gebhart/patrepeval huggingface dataset:
Linkage and association of CYP17 gene in hereditary and sporadic prostate cancer (2001)

Androgens are essential for prostate development, growth and maintenance and the association between androgen levels and prostate cancer is well established. Since the CYP17 gene encodes the enzyme cytochrome P450c17alpha, which mediates 17alpha-hydroxylase and 17,20-lyase activities in the androgen biosynthesis pathway, sequence variations in the gene and association with increased risk to prostate cancer has been studied. In particular, several groups have studied the association between a polymorphism in the 5' promoter region and prostate cancer using a population-based association approach. However, the results from these studies were inconclusive. To further study this polymorphism and its possible role in hereditary prostate cancer (HPC), we performed a genetic linkage analysis and family-based association analysis in 159 families, each of which contains at least 3 first-degree relatives with prostate cancer. In addition, we performed a population-based association analysis to compare the risk of this polymorphism to hereditary and sporadic prostate cancer in 159 HPC probands, 249 sporadic prostate cancer patients and 211 unaffected control subjects. Evidence for linkage at the CYP17 gene region was found in the total 159 HPC families (LOD = 1.3, p = 0.01, at marker D10S222). However, family-based association tests did not provide evidence for overtransmission of either allele of the CYP17 polymorphism to affected individuals in the HPC families. The allele and genotype frequencies of the polymorphism were not statistically different among the HPC probands, sporadic cases and unaffected control subjects. In conclusion, our results suggest that the CYP17 gene or other genes in the region may increase the susceptibility to prostate cancer in men; however, the polymorphism in the 5' promoter region has a minor role if any in increasing prostate cancer susceptibility in our study sample.
In silico identification of vaccine candidates against enteric pathogens by a comparative genome sequence approach (2010)

Enteropathogens are among the most important human pathogens. Enteric pathogens including Shigella spp, Es- cherichia coli, Vibrio cholerae, Salmonella spp. and Yersinia enterocolitica account for a significant percentage of diarrheal diseases in the developing world. The antigenic diversity among various circulating strains of these pathogens is a cause of concern to those developing effective vaccines. In this context, we searched for any conserved bacterial cell surface located proteins which are shared among most of the above mentioned pathogens that could be used as potential vaccine candidates to neutralize most of them if not all of them. Various in silico procedures were applied to identify such vaccine candidates by adopting a scheme of stepwise eliminations. The study resulted in identifying total 11 expressed (protein producing) genes of interest; of these 3 appeared to be strong vaccine candidates, and could also act as good diagnostic markers for discrimination of closely related diarrheagenic bacterial species.
β‐catenin accumulation and mutation of the CTNNB1 gene in hepatoblastoma (1999)

Hepatoblastoma is a rare malignant tumor of the liver that occurs in children at an average age of 2 to 3 years. Epidemiologic studies have shown an increased frequency of this tumor type in families affected by adenomatous polyposis coli. In addition to the epidemiologic data, molecular genetic studies suggest that inactivation of the APC tumor suppressor may be involved in hepatoblastoma tumorigenesis. A major function of APC is the downregulation of β-catenin, a transcription-activating protein with oncogenic potential. In an ongoing immunohistochemical study of β-catenin expression in sporadic cases of tumor types that are associated with adenomatous polyposis coli, we observed increased β-catenin levels in the cytoplasm and in the nuclei of three investigated hepatoblastomas. Sequencing of exon 3 of the β-catenin gene (CTNNB1) revealed an activating mutation in one of the tumor samples. Our data indicate for the first time that β-catenin accumulation may play a role in the development of hepatoblastoma and that activating mutations of the β-catenin gene may substitute biallelic APC inactivation in this tumor type. Genes Chromosomes Cancer 25:399–402, 1999. © 1999 Wiley-Liss, Inc.
Label-Free Biosensor Arrays Based on Silicon Ring Resonators and High-Speed Optical Scanning Instrumentation (2010)

