gebhart/patrepeval huggingface dataset:
Multilevel matrix decomposition algorithm for analysis of electrically large electromagnetic problems in 3-D (1999)

The multilevel matrix decomposition algorithm (MLMDA) has been implemented in 3-D for the solution of large electromagnetic problems. The electric field integral equation is solved for arbitrary surfaces discretized using N Rao, Wilton, and Glisson basis functions. The MLMDA accelerates the matrix–vector products in a conjugate gradient or biconjugate gradient iterative solution of the resulting system of equations. The computational cost of each iteration is proportional to N log2 N for very large problems, and is particularly small for planar or piecewise planar objects. ©1999 John Wiley & Sons, Inc. Microwave Opt Technol Lett 22: 177–182, 1999.
Tracking neuronal fiber pathways in the living human brain (1999)

Functional imaging with positron emission tomography and functional MRI has revolutionized studies of the human brain. Understanding the organization of brain systems, especially those used for cognition, remains limited, however, because no methods currently exist for noninvasive tracking of neuronal connections between functional regions [Crick, F. & Jones, E. (1993) Nature (London) 361, 109-110]. Detailed connectivities have been studied in animals through invasive tracer techniques, but these invasive studies cannot be done in humans, and animal results cannot always be extrapolated to human systems. We have developed noninvasive neuronal fiber tracking for use in living humans, utilizing the unique ability of MRI to characterize water diffusion. We reconstructed fiber trajectories throughout the brain by tracking the direction of fastest diffusion (the fiber direction) from a grid of seed points, and then selected tracks that join anatomically or functionally (functional MRI) defined regions. We demonstrate diffusion tracking of fiber bundles in a variety of white matter classes with examples in the corpus callosum, geniculo-calcarine, and subcortical association pathways. Tracks covered long distances, navigated through divergences and tight curves, and manifested topological separations in the geniculo-calcarine tract consistent with tracer studies in animals and retinotopy studies in humans. Additionally, previously undescribed topologies were revealed in the other pathways. This approach enhances the power of modern imaging by enabling study of fiber connections among anatomically and functionally defined brain regions in individual human subjects.
Rational Design of Artificial Zinc-Finger Proteins Using a Nondegenerate Recognition Code Table (2002)

We have developed a novel and simple method to rationally design artificial zinc-finger proteins (AZPs) targeting diverse DNA sequences using a nondegenerate recognition code table. The table was constructed based on known and potential DNA base-amino acid interactions. The table permits identification of an amino acid for each position (-1, 2, 3, and 6) of the alpha-helical region of the zinc-finger domain (position 1 is the starting amino acid in the alpha-helix) from overlapping 4-bp sequences in a given DNA target. Based on the table, we designed ten 3-finger AZPs, each of which targeted an arbitrarily chosen 10-bp DNA sequence, and characterized the binding properties. In vitro DNA-binding assays showed five of the AZPs tightly and specifically bound to their targets containing more than three guanine bases in the first 9-bp region. In addition, 6-finger AZPs, each of which was produced by combining two functional 3-finger AZPs, bound to their 19-bp targets with the dissociation constant of less than 3 pM. The in vivo functionality of the AZP was tested using Arabidopsis protoplasts. The AZP fused to a transcriptional activation domain efficiently activated expression of a reporter gene linked to a native promoter containing the AZP target site. Our simple AZP design method will provide a powerful approach to manipulation of endogenous gene expression by enabling rapid creation of numerous artificial DNA-binding proteins.
Optical 4x4 hitless slicon router for optical networks-on-chip (NoC) (2008)

We demonstrate here a spatially non-blocking optical 4x4 router with a footprint of 0.07 mm(2) for use in future integrated photonic interconnection networks. The device is dynamically switched using thermo-optically tuned silicon microring resonators with a wavelength shift to power ratio of 0.25nm/mW. The design can route four optical inputs to four outputs with individual bandwidths of up to 38.5 GHz. All tested configurations successfully routed a single-wavelength laser and provided a maximum extinction ratio larger than 20 dB.
Wheat Puroindolines Enhance Fungal Disease Resistance in Transgenic Rice (2001)

