gebhart/patrepeval huggingface dataset:
Evaluation of tissue‐specific promoters in carcinomas of the cervix uteri (2004)

Our study demonstrates that the promoters for MK and VEGF are active in cervical cancer. We believe that both promoters can be successfully employed as TSPs for gene therapy targeted to cervical cancer.
Dermal mast cell degranulation in systemic sclerosis (1990)

Paired biopsy samples from involved and uninvolved skin were obtained from 19 patients with generalized scleroderma (11 with early, progressive disease and 8 with late, improving disease). Skin biopsy samples were double stained for mast cell granules and for mast cell membrane. The number of mast cells was increased in patients with systemic sclerosis (SSc), in both involved and uninvolved skin and in both early and late disease. There was an increase in the number of degranulated mast cells in the involved skin of patients with both early and late disease and in the not-yet-involved skin of patients with early disease; however, there was no increase in the number of degranulated mast cells in areas of previously involved but now normal skin of patients with late disease. Increases in mast cell number and degranulation precede clinically apparent dermal fibrosis in SSc. These observations and the absence of mast cell degranulation in regressing skin suggest a participatory role of the mast cell in the clinical progression of skin changes in SSc.
Use of the Avidin-Biotin Complex for Specific Staining of Biological Membranes in Electron Microscopy (1974)

To expand the electron microscopist's options in localization and visualization, a new and general staining technique has been tested. The avidin-biotin complex serves as a coupling between the electron-dense marker, ferritin, and points of interest in biological samples. When specific cellular components are tagged with biotin, those components may be visualized with ferritin-linked avidin. Because of the remarkably strong affinity of avidin and biotin (characterized by an association constant of 10(15) M(-1)), the staining is rapid and stable. The preparation of ferritin-avidin conjugate is described, and examples are presented of the application of this complex to biotin-tagged membranes. The ghosts of Acholeplasma laidlawii have been treated with biotinyl-N-hydroxysuccinimide ester to label protein amino groups. Erythrocyte membrane oligosaccharides have been oxidized by periodate or by galactose oxidase, and the resulting aldehydes labeled with biotin hydrazide. The avidin-biotin complex in electron microscopy seems especially appropriate for seqential staining procedures, as well as for visualization of reaction sites of biotin-labeled, low-molecular-weight reagents.
Overexpression of the Wilms' tumor gene WT1 in primary astrocytic tumors (2004)

Expression of the Wilms' tumor gene W T1 in primary astrocytic tumors was examined using a quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR) or immunohistochemistry. Real-time RT-PCR showed that W T1 mRNA was expressed at various levels in all of the 25 astrocytic tumors examined. Immunohistochemical analysis showed that W T1 protein was expressed in 5 of 6 low-grade astrocytic tumors (grade I-II) and all of 18 high-grade ones (grade III-IV), and that expression levels of W T1 protein in high-grade tumors were significantly higher than those in low-grade ones. W T1 protein was not detected in the normal glial cells contained in the tumor specimens. Furthermore, treatment with W T1 antisense oligomers specifically inhibited growth of glioblastoma cell lines, U87-MG, A172, and T-98G. These results may indicate that the W T1 gene plays an important role in tumorigenesis of primary astrocytic tumors.
Calculation of critical layer thickness versus lattice mismatch for GexSi1−x/Si strained-layer heterostructures (1985)

A calculation of the critical layer thickness hc for growth of GexSi1−x strained layers on Si substrates is presented for 0≤x≤1.0. The present results are obtained assuming misfit dislocation generation is determined solely by energy balance. This approach differs therefore from previous theories (e.g., Matthews et al.), in which the absence of mechanical equilibrium for grown-in threading dislocations determines the onset of the generation of interfacial misfit dislocations. It is assumed that interfacial misfit dislocations will be generated when the areal strain energy density of the film exceeds the energy density associated with the formation of a screw dislocation at a distance from the free surface equal to the film thickness h. For films thicker than this critical value, screw (and edge) dislocations will be generated at the film/substrate interface. Values obtained for the critical thickness versus lattice mismatch are in excellent agreement with measurements of hc for GexSi1−x strained layers on Si substrates.
Patterning of various silicon structures via polymer lithography and catalytic chemical etching (2011)

We demonstrate a facile fabrication of a rich variety of silicon patterns with different length scales by combining polymer lithography and a metal-assisted chemical etching method. Several types of polymer patterns were fabricated on silicon substrates, and silver layers were deposited on the patterned silicon surfaces and used to etch the silicon beneath. Various silicon patterns including topographic lines, concentric rings, and square arrays were created at a micro- and nanoscale after etching the silicon and subsequent removal of the patterned polymer masks. Alternatively, the arrays of sub-30 nm silicon nanowires were produced by a chemical etching of the silicon wafer which was covered with highly ordered polystyrene-block-polyvinylpyridine (PS-b-PVP) micellar films. In addition, silicon nanohole arrays were also generated by etching with hexagonally packed silver nanoparticles that were prepared using PS-b-PVP block copolymer templates.
Sequence of the bchG gene from Chloroflexus aurantiacus: relationship between chlorophyll synthase and other polyprenyltransferases (1996)

The sequence of the Chloroflexus aurantiacus open reading frame thought to be the C. aurantiacus homolog of the Rhodobacter capsulatus bchG gene is reported. The BchG gene product catalyzes esterification of bacteriochlorophyllide a by geranylgeraniol-PPi during bacteriochlorophyll a biosynthesis. Homologs from Arabidopsis thaliana, Synechocystis sp. strain PCC6803, and C. aurantiacus were identified in database searches. Profile analysis identified three related polyprenyltransferase enzymes which attach an aliphatic alcohol PPi to an aromatic substrate. This suggests a broader relationship between chlorophyll synthases and other polyprenyltransferases.
Internet accounting (2001)

This article provides an introduction to Internet accounting and discusses the status of related work within the IETF and IRTF, as well as certain research projects. Internet accounting is different from accounting in POTS. To understand Internet accounting, it is important to answer questions like "what is being paid for" and "who is being paid". With respect to the question "what is being paid for" a distinction can be made between transport accounting and content accounting. Transport accounting is interesting since techniques like DiffServ enable the provision of different quality of service classes; each class will be charged differently to avoid all users selecting the same top-level class. The interest in content accounting finds its roots in the fast growth of commercial offerings over the Internet; examples of such offerings include remote video and software distribution. The question "who is being paid" has two possible answers: the network provider or the owner of the content. The case in which the network provider issues the bill is called provider-based accounting. Since this case will become more and more important, this article introduces a new architecture for provider-based accounting.
The polymerase chain reaction (1992)

Abstract The polymerase chain reaction (PCR), now a key tool in molecular biology, provides a rapid and powerful technique for the in vitro amplification of DNA sequences (see refs 1-3 for reviews). The PCR is now routinely used for gene cloning, analysis, and manipulation in many molecular biology laboratories. It has also found wide application in medicine; including diagnosis of genetic disease, mutational analysis, forensic pathology, and is proving important in such programmes as the mapping and sequencing of the human genome. The PCR has great potential for the study of plant-pathogen interactions in facilitating both gene cloning and genome analysis. Indeed, in biotrophic interactions where the host-pathogen interface is restricted to a small number of specialized cells, the PCR may provide the only mechanism for the investigation of changes in gene expression.
A Potential Suppressive Effect of Natural Antisense IL-1β RNA on Lipopolysaccharide-Induced IL-1β Expression (2013)

Although more than half of genomic loci are believed to have antisense transcription, whether antisense transcription is involved in cytokine expression has not been studied. In this study, we show that some loci of innate immunity related genes do have antisense transcripts. We investigated the effect of several antisense RNAs, including anti-4-1BBL, anti-p100, and anti-IL-1β, on their cognate sense gene's expression in macrophages. We found that overexpression of antisense IL-1β transcript suppressed IL-1β expression. Anti-IL-1β is complementary to the sequence in the 5' upstream region of the IL-1β promoter. Its mediated inhibition of IL-1β production occurred at the transcriptional level. Anti-IL-1β did not alter the methylation status of the IL-1β promoter. However, chromatin immunoprecipitation assays revealed that the anti-IL-1β transcript can change the chromatin structure of the IL-1β promoter by decreasing H3K4 trimethylation on the promoter, which is at least part of the mechanism underlying the reduced binding of RNA polymerase II to the IL-1β promoter upon anti-IL-1β expression. Our data suggest that some antisense transcripts of innate immunity-related genes play a role by regulating cytokine expression.
Immunomodulatory Gene Therapy With Interleukin 12 and 4-1BB Ligand: Long- Term Remission of Liver Metastases in a Mouse Model (2000)

Adenovirus-mediated transfer of IL-12 and 4-1BBL genes directly into liver tumors resulted in tumor regression that required both NK and CD8+ T cells and generated a potent, long-lasting antitumor immunity.
Male‐specific expression of Aldh1a1 in mouse and chicken fetal testes: Implications for retinoid balance in gonad development (2009)

Balanced production and degradation of retinoids is important in regulating development of several organ systems in the vertebrate embryo. Among these, it is known that retinoic acid (RA), and the retinoid-catabolyzing enzyme CYP26B1 together regulate the sex-specific behavior of germ cells in developing mouse gonads. We report here that the gene encoding a cytosolic class-1 aldehyde dehydrogenase, ALDH1A1, a weak catalyst of RA production, is strongly expressed in a male-specific manner in somatic cells of the developing mouse testis, beginning shortly after Sry expression is first detectable. This expression pattern is conserved in the developing male gonad of the chicken and is dependent on the testis-specific transcription factor SOX9. Our data suggest that low levels of RA may be required for early developmental events in the testis, or that Aldh1a1 expression in the fetus may prefigure a later requirement for ALDH1A1 in regulating spermatogenesis postnatally.
Hydrogen energy future with formic acid: a renewable chemical hydrogen storage system (2015)

Formic acid, the simplest carboxylic acid, could serve as one of the better fuels for portable devices, vehicles and other energy-related applications in the future.
Huntingtin-associated Protein 1 Interacts with Hepatocyte Growth Factor-regulated Tyrosine Kinase Substrate and Functions in Endosomal Trafficking (2002)

Huntingtin-associated protein 1 (HAP1) is a novel protein of unknown function with a higher binding affinity for the mutant form of Huntington's disease protein huntingtin. Here we report that HAP1 interacts with hepatocyte growth factor-regulated tyrosine kinase substrate (Hrs), a mammalian homologue of yeast vacuolar protein sorting protein Vps27p involved in the endosome-to-lysosome trafficking. This novel interaction was identified in a yeast two-hybrid screen using full-length Hrs as bait, and confirmed by<i>in vitro</i> binding assays and co-immunoprecipitation experiments. Deletion analysis reveals that the association of HAP1 with Hrs is mediated via a coiled-coil interaction between the central coiled-coil domains of both proteins. Immunofluorescence and subcellular fractionation studies show that HAP1 co-localizes with Hrs on early endosomes. Like Hrs, overexpression of HAP1 causes the formation of enlarged early endosomes, and inhibits the degradation of internalized epidermal growth factor receptors. Whereas overexpression of HAP1 does not affect either constitutive or ligand-induced receptor-mediated endocytosis, it potently blocks the trafficking of endocytosed epidermal growth factor receptors from early endosomes to late endosomes. These findings implicate, for the first time, the involvement of HAP1 in the regulation of vesicular trafficking from early endosomes to the late endocytic compartments.
Lower Cost CPV 3-Sun Mirror Modules (2007)