A platform for performing rapid, real-time binding assays on sensor arrays based on silicon ring resonators is presented in this paper. An array of 32 sensors is interrogated simultaneously. Using eight sensors as controls, 24 simultaneous binding curves are produced. The bulk refractive index sensitivity of the system was demonstrated down to 7.6 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-7</sup> and sensor-to-sensor variability is 3.9%. Using an 8-min incubation, real-time binding was observed over 8-logs of concentration down to 60 fM using immobilized biotin to capture streptavidin diluted in bovine serum albumin solution. Multiplexing in complex media is demonstrated with two DNA oligonucleotide probes. Time to result and repeatability are demonstrated to be adequate for clinical applications.
Role of microRNA in melanoma progression (2006)

1Department of Dermatology and Venereology 2Department of Immunogenetics Abstracts of the Perspectives in Melanoma X and The Third Annual International Melanoma Research Congress, 14–16 September 2006, Noordwijk, The Netherlands
Temperature-dependent photoluminescence properties of Mn:ZnCuInS nanocrystals (2015)

Different particle sizes of colloidal Mn doped ZnCuInS (Mn:ZCIS) nanocrystals were prepared with different reaction times in a noncoordinating solvent. Different test methods were used to reveal the successful incorporation of Mn2+ ion into ZCIS nanocrystals for obtaining the Mn d-state emission. We investigated the temperature-dependent PL spectra of Mn:ZCIS nanocrystals show a redshift with decreasing intensity at low temperature (20–300 K). The energy levels, FWHM of the PL peak and PL Intensity of nanocrystals with different diameters were investigated as a function of temperature in the range 20−300 K. We found that the variation of both energy level and PL peak broadening for Mn:ZCIS nanocrystals were most likely caused by the coupling of the carrier to acoustic phonon.
Integrated THz technology for label-free genetic diagnostics (2002)

We report on a promising approach for the label-free analysis of DNA molecules using direct probing of the binding state of DNA with electromagnetic waves at THz frequencies. Passive THz resonator devices based on planar waveguides are used as sample carriers and transducers for THz transmission analysis. In comparison to a formerly used free-space detection scheme, this method provides a drastically enhanced sensitivity enabling analysis down to femtomol levels. We examine the potential of our approach on biologically relevant DNA samples and demonstrate the detection of single base mutations on DNA molecules.
Sequential Biochemical and Mechanical Stimulation in the Development of Tissue-Engineered Ligaments (2008)

Application of stimuli in sequence to developing cultures in vitro offers the potential to intricately direct cell development and differentiation by following the template of native tissue behavior. We hypothesize that administration of mechanical stimulation at the peak of growth factor-induced cell activity will differentiate bone marrow stromal cells (BMSCs) along a fibroblast lineage and enhance in vitro ligament development through enhanced matrix ingrowth, matrix metalloproteinase-2 (MMP-2) production, collagen type I production, and extracellular matrix (ECM) alignment. BMSC-seeded silk matrices were cultured in a static growth-factor-free environment for 5 days prior to loading into bioreactor vessels to first establish an appropriate dynamic rotational regime, as determined through assessment of cell activity, histology, and surface topography. Once the regime was determined, seeded matrices initially cultured in basic fibroblast growth factor (bFGF), epidermal growth factor (EGF), or growth-factor-free control medium for 5 days were loaded into the bioreactor for 9 days of mechanical stimulation. Our findings indicated that the sequential application of mechanical stimulation following growth factor supplemented static culture-induced cell differentiation toward a fibroblast lineage, enhancing matrix ingrowth, cell and ECM alignment, and total collagen type I produced compared to respective static cultures. The current results suggest a dynamic culturing regime in the development of engineered tissues.
Stress induces tRNA cleavage by angiogenin in mammalian cells (2008)

tRNAs play a central role in protein translation, acting as the carrier of amino acids. By cloning microRNAs, we unexpectedly obtained some tRNA fragments generated by tRNA cleavage in the anticodon loop. These tRNA fragments are present in many cell lines and different mouse tissues. In addition, various stress conditions can induce this tRNA cleavage event in mammalian cells. More importantly, angiogenin (ANG), a member of RNase A superfamily, appears to be the nuclease which cleaves tRNAs into tRNA halves in vitro and in vivo. These results imply that angiogenin plays an important physiological role in cell stress response, except for the known function of inducing angiogenesis.
DETECTION OF SALMONELLA TYPHI BY NESTED POLYMERASE CHAIN REACTION IN BLOOD, URINE, AND STOOL SAMPLES (2007)

A nested polymerase chain reaction (PCR) specific for Salmonella enterica serovar Typhi was used for the detection of the pathogen in blood, urine, and stool samples from 131 patients with clinical suspicion of typhoid fever. The sensitivity of blood culture, the PCRs with blood, urine, and feces, and the Widal test were 61.8%, 84.5%, 69.3%, 46.9%, and 39.0%, respectively. The sensitivity of the PCRs with blood (P < 0.001) and urine (P = 0.01) were significantly higher, and the sensitivity of the PCR with feces (P > 0.05) was similar to that of blood culture. Combined, the PCRs on urine and feces showed positive results for 16 (70%) of 23 typhoid patients with negative results with blood culture and PCR with blood. These results show that the PCR with blood is a sensitive method for the diagnosis of typhoid fever, and that the PCRs with urine and feces could be useful complementary tests.
Einleitung (1997)

Zusammenfassung“The general job-shop problem is a fascinating challenge. Although it is easy to state, and to visualize what is required, it is extremely difficult to make any progress whatever toward a solution. Many proficient people have considered the problem, and all have come away essentially empty-handed. Since this frustration is not reported in the literature, the problem continues to attract investigators, who just cannot believe that a problem so simply structured can be so difficult, until they have tried it.”1
A Proposed Role for the Azotobacter vinelandii NfuA Protein as an Intermediate Iron-Sulfur Cluster Carrier (2008)

Iron-sulfur clusters ([Fe-S] clusters) are assembled on molecular scaffolds and subsequently used for maturation of proteins that require [Fe-S] clusters for their functions. Previous studies have shown that Azotobacter vinelandii produces at least two [Fe-S] cluster assembly scaffolds: NifU, required for the maturation of nitrogenase, and IscU, required for the general maturation of other [Fe-S] proteins. A. vinelandii also encodes a protein designated NfuA, which shares amino acid sequence similarity with the C-terminal region of NifU. The activity of aconitase, a [4Fe-4S] cluster-containing enzyme, is markedly diminished in a strain containing an inactivated nfuA gene. This inactivation also results in a null-growth phenotype when the strain is cultivated under elevated oxygen concentrations. NifU has a limited ability to serve the function of NfuA, as its expression at high levels corrects the defect of the nfuA-disrupted strain. Spectroscopic and analytical studies indicate that one [4Fe-4S] cluster can be assembled in vitro within a dimeric form of NfuA. The resultant [4Fe-4S] cluster-loaded form of NfuA is competent for rapid in vitro activation of apo-aconitase. Based on these results a model is proposed where NfuA could represent a class of intermediate [Fe-S] cluster carriers involved in [Fe-S] protein maturation.
Catalytic Enantioselective Negishi Reactions of Racemic Secondary Benzylic Halides (2005)

This report describes the first enantioselective cross-couplings of racemic secondary benzylic halides, specifically, nickel-catalyzed Negishi reactions of bromides and chlorides. The catalyst components are commercially available and air-stable, and the reaction is not highly oxygen- or moisture-sensitive (it can be set up in the air). The method has been applied to the catalytic enantioselective synthesis of intermediates employed by others in the generation of bioactive compounds (e.g., trikentrin A and an androgen receptor agonist).
Analysis of depletion-region collection in GaInNAs solar cells (2005)

We provide qualitative insight into depletion-region collection in GaInNAs cells to (1) understand the effect of diffusion length L on the QE; and (2) describe the magnitude of L required to get adequate current from the cell. We use Wolf's equations for the QE including a drift field E, and model E as being equal to the junction built-in voltage distributed uniformly across the depletion region. This allows us to calculate the QE as a function of L and depletion width W/sub D/. We show that if L is sufficiently small, increasing W/sub D/ can actually decrease the QE. To determine how long L needs to be in a practical GaInNAs junction, we calculate from the QE the short-circuit current density as a function of W/sub D/ and L. This allows us to estimate that L/sub ambipolar/ needs to be greater than roughly 1 /spl mu/m in order to obtain enough photocurrent for the 4-junction application, giving guidance to the experimental effort to develop such cells.
Beneficial effects of colestipol-niacin on coronary atherosclerosis. A 4-year follow-up (1990)

