gebhart/patrepeval huggingface dataset:
Morphologic and Molecular Evolutionary Pathways of Low Nuclear Grade Invasive Breast Cancers and Their Putative Precursor Lesions: Further Evidence to Support the Concept of Low Nuclear Grade Breast Neoplasia Family (2008)

We have previously provided evidence showing an association between some precursor lesions with low nuclear grade breast carcinomas (LNGBCs). In this study, further immunophenotypic support to our proposed route of pathogenesis of LNGBC and their precursor lesions was provided. Precursor lesions including columnar cell lesions, atypical ductal hyperplasia, ductal carcinoma in situ, usual epithelial hyperplasia, and lobular neoplasia were compared with matching "morphologically normal" terminal lobular duct units and matching invasive carcinoma. The epithelial cells in the putative precursor flat epithelial atypia, atypical ductal hyperplasia, lobular neoplasia, ductal carcinoma in situ lesions, and their coexisting LNGBC were negative for basal and myoepithelial markers, but positive for CK19/18/8, estrogen receptor (ER)-alpha, Bcl-2, and cyclin D1. The ER-alpha/ER-beta expression ratio increased during carcinogenesis, as did expression of cyclin D1 and Bcl-2. p53 immunopositivity was found 3% in LNGBC versus 43% in high nuclear grade breast carcinoma (HNGBC), whereas ataxia telangiectasia mutated expression was absent or reduced in 22% of LNGBC versus 53% of HNGBC cases. In summary, our findings support the concept that flat epithelial atypia is the earliest morphologically identifiable nonobligate precursor lesion of LNGBC. These may represent a family of precursor, in situ and invasive neoplastic lesions belonging to the luminal "A" subclass of breast cancer. The balance between ER-alpha and ER-beta expression may be important in driving cyclin D-1 and Bcl-2 expression. Ataxia telangiectasia mutated may be one of the alternative regulatory mechanisms to TP53 mutation or dysfunction in low-grade and high-grade breast carcinoma. Our findings support the concept that progression of LNGBC to HNGBC (basal-like or HER2+) phenotype is an unlikely biologic phenomenon.
Bromination of substituted methylcoumarins with N-bromo-succinimide. (1974)

Chemistry Department, Faculty of Science, M. S. University of Baroda, Baroda-2. <em>Manuscript received 12 January 1974; accepted 11 July 1974.</em> Bromination of 7-methoxy-5-methylcoumarin, 5-methoxy-4-, 7-dimethylcoumarin and 7-meth­oxy-4, 8-dimethylcoumarin with N-bromosuccininide gave 7-me thox y-5-bromomethylcoumarin, 5-methoxy-4-methyl-7-bromomethylcoumarin and 7-methoxy-4-methyl-8-bromomethylcoumarin, while 5-hydroxy-4, 7-dimethylcoumarin gave 5-hydroxy-6-bromo-4, 7-dimethylcoumariu under similar conditions.
Involvement of the Molecular Chaperone Ydj1 in the Ubiquitin-Dependent Degradation of Short-Lived and Abnormal Proteins in <i>Saccharomyces cerevisiae</i> (1996)

In Escherichia coli and mitochondria, the molecular chaperone DnaJ is required not only for protein folding but also for selective degradation of certain abnormal polypeptides. Here we demonstrate that in the yeast cytosol, the homologous chaperone Ydj1 is also required for ubiquitin-dependent degradation of certain abnormal proteins. The temperature-sensitive ydj1-151 mutant showed a large defect in the overall breakdown of short-lived cell proteins and abnormal polypeptides containing amino acid analogs, especially at 38 degrees C. By contrast, the degradation of long-lived cell proteins, which is independent of ubiquitin, was not altered nor was cell growth affected. The inactivation of Ydj1 markedly reduced the rapid, ubiquitin-dependent breakdown of certain beta-galactosidase (beta-gal) fusion polypeptides. Although degradation of N-end rule substrates (arginine-beta-gal and leucine-beta-gal) and the B-type cyclin Clb5-beta-gal occurred normally, degradation of the abnormal polypeptide ubiquitin-proline-beta-gal (Ub-P-beta-gal) and that of the short-lived normal protein Gcn4 were inhibited. As a consequence of reduced degradation of Ub-P-beta-gal, the beta-gal activity was four to five times higher in temperature-sensitive ydj1-151 mutant cells than in wild-type cells; thus, the folding and assembly of this enzyme do not require Ydj1 function. In wild-type cells, but not in ydj1-151 mutant cells, this chaperone is associated with the short-lived substrate Ub-P-beta-gal and not with stable beta-gal constructs. Furthermore, in the ydj1-151 mutant, the ubiquitination of Ub-P-beta-gal was blocked and the total level of ubiquitinated protein in the cell was reduced. Thus, Ydj1 is essential for the ubiquitin-dependent degradation of certain proteins. This chaperone may facilitate the recognition of unfolded proteins or serve as a cofactor for certain ubiquitin-ligating enzymes.
Changes in the sebaceous gland in patients with male pattern hair loss (androgenic alopecia) (2015)

The overgrowth (multilobulation) of the sebaceous gland and relative preservation of the follicular stem cells suggest that the changes in the sebaceous gland could be an important factor in the pathology of AGA.
Autocrine regulation of collagenase 3 (matrix metalloproteinase 13) during osteoarthritis (2000)

These data show that TGFbeta1 has antagonistic effects upon OA chondrocytes, in contrast to the effects seen with TNFalpha. The cyclical course of OA, where a period of active disease is followed by a period of remission, can be explained by a sequential pattern of cytokine stimulation followed by a feedback inhibition of autocrine cytokine production and cytokine receptor expression, thus affecting collagenase synthesis.
Differential Effects of Structural Modifications on the Competition of Chalcones for the PIB Amyloid Imaging Ligand-Binding Site in Alzheimer’s Disease Brain and Synthetic Aβ Fibrils (2015)

Alzheimer's disease (AD) is a complex brain disorder that still remains ill defined. In order to understand the significance of binding of different clinical in vivo imaging ligands to the polymorphic pathological features of AD brain, the molecular characteristics of the ligand interacting with its specific binding site need to be defined. Herein, we observed that tritiated Pittsburgh Compound B ((3)H-PIB) can be displaced from synthetic Aβ(1-40) and Aβ(1-42) fibrils and from the PIB binding complex purified from human AD brain (ADPBC) by molecules containing a chalcone structural scaffold. We evaluated how substitution on the chalcone scaffold alters its ability to displace (3)H-PIB from the synthetic fibrils and ADPBC. By comparing unsubstituted core chalcone scaffolds along with the effects of bromine and methyl substitution at various positions, we found that attaching a hydroxyl group on the ring adjacent to the carbonyl group (ring I) of the parent member of the chalcone family generally improved the binding affinity of chalcones toward ADPBC and synthetic fibrils F40 and F42. Furthermore, any substitution on ring I at the ortho-position of the carbonyl group greatly decreases the binding affinity of the chalcones, potentially as a result of steric hindrance. Together with the finding that neither our chalcones nor PIB interact with the Congo Red/X-34 binding site, these molecules provide new tools to selectively probe the PIB binding site that is found in human AD brain, but not in brains of AD pathology animal models. Our chalcone derivatives also provide important information on the effects of fibril polymorphism on ligand binding.
Effect of Dislocations on Breakdown in Silicon <i>p-n</i> Junctions (1958)

The light emission patterns of silicon diffused p-n junctions at breakdown have been compared with the etch-pit patterns that reveal dislocations. It is concluded that avalanche breakdown microplasmas occur preferentially where dislocations pass through the junction. In narrow p-n junctions, large numbers of dislocations result in enhanced internal field emission and, consequently, a soft reverse characteristic. A qualitative correlation is found between the nature of the light emission pattern (spots for avalanche breakdown, glow for field emission) and the quality of the reverse characteristic. Possible reasons why breakdown should occur preferentially at dislocations are discussed though no precise conclusion is reached. Peculiar singularities observed in the light emission patterns of some junctions were found to coincide with crystal abnormalities revealed in the etch patterns.
Communication theory perspective on antenna selection for compact transceivers (2012)

Traditional antenna selection applied to MIMO systems ignores the presence of unselected (or inactive) antennas. However, compact arrays offer a unique advantage in that mutual coupling can be exploited to improve the system performance. Previous studies on selection with coupling have not considered the effects of the inactive-antenna terminations and lack detailed transceiver modeling. In this work, we present a communication-theoretic analysis and design of antenna selection systems for compact transceivers. We also propose a simple parasitic antenna selection technique that can significantly outperform traditional selection when coupling is present.
Characterization of a new open cylindrical ion cyclotron resonance cell with unusual geometry (2007)

