gebhart/patrepeval huggingface dataset:
Parallel Tag Clouds to explore and analyze faceted text corpora (2009)

Do court cases differ from place to place? What kind of picture do we get by looking at a country's collection of law cases? We introduce parallel tag clouds: a new way to visualize differences amongst facets of very large metadata-rich text corpora. We have pointed parallel tag clouds at a collection of over 600,000 US Circuit Court decisions spanning a period of 50 years and have discovered regional as well as linguistic differences between courts. The visualization technique combines graphical elements from parallel coordinates and traditional tag clouds to provide rich overviews of a document collection while acting as an entry point for exploration of individual texts. We augment basic parallel tag clouds with a details-in-context display and an option to visualize changes over a second facet of the data, such as time. We also address text mining challenges such as selecting the best words to visualize, and how to do so in reasonable time periods to maintain interactivity.
Comparison of Tazarotene and Minocycline Maintenance Therapies in Acne Vulgaris (2006)

A high percentage of patients with moderately severe to severe acne can maintain improvement in their condition with topical retinoid monotherapy. Maintenance with combination tazarotene and minocycline therapy showed a trend for greater efficacy but no statistical significance vs tazarotene alone. Topical retinoid monotherapy should be considered for maintenance to help minimize antibiotic exposure.
Short Hairpin RNA (shRNA): Design, Delivery, and Assessment of Gene Knockdown (2010)

Shortly after the cellular mechanism of RNA interference (RNAi) was first described, scientists began using this powerful technique to study gene function. This included designing better methods for the successful delivery of small interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs) into mammalian cells. While the simplest method for RNAi is the cytosolic delivery of siRNA oligonucleotides, this technique is limited to cells capable of transfection and is primarily utilized during transient in vitro studies. The introduction of shRNA into mammalian cells through infection with viral vectors allows for stable integration of shRNA and long-term knockdown of the targeted gene; however, several challenges exist with the implementation of this technology. Here we describe some well-tested protocols which should increase the chances of successful design, delivery, and assessment of gene knockdown by shRNA. We provide suggestions for designing shRNA targets and controls, a protocol for sequencing through the secondary structure of the shRNA hairpin structure, and protocols for packaging and delivery of shRNA lentiviral particles. Using real-time PCR and functional assays we demonstrate the successful knockdown of ASC, an inflammatory adaptor molecule. These studies demonstrate the practicality of including two shRNAs with different efficacies of knockdown to provide an additional level of control and to verify dose dependency of functional effects. Along with the methods described here, as new techniques and algorithms are designed in the future, shRNA is likely to include further promising application and continue to be a critical component of gene discovery.
The Sequence Alignment/Map format and SAMtools (2009)

http://samtools.sourceforge.net.
35 IN VITRO BOVINE EMBRYO DEVELOPMENT AFTER NUCLEAR TRANSFER BY HANDMADE CLONING USING A MODIFIED WOW CULTURE SYSTEM (2005)