Antimicrobial peptides play a role in the immune systems of animals and plants by limiting pathogen infection and growth. The puroindolines, endosperm-specific proteins involved in wheat seed hardness, are small proteins reported to have in vitro antimicrobial properties. Rice, the most widely used cereal crop worldwide, normally does not contain puroindolines. Transgenic rice plants that constitutively express the puroindoline genes pinA and/or pinB throughout the plants were produced. PIN extracts of leaves from the transgenic plants reduced in vitro growth of Magnaporthe grisea and Rhizoctonia solani, two major fungal pathogens of rice, by 35 to 50%. Transgenic rice expressing pinA and/or pinB showed significantly increased tolerance to M. grisea (rice blast), with a 29 to 54% reduction in symptoms, and R. solani (sheath blight), with an 11 to 22% reduction in symptoms. Puroindolines are effective in vivo in antifungal proteins and could be valuable new tools in the control of a wide range of fungal pathogens of crop plants.
Vitamin D analogues for secondary hyperparathyroidism (2002)

Secondary hyperparathyroidism (2HPT), a common disorder in patients with chronic renal failure, develops in response to phosphate retention and low serum 1,25-dihydroxyvitamin D(3) (1,25(OH)(2)D(3), calcitriol). Replacement therapy with calcitriol or its precursor 1alpha-hydroxyvitamin D(3) (1alphaOHD(3), alfacalcidol) often produces hypercalcaemia, especially when combined with calcium-based phosphate binders. In addition, these vitamin D compounds can aggravate the hyperphosphataemia in these patients. Several vitamin D analogues have been developed that retain the direct suppressive action of 1,25(OH)(2)D(3) on the parathyroid glands but have less calcaemic activity, thereby offering a safer and more effective means of controlling 2HPT. 1,25-Dihydroxy-19-norvitamin D(2) (19-norD(2)) and 1alpha-hydroxyvitamin D(2) (1alphaOHD(2)) are available in the US and 1,25-dihydroxy-22-oxavitamin D(3) (22-oxacalcitriol, OCT) and 1,25-dihydroxy-26,26,26,27,27,27-hexafluorovitamin D(3) (1,25(OH)(2)26,27F6 D(3), falecalcitriol) have been approved for use in Japan. Animal studies have demonstrated that OCT and 19-norD(2) have a wider therapeutic window for suppression of parathyroid hormone (PTH) because of their lower calcaemic and phosphataemic activities. The low calcaemic activity of OCT has been attributed to its rapid clearance, which prevents sustained effects on intestinal calcium absorption and bone resorption, but still allows a prolonged suppression of PTH gene expression and parathyroid cell growth. The calcaemic activity of 19-norD(2) diminishes with the duration of treatment by as yet unknown mechanisms. The lower toxicity of 1alphaOHD(2), compared with 1alphaOHD(3), has also been noted with chronic, but not acute administration, perhaps due to differential metabolism. The unique actions of falecalcitriol may also result from an altered metabolism. A clear understanding of the molecular basis for the selectivity of vitamin D analogues on parathyroid function may allow the design of even more effective analogues.
HLA-DR meets ERK (2010)

In this issue of Blood, Stein and colleagues present a novel mechanism by which MHC class II antibodies induce apoptosis in lymphoid malignancies. These are important findings that provide fresh insight into a common antibody target.
A Low-Phase-Noise Low-Power 27-GHz SiGe-VCO using Merged-Transformer Matching Circuit Technique (2007)

A 27-GHz voltage-controlled oscillator MMIC (VCO-MMIC), featuring low phase noise of -115dBc/Hz at a 1-MHz offset frequency and large output power of +3.7 dBm with low DC-power dissipation of 111 mW, was developed using a 0.18- <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">μ</i> m SiGe BiCMOS process. A novel merged-transformer matching circuit, in which an inductor in an oscillation loop is reused as a primary inductor of the transformer, contributes to reducing the DC-power dissipation keeping a large output power. This matching circuit is also effective to suppress the bad influence due to the parasitic capacitance of the transformer. The figure of merit (FOM) of the VCO-MMIC is -187 dB. In our knowledge, this value indicates the best performance in 30-GHz class VCO-MMICs fabricated using Si-based technology.
Detection of magnetic nanoparticles in tissue using magneto-motive ultrasound (2006)

The purpose of this study was to demonstrate the magneto-motive ultrasonic detection of superparamagnetic iron oxide (SPIO) nanoparticles as a marker of macrophage recruitment in tissue. The capability of ultrasound to detect SPIO nanoparticles (core diameter ∼20 nm) taken up by murine liver macrophages was investigated. Eight mice were sacrificed two days after the intravenous administration of four SPIO doses (1.5, 1.0, 0.5, and 0.1 mmol Fe/kg body weight). In the iron-laden livers, ultrasound Doppler measurements showed a frequency shift in response to an applied time-varying magnetic field. M-mode scan and colour power Doppler images of the iron-laden livers also demonstrated nanoparticle movement under focused magnetic field excitation. In the livers of two saline injected control mice, no movement was observed using any ultrasound imaging modes. The results of our experiments indicate that ultrasound imaging of magneto-motive excitation is a candidate imaging modality to identify tissue-based macrophages containing SPIO nanoparticles.
General and Direct Synthesis of 3-Aminoindolizines and Their Analogues via Pd/Cu-Catalyzed Sequential Cross-Coupling/Cycloisomerization Reactions (2007)

[reaction: see text] An efficient and one-step synthesis of 3-aminoindolizines or benz[e]indolizines from the reactions of propargyl amines or amides with heteroaryl bromides was developed. This methodology is realized by a tandem reaction using Pd/Cu catalysts, which could catalyze coupling and cycloisomerization reactions in the same vessel.
Distribution of microsomal glutathione transferase 1 in mammalian tissues (1999)

An extensive Northern blot analysis of microsomal glutathione transferase 1 in human and rat tissues was performed. When normalized against the glyceraldehyde-3-phosphate dehydrogenase or actin expression it was evident that the predominant expression occurs in liver and pancreas. An ontogenetic, as well as a functional, basis for the high levels in these two organs is possible. The relative expression levels in man ranged from: liver and pancreas (100%), to kidney, prostate, colon (30-40%), heart, brain, lung, testis, ovary, small intestine (10-20%), placenta, skeletal muscle, spleen, thymus and peripheral blood leucocytes (1-10%). Liver-enriched expression was detected in human fetal tissues with lung and kidney displaying lower levels (10-20%). No transcripts could be detected in fetal brain or heart. When comparing the expression levels between rat and man it is apparent that human extrahepatic mRNA levels are much higher relative to liver. Rat microsomal glutathione transferase mRNA expression ranges from 0.2 to 10% that of liver, with adrenal, uterus, ovary and stomach displaying the highest levels of the organs tested. Based on these observations, and the fact that the enzyme is encoded by a highly conserved single-copy gene, it is suggested that microsomal glutathione transferase 1 performs essential functions vital to most mammalian cell types. We suggest that protection against oxidative stress constitutes one such function. Human expressed sequence tag (EST) characterization yielded four alternate mRNA transcripts with different 5'-ends (four alternate noncoding exons 1). The predominant exon (based on the observed EST frequency) revealed a tissue distribution similar to that obtained using the reading frame as probe. Thus, it appears that one exon preferentially gives rise to mature mRNA in the human tissues examined. This exon is different from the one reported in the original cDNA characterized.
Formation of gamma-glutamycyst(e)ine in vivo is catalyzed by gamma-glutamyl transpeptidase. (1981)

These studies indicate that gamma-glutamylcyst(e)ine, found in the urine of a patient with gamma-glutamyl transpeptidase deficiency and also in the urine of experimental animals injected with glutathione or with inhibitors of gamma-glutamyl transpeptidase, is formed by the action of gamma-glutamyltranspeptidase. The evidence demonstrates that transpeptidation between glutathione and cystine occurs in vivo and also that this reaction constitutes a significant physiological function of the enzyme. The appearance of large amounts of gamma-glutamylcyst(e)ine in the urine seems to reflect an inhibitory effect of glutathione on the transport of gamma-glutamylcyst(e)ine into cells. The findings also indicate that conversion of glutathione to gamma-glutamylcysteine by hydrolytic cleavage of the COOH-terminal glycine moiety of glutathione (or analogous cleavage of glutathione disulfide) is not a quantitatively significant pathway. The results reported here show that gamma-glutamyl transpeptidase activity is not completely absent in a patient found to have a deficiency of this enzyme and that the activity of the enzyme is not abolished in experimental animals treated with potent gamma-glutamyl transpeptidase inhibitors.
Diaminoalkanes with an odd number of carbon atoms induce compaction of a single double‐stranded DNA chain (1995)

