gebhart/patrepeval huggingface dataset:
Low Rate Sampling of Pulse Streams with Application to Ultrasound Imaging (2010)

Abstract—Signals comprised of a stream of short pulses appear in many applications including bio-imaging, radar, and ultrawideband communication. Recently, a new framework, referred to as finite rate of innovation, has paved the way to low rate sampling of such pulses by exploiting the fact that only a small number of parameters per unit time are needed to fully describe these signals. Unfortunately, for high rates of innovation, existing approaches are numerically unstable. In this paper we propose a general sampling approach which leads to stable recovery even in the presence of many pulses. We begin by deriving a condition on the sampling kernel which allows perfect reconstruction of periodic streams of pulses from a minimal number of samples. This extends previous work which assumes that the sampling kernel is an ideal low-pass filter. A compactly supported class of filters, satisfying the mathematical condition, is then introduced, leading to a sampling framework based on compactly supported kernels. We then extend our periodic solution to finite and infinite streams, and show that our method is numerically stable even for a large number of pulses per unit time. High noise robustness is demonstrated as well when the time delays are sufficiently separated. Finally, we apply our results to ultrasound imaging data, and show that our techniques result in substantial rate reduction with respect to traditional ultrasound sampling schemes. Index Terms—Analog-to-digital conversion, annihilating filters, finite rate of innovation, generalized sampling, perfect reconstruction, ultrasound imaging. I.
Magnesium and Mortality in Patients with Diabetes and Early Chronic Kidney Disease (2014)

An observational, prospective study involving 191 patients was conducted in our outpatient diabetic nephropathy clinic from December
Oxygen radicals stimulate intracellular proteolysis and lipid peroxidation by independent mechanisms in erythrocytes. (1987)

Exposure of red blood cells to oxygen radicals can induce hemoglobin damage and stimulate protein degradation, lipid peroxidation, and hemolysis. To determine if these events are linked, rabbit erythrocytes were incubated at 37 degrees C with various oxygen radical-generating systems and antioxidants. Protein degradation, measured by the production of free alanine, increased more than 11-fold in response to xanthine (X) + xanthine oxidase (XO). A similar increase in proteolysis occurred when the cells were incubated with acetaldehyde plus XO, with ascorbic acid plus iron (Asc + Fe), or with hydrogen peroxide (H2O2) alone. Upon addition of XO, increased proteolysis was evident within 5 min and was linear for up to 5 h. In contrast, lipid peroxidation, as shown by the production of malonyldialdehyde, conjugated dienes, or lipid hydroperoxides was observed only after 2 h of incubation with X + XO, acetaldehyde + XO, or H2O2. Ascorbate plus Fe2+ induced both protein degradation and lipid peroxidation; however, the addition of various antioxidants (urate, xanthine, glucose, or butylated hydroxytoluene) decreased lipid peroxidation without affecting proteolysis. Thus, these processes seem to occur by distinct mechanisms. Furthermore, at low concentrations of XO, protein degradation was clearly increased in the absence of detectable lipid peroxidation products. Hemolysis occurred only in a small number of cells (9%) and followed the appearance of lipid peroxidation products. Thus, an important response of red cells to oxygen radicals is rapid degradation of damaged cell proteins. Increased proteolysis seems to occur independently of membrane damage and to be a more sensitive indicator of cell exposure to oxygen radicals than is lipid peroxidation.
Protease B of the Lysosomelike Vacuole of the Yeast Saccharomyces Cerevisiae Is Homologous to the Subtilisin Family of Serine Proteases (1987)

The PRB1 gene of Saccharomyces cerevisiae encodes the vacuolar endoprotease protease B. We have determined the DNA sequence of the PRB1 gene and the amino acid sequence of the amino terminus of mature protease B. The deduced amino acid sequence of this serine protease shares extensive homology with those of subtilisin, proteinase K, and related proteases. The open reading frame of PRB1 consists of 635 codons and, therefore, encodes a very large protein (molecular weight, greater than 69,000) relative to the observed size of mature protease B (molecular weight, 33,000). Examination of the gene sequence, the determined amino-terminal sequence, and empirical molecular weight determinations suggests that the preproenzyme must be processed at both amino and carboxy termini and that asparagine-linked glycosylation occurs at an unusual tripeptide acceptor sequence.
Two trans-Acting Metalloregulatory Proteins Controlling Expression of the Copper-ATPases of Enterococcus hirae* (1995)

