gebhart/patrepeval huggingface dataset:
Cold injury in mice: a model to study mechanisms of brain edema and neuronal apoptosis (1999)

Small rodents, mice in particular, have been widely used for genetic manipulation because of the extensive knowledge in development, embryology and other molecular aspects of this species. However, the use of mice for neurobiology research in the area of brain edema and neuronal injury has not been common. Here we summarize the studies of cold injury-induced brain edema and neuronal apoptosis using mice. Blood-brain barrier (BBB) permeability, demonstrated by extravasation of a serum albumin tracer, Evans Blue, was increased immediately after the injury and returned to the control level by 24 hr. Water content was maximized at 24 hr, whereas a secondary lesion gradually progressed up to 72 hr after cold injury. The mechanism of the development of the cold injury-induced edema and the secondary lesion, involving of oxygen radicals in particular, was determined using superoxide dismutase (SOD)-1 transgenic (Tg) mice with overexpressed copper, zinc-SOD. All of the parameters, BBB permeability, water content and secondary lesion, were attenuated in the Tg mice as compared to littermate non-Tg mice. This clearly demonstrates that oxygen radicals, superoxide anion in particular, mediate cold injury. We also studied whether apoptosis contributes to brain injury following cold injury. Staining with terminal deoxynucleotidyl transferase-mediated uridine 5'-triphosphate-biotin nick end labeling showed the apoptotic cells widespread throughout the entire lesion while still remaining in the margin. DNA laddering was exhibited by gel electrophoresis. These studies indicate that oxidative mediates the development of cold injury-induced edema and the secondary injury, and induces apoptotic cell death. We believe that cold injury in mice provides a simple animal model to study the pathogenesis of brain edema and apoptosis in genetically altered animals.
Differential production of parasiticein, an elicitor of necrosis and resistance in tobacco, by isolates of Phytophthora parasitica (1992)

Fifteen isolates of Phytophthora parasitica , nine from tobacco (causing black shank disease) and six from other host plants, were compared by root inoculation with regard to their pathogenicity to young tobacco plants. A progressive invasion of the aerial parts over 1 week was observed only with the black shank isolates, while the non‐tobacco isolates induced leaf necrosis within 2 days. Similar necrosis occurred when the roots of tobacco plants were dipped in diluted culture filtrates from non‐tobacco isolates, but not in those from tobacco isolates. The necrosis‐inducing filtrates were shown to contain a c. 10‐kDa protein band which was not present in the other filtrates. This protein (named parasiticein) was purified by ion‐exchange chromatography to homogeneity in SDS‐PAGE and reverse‐phase HPLC. Parasiticein was serologically related to cryptogein, a member of the elicitin family of proteinaceous elicitors previously described from other Phytophthora species. Like the other elicitins, parasiticein induced necrosis in tobacco plants and protected them against black shank. It most closely resembled capsicein in being acidic and in inducing resistance at concentrations (10–100 μg per plant) that caused little leaf necrosis. It is suggested that the absence of parasiticein production by the black shank isolates might be a factor involved in their specific pathogenicity to tobacco.
Wide-band receiver architecture with flexible blocker filtering techniques (2010)

Wide-band filterless RF front-ends are yet unpractical because of the stringent linearity requirements imposed by out-of-band blockers. A base-band to radio-frequency feedback receiver (BB-RF-FBRX) architecture is proposed in this paper, which reflects the base-band selectivity to the RF input. The aim of this architecture is to eliminate surface acoustic wave (SAW) filters between the antenna and the low noise amplifier (LNA). Two variants of BB-RF feedback are analyzed and explored by simulation. The most promising positive feed-back architecture should allow up to 19 dB rejection of out-of-band interferers.
Glucose-regulated stresses cause decreased expression of cyclin D1 and hypophosphorylation of retinoblastoma protein in human cancer cells. (1996)

Glucose-regulated stress response of cancer cells occurs during the growth of solid tumors and is induced in culture by treatments with various agents, including 2-deoxyglucose, glucosamine, and calcium ionophore A23187. We previously reported that the three stressors commonly induced cell-cycle arrest in the G1 phase and resistance to antitumor drugs in human cancer A2780 and HT-29 cells. In this study, we investigated the mechanisms of stress-induced G1 arrest by determining the expression of cell-cycle-regulating proteins. Among G1 cyclins and cyclin-dependent kinases (cdk) examined, the expression levels of cyclin D1 preferentially decreased in the stressed cells. A time-course study showed that the decrease in cyclin D1 coincided with the appearance of hypophosphorylated retinoblastoma protein (pRb), which is the growth suppressive form. These findings suggest that the stress-induced G1 arrest is mediated through the down-regulation of cyclin D1-associated kinases (cdk4/6), pRb kinases during G1 phase. This was also supported by decreased cdk4 expression in stressed HT-29 cells. In addition, p21WAF1, a cdk inhibitor, was induced in the stressed cells, particularly A23187-treated cells. A23187, compared with the other stressors, caused extreme pRb hypophosphorylation, suggesting that p21WAf1 is involved in the regulation of pRb phosphorylation in the stressed cells. Our present findings could explain a molecular-based mechanism of a growth-arrested quiescent state and also resistance to chemotherapy of solid tumor cells.
Kinetics of a Cellular Nitric Oxide/cGMP/Phosphodiesterase-5 Pathway (2004)

Rat platelets served as a model to evaluate quantitatively how guanylate cyclase (GC)-coupled nitric oxide (NO) receptors and phosphodiesterases (here phosphodiesterase-5) interact to transduce NO signals in cells. The platelets expressed mRNA only for the alpha(1) and beta(1) GC-coupled receptor subunits. In intact platelets, the potency of NO for elevating cGMP (EC(50) = 10 nm) was lower than in lysed platelets (EC(50) = 1.7 nm). The limiting activities of GC and phosphodiesterase in intact platelets were both very high, being equivalent to about 100 microm/s. With low phosphodiesterase activity (imposed by 100 microm sildenafil), the cGMP response over time was hyperbolic in shape for a range of NO concentrations or GC activities due to GC desensitization. Without a phosphodiesterase inhibitor, NO generated only brief cGMP transients, peaking after 2-5 s but amounting maximally to about 150 microm cGMP. The transients were caused partly by GC desensitization, which varied in rate (half-time up to 3 s) and extent (up to 80%) depending on the NO concentration, and partly by an enhancement of the phosphodiesterase catalytic activity with time, which was deduced to be up to 30-fold and to occur with a half-time of up to 5 s. The results were simulated by a quantitative model, which also explains the varied shapes of cGMP responses to NO found in other cells. Downstream phosphorylation in platelets was detectable within 2 s, and, with continuous exposure (1 min), this pathway could be engaged by subnanomolar NO concentrations (EC(50) = 0.5 nm).
The Potential of Cellulosic Ethanol Production from Municipal Solid Waste: A Technical and Economic Evaluation (2009)

Municipal solid waste (MSW) is an attractive cellulosic resource for sustainable production of transportation fuels and chemicals because of its abundance, the need to find uses for this problematic waste, and its low and perhaps negative cost. However, significant heterogeneity and possible toxic contaminants are barriers to biological conversion to ethanol and other products. In this study, we obtained six fractions of sorted MSW from a waste processing facility in Fontana, California: 1) final alternative daily cover (ADC Final), 2) ADC green, 3) woody waste, 4) grass waste, 5) cardboard, and 6) mixed paper. Application of dilