MS Total Ion Current (2013)

Label-free quantitative strategies are commonly used in shotgun proteomics to detect differences in protein abundance between biological sample groups. Here, we have employed a combination of two such approaches, spectral counting (SpC) and average MS/MS total ion current (MS(2) TIC), for the analysis of rat kidney mitochondria in response to metabolic acidosis. In total, 49 proteins were observed to be significantly altered in response to metabolic acidosis (p-value < 0.05). Of these, 32 proteins were uniquely observed as significantly different by SpC, 14 by MS(2) TIC, and only 3 by both approaches. Western blot analysis was performed on a subset of these proteins to validate the observed abundance differences. This study illustrates the utility and ease of combining these two label-free quantitative approaches to increase the number of detected protein abundance differences in the shotgun analysis of complex biological samples.
Modulation of the Intestinal Microbiota Alters Colitis-Associated Colorectal Cancer Susceptibility (2009)

It is well established that the intestinal microbiota plays a key role in the pathogenesis of Crohn's disease (CD) and ulcerative colitis (UC) collectively referred to as inflammatory bowel disease (IBD). Epidemiological studies have provided strong evidence that IBD patients bear increased risk for the development of colorectal cancer (CRC). However, the impact of the microbiota on the development of colitis-associated cancer (CAC) remains largely unknown. In this study, we established a new model of CAC using azoxymethane (AOM)-exposed, conventionalized-Il10(-/-) mice and have explored the contribution of the host intestinal microbiota and MyD88 signaling to the development of CAC. We show that 8/13 (62%) of AOM-Il10(-/-) mice developed colon tumors compared to only 3/15 (20%) of AOM- wild-type (WT) mice. Conventionalized AOM-Il10(-/-) mice developed spontaneous colitis and colorectal carcinomas while AOM-WT mice were colitis-free and developed only rare adenomas. Importantly, tumor multiplicity directly correlated with the presence of colitis. Il10(-/-) mice mono-associated with the mildly colitogenic bacterium Bacteroides vulgatus displayed significantly reduced colitis and colorectal tumor multiplicity compared to Il10(-/-) mice. Germ-free AOM-treated Il10(-/-) mice showed normal colon histology and were devoid of tumors. Il10(-/-); Myd88(-/-) mice treated with AOM displayed reduced expression of Il12p40 and Tnfalpha mRNA and showed no signs of tumor development. We present the first direct demonstration that manipulation of the intestinal microbiota alters the development of CAC. The TLR/MyD88 pathway is essential for microbiota-induced development of CAC. Unlike findings obtained using the AOM/DSS model, we demonstrate that the severity of chronic colitis directly correlates to colorectal tumor development and that bacterial-induced inflammation drives progression from adenoma to invasive carcinoma.
Slow-Cycling Therapy-Resistant Cancer Cells (2011)

Tumor recurrence after chemotherapy is a major cause of patient morbidity and mortality. Recurrences are thought to be secondary to small subsets of cancer cells that are better able to survive traditional forms of chemotherapy and thus drive tumor regrowth. The ability to isolate and better characterize these therapy-resistant cells is critical for the future development of targeted therapies aimed at achieving more robust and long-lasting responses. Using a novel application for the proliferation marker carboxyfluorescein diacetate, succinimidyl ester (CFSE), we have identified a population of slow-cycling, label-retaining tumor cells in both in vitro sphere cultures and in vivo xenograft models. Strikingly, label-retaining cells exhibit a multifold increase in ability to survive traditional forms of chemotherapy and reenter the cell cycle. Further, we demonstrate the innovative application of CFSE to live sort slow-cycling tumor cells and validate their chemoresistance and tumorigenic potential.
T-cell apoptosis and suppression of T-cell receptor/CD3-zeta by Fas ligand-containing membrane vesicles shed from ovarian tumors. (2003)

Our results suggest that FasL associated with tumor-derived MFs is responsible for apoptosis of T lymphocytes and a concomitant loss of zeta-chain expression in patients with ovarian carcinoma.
Chlamydia trachomatis Mip‐like protein has peptidylprolyl cis/trans isomerase activity that is inhibited by FK506 and rapamycin and is implicated in initiation of chlamydial infection (1993)