Enterococcus hirae possesses two P-type ATPases, CopA and CopB, that are involved in copper homeostasis. These enzymes are induced by extracellular copper concentrations that are either too low or too high for optimal growth. To identify the regulatory proteins involved in induction, the DNA upstream of copA was cloned and sequenced. Following a putative promoter region, it contains two genes, copY and copZ, that encode proteins of 145 and 69 amino acids, respectively. Both proteins contain metal binding motifs and exhibit significant sequence similarity to known regulatory proteins. Gene disruption of copY by reverse genetics caused constitutive overexpression of CopA and CopB, generating a copper-dependent phenotype. In contrast, disruption of copZ suppressed the expression of the two copper-ATPases, rendering the cells copper-sensitive. Both null mutations could be complemented in trans with plasmids bearing copY or copZ. Thus, copY and copZ encode trans-acting metalloregulatory proteins that are required for induction of the cop operon by copper. In this mechanism, CopY apparently acts as a metal-fist type repressor and CopZ as an activator.
Direct Reading Spectrometer Optimization Using Two Complementary Concave Holographic Gratings (1984)

A direct reading spectrometer utilizing two concave holographic gratings is able to analyze as many as 40 elements simultaneously over the spectral range 170-900nm. This paper provides a discussion of the basic concepts, problems, and solutions involved in spectrometer optimization and aberration corrected grating design.
Microbial models of mammalian metabolism: stereospecificity of ketone reduction with pentoxifylline (1985)

The absolute configuration of pentoxifylline alcohol produced by the microbial reduction of pentoxifylline using Rhodotorula rubra (ATCC 20129) was determined by O.R.D. spectroscopy and p.m.r. studies on the R-(+)-alpha-methoxy-alpha-(trifluoromethyl) phenylacetate (MTPA) ester. The development of a reverse-phase h.p.l.c. method for resolving the diastereomeric R-(+)-MTPA esters of racemic pentoxifylline alcohol and assignment of the elution order, allowed for the determination of the stereochemical purity of pentoxifylline alcohol produced by 13 microbial cultures shown previously to reduce pentoxifylline. A marked preference for S-alcohol production was observed with five organisms exhibiting complete stereoselectivity towards S-alcohol generation, and two producing the racemic alcohol.
CCR 2 + monocytes infiltrate atrophic lesions in age‐related macular disease and mediate photoreceptor degeneration in experimental subretinal inflammation in Cx3cr1 deficient mice (2013)

Atrophic age-related macular degeneration (AMD) is associated with the subretinal accumulation of mononuclear phagocytes (MPs). Their role in promoting or inhibiting retinal degeneration is unknown. We here show that atrophic AMD is associated with increased intraocular CCL2 levels and subretinal CCR2(+) inflammatory monocyte infiltration in patients. Using age- and light-induced subretinal inflammation and photoreceptor degeneration in Cx3cr1 knockout mice, we show that subretinal Cx3cr1 deficient MPs overexpress CCL2 and that both the genetic deletion of CCL2 or CCR2 and the pharmacological inhibition of CCR2 prevent inflammatory monocyte recruitment, MP accumulation and photoreceptor degeneration in vivo. Our study shows that contrary to CCR2 and CCL2, CX3CR1 is constitutively expressed in the retina where it represses the expression of CCL2 and the recruitment of neurotoxic inflammatory CCR2(+) monocytes. CCL2/CCR2 inhibition might represent a powerful tool for controlling inflammation and neurodegeneration in AMD.
Human Papillomavirus and head and neck cancer: Epidemiology and molecular biology (1998)

The prevalence of HPV, particularly the high-risk types, suggests a potential etiologic role for the virus in head and neck cancer. Molecular biology has provided important data on the interaction of the HPV oncoproteins with genes important in cell cycle control. Nonetheless, more basic research is needed to describe the physical state of the virus in a variety of cell types and the interaction with other genes. In addition, epidemiologic research is required to further understand the association between HPV and demographic and other risk factors as well as possible routes of transmission. Finally, much work is warranted to provide a definitive assessment of the prognostic significance of HPV in head and neck cancer.
Reduction of sidewall defect induced leakage currents by the use of nitrided field oxides in silicon selective epitaxial growth isolation for advanced ultralarge scale integration (2000)

