gebhart/patrepeval huggingface dataset:
Zonal Distribution of Prostatic Adenocarcinoma (1988)

For 104 prostate glands obtained at radical prostatectomy for adenocarcinoma, we mapped the tumor outline and determined the tumor volume, grade, and location relative to the transition zone boundary and location of the central zone. Among the 88 cancers whose probable zone of origin could be identified, 68% arose in the peripheral zone, 24% arose in the transition zone, and 8% arose in the central zone. Transition zone carcinomas had usually been diagnosed by transurethral resection (TUR) and often appeared to arise within BPH nodules; only two of 67 non-transition zone carcinomas had been diagnosed at TUR. Two-thirds of 21 transition zone cancers showed a distinctive histologic appearance; they were made up of columnar clear cells lining glands of widely variable size and contour. The transition zone boundary appeared to act as a barrier to the spread of non-transition zone carcinomas. We conclude that carcinoma typically arises in the region of the prostate that is susceptible to benign prostatic hyperplasia and that the great majority of Stage A (TUR) cancers are transition zone cancers. Non-transition zone cancers detectable at TUR are predominantly large tumors that are poorly differentiated and lack the clear cell histologic pattern.
CD34+ or CD34−: Does it Really Matter? (1999)

T HE CELL SURFACE glycoprotein CD34 has been the focus of intense interest ever since its discovery on a small fraction of human bone marrow cells.[1][1] The CD34+population appears responsible for most, if not all, of the hematopoietic activity in bone marrow, including colony formation in short-
Molecular Mechanism of Substrate Specificity for Heparan Sulfate 2-O-Sulfotransferase (2014)

Heparan sulfate (HS) is an abundant polysaccharide in the animal kingdom with essential physiological functions. HS is composed of sulfated saccharides that are biosynthesized through a complex pathway involving multiple enzymes. In vivo regulation of this process remains unclear. HS 2-O-sulfotransferase (2OST) is a key enzyme in this pathway. Here, we report the crystal structure of the ternary complex of 2OST, 3'-phosphoadenosine 5'-phosphate, and a heptasaccharide substrate. Utilizing site-directed mutagenesis and specific oligosaccharide substrate sequences, we probed the molecular basis of specificity and 2OST position in the ordered HS biosynthesis pathway. These studies revealed that Arg-80, Lys-350, and Arg-190 of 2OST interact with the N-sulfo groups near the modification site, consistent with the dependence of 2OST on N-sulfation. In contrast, 6-O-sulfo groups on HS are likely excluded by steric and electrostatic repulsion within the active site supporting the hypothesis that 2-O-sulfation occurs prior to 6-O-sulfation. Our results provide the structural evidence for understanding the sequence of enzymatic events in this pathway.
Innate Vα14+ natural killer T cells mature dendritic cells, leading to strong adaptive immunity (2007)

The observation that the glycolipid alpha-galactosylceramide (alpha-GalCer) is a potent stimulator of natural killer T (NKT) cells has provided an important means for investigating NKT cell biology. alpha-GalCer is presented on CD1d to the invariant NKT receptor, leading to interleukin-12 (IL-12) production by dendritic cells (DCs) and to NK cell activation. We review our research on the tumor-protective properties of alpha-GalCer, particularly the major role played by DCs. We compared administration of alpha-GalCer on mature DCs with soluble glycolipid and found that DCs induced more prolonged interferon-gamma (IFN-gamma) production by NKT cells and better protection against B16 melanoma. Human alpha-GalCer-loaded DCs also expanded NKT cell numbers in cancer patients. alpha-GalCer-activated NKT cells were then found to induce DC maturation in vivo. The maturing DCs produced IL-12, upregulated co-stimulatory molecules, and induced adaptive immunity to captured cellular antigens, including prolonged, combined CD4(+)/CD8(+) T-cell immunity to dying tumor cells. Surprisingly, co-stimulator-poor tumor cells, if directly loaded with alpha-GalCer ('tumor/Gal') and injected intravenously, also induced strong NKT- and NK-cell responses. The latter killed the tumor/Gal, which were subsequently cross presented by CD1d on DCs to elicit DC maturation and prolonged adaptive T-cell immunity, which lasted 6-12 months. These findings help explain tumor protection via alpha-GalCer and urge development of the DC-NKT axis to provide innate and adaptive immunity to human cancers.
Assessment of Purity and Screening of Peptide Libraries by Nested Ion Mobility-TOFMS:  Identification of RNase S-Protein Binders (2000)