The effect of the microenvironment on embryo development during in vitro culture of zona-free embryos after nuclear transfer is still unclear. The aim of this experiment was to determine the effect of the dimensions of the well (WOW; Vajta et al . 2000 Mol. Reprod. Dev. 55, 256-264) culture system on the in vitro development of handmade cloned bovine embryos to the blastocyst stage. Appropriately ground steel needles were pressed slightly by hand to the bottom of the well of a polystyrene four-well dish (176740, Nunc, Life Technologies AS, Roskilde, Denmark). Embryos were produced by the handmade cloning (HMC) technique (Vajta et al . 2003 Biol. Reprod. 68, 571-578) with modifications, using primary cultures of skin fibroblast cells from an adult cow as nuclear donors. Cumulus-oocyte complexes were in vitro -matured in M-199 supplemented with 10% estrous cow serum (ECS), FSH, hCG, and estradiol (E2) for 17 h. After maturation, cumulus cells were removed by pipetting. Following zona pellucida removal in 0.5% protease (Sigma, Brazil), zona-free oocytes were incubated for 15 min in 5 mg/mL cytochalasin B (Sigma) and subsequently hand-bisected and screened for nuclear material under UV light after incubation in 10 mg/mL bisbenzimide (Hoechst 33342). Next, two enucleated halves and one donor cell were aggregated after a quick exposure to phytohemagglutinin (PHA) and subsequently fused by two electrical DC pulses of 1 kV/cm for 20 µs, in a BTX 453 chamber coupled to an ECM 2001 Electro Cell Manipulator System (BTX, Inc., San Diego, CA, USA), with additional exposure to brief pre- and post-fusion AC pulses of 15 V. Reconstructed embryos were chemically activated in 5 mM ionomycin (Sigma) for 5 min, followed by 2 mM 6-DMAP (Sigma) for 2.5 h. Finally, activated reconstructed cloned embryos were in vitro -cultured in one of two WOW culture systems (larger vs. smaller micro-wells) in 4-well plates containing 400 mL modified SOF medium supplemented with 10% ECS, under mineral oil, at 5% CO2, 5% O2 and 90% N2, and 39°C for 7 days. In Group 1 (large-size micro-well), embryos were cultured in individual cylindrical micro-wells with an inner diameter and depth of approximately 280 and 250 mm, respectively, whereas in Group 2 (small size micro-well), embryos were cultured in individual conical micro-wells with approximately 130 mm inner diameter and 150 mm depth. Data analysis was performed by the chi-square test. After four replicates, cleavage rates were significantly higher ( P &amp;lt; 0.05) in Group 2 (51/63, 80.9%) than in Group 1 (43/67, 64.1%). Embryo development to the blastocyst stage was also greater ( P &amp;lt; 0.05) in the small micro-wells (16/63, 25.3%) than in the large ones (8/67, 11.9%). In summary, these results show a significant increase in cleavage and blastocyst developmental rates in handmade cloned embryos cultured in a modified WOW system using individual small size micro-wells, suggesting that a small, tighter micro-well provides favorable in vitro conditions for embryo development.
Serum cystatin C, determined by a rapid, automated particle-enhanced turbidimetric method, is a better marker than serum creatinine for glomerular filtration rate (1994)

We describe a fully automated particle-enhanced turbidimetric assay for cystatin C in undiluted serum and EDTA-plasma. The throughput is 90 samples per hour and urgent samples can be analyzed in 7 min. The assay range (0.4-14.1 mg/L) covers the concentration range in health and disease. The within- and between-run imprecision is 0.9% and 2.2%, respectively. Analytical recovery of additions of recombinant cystatin C averaged 98%. Rheumatoid factors (< or = 323,000 IU/L), bilirubin (< or = 150 mumol/L), hemoglobin (< or = 1.2 g/L), and triglycerides (< or = 8.5 mmol/L) do not interfere in the assay. In view of the superior (by ROC analysis) diagnostic accuracy of serum concentrations of cystatin C for reduced glomerular filtration rate (GFR) in comparison with creatinine, cystatin C seems an attractive alternative to creatinine for estimation of GFR.
Reaction of Silicate Minerals To Form Tetramethoxysilane (2002)

Several silicon dioxide sources were used as reagents in the base-mediated reaction with dimethyl carbonate (DMC) to make tetramethoxysilane (Q'). Several commercially available diatomaceous earth materials were investigated. High throughput screening was employed to explore over 200 silicate rocks and minerals as alternative silicon dioxide sources for formation of Q' from DMC and base. Amorphous silicon dioxide materials are effective reagents for the Q' forming reaction. Effective silicon dioxide sources in addition to the diatomaceous earth materials include opal and various synthetic silicates (Li, Co, and Ca).
Cyclic Ruthenium-Alkylidene Catalysts for Ring-Expansion Metathesis Polymerization (2008)

A series of cyclic Ru-alkylidene catalysts have been prepared and evaluated for their efficiency in ring-expansion metathesis polymerization (REMP). The catalyst structures feature chelating tethers extending from one N-atom of an N-heterocyclic carbene (NHC) ligand to the Ru metal center. The catalyst design is modular in nature, which provided access to Ru complexes having varying tether lengths, as well as electronically different NHC ligands. Structural impacts of the tether length were unveiled through (1)H NMR spectroscopy as well as single-crystal X-ray analyses. Catalyst activities were evaluated via polymerization of cyclooctene, and key data are provided regarding propagation rates, intramolecular chain transfer, and catalyst stabilities, three areas necessary for the efficient synthesis of cyclic poly(olefin)s via REMP. From these studies, it was determined that while increasing the tether length of the catalyst leads to enhanced rates of polymerization, shorter tethers were found to facilitate intramolecular chain transfer and release of catalyst from the polymer. Electronic modification of the NHC via backbone saturation was found to enhance polymerization rates to a greater extent than did homologation of the tether. Overall, cyclic Ru complexes bearing 5- or 6-carbon tethers and saturated NHC ligands were found to be readily synthesized, bench-stable, and highly active catalysts for REMP.
Transport and Sensing in Nanofluidic Devices (2011)