The Mip-like protein of Chlamydia trachomatis has sequence similarity with both the Mip protein of Legionella pneumophila, a virulence factor necessary for optimal intracellular infection, and FK506-binding proteins (FKBPs) of both prokaryotic and eukaryotic origin. FKBPs contain a site for peptidyl-prolyl cis/trans isomerase activity, which is blocked upon binding of the drugs, FK506 or rapamycin. In this paper we report that the recombinant chlamydial Mip-like protein exhibits a peptidyl-prolyl cis/trans isomerase activity which is inhibited by either rapamycin or FK506. To assess the role of the Mip-like protein in chlamydial infection, rapamycin or FK506 (25 microM), were used in either treatment of chlamydial organisms prior to inoculation, or were present at different intervals through the infection. Pretreatment of organisms alone reduced infectivity for McCoy cells by 30%, with inhibition rising to 80% on more prolonged exposure from 0 to 8h and 8 to 16h post-inoculation and declining thereafter. When drug was present during the developmental cycle at intervals from 0 to 24h post-inoculation abnormal chlamydiae were induced in residual inclusions. The results suggest that inhibition of the isomerase of the Mip-like protein interferes with one or more early events in the infective process that determine productive intracellular infection.
Structural characterization of factor I mediated cleavage of the third component of complement (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructural characterization of factor I mediated cleavage of the third component of complementAlvin E. Davis III and Richard A. HarrisonCite this: Biochemistry 1982, 21, 23, 5745–5749Publication Date (Print):November 9, 1982Publication History Published online1 May 2002Published inissue 9 November 1982https://pubs.acs.org/doi/10.1021/bi00266a003https://doi.org/10.1021/bi00266a003research-articleACS PublicationsRequest reuse permissionsArticle Views93Altmetric-Citations61LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Enrichment map profiling of the cancer invasion front suggests regulation of colorectal cancer progression by the bone morphogenetic protein antagonist, gremlin‐1 (2013)

The cancer invasion front (CIF), a spatially-recognized area due to the frequent presence of peritumoral desmoplastic reaction, represents a cancer site where many hallmarks of cancer metastasis occur. It is now strongly suggested that the desmoplastic microenvironment holds crucial information for determining tumor development and progression. Despite extensive research on tumor-host cell interactions at CIFs, the exact paracrine molecular network that is hardwired into the proteome of the stromal and cancer subpopulations remains partially understood. Here, we interrogated the signaling pathways and the molecular functional signatures across the proteome of a desmoplastic coculture model system of colorectal cancer progression. We discovered a group of bone morphogenetic protein (BMP) antagonists that coordinates major biological programs in CIFs, including cell proliferation, invasion, migration and differentiation processes. Using a mathematical model of cancer cell progression, coupled to in vitro cell migration assays, we demonstrated that the prominent BMP antagonist gremlin-1 (GREM1) may trigger motility of cancer cell cohorts. Our data collectively demonstrate that the desmoplastic CIFs deploy a microenvironmental signature, based on BMP antagonism, in order to regulate the motogenic fates of cancer cell cohorts invading the adjacent stroma.
Differentiation of HPV-Containing Cells Using Organotypic (2005)

The study of human papillomaviruses (HPVs) has been challenging due to the differentiation-dependent aspects of their productive life cycles. The use of HPV virions, isolated from tissues, to study viral pathogenesis has been complicated due to the low numbers of HPV virions synthesized and inefficient infection of cells in tissue culture. As an alternative approach, genetic methods have been developed to study the papillomavirus life cycle in its natural host, human keratinocytes. Techniques have been developed to transfect keratinocytes with cloned HPV DNA and to isolate cell lines that maintain viral DNA as extra-chromosomal elements. Since the productive phase of the HPV life cycle is dependent on differentiation, in vitro tissue-culture models have also been used to recapitulate epithelial differentiation. Differentiation in organotypic raft cultures as well as upon suspension in semi-solid media have been used to study both early and late stages of the viral life cycle.