In a series of patent applications filed between 2002 and 2005, JX Crystals Inc described a evolutionary lower-cost low-concentration planar solar photovoltaic module that uses multiple linear rows of silicon cells and standard one-sun circuit laminations incorporating glass and EVA weather proofing encapsulations. The three novel features that we described are interdependent and integrated together to yield lower cost PV modules. These 3 novel features are: (1) The use of rows of linear mirrors or linear Fresnel lenses aligned with the cell rows and concentrating the sunlight onto the cell rows. (2) The addition of a thin aluminum sheet heat spreader on the back of the circuit lamination to spread the heat away from the cell rows so that the cell operating temperature remains acceptably low. (3) The incorporation of slots in the back of the aluminum sheet heat spreader to accommodate the differences in thermal expansion between the silicon cells, the glass, and the aluminum so that the circuit interconnectivity is maintained over time. Various embodiments of this planar linear concentrator panel are shown in figures 1 to 5. Figures 1 and 2 show the original planar linear concentrator module concept from July of 2002 with either mirrors (figuremore » 1) or linear Fresnel lenses (figure 2). The idea was expanded in 2003 with the idea of an aluminum sheet heat spreader added to the back of a standard PV circuit lamination as shown in figure 3. In 2003, we also transitioned from half cells to third cells using SunPower cells as shown in figure 4. JX Crystals Inc then received funding for the 3-sun PV mirror module concept from the Shanghai Science and Technology Commission in 2003 and from the Shanghai Flower Port and the Shanghai Import and Export Trading Company in 2005. This funding led to a 800 panel pilot production run of our JX Crystals designed 3-sun module in 2006. 672 of these panels were installed in a 100 kW demonstration and an additional 24 panels were installed in a second 4 kW demonstration both at the Flower Port in Shanghai. Both of these systems were completed in 2006. Our 3-sun PV Panel concept has been described previously (see references 1, 2, & 3 available at www.jxcrystals.com under publication tab). We are now interested in bringing this potentially lower cost 3-sun technology back to the US. For any new technology, three issues need to be addressed. They are performance, durability, and cost. These topics are addressed in the next 3 sections.« less
Understanding deep learning requires rethinking generalization (2016)

Despite their massive size, successful deep artificial neural networks can exhibit a remarkably small difference between training and test performance. Conventional wisdom attributes small generalization error either to properties of the model family, or to the regularization techniques used during training. Through extensive systematic experiments, we show how these traditional approaches fail to explain why large neural networks generalize well in practice. Specifically, our experiments establish that state-of-the-art convolutional networks for image classification trained with stochastic gradient methods easily fit a random labeling of the training data. This phenomenon is qualitatively unaffected by explicit regularization, and occurs even if we replace the true images by completely unstructured random noise. We corroborate these experimental findings with a theoretical construction showing that simple depth two neural networks already have perfect finite sample expressivity as soon as the number of parameters exceeds the number of data points as it usually does in practice. We interpret our experimental findings by comparison with traditional models.
TREATMENT OF CORNEAL ALLOGRAFT REJECTION WITH THE CYTOTOXIN IL-2-PE40 (1991)

IL-2-PE40 is a recombinant chimeric protein composed of IL-2, fused to a modified pseudomonas exotoxin. This molecule is extremely toxic to activated T cells expressing high-affinity IL-2R. We used this new molecule for selective immunosuppression to treat corneal allograft rejection in the rat, using Fisher and Lewis rats, a strain combination differing only in medial and minor histocompatibility antigens. The effect of IL-2-PE40 on the immunologic response was studied using both a heterotopic corneal graft model and orthotopic grafts. At the dose of 0.31 micrograms/g given intraperitoneally every 12 hr, IL-2-PE40 produced a significant reduction of both total lymph node cells and cytotoxic-T-cell (CTL) activity in draining lymph nodes (DLN) of heterotopically grafted animals. IL-2-PE40 treatment also significantly reduced the clinical rejection score and cumulative rejection rate (CRR) in orthotopic grafts and appears to be a very effective immunosuppressive agent.
Separation of Spores and Parasporal Crystals of Bacillus thuringiensis in Gradients of Certain X-Ray Contrasting Agents (1975)

Spores and parasporal crystals of Bacillus thuringiensis can be separated at moderate centrifugation speeds (10,000 to 12,000 rpm) in gradients of Renografin or sodium diatrizoate.
Combination chemotherapy studies with gemcitabine. (1997)