Ion transport and sensing in nanofluidic devices are receiving a great deal of attention because of their unique transport properties and potential analytical applications. Some aspects of microscale transport transfer directly to the nanoscale, but nanofluidic systems can be significantly influenced by phenomena such as double-layer overlap, surface charge, ion-current rectification, diffusion, and entropic forces, which are either insignificant or absent in larger microchannels. Micro- and nanofabrication techniques create features with a wide range of well-defined geometries and dimensions in synthetic and solid-state substrates. Moreover, these techniques permit coupling of multiple nano- and microscale elements, which can execute various functions. We discuss basic nanofluidic architectures, material transport properties through single and multiple nanochannels, and characterization of single particles by resistive-pulse sensing.
Multicomponent reactions provide key molecules for secret communication (2018)

A convenient and inherently more secure communication channel for encoding messages via specifically designed molecular keys is introduced by combining advanced encryption standard cryptography with molecular steganography. The necessary molecular keys require large structural diversity, thus suggesting the application of multicomponent reactions. Herein, the Ugi four-component reaction of perfluorinated acids is utilized to establish an exemplary database consisting of 130 commercially available components. Considering all permutations, this combinatorial approach can unambiguously provide 500,000 molecular keys in only one synthetic procedure per key. The molecular keys are transferred nondigitally and concealed by either adsorption onto paper, coffee, tea or sugar as well as by dissolution in a perfume or in blood. Re-isolation and purification from these disguises is simplified by the perfluorinated sidechains of the molecular keys. High resolution tandem mass spectrometry can unequivocally determine the molecular structure and thus the identity of the key for a subsequent decryption of an encoded message.
Poly(vinyl alcohol) hydrogel as an artificial articular cartilage: Evaluation of biocompatibility (1991)

We have developed a new poly(vinyl alcohol) hydrogel (PVA-H) of increased physical strength through a new manufacturing process. Its mechanical properties have been found to be preferable as a substitute for articular cartilage. To evaluate its biocompatibility as an artificial articular cartilage, a series of in vivo tests within the intraarticular, as well as the intramuscular, environment were conducted. Tissue reactions of cartilage, bone, synovium, and muscle to PVA-H were studied histologically. In the experimental group, in which PVA-H was implanted, inflammatory reactions of all of these tissues were very slight. In the control group, in which ultra-high molecular weight polyethylene (UHMWPE) was implanted, although tissue reactions of bone and muscle were as slight as in the experimental group, those of cartilage and synovium were somewhat more conspicuous. By way of these findings, the better biocompatibility of PVA-H was documented.
0.1 dB/cm waveguide losses in single-mode SOI rib waveguides (1996)

Waveguide losses as low as 0.1 dB/cm at a wavelength of /spl lambda/=1.3 μm have been achieved in SOI rib waveguides fabricated by wet chemical etching. The single-mode waveguides have a large cross section yielding field mismatch losses to a standard single-mode fiber of only 0.17 dB/facet (both polarizations). Polarization independent fiber-chip-fiber insertion losses of 0.9 dB (best 0.5 dB) at a chip length of 60 mm have been measured.
Reviews (1990)

Slow Burn: A Photodocument of Centralia, Pennsylvania. Photographs and Text by Renee Jacobs. Introduction by Margaret O. Kirk. Philadelphia: University of Pennsylvania Press, 1986.176 p. $26.95 pb. Coming of Age in Buffalo: Youth and Authority in the Postwar Era by William Graebner. Philadelphia: Temple University Press, 1990.153 p. $24.954 cloth. The Contest of Meaning: Critical Histories of Photography, edited by Richard Bolton. Cambridge, MA: MIT Press, 1989. 407 p. $40.00 cloth. Mind's Eye, Mind's Truth: FSA Photography Reconsidered by James Curtis. Philadelphia: Temple University Press, 1989. 152p. $29.95 cloth. The Fight for Newton Corner: A Study of Neighborhood Development by Jon Chase. Massachusetts Foundation for Humanities and Public Policy, 1987. 94 photographs, 80 p. $14.95 pb. Exhibit Review: Webs of Meaning. Visual Sociology at Mendenhall Gallery
Training Viruses to Attack Cancers (1998)