A new cylindrical ion cyclotron resonance cell with electrodes of different diameters is characterized. It consists of a central segmented electrode for ion trapping and detection and two planar trapping electrodes with a center bore, to which two small tube electrodes are fitted. The cell can trap either positive or negative ions or both ion polarities in the center region. For trapping both ion polarities, an unsymmetrical double well potential can be generated. Ions generated from SF(6) by electron impact or electron attachment are investigated. In depth analysis of radial excitation patterns of positive and negative ions trapped simultaneously in different stability regions reveals sharp discrimination in the extent of radial acceleration. SIMION simulations of the radial excitation show different trajectories of positive and negative ions. Axial component of radial dipolar excitation field exists in the terminal stability regions.
The development of indigo reduction methods and pre‐reduced indigo products (2009)

The continuing importance of blue denim maintains indigo as an important vat dye industrially. In this review, we examine the various methods that have been used in the past and are currently used to reduce and dissolve indigo for dyeing. We discuss recent insights into the bacterial fermentation technology, the advantages and disadvantages of the direct chemical methods that have predominated for the last century and potentially cleaner technologies of catalytic hydrogenation and electrochemistry, which are becoming increasingly important. With considerations of environmental impact high on the dyeing industry’s agenda, we also discuss the developments that have led to the production of pre‐reduced indigo.
Cyclodextrin-modified solvent extraction for polynuclear aromatic hydrocarbons (1988)

The extraction efficiencies of several polynuclear aromatic hydrocarbons (PAHs) between Isopropyl ether/water and between Isopropyl ether: 1-butanol (1:4)/water are measured in the presence of an aqueous γ-cyclodextrin (CDx) modifier at room temperature. The distribution of certain PAHs Into the aqueous phase is Increased by the presence of 10-2M γ -cdx. For compounds such as perylene and coronene, which show the most marked effects, the extraction efficiencies Into the aqueous phase from pure Isopropyl ether are 95.1% and 93.7%, respectively, when the CDx modifier Is used. In the mixed solvent system with 1-butanol, these values are 63.4% and 98.1 %, respectively. In both systems, the Increased distribution into water is based in part on the size relationship between the PAH and the CDx cavity. In the case of relatively small molecules like anthracene, little or no extraction Is observed in the presence of the CDx modifier. This type of extraction system may be useful for selective extraction of large PAHs from mixtures. Extraction results for a variety of PAHs are presented and discussed. © 1988, American Chemical Society. All rights reserved.
Evidence for DNA Translocation by the ISWI Chromatin-Remodeling Enzyme (2003)

The ISWI proteins form the catalytic core of a subset of ATP-dependent chromatin-remodeling activities. Here, we studied the interaction of the ISWI protein with nucleosomal substrates. We found that the ability of nucleic acids to bind and stimulate the ATPase activity of ISWI depends on length. We also found that ISWI is able to displace triplex-forming oligonucleotides efficiently when they are introduced at sites close to a nucleosome but successively less efficiently 30 to 60 bp from its edge. The ability of ISWI to direct triplex displacement was specifically impeded by the introduction of 5- or 10-bp gaps in the 3'-5' strand between the triplex and the nucleosome. In combination, these observations suggest that ISWI is a 3'-5'-strand-specific, ATP-dependent DNA translocase that may be capable of forcing DNA over the surface of nucleosomes.
Design and implementation of an Android host-based intrusion prevention system (2014)

Android has a dominating share in the mobile market and there is a significant rise of mobile malware targeting Android devices. Android malware accounted for 97% of all mobile threats in 2013 [26]. To protect smartphones and prevent privacy leakage, companies have implemented various host-based intrusion prevention systems (HIPS) on their Android devices. In this paper, we first analyze the implementations, strengths and weaknesses of three popular HIPS architectures. We demonstrate a severe loophole and weakness of an existing popular HIPS product in which hackers can readily exploit. Then we present a design and implementation of a secure and extensible HIPS platform---"Patronus." Patronus not only provides intrusion prevention without the need to modify the Android system, it can also dynamically detect existing malware based on runtime information. We propose a two-phase dynamic detection algorithm for detecting running malware. Our experiments show that Patronus can prevent the intrusive behaviors efficiently and detect malware accurately with a very low performance overhead and power consumption.
A Silicon-Chip Source of Bright Photon-Pair Comb (2012)

Integrated quantum photonics relies critically on the purity, scalability, integrability, and flexibility of a photon source to support diverse quantum functionalities on a single chip. Up to date, it remains an open challenge to realize an efficient monolithic photon-pair source for on-chip application. Here we report a device on the silicon-on-insulator platform that utilizes dramatic cavity enhanced four-wave mixing in a high-Q silicon microdisk resonator. The device is able to produce high-purity photon pairs in a comb fashion, with an unprecedented spectral brightness of $6.24 \times 10^7 {\rm pair/s/mW^2/GHz}$ and photon-pair correlation with a coincidence-to-accidental ratio of $1386 \pm 278$ while pumped with a continuous-wave laser. The superior performance, together with the structural compactness and CMOS compatibility, opens up a great avenue towards quantum silicon photonics with unprecedented capability of multi-channel parallel information processing for both integrated quantum computing and long-haul quantum communication.
A Migrating Oropharyngeal Foreign Body Presenting as Acute Supraglottic Laryngitis (2004)

Management of a patient who has a fish bone lodged in the soft tissues of the neck presents a diagnostic and therapeutic dilemma. A patient who came to our hospital with typical symptoms of acute supraglottic laryngitis and a vague history of foreign-body ingestion was proven to have an incarcerated oropharyngeal fish bone. A neck CT scan with multi-plane reformatted oblique sagittal images proved to be helpful in locating the embedded foreign body before neck exploration. To our knowledge the use of such a diagnostic tool for this purpose has not previously been reported.
A 1.4 watt Q-band GaAs PHEMT MMIC (2002)

A Q-band three-stage monolithic GaAs PHEMT amplifier with an output power of 1.4 W from 42 to 45 GHz has been developed. Power added efficiency between 14 and 18% with an associated gain of 12.5 dB was measured when biased at Vds=6.0 V and Idsq=1000 mA. When biased at Vds=5.0 V, Idsq=1000 mA this amplifier has demonstrated over 1.1 W of output power with an associated gain of 11.5 to 12.5 dB from 41 to 46 GHz. Similar performances were also measured when the design was transferred from 2 mil thick 3 inch diameter pilot process line to the 2 mil thick, 4 inch diameter manufacturing process line.
Language and Style (2018)

“Have something to say, and say it as clearly as you can. That is the only secret
of style.” --Matthew Arnold Deserved or not, scientists and engineers have a reputation as bad writers. An
average person reading a scientific journal paper will likely come away numb
within a few sentences. Much of that is due to the complexity of the subject and a writing style that assumes a readership of knowledgeable peers. Some of that
reputation is deserved, as many writers in our field either do not value clear and
concise prose or do not know how to achieve it. If you feel that you are not as good a writer as you want to be, what can be
done? Specifically, how can you improve your writing for a scientific journal
paper? Style is a layered concept, and learning to improve your style means
mastering words and grammar first, clear and accurate sentences next, then
paragraphs that communicate complex thoughts well, and finally an organized
whole that contributes to the accumulated knowledge of science (see Chapter 2). If that sounds like a big task, it is because it is. Much of the job of learning to write well is independent of genre (at least in
the case of nonfiction writing). But some aspects of writing a good scientific paper are unique to the scientific style. Thus, I’ll begin by talking about good writing in general and end with the scientific style in particular.
THE MORSE TEST (1962)

The determination of IHP by means of the Morse Test is used in most college courses on heat engines and automobile work.
Uncoupling proteins 2 and 3: potential regulators of mitochondrial energy metabolism. (2000)

Mitochondria use energy derived from fuel combustion to create a proton electrochemical gradient across the mitochondrial inner membrane. This intermediate form of energy is then used by ATP synthase to synthesize ATP. Uncoupling protein-1 (UCP1) is a brown fat-specific mitochondrial inner membrane protein with proton transport activity. UCP1 catalyzes a highly regulated proton leak, converting energy stored within the mitochondrial proton electrochemical potential gradient to heat. This uncouples fuel oxidation from conversion of ADP to ATP. In rodents, UCP1 activity and brown fat contribute importantly to whole-body energy expenditure. Recently, two additional mitochondrial carriers with high similarity to UCP1 were molecularly cloned. In contrast to UCP1, UCP2 is expressed widely, and UCP3 is expressed preferentially in skeletal muscle. Biochemical studies indicate that UCP2 and UCP3, like UCP1, have uncoupling activity. While UCP1 is known to play an important role in regulating heat production during cold exposure, the biological functions of UCP2 and UCP3 are unknown. Possible functions include 1) control of adaptive thermogenesis in response to cold exposure and diet, 2) control of reactive oxygen species production by mitochondria, 3) regulation of ATP synthesis, and 4) regulation of fatty acid oxidation. This article will survey present knowledge regarding UCP1, UCP2, and UCP3, and review proposed functions for the two new uncoupling proteins.
Listening Outside and Within (1996)

(1996). Listening Outside and Within. Journal of Museum Education: Vol. 21, Determining Museum Effectiveness: Visitor Studies Today, pp. 26-27.
Overexpression of the Arabidopsis 14-3-3 Protein GF14λ in Cotton Leads to a “Stay-Green” Phenotype and Improves Stress Tolerance under Moderate Drought Conditions (2004)

The Arabidopsis gene GF14 lambda that encodes a 14-3-3 protein was introduced into cotton plants to explore the physiological roles that GF14 lambda might play in plants. The expression level of GF14 lambda under the control of the cauliflower mosaic virus 35S promoter varied in transgenic cotton plants, and lines that expressed GF14 lambda demonstrated a "stay-green" phenotype and improved water-stress tolerance. These lines wilted less and maintained higher photosynthesis than segregated non-transgenic control plants under water-deficit conditions. Stomatal conductance appears to be the major factor for the observed higher photosynthetic rates under water-deficit conditions. The stomatal aperture of transgenic plants might be regulated by GF14 lambda through some transporters such as H(+)-ATPase whose activities are controlled by their interaction with 14-3-3 proteins. However, since 14-3-3 proteins interact with numerous proteins in plant cells, many metabolic processes could be affected by the GF14 lambda overexpression. Whatever the mechanisms, the traits observed in the GF14 lambda-expressing cotton plants are beneficial to crops under certain water-deficit conditions.
Evaluation of Yucatan Micropig Skin for Use as an in Vitro Model for Skin Permeation Study. (1997)

Skin permeation rates of five non-steroidal anti-inflammatory drugs, three of them lipophilic (ibuprofen, indomethacin and ketoprofen) and two hydrophilic (sodium diclofenac and antipyrine), through Yucatan hairless micropig (YMP) full-thickness skin were determined in vitro using Franz-type diffusion cells, and the usefulness of YMP skin as an animal model skin was investigated. Five-month-old YMP skin showed small variation with respect to drug permeation rates, if the region of skin site was the same. But skin from 6-month-old YMPs showed faster and varied permeation rates due to skin defects. In the case of hydrophilic drugs, no effects on permeation due to the region from which the skin was obtained were observed, although higher permeation rates were observed through the flank than through dorsal skin in the case of ibuprofen and ketoprofen. For YMP skin, the permeation coefficients of drugs were lower than those for hairless rat skin, especially for hydrophilic drugs. Compared with reported human data on permeation coefficients, the permeation coefficients of drugs through YMP skin were 1/2-1/8 of those through human skin, regardless of whether the drugs were hydrophilic or lipophilic. YMP skin could be used as an in vitro animal skin model because of the reproducibility of the permeation rate of drugs through this skin and its similarity to human skin.
Highly Efficient Infectious Cell Culture of Three Hepatitis C Virus Genotype 2B Strains and Sensitivity to Lead Protease, Nonstructural Protein 5A, and Polymerase Inhibitors (2013)

Highly efficient HCV full-length 2b culture systems can be established by using consensus clones with defined mutations. Lead protease and NS5A inhibitors, as well as polymerase inhibitors sofosbuvir, mericitabine, and BI207127, show cross-activity against full-length 1a, 2a, and 2b viruses, but important sensitivity differences exist at the isolate level. Infectious cultures for different HCV strains will advance studies on viral biology and pathogenesis and promote individualized patient treatment.