Gemcitabine (2',2'-difluorodeoxycytidine) is an antineoplastic agent with clinical activity against ovarian carcinoma, small cell and non-small cell lung cancers, head and neck cancer, bladder cancer, breast cancer, and pancreatic cancer. Cisplatin (CDDP), etoposide (VP-16), and mitomycin C (MMC) are well-known anticancer agents that are also active against many of these types of cancer. Because of the low toxicity profile of gemcitabine and the differences in mechanism of cytotoxicity, combinations of these drugs with gemcitabine were studied in vitro and in vivo. Cells were exposed in vitro for 1, 4, 24, or 72 hours to gemcitabine in combination with these drugs, either simultaneously or sequentially in a constant ratio. Another approach consisted of exposure to a combination of the approximate IC25 of one drug and varying concentrations of the other drug. Synergism for several of these combinations was found in the human ovarian cancer cell line A2780, its CDDP-resistant variant ADDP, its gemcitabine-resistant variant AG6000, and in the non-small cell lung cancer cell lines H322 and Lewis lung (LL) after a 72-hour drug treatment. Studies of the possible mechanisms of action initially focused on the major metabolic features of each drug. CDDP did not enhance the accumulation of gemcitabine triphosphate and caused only marginal changes in the extent of DNA double-strand breaks (DSBs) induced by gemcitabine in these cell lines. Gemcitabine increased platinum accumulation only in the ADDP cell line, but the DNA platination was enhanced in the A2780, ADDP, AG6000, and LL cell lines. MMC did not influence the formation of DSBs by gemcitabine in the LL cell line. The combination of VP-16 and gemcitabine, however, resulted in the formation of more DSBs in this cell line than each drug alone. This effect was even more pronounced when cells were exposed to VP-16 4 hours before gemcitabine. In vivo, the antitumor activity of a combination of 50 mg/kg gemcitabine and 6 mg/kg CDDP was more effective against LL tumors than each compound alone. In conclusion, gemcitabine is an attractive drug to combine with a wide range of anticancer drugs; synergism is often schedule dependent.
Videotape Editing Systems Using Microprocessors (1978)

Following a short overview of videotape editing history, the modern approach is described — using a controller built around a microprocessor or “computer on a chip” rather than hardwired logic. A good editing controller should be directly interfaced with the individual editing machine; it must “know” all the relevant characteristics of the machine for correct control and at the same time must have easily understandable displays and a simple, functional control panel for easy operation. Two specific microprocessor-controlled editing systems designed to operate with the TR-600 quadruplex VTR are discussed; these are the AE-600, a sophisticated time-code editing system (able to control up to eight TR-600's) using the Intel 8080 microprocessor with 15K bytes of memory, and the SE-1 “simple editing system” using the CDP1802 microprocessor with 2K bytes of memory. The mechanics of editing with time code are discussed briefly.
Induction of the Bacillus subtilis ptsGHI operon by glucose is controlled by a novel antiterminator, GlcT (1997)

Glucose is the preferred carbon and energy source of Bacillus subtilis. It is transported into the cell by the glucose-specific phosphoenolpyruvate:sugar phosphotransferase system (PTS) encoded by the ptsGHI locus. We show here that these three genes (ptsG, ptsH, and ptsI) form an operon, the expression of which is inducible by glucose. In addition, ptsH and ptsl form a constitutive ptsHI operon. The promoter of the ptsGHI operon was mapped and expression from this promoter was found to be constitutive. Deletion mapping of the promoter region revealed the presence of a transcriptional terminator as a regulatory element between the promoter and coding region of the ptsG gene. Mutations within the ptsG gene were characterized and their consequences on the expression of ptsG studied. The results suggest that expression of the ptsGHI operon is subject to negative autoregulation by the glucose permease, which is the ptsG gene product. A regulatory gene located upstream of the ptsGHI operon, termed glcT, was also identified. The GlcT protein is a novel member of the BglG family of transcriptional antiterminators and is essential for the expression of the ptsGHI operon. A deletion of the terminator alleviates the need for GlcT. The activity of GlcT is negatively regulated by the glucose permease.