ONCOLOGYA growing assortment of viruses that replicate in and kill cancer cells, but not normal tissue, may be new weapons in the war on cancer. So far, researchers have come up with a half-dozen of these tumor-killing, or oncolytic, viruses, the latest of which is a reovirus described on page [1332][1]. The reovirus--a type of virus that doesn't cause problems in humans--is not yet in clinical trials, but two other viruses are, and early results from one indicate that it can shrink tumors, particularly when used in conjunction with other therapies. Also in the works are oncolytic viruses that not only kill cancer cells but also carry genes that make the cells more susceptible to radiation or chemotherapy, thereby delivering a double blow to the tumor.

 [1]: http://www.sciencemag.org/cgi/content/short/282/5392/1332
Insulin-Like Growth Factor Binding Protein 2 (IGFBP-2) Promotes Growth and Survival of Breast Epithelial Cells: Novel Regulation of the Estrogen Receptor (2013)

In breast tumors IGF binding protein-2 (IGFBP-2) is elevated, and the presence of IGFBP-2 has been shown to correlate with malignancy. However, how IGFBP-2 contributes to the malignant state is still unclear. Silencing IGFBP-2 blocked cell proliferation and in MCF-7 cells increased cell death, indicating that IGFBP-2 was acting in both a mitogenic and a survival capacity. Exogenous IGFBP-2 acting via integrin receptors to reduce phosphatase and tensin homolog deleted from chromosome 10 (PTEN) levels protected these cells against death induced by various chemotherapeutic agents. This was dependent on a functional estrogen receptor (ER)-α because silencing ER-α blocked the ability of IGFBP-2 to confer cell survival. Loss of IGFBP-2 increased levels of PTEN and improved chemosensitivity of the cells, confirming its role as a survival factor. Silencing IGFBP-2 had no effect on the response to IGF-II, but responses to estrogen and tamoxifen were no longer observed due to loss of ER-α, which could be prevented by the inhibition of PTEN. Conversely, exogenous IGFBP-2 increased ER-α mRNA and protein in both normal and cancer cells via its interaction with integrin receptors. These actions of IGFBP-2 on ER-α involved the IGF-I receptor and activation of phosphatidylinositol 3-kinase in the cancer cells but were independent of this in normal breast cells. The production of IGFBP-2 by breast cancer cells enhances their proliferative potential, increases their survival, and protects them against chemotherapy-induced death. IGFBP-2 not only modulates IGFs and directly regulates PTEN but also has a role in maintaining ER-α expression.
Promyelocytic Leukemia (Pml) Nuclear Bodies Are Protein Structures That Do Not Accumulate RNA (2000)

The promyelocytic leukemia (PML) nuclear body (also referred to as ND10, POD, and Kr body) is involved in oncogenesis and viral infection. This subnuclear domain has been reported to be rich in RNA and a site of nascent RNA synthesis, implicating its direct involvement in the regulation of gene expression. We used an analytical transmission electron microscopic method to determine the structure and composition of PML nuclear bodies and the surrounding nucleoplasm. Electron spectroscopic imaging (ESI) demonstrates that the core of the PML nuclear body is a dense, protein-based structure, 250 nm in diameter, which does not contain detectable nucleic acid. Although PML nuclear bodies contain neither chromatin nor nascent RNA, newly synthesized RNA is associated with the periphery of the PML nuclear body, and is found within the chromatin-depleted region of the nucleoplasm immediately surrounding the core of the PML nuclear body. We further show that the RNA does not accumulate in the protein core of the structure. Our results dismiss the hypothesis that the PML nuclear body is a site of transcription, but support the model in which the PML nuclear body may contribute to the formation of a favorable nuclear environment for the expression of specific genes.
Kinetics of hybridization of mRNA of c-myc oncogene with 111In-labeled antisense oligodeoxynucleotide probes by high-pressure liquid chromatography. (1994)