The Cholesterol Lowering Atherosclerosis Study (CLAS) was a randomized, placebo-controlled, angiographic trial testing combined colestipol-niacin therapy in 162 subjects. Two-year results (CLAS-I) showed decreased atherosclerosis progression and increased regression. We now describe a subgroup of 103 subjects treated for 4 years (CLAS-II). Changes in blood lipid, lipoproteincholesterol, and apolipoprotein levels were maintained, and at 4 years significantly more drug-treated subjects demonstrated nonprogression (52% drug- vs 15% placebo-treated) and regression (18% drug- vs 6% placebo-treated) in native coronary artery lesions. Significantly fewer drug-treated subjects developed new lesions in native coronary arteries (14% drug- vs 40% placebo-treated) and bypass grafts (16% drug- vs 38% placebo-treated). These results confirm CLAS-I findings and indicate that regression can continue for 4 years. They reaffirm the need for early initiation of vigorous long-term lipid lowering therapy in coronary bypass subjects. (<i>JAMA</i>. 1990;264:3013-3017)
Significance of MMP-2 and TIMP-2 mRNA expressions on glomerular cells in the development of glomerulosclerosis. (2004)

The results suggest that the over-expressions of MMP-2 and TIMP-2 mRNA on glomerular cells might play a critical role in the development of glomerulosclerosis.
Implantation of bone marrow‐derived mesenchymal stem cells demonstrates improved outcome in horses with overstrain injury of the superficial digital flexor tendon (2011)

This study has provided evidence for the long-term efficacy of MSC treatment for tendinopathy in racehorses and provides support for translation to human tendon injuries.
History Matching for Lauchstaedt Underground Gas Storage (1998)

Abstract Underground gas storage Lauchstaedt (East Germany) is represented by fractured reservoir. For adequate representation of considered deposit, an idea of two-layered reservoir has been chosen. One layer was responsible for the system of fractures, whereas another one corresponded to matrix blocks description. For this storage an automatic history matching procedure has been implemented that was based upon optimal control theory approach. Objective function to be minimized included the sum of least square mismatches of observed and calculated well's reservoir pressures. A conjugate gradient method was implemented to minimize given objective function. Applied history matching algorithm implied solution of forward and adjoint boundary value problems. A set of control parameters contained porosity and permeability of fractures and matrix blocks. The problem of reservoir petrophysical properties estimation was investigated in 3D statement. Developed history matching algorithm turned out to be very efficient. A very good fit of observed and calculated well's grid block pressures has been reached after 8 iterations of gradient search procedure, nevertheless 10 control parameters were introduced. The most sensitive parameter happened to be porosity. It resulted in initial gas in place overestimation by 15% comparing with registered one. It was also obtained a good match of observed and calculated pressures after manual history matching procedure for reservoir described as dual porosity layer. Only two matching parameters have been introduced in this case, namely P. 263
Carcinoembryonic Antigen as a Target for Therapeutic Anticancer Vaccines: A Review (2002)

Tolerance to CEA in patients with cancer can be overcome with several different vaccination approaches, and such vaccinations are safe and immunologically active. Poxvirus-based vaccines can reproducibly generate T-cell responses to CEA and to tumors expressing CEA. Clinical activity has been seen with poxvirus or dendritic cell approaches. Other approaches are also being explored.
Identification of Epigenetically Silenced Genes in Tumor Endothelial Cells (2007)

Tumor angiogenesis requires intricate regulation of gene expression in endothelial cells. We recently showed that DNA methyltransferase (DNMT) and histone deacetylase (HDAC) inhibitors directly repress endothelial cell growth and tumor angiogenesis, suggesting that epigenetic modifications mediated by DNMTs and HDAC are involved in regulation of endothelial cell gene expression during tumor angiogenesis. To understand the mechanisms behind the epigenetic regulation of tumor angiogenesis, we used microarray analysis to perform a comprehensive screen to identify genes down-regulated in tumor-conditioned versus quiescent endothelial cells, and reexpressed by 5-aza-2'-deoxycytidine (DAC) and trichostatin A (TSA). Among the 81 genes identified, 77% harbored a promoter CpG island. Validation of mRNA levels of a subset of genes confirmed significant down-regulation in tumor-conditioned endothelial cells and reactivation by treatment with a combination of DAC and TSA, as well as by both compounds separately. Silencing of these genes in tumor-conditioned endothelial cells correlated with promoter histone H3 deacetylation and loss of H3 lysine 4 methylation, but did not involve DNA methylation of promoter CpG islands. For six genes, down-regulation in microdissected human tumor endothelium was confirmed. Functional validation by RNA interference revealed that clusterin, fibrillin 1, and quiescin Q6 are negative regulators of endothelial cell growth and angiogenesis. In summary, our data identify novel angiogenesis-suppressing genes that become silenced in tumor-conditioned endothelial cells in association with promoter histone modifications and reactivated by DNMT and HDAC inhibitors through reversal of these epigenetic modifications, providing a mechanism for epigenetic regulation of tumor angiogenesis.
Cytotoxic T lymphocytes inhibit hepatitis B virus gene expression by a noncytolytic mechanism in transgenic mice. (1994)

During hepatitis B virus (HBV) infection, distinct host-virus interactions may establish the patterns of viral clearance and persistence and the extent of virus-associated pathology. It is generally thought that HBV-specific class I-restricted cytotoxic T lymphocytes (CTLs) play a critical role in this process by destroying infected hepatocytes. This cytopathic mechanism, however, could be lethal if most of the hepatocytes are infected. In the current study, we demonstrate that class I-restricted HBV-specific CTLs profoundly suppress hepatocellular HBV gene expression in HBV transgenic mice by a noncytolytic process, the strength of which greatly exceeds the cytopathic effect of the CTLs in magnitude and duration. We also show that the regulatory effect of the CTLs is initially mediated by interferon gamma and tumor necrosis factor alpha, is delayed in onset, and becomes independent of these cytokines shortly after it begins. The data indicate that the anti-viral CTL response activates a complex regulatory cascade that inhibits hepatocellular HBV gene expression without killing the cell. The extent to which this mechanism contributes to viral clearance or viral persistence during HBV infection remains to be determined.
Analysis of cellular sensitization with cisplatin-induced apoptosis by glucose-starved stress in cisplatin-sensitive and -resistant A431 cell line. (2001)

Most solid tumors show resistance to current chemotherapy. This drug resistance can be associated with stress conditions, such as glucose starvation, low pH and hypoxia. These conditions are not observed in normal tissues. These tumor specific conditions commonly cause the glucose-regulated stress response of cancer cells. This stress response leads to induction of resistance to multiple anticancer drugs, such as etoposide, doxorubicin, camptothecin and vincristine. An examination was made of the effect of the glucose-regulated protein (GRP)-inducing conditions on cellular sensitivity to cisplatin (CDDP), which is a widely used drug against solid tumors.We used CDDP resistant subline A431/CDDP2 from human epidermoid carcinoma cell line A431 as previously established. Glucose-starved response showed GRP78 protein by Western blotting. We generated the glucose-starved condition by exposing cells to 2-deoxyglucose (2-DG) and examined cellular sensitivity to CDDP. We next examined CDDP induced apoptosis in glucose-starved condition. Furthermore, we determined the JNK1/SAPK and caspase-3 protein levels by Western blotting.The glucose-starved condition was up-regulate GRP78 in the parent A431 cell (A431/P). On the other hand, in A431/CDDP2, GRP78 levels were not changed. The GRP78 inducing stress condition led to cellular sensitization to CDDP in A431/P cells only. DNA fragmentation of A431/P treated with 2-DG increased CDDP-induced apoptosis. A431/CDDP2 was not different with CDDP induced apoptosis in glucose-starved stress condition. The reduction of CDDP-induced apoptosis under glucose-starved stress condition was influenced by JNK1/SAPK and caspase-3 proteins.These results indicated that the glucose-starved stress condition was associated with increased sensitivity to CDDP in the up-regulated GRP78 cells. Furthermore, the reduction of CDDP-induced apoptosis can be considered as one of the CDDP resistant mechanisms in a glucose-starvation condition.