Combinatorial peptide synthesis in combination with affinity selection and high-resolution ion mobility/time-of-flight mass spectrometry (IM/TOFMS) analysis has been used to investigate the binding of a series of 96 related eight-residue peptides (with the general sequence NH2-GX1X2FX3X4X5G-CO2H, where X1 = L, F, V, Y; X2 = N, F; X3 = E, V, T; X4 = V, L; X5 = V, L) to the ribonuclease S protein. A key advantage of this strategy is that the IM/ TOFMS approach allows the relative abundances of individual library components (including numerous sequence and structural isomers) to be characterized before and after screening. The relative binding interactions of different sequences are assessed by comparing IM/TOFMS data for those components that pass through the column (as well as those that bind) to data for the library prior to screening. The high-affinity sequences that are found in this study are compared with those selected from much larger combinatorial libraries. The results suggest that many expected sequences in the large libraries may be missing (e.g., due to issues such as failure of specific steps during the synthesis or differences in solubility). Comparison of the binding sequences obtained in these studies and those reported previously indicates that screening results from large libraries should be interpreted with caution.
[Specific features of normal vaginal microflora in girls of preschool age]. (2004)

The study of the vaginal microbial cenosis in 20 healthy girls aged 3-7 years did not confirm the notion on the dominating role of cocci (including epidermal staphylococci). The associations of 2-5 different microorganisms represented by more than 20 species in an amount of 4-6 Ig PFC/g of discharge were established. In the overwhelming majority of the examinees (84.2%) the microbial associations of the vagina were found to contain bifidobacteria. Gram positive cocci (staphylococci and streptococci) took the 2nd and 3rd places in the isolation rates and were detected in vaginal associations in 78.9% of the girls. Staphylococci were represented by 5 coagulase-negative staphylococcal species with S. simulans and S. epidermidis prevailing. Hemolytic streptococci variants alpha and beta were isolated in the proportion of 2:1. The latter belonged to serogroups C and F. No S. aureus, Lactobacillus sp., streptococci of groups A and B, yeast-like fungi were detected. Genital mycoplasms (M. hominis) could rarely be found in the vaginal discharge of the girls aged 3-7 years (5.3%). No resident and transitory components could be isolated from the normal vaginal microflora and no quantitative domination of any bacterial species (genus) was shown. The concentrations of all organisms in this association were moderate or low.
Interference of Antibody Production to Hepatitis B Surface Antigen in a Combination Hepatitis A/Hepatitis B Vaccine (1999)

A randomized trial comparing 3 manufacturing consistency lots of a combination hepatitis A/hepatitis B vaccine to each other and to hepatitis A vaccine and hepatitis B vaccine given separately and concurrently was done to evaluate safety, tolerability, and immunogenicity. Healthy volunteers >/=11 years of age were divided into 4 groups. Each of 3 groups received a separate consistency lot of the combination vaccine, and 1 group received separate but concurrent injections of hepatitis A and hepatitis B vaccines. Injections were given at weeks 0 and 24. The combination vaccine was generally well tolerated. The hepatitis A portion of the combination vaccine produced clinically acceptable high seropositivity rates 4 and 52 weeks after the first injection. The hepatitis B portion of the vaccine did not produce clinically acceptable seropositivity rates 4 weeks after the second injection. Lack of antibody production may be attributed, at least in part, to immunologic interference.
Fat paradox of steatohepatitis (2008)

Alcoholic and non-alcoholic steatohepatitis (ASH and NASH) constitute two major types of chronic liver disease with worldwide prevalence and are histologically indistinguishable with shared pathogenetic mechanisms. More importantly, they have synergistic interactions for liver pathology. Comparative studies on ASH and NASH have been hampered by the use of different animal models with confounding variables, particularly those with extreme genetic, toxic, and malnutrition etiologies. The mouse intragastric model circumvents these problems and reproduces the natural course and etiological background of ASH and NASH. Further, our recent work reproduces a profound synergism between the two in the model. Intracellular accumulation of neural lipids is a hallmark biochemical feature of ASH and NASH. Although impaired lipid oxidation and export may contribute to this pathological change, enhanced lipogenic regulation is frequently encountered, as characterized by induction of lipogenic or adipogenic transcription factors (peroxisome proliferator-activated receptor [PPAR gamma], liver X receptor alpha[LXR alpha], sterol-regulatory element-binding protein-1c [SREBP-1c]). In contrast, we have recently defined transdifferentiation of hepatic stellate cells (HSC), a pivotal event in liver fibrogenesis, as an 'antilipogenic' or 'anti-adipogenic' phenomenon. Thus, there is an apparent paradox between hepatocytes and HSC in steatohepatitis in terms of the outcome of lipogenic regulation. Our recent work suggests that defective insulin signaling in activated HSC may be responsible for this paradox. Further, activated Wnt signaling is implicated in 'anti-adipogenic' stellate cell transdifferentiation in liver fibrogenesis.
Prelesional complement activation in experimental atherosclerosis. Terminal C5b-9 complement deposition coincides with cholesterol accumulation in the aortic intima of hypercholesterolemic rabbits. (1989)

Cholesterol accumulation in the tunica intima of large and medium sized arteries is a characteristic of atherosclerotic lesion development. Cholesterol activates the complement system in vitro generating C5b-9 complexes, and C5b-9 antigens have been observed in atherosclerotic lesions. We therefore investigated whether complement activation correlates temporally with accumulation of intimal cholesterol in vivo. Frozen sections of aortic tissue from rabbits fed a 0.3% cholesterol diet for 0, 2, 6, and 10 weeks were stained with antibodies directed against neoantigens of the C5b-9 complex. Lipids were detected with oil red O, filipin, and antibodies against apoprotein B. C5b-9 complexes were observed to colocalize with extracellular lipid in the subendothelial space beginning at 2 weeks on the diet and extending past 10 weeks. Quantitation of aorta extracted C5b-9 complexes by an enzyme-linked immunosorbent assay revealed a progressive increase in aortic C5b-9 content as a function of time on the cholesterol diet. An approximately 30-fold increase in aortic C5b-9 occurred between 0 and 10 weeks on the diet, whereas plasma C5b-9 remained at normal levels throughout this time. Aortic cholesterol and triglyceride levels approximately doubled between 0 and 10 weeks on the diet and plasma cholesterol increased nearly 50-fold. Intimal C5b-9 deposition preceded monocyte infiltration and foam cell development. The data indicates that early cholesterol accumulation in the aortic intima results in complement activation. Since complement activation products are chemotactic for monocytes and promote their adhesion to the endothelium, complement may provide a mechanism by which monocytes are attracted to arterial regions of lipid accumulation.
Notes on methodology (1985)

I want to propose that a domain of research exists that is not part of any other established science. The domain is one that those who are pursuing it have come to call ethnomethodology/conversation analysis. That domain seeks to describe methods persons use in doing social life. It is our claim that, although the range of activities this domain describes may be as yet unknown, the mode of description, the way it is cast, is intrinsically stable.
Human breast cancer stem cell markers CD44 and CD24: enriching for cells with functional properties in mice or in man? (2007)

Identification of breast cancer stem cells as the cells within breast tumors that have the ability to give rise to cells that make up the bulk of the tumor mass has shifted the focus of cancer research. However, there is still much debate concerning the unique nature of the markers that distinguish cancer stem cells in the breast. As such, understanding whether CD44+/CD24- breast cancer cells are merely more successful in overcoming an engraftment incompatibility that exists when injecting human cells into the mouse adipose tissue or are indeed bona fide cancer stem cells is of great importance.
Emerging 3DVLSI: Opportunities and challenges (2015)

As the semiconductor industry continues to drive the CMOS scaling roadmap, traditional cost reduction and the accompanied power/performance/area (PPAC) advantages of successive technology nodes are diminishing to a myriad of process integration challenges and increasing variability, reliability, power and thermal constraints. 3D technologies have been explored as potential alternatives to address various system integration needs and to extend the economic scaling roadmap. Among them, 3D VLSI (3DV) technologies emerge as the most plausible candidates. Unlike packaging-driven 3D technologies (e.g., 2.5D, TSV-based 3D, etc.), the emerging 3DV offers over 1000X more vertical connections approaching the same order of magnitude as 2D VLSI vias. Such a high density of vertical interconnects allows us to envision a cost effective 3D system-on-chip (3D SoC) solution that integrates digital, analog, RF, sensors, power etc. into a single chip device, further expand the PPAC roadmap and drive the next wave of semiconductor growth in the emerging markets of internet of everything (IoE), electronic health (eHealth) and electronic medical (eMedic). In this article, we will discuss the 3DV integration opportunities and associated design and technology challenges.
Automatic Photo Adjustment Using Deep Neural Networks (2016)