We have performed direct observations on the conformational change of a single double-stranded T4 DNA molecule induced by diaminoalkanes, NH3+(CH2)nNH3+(n = 1-6), by use of fluorescence microscopy. It was found that diamines with three and five methylene groups show a significant effect on the compaction of individual single DNA molecules. On the other hand, diamines with two, four and six methylene groups are not effective in the compaction of DNA. Such a drastic difference in the action of diamines suggests that not only the number of charge but also the length between the amino groups in the diamines plays an essential role in their interactions with DNA.
Oxygen Reduction on Small Supported Platinum Particles (1986)

A series of four catalysts with 5, 10, 20, and 30 weight percent of Pt on carbon has been prepared and incorporated into Teflon‐bonded electrodes. The mean Pt crystallite sizes, as determined by chemisorption, were less than 1, 1.1, 1.4, and 4.1 nm. Also, a Teflon‐bonded Pt‐black electrocatalyst with a Pt crystallite size of 12 nm was prepared. These electrodes were used for the cathodic reduction of dioxygen in at 298 K. The turnover frequency decreased by a factor of 20 with decreasing particle size. Since surface area per weight of metal increases as particle size decreases, the optimum Pt crystallite diameter is about 3 nm.
Impaired Nuclear Nrf2 Translocation Undermines the Oxidative Stress Response in Friedreich Ataxia (2009)

Thus, the defective machinery for ISP synthesis by causing mitochondrial iron dysmetabolism increases hydrogen peroxide production that accounts for the increased susceptibility to oxidative stress.
Functional analysis of the Salmonella typhimurium invasion genes invl and invJ and identification of a target of the protein secretion apparatus encoded in the inv locus (1995)

Summary We have carried out a functional analysis of invl and invJ , two Saimonella typhimurium genes required for this organism to gain access So cultured mammalian cells. These genes are located immediately downstream of invC , a previously identified gene also required for bacterial invasion. Non‐polar mutations in either of these genes rendered S. typhimurium severely defective for entry into cultured epithelial cells, although these mutations did not affect the ability of these organisms to attach to those cells. Nucleotide sequence analysis revealed that the invl and invJ genes encode proteins with molecular weights of 18077 and 36415, respectively. Polypeptides of similar sizes were observed when these genes were expressed in a bacteriophage T7 RNA polymerase‐based expression system. Comparison of the predicted sequences of Invl and InvJ with translated sequences in the existing databases indicated that these proteins are Identical to the previously identified S. typhimurium SpaM and SpaN proteins. Further analysis of these sequences revealed regions of homology between Invl and the N ‐terminus of lpaB of Shigella spp. and between InvJ and EaeB of enteropathogenic Escherichia coli. Localization studies by immunoblot analysis indicated that InvJ is secreted to the culture supernatant, a surprising finding since this protein also lacks a typical signal sequence. Mutations in invG and inyC , two members of the Salmonella inv locus, effectively prevented the transport of InvJ to the culture supernatant. Thus, InvJ is the first identified target of the protein secretion apparatus encoded in the inv locus and therefore a candidate to have effector functions related to bacterial entry.
Aberrant Phosphorylation of SMAD4 Thr277-Mediated USP9x–SMAD4 Interaction by Free Fatty Acids Promotes Breast Cancer Metastasis (2017)