Antisense oligodeoxynucleotides (ASON) were labeled with gamma-emitting 123I, 99mTc and 111In radionuclides. The hybridization kinetics of 111In-labeled ASON probes [phosphorothioate (S) and phosphodiester (O)] with intact leukemic cells (P388) and purified mRNA was studied by gel filtration technique. The 15-mer oligodeoxynucleotide (ON) sequence was synthesized, amino linked and coupled to diethylenetriaminepentaacetic acid (DTPA)-isothiocyanate, and aliquots were lyophilized to make a kit for convenient preparation. 111In radionuclide was chelated to DTPAASON derivatives and free 111In was separated by gel filtration. The probe was incubated with P388 cells and mRNA extract of P388 cells. Hybridization kinetics was studied by measuring the free and mRNA-bound probe separated by the HPLC technique. The distribution of radioactivity associated with proteins, DNA and mRNAs was directly measured with a gamma camera and further quantified with an ionization chamber. The kinetics of direct and indirect hybridization of 111In-labeled antisense probes with mRNA and intact cells was similar.
ACEI of Trichoderma reesei Is a Repressor of Cellulase and Xylanase Expression (2003)

We characterized the effect of deletion of the Trichoderma reesei (Hypocrea jecorina) ace1 gene encoding the novel cellulase regulator ACEI that was isolated based on its ability to bind to and activate in vivo in Saccharomyces cerevisiae the promoter of the main cellulase gene, cbh1. Deletion of ace1 resulted in an increase in the expression of all the main cellulase genes and two xylanase genes in sophorose- and cellulose-induced cultures, indicating that ACEI acts as a repressor of cellulase and xylanase expression. Growth of the strain with a deletion of the ace1 gene on different carbon sources was analyzed. On cellulose-based medium, on which cellulases are needed for growth, the Deltaace1 strain grew better than the host strain due to the increased cellulase production. On culture media containing sorbitol as the sole carbon source, the growth of the strain with a deletion of the ace1 gene was severely impaired, suggesting that ACEI regulates expression of other genes in addition to cellulase and xylanase genes. A strain with a deletion of the ace1 gene and with a deletion of the ace2 gene coding for the cellulase and xylanase activator ACEII expressed cellulases and xylanases similar to the Deltaace1 strain, indicating that yet another activator regulating cellulase and xylanase promoters was present.
Basis of microheterogeneity of myelin basic protein. (1976)

The basic protein of bovine central nervous system myelin contains a single polypeptide chain of 170 amino acids. Multiple components of basic protein have been observed on disc gel electrophoresis and ion exchange chromatography at alkaline pH, but the basis of the microheterogeneity has not been established. In the present study myelin basic protein from bovine spinal cord was chromatographed on carboxymethylcellulose at pH 10.4 in glycine buffer/2 M urea. Three major peaks were obtained, identified as components 4, 5, and 6 in the oder of their elution from the column by a linear salt gradient. The amino acid compositions of tryptic peptides from components 4 and 6 were identical and the COOH-terminal sequence, Ala-Arg-Arg, was intact for all three components. Component 4 was found to differ from component 6 by partial phosphorylation of threonine 98 and serine 165. This modification was estimated to account for 50% of component 4. Component 5 differed from component 6 by partial deamidation of glutamine residues 103 and 147, which accounted for 80% of this component. These modified glutamine residues were also present in component 4 and constituted another 15% of this component. It was considered that component 6 was the native, unmodified species of basic protein and that component 4 differed by a net negative charge of 2, and component 5 by a net negative charge of.1 as a result of these modifications. The nonrandom nature of the modifications suggested the involvement of specific enzymes.
Loss of Heterozygosity in Normal Tissue Adjacent to Breast Carcinomas (1996)

Loss of heterozygosity (LOH) was detected in morphologically normal lobules adjacent to breast cancers. The most frequent aberration was at chromosome 3p22-25; of ten cases with this LOH in the carcinoma, six displayed the same LOH in adjacent normal lobules. This suggests that in a subset of sporadic breast cancers, a tumor suppresser gene at 3p22-25 may be important in initiation or early progression of tumorigenesis. Among sixteen breast cancers with LOH at 17p13.1 and five breast cancers with LOH at 11p15.5, one case each displayed the same LOH in adjacent normal lobules. Thus the molecular heterogeneity that characterizes invasive breast cancers may occur at the earliest detectable stages of progression.