Defects in the near sidewall region in selective epitaxial growth of silicon have prevented its widespread use as a viable dielectric isolation technology. The main cause of these defects has been demonstrated to be thermal stress due to mismatch in the coefficient of thermal expansion between silicon and silicon dioxide. This article presents the detailed electrical characterization of these sidewall defects using P+/N junction diodes fabricated using silicon dioxide and thermally nitrided silicon dioxide as the field insulator. It is shown that the use of field oxide which was nitrided at 1100 °C for 60 min in ammonia gas ambient reduced the reverse saturation current density in the diodes by a factor of 6 and also improved the forward recombination and ideality factors when compared to standard thermal field oxide isolated diodes. The improvement of the sidewall quality was attributed to a reduction in thermal stress due to the modification of the coefficient of thermal expansion of nitrided silicon oxide.
An Independent, Temperature-Controllable Microelectrode Array (2004)

Rapid, localized temperature control and negligible power consumption are key requisites for realizing effective parallel and sequential processing in the miniaturized, integrated biomedical microdevices where temperature-dependent biochemical reactions and fluid flow occur. In this study, an independent, temperature-controllable microelectrode array, with excellent temperature control rates and minimal power consumption, has been developed using microelectromechanical systems technology. The microfabricated array consists of Pt microelectrodes (100-microm diameter), with n-doped polysilicon microheaters (1.4-k Omega resistance), and vacuum-sealed cavities of depth 6.2 microm and diameter 200 microm. The thermal characteristics of each microelectrode were evaluated electrochemically through surface temperature measurements. The large heater power coefficient (2.1 +/- 0.1 degrees C mW(-1)) and the short heating and cooling times (less than 0.2 s for T(0.95)) are consequences of the vacuum-sealed cavities, which facilitate good thermal isolation and low thermal mass. The temperature of each microelectrode is independently controlled by a dedicated microheater, without thermally influencing the adjacent microelectrodes significantly.
Synthesis of New Chiral 2,2‘-Bipyridyl-Type Ligands, Their Coordination to Molybdenum(0), Copper(II), and Palladium(II), and Application in Asymmetric Allylic Substitution, Allylic Oxidation, and Cyclopropanation (2001)

A series of chiral bipyridine-type ligands 5−12 has been synthesized via a de novo construction of the pyridine nucleus. The chiral moieties of the ligands originate from the monoterpene realm, namely, pinocarvone (13 → 6, 7, and 9), myrtenal (18 → 5), nopinone (21 → 8 and 10), and menthone (28 → 11 and 12); the first three precursors can be obtained in one step from β- and α-pinene, respectively. Complexes of these ligands with molybdenum(0) (38−40) and copper(II) (41) have been characterized by single-crystal X-ray crystallography. While complex 38 exhibits polymorphism (monoclinic and tetragonal forms crystallize from the same batch), 41 is characterized by a tetrahedrally distorted geometry of the metal coordination. The Mo and Pd complexes exhibit modest asymmetric induction in allylic substitution (43 → 44), and the Cu(I) counterpart of 41, derived from 10 (PINDY) and Cu(OTf)2, shows promising enantioselectivity (49−75% ee) and reaction rate (≥30 min at room temperature) in allylic oxidation of cyclic olefins (47 → 48). The Cu(I) complex of 11 (MINDY) proved effective in cyclopropanation (49 → 50) with up to 72% ee.
Attenuation of early and late phase allergen-induced bronchoconstriction in asthmatic subjects by a 5-lipoxygenase activating protein antagonist, BAYx 1005 (1997)

These results show that antagonism of 5-lipoxygenase activating protein can attenuate allergen-induced bronchoconstrictor responses and support an important role for the cysteinyl leukotrienes in mediating these asthmatic responses.
Effects of salinity and toxic heavy metals on oxygen release by Fucus vesiculosus L. (1991)

Continuous measurements with an oxygen electrode applied to thalloid algal material were used to determine 02 production/consumption at light and dark phases in an open system. The balance of photosynthesis-related 02 release by Fucus vesiculosus L. in seawater shows a decrease within only 20 min. after addition of Cu(II)SO4&#1468;5 H20 at condensations known to be toxic. Short response time and continuous recording allowed to show that in the case of ZnCl2 addition, the increase in 02 release is followed by a decrease. Effects of interactions between zinc and copper compounds and seawater salinities can be recorded in the same way.
Synthetic receptors as sensor coatings for molecules and living cells (2001)

Non-covalent molecularly imprinted polymers are applied as sensitive coatings to planar waveguides and mass-sensitive devices for the selective detection of various groups of analytes in the gaseous and aqueous phases. Cavity imprinting in the bulk of the sensor material as well as surface imprinting techniques are used to enrich analytes ranging from sub-nanometres to micrometres in analyte size. The coated devices provide sensitivity to e.g. polycyclic aromatic hydrocarbons, xanthine derivatives, complex coffee samples and whole microorganisms.
Phosphoproteomics reveals malaria parasite Protein Kinase G as a signalling hub regulating egress and invasion (2015)

Our understanding of the key phosphorylation-dependent signalling pathways in the human malaria parasite, Plasmodium falciparum, remains rudimentary. Here we address this issue for the essential cGMP-dependent protein kinase, PfPKG. By employing chemical and genetic tools in combination with quantitative global phosphoproteomics, we identify the phosphorylation sites on 69 proteins that are direct or indirect cellular targets for PfPKG. These PfPKG targets include proteins involved in cell signalling, proteolysis, gene regulation, protein export and ion and protein transport, indicating that cGMP/PfPKG acts as a signalling hub that plays a central role in a number of core parasite processes. We also show that PfPKG activity is required for parasite invasion. This correlates with the finding that the calcium-dependent protein kinase, PfCDPK1, is phosphorylated by PfPKG, as are components of the actomyosin complex, providing mechanistic insight into the essential role of PfPKG in parasite egress and invasion.
Genetic Contribution of Tumor Necrosis Factor (TNF)‐α Gene Promoter (−1031, −863 and −857) and TNF Receptor 2 Gene Polymorphisms in Endometriosis Susceptibility (2004)

Our results indicated that TNFA promoter polymorphism was associated with susceptibility to endometriosis. However, this association was not independent of HLA-class I polymorphisms.
Electrospinning Bombyx mori Silk with Poly(ethylene oxide) (2002)

Electrospinning for the formation of nanoscale diameter fibers has been explored for high-performance filters and biomaterial scaffolds for vascular grafts or wound dressings. Fibers with nanoscale diameters provide benefits due to high surface area. In the present study we explore electrospinning for protein-based biomaterials to fabricate scaffolds and membranes from regenerated silkworm silk, Bombyx mori, solutions. To improve processability of the protein solution, poly(ethylene oxide) (PEO) with molecular weight of 900,000 was blended with the silk fibroin. A variety of compositions of the silk/PEO aqueous blends were successfully electrospun. The morphology of the fibers was characterized using high-resolution scanning electron microscopy. Fiber diameters were uniform and less than 800 nm. The composition was estimated by X-ray photoelectron spectroscopy to characterize silk/PEO surface content. Aqueous-based electrospining of silk and silk/PEO blends provides potentially useful options for the fabrication of biomaterial scaffolds based on this unique fibrous protein.
A Binding Domain on Mesothelin for CA125/MUC16 (2008)

Ovarian cancer and malignant mesothelioma frequently express both mesothelin and CA125 (also known as MUC16) at high levels on the cell surface. The interaction between mesothelin and CA125 may facilitate the implantation and peritoneal spread of tumors by cell adhesion, whereas the detailed nature of this interaction is still unknown. Here, we used truncated mutagenesis and alanine replacement techniques to identify a binding site on mesothelin for CA125. We examined the molecular interaction by Western blot overlay assays and further quantitatively analyzed by enzyme-linked immunosorbent assay. We also evaluated the binding on cancer cells by flow cytometry. We identified the region (296-359) consisting of 64 amino acids at the N-terminal of cell surface mesothelin as the minimum fragment for complete binding activity to CA125. We found that substitution of tyrosine 318 with an alanine abolished CA125 binding. Replacement of tryptophan 321 and glutamic acid 324 with alanine could partially decrease binding to CA125, whereas mutation of histidine 354 had no effect. These results indicate that a conformation-sensitive structure of the region (296-359) is required and sufficient for the binding of mesothelin to CA125. In addition, we have shown that a single chain monoclonal antibody (SS1) recognizes this CA125-binding domain and blocks the mesothelin-CA125 interaction on cancer cells. The identified CA125-binding domain significantly inhibits cancer cell adhesion and merits evaluation as a new therapeutic agent for preventing or treating peritoneal malignant tumors.
Synthesis and Transporter Binding Properties of 3β-(4‘-Alkyl-, 4‘-alkenyl-, and 4‘-alkynylphenyl)nortropane-2β-carboxylic Acid Methyl Esters:  Serotonin Transporter Selective Analogs (1996)