Photo retouching enables photographers to invoke dramatic visual impressions by artistically enhancing their photos through stylistic color and tone adjustments. However, it is also a time-consuming and challenging task that requires advanced skills beyond the abilities of casual photographers. Using an automated algorithm is an appealing alternative to manual work, but such an algorithm faces many hurdles. Many photographic styles rely on subtle adjustments that depend on the image content and even its semantics. Further, these adjustments are often spatially varying. Existing automatic algorithms are still limited and cover only a subset of these challenges. Recently, deep learning has shown unique abilities to address hard problems. This motivated us to explore the use of deep neural networks (DNNs) in the context of photo editing. In this article, we formulate automatic photo adjustment in a manner suitable for this approach. We also introduce an image descriptor accounting for the local semantics of an image. Our experiments demonstrate that training DNNs using these descriptors successfully capture sophisticated photographic styles. In particular and unlike previous techniques, it can model local adjustments that depend on image semantics. We show that this yields results that are qualitatively and quantitatively better than previous work.
A simple strategy for quantum dot assisted selective detection of cadmium ions (2008)

Here we report a simple strategy for selective detection of cadmium ions by manipulating the electron transfer pathways of surface-engineered quantum dots.
Developmental Changes of C-Series Polysialogangliosides in Chick Brains Revealed by Mouse Monoclonal Antibodies M6704 and M7103 with Different Epitope Specificities1 (1988)

We have established many mouse monoclonal antibodies detecting developmentally regulated antigens in chicken embryonic neural tissues of the otic vesicles and neural tube by immunizing mice with the membrane fraction of the neural tube and somite prepared from 3-d chick embryos. Among them, three monoclonal antibodies (MAbs) M6703, M6704, and M7103 were shown to react with the gangliosides isolated from chicken embryonic brains. The precise specificity of the antibodies was determined mainly by enzyme-immunostaining on thin layer plates. MAbs M6703 and M6704 bound to C-series polysialogangliosides including GT3, GT2, GT1c, GQ1c, and GP1c isolated from cod fish brains, but never to A-series, B-series, or X-series gangliosides. On the other hand, MAb M7103 antibody has a rather narrow specificity, reacting with GT1c, GQ1c, and GP1c, but not with ganglioside GT3. This indicates that the epitopes defined by these two MAbs are not with ganglioside GT3. This indicates that the epitopes defined by these two MAbs are different from each other. MAbs M6703 and M6704 recognize a trisialosyl residue, NeuAc alpha 2-8NeuAc alpha 2-8NeuAc alpha 2-3, while M7103 requires both a trisialosyl residue and the gangliotetraosy backbone structure for binding. As compared to similar MAbs which have been reported in the literature. M6703 and M6704 are unique in that they react equally with all of the C-series gangliosides and belong to the IgG3 subclass.(ABSTRACT TRUNCATED AT 250 WORDS)
Altered renal hemodynamics is associated with glomerular lipid accumulation in obese Dahl salt-sensitive leptin receptor mutant rats (2020)

The present study examined whether development of renal injury in the nondiabetic obese Dahl salt-sensitive leptin receptor mutant (SS<sup>LepR</sup>mutant) strain is associated with elevations in glomerular filtration rate and renal lipid accumulation. Baseline mean arterial pressure at 6 wk of age was similar between Dahl salt-sensitive wild-type (SS<sub>WT</sub>) and SS<sup>LepR</sup>mutant rats. However, by 18 wk of age, the SS<sup>LepR</sup>mutant strain developed hypertension, while the elevation in mean arterial pressure was not as severe in SS<sub>WT</sub> rats (192 ± 4 and 149 ± 6 mmHg, respectively). At baseline, proteinuria was fourfold higher in SS<sup>LepR</sup>mutant than SS<sub>WT</sub> rats and remained elevated throughout the study. The early development of progressive proteinuria was associated with renal hyperfiltration followed by a decline in renal function over the course of study in the SS<sup>LepR</sup>mutant compared with SS<sub>WT</sub> rats. Kidneys from the SS<sup>LepR</sup>mutant strain displayed more glomerulosclerosis and glomerular lipid accumulation than SS<sub>WT</sub> rats. Glomeruli were isolated from the renal cortex of both strains at 6 and 18 wk of age, and RNA sequencing was performed to identify genes and pathways driving glomerular injury. We observed significant increases in expression of the influx lipid transporters, chemokine (C-X-C motif) ligand 16 (Cxcl16) and scavenger receptor and fatty acid translocase (Cd36), respectively, and a significant decrease in expression of the efflux lipid transporter, ATP-binding cassette subfamily A member 2 (<i>Abca2</i>; cholesterol efflux regulatory protein 2), in SS<sup>LepR</sup>mutant compared with SS<sub>WT</sub> rats at 6 and 18 wk of age, which were validated by RT-PCR analysis. These data suggest an association between glomerular hyperfiltration and glomerular lipid accumulation during the early development of proteinuria associated with obesity.
A fast algorithm for finding dominators in a flowgraph (1979)

A fast algorithm for finding dominators in a flowgraph is presented. The algorithm uses depth-first search and an efficient method of computing functions defined on paths in trees. A simple implementation of the algorithm runs in O ( m log n ) time, where m is the number of edges and n is the number of vertices in the problem graph. A more sophisticated implementation runs in O ( m α( m , n )) time, where α( m , n ) is a functional inverse of Ackermann's function. Both versions of the algorithm were implemented in Algol W, a Stanford University version of Algol, and tested on an IBM 370/168. The programs were compared with an implementation by Purdom and Moore of a straightforward O ( mn )-time algorithm, and with a bit vector algorithm described by Aho and Ullman. The fast algorithm beat the straightforward algorithm and the bit vector algorithm on all but the smallest graphs tested.
An atherogenic diet rapidly induces VCAM-1, a cytokine-regulatable mononuclear leukocyte adhesion molecule, in rabbit aortic endothelium. (1993)

Accumulation of monocyte-derived foam cells in focal areas of the arterial intima is a key step in early atherogenesis. We investigated the expression of vascular cell adhesion molecule-1 (VCAM-1), a mononuclear leukocyte adhesion molecule, in the arterial endothelium during the early phases of diet-induced atherogenesis in rabbits in vivo and the regulation of VCAM-1 expression by cytokines in rabbit aortic organoid cultures in vitro. Rabbits were fed either an atherogenic diet (containing 0.3% cholesterol, 9% coconut oil, and 1% corn oil) or an isocaloric control diet (10% corn oil) for 4 days or 1, 3, 6, or 13 weeks. The endothelium in the ascending aorta focally expressed VCAM-1 after only 1 week on the atherogenic diet but before the first appearance of intimal macrophages, as judged by immunohistochemical staining of serial sections. The rabbits that consumed the atherogenic diet for 3 weeks or longer developed lesions in the intima composed of macrophages bearing class II major histocompatibility antigen (MHC-II). Endothelial cells continued to focally express VCAM-1 at sites of MHC-II-positive intimal macrophages for up to 13 weeks. The ascending aortas of control rabbits lacked VCAM-1 or MHC-II-positive endothelium or macrophages at all times studied. These observations demonstrate the focal activation of arterial endothelium as early as 7 days after initiation of an atherogenic diet (at serum cholesterol levels of 308 +/- 57 mg/dl).(ABSTRACT TRUNCATED AT 250 WORDS)
Structure of outer membrane protein G by solution NMR spectroscopy (2007)

The bacterial outer membrane protein G (OmpG), a monomeric pH-gated porin, was overexpressed in Escherichia coli and refolded in beta-octyl glucoside micelles. After transfer into dodecylphosphocholine micelles, the solution structure of OmpG was determined by solution NMR spectroscopy at pH 6.3. Complete backbone assignments were obtained for 234 of 280 residues based on CA, CB, and CO connection pathways determined from a series of TROSY-based 3D experiments at 800 MHz. The global fold of the 14-stranded beta-barrel was determined based on 133 long-range NOEs observed between neighboring strands and local chemical shift and NOE information. The structure of the barrel is very similar to previous crystal structures, but the loops of the solution structure are quite flexible.
Doping sources for growth of group III-nitrides (1996)

One of the many challenges associated with the development of group 3-nitride materials is the control and understanding of their electrical behavior. While highly successful light emitting diodes have been achieved, more advanced structures will require significant improvement in the doping levels and profiles. This paper reviews the current status of doping in these materials and offer suggestions for approaches which may significantly improve the ability to create complicated dopant profiles in these materials. 38 refs., 9 figs.