Obesity increases the risk of distant metastatic recurrence and reduces breast cancer survival. However, the mechanisms behind this pathology and identification of relevant therapeutic targets are poorly defined. Plasma free fatty acids (FFA) levels are elevated in obese individuals. Here we report that TGFβ transiently activates ERK and subsequently phosphorylates SMAD4 at Thr277, which facilitates a SMAD4-USP9x interaction, SMAD4 nuclear retention, and stimulates TGFβ/SMAD3-mediated transcription of Twist and Snail. USP9x inhibited the E3 ubiquitin-protein ligase TIF1γ from binding and monoubiquitinating SMAD4, hence maintaining the SMAD4 nuclear retention. FFA further facilitated TGFβ-induced ERK activation, SMAD4 phosphorylation, and nuclear retention, promoting TGFβ-dependent cancer progression. Inhibition of ERK and USP9x suppressed obesity-induced metastasis. In addition, clinical data indicated that phospho-ERK and -SMAD4 levels correlate with activated TGFβ signaling and metastasis in overweight/obese patient breast cancer specimens. Altogether, we demonstrate the vital interaction of USP9x and SMAD4 for governing TGFβ signaling and dyslipidemia-induced aberrant TGFβ activation during breast cancer metastasis. <i>Cancer Res; 77(6); 1383-94. ©2017 AACR</i>.
ΔNp73, A Dominant-Negative Inhibitor of Wild-type p53 and TAp73, Is Up-regulated in Human Tumors (2002)

p73 has significant homology to p53. However, tumor-associated up-regulation of p73 and genetic data from human tumors and p73-deficient mice exclude a classical Knudson-type tumor suppressor role. We report that the human TP73 gene generates an NH(2) terminally truncated isoform. DeltaNp73 derives from an alternative promoter in intron 3 and lacks the transactivation domain of full-length TAp73. DeltaNp73 is frequently overexpressed in a variety of human cancers, but not in normal tissues. DeltaNp73 acts as a potent transdominant inhibitor of wild-type p53 and transactivation-competent TAp73. DeltaNp73 efficiently counteracts transactivation function, apoptosis, and growth suppression mediated by wild-type p53 and TAp73, and confers drug resistance to wild-type p53 harboring tumor cells. Conversely, down-regulation of endogenous DeltaNp73 levels by antisense methods alleviates its suppressive action and enhances p53- and TAp73-mediated apoptosis. DeltaNp73 is complexed with wild-type p53, as demonstrated by coimmunoprecipitation from cultured cells and primary tumors. Thus, DeltaNp73 mediates a novel inactivation mechanism of p53 and TAp73 via a dominant-negative family network. Deregulated expression of DeltaNp73 can bestow oncogenic activity upon the TP73 gene by functionally inactivating the suppressor action of p53 and TAp73. This trait might be selected for in human cancers.
Diabetic Retinopathy and Metabolic Control (1993)

Retinopathy is probably the first long-term complication of diabetes mellitus to become clinically evident, possibly because the retina is the only microvascular bed that can be observed directly and repeatedly. This makes it a good model for studying the pathogenesis and natural history of diabetic microangiopathy. Most of the proposals to account for its pathogenesis invoke mechanisms that depend directly on the circulating and tissue levels of glucose: protein glycosylation, activation of the "polyol pathway", abnormalities of vascular endothelium, altered capillary blood flow. Several population studies and clinical trials suggest that the degree of metabolic control maintained over the years influences the rates of appearance and progression of retinopathy. However, on an individual basis, factors independent of control may intervene, making some patients more or less prone to this complication. Animal models also suggest that the progression of retinopathy may become irreversible from its very early stages. From a clinical point of view, it is difficult to establish a satisfactory definition of "good" control and approaching it may increase the risk of dangerous hypoglycemia and weight gain. Diabetes and eye specialists are thus left to strive for the best possible, sensible, metabolic control but must also rely on early diagnosis and treatment for the sight-threatening complications of diabetes.
Chickenpox Hospitalizations Among Residents of Olmsted County, Minnesota, 1962 Through 1981 (1984)

Age-specific incidence rates were determined for hospitalizations resulting from complications of chickenpox. We reviewed medical records for all Olmsted County, Minnesota, residents hospitalized for chickenpox during the 20-year period 1962 through 1981. Incidence rates based on these 25 cases showed good agreement with national rates computed from information compiled by the Commission on Professional and Hospital Activities for 669 statistically selected patients, representing about 5% of US varicella hospitalizations from January 1979 through June 1982 (about 4,000 hospitalizations annually). The most common complications were bacterial superinfections in children younger than 5 years old, varicella encephalitis (mainly acute cerebellar ataxia) and dehydration in 5- to 9-year-olds, and varicella pneumonia in adults. The high prevalence of chickenpox and its association with infectious and neurologic complications make it a continuing source of morbidity.