New methods for the synthesis of 3 beta-(4'-alkyl-, 4'-alkenyl-, and 4'-alkynylphenyl)nortropane-2 beta-carboxylic acid methyl esters 2-4, respectively, were developed. These methods involved coupling of the appropriate organometallic reagents to 3 beta-(4'-iodophenyl)tropane-2 beta-carboxylic acid methyl ester (6a, RTI-55) or to an N-protected derivative of 6a followed by N-demethylation or removal of the protecting group. Some analogs were prepared by catalytic reduction of the alkene and alkene analogs 3 and 4 or by isomerization of the alkenes 3. The analogs 2-4 were evaluated for inhibition of radioligand binding to the serotonin (5-HT), dopamine (DA), and norepinephrine (NE) transporters. 3 beta-(4'-Isopropenyl- and 4'-cis-propenylphenyl)nortropane-2 beta-carboxylic acid methyl esters (3b,d), which possessed IC50 values of 0.6 and 1.15 nM, respectively, were the most potent analogs at the 5-HT transporter, and with NE/5-HT IC50 ratios of 240 and 128 nM, respectively, they were selective for the 5-HT relative to the NE transporter. Since interaction with the serotonin transporter may modulate the pharmacological effects resulting from binding to the dopamine transporter, 3 beta-(4'-isopropenylphenyl)tropane-2 beta-carboxylic acid methyl ester (11b) which has good affinity for both the 5-HT and DA transporters but low affinity at the NE transporter may be useful for studying this interaction.
Chiral magnetization textures stabilized by the Dzyaloshinskii-Moriya interaction during spin-orbit torque switching (2014)

We study the effect of the Dzyaloshinskii-Moriya interaction (DMI) on current-induced magnetic switching of a perpendicularly magnetized heavy-metal/ferromagnet/oxide trilayer both experimentally and through micromagnetic simulations. We report the generation of stable helical magnetization stripes for a sufficiently large DMI strength in the switching region, giving rise to intermediate states in the magnetization and confirming the essential role of the DMI on switching processes. We compare the simulation and experimental results to a macrospin model, showing the need for a micromagnetic approach. The influence of the temperature on the switching is also discussed.
Corrosion and surface chemistry of metals (2007)

Providing a carefully developed and comprehensive overview of the corrosion chemistry of metallic materials, this book covers the principal methods of corrosion prevention. It includes a systematic study of the physical chemistry of the surface supported by state-of-the-art analysis methods. The author builds a scientific foundation by developing t
Duration of mucociliary dysfunction following antigen challenge (1983)

Antigen-induced bronchospasm is associated with an impairment of airway mucociliary clearance, but the duration of this defect has not been examined. In the present study, we determined the time course of mucociliary dysfunction following inhalation challenge with Ascaris suum extract in conscious sheep with hypersensitivity to this antigen. Tracheal mucous velocity (TMV) as an index of mucociliary function, pulmonary resistance (RL), and arterial oxygen tension (Pao2) were measured prior to, immediately after, and serially for 8 h after inhalation challenge. TMV and Pao2 were then measured periodically for at least 2 wk. Immediately after A. suum challenge, mean RL increased to 264% of base line (P less than 0.05), and mean Pao2 decreased to 61% of base line (P less than 0.05). By 2 h postchallenge, mean RL and Pao2 had returned to base line but mean TMV had fallen to 61% of base line (P less than 0.05). Mean TMV reached a minimum of 35% of base line after 5 h (P less than 0.05) and remained significantly depressed between 37% and 54% of base line for 7 days; by day 9, mean TMV had returned to base line. Inhalation challenge with a control antigen (ragweed) failed to alter mean TMV, RL, and Pao2 during the first 8 h and TMV and Pao2 at any time throughout the 2-wk observation period.(ABSTRACT TRUNCATED AT 250 WORDS)
Phase II Trial of Trastuzumab in Combination With Cytotoxic Chemotherapy for Treatment of Metastatic Osteosarcoma With Human Epidermal Growth Factor Receptor 2 Overexpression: A Report From the Children's Oncology Group (2012)

Despite intensive chemotherapy plus trastuzumab for patients with HER2-positive disease, the outcome for all patients was poor, with no significant difference between the HER2-positive and HER2-negative groups. Although our findings suggest that trastuzumab can be safely delivered in combination with anthracycline-based chemotherapy and dexrazoxane, its therapeutic benefit remains uncertain. Definitive assessment of trastuzumab's potential role in treating osteosarcoma would require a randomized study of patients with HER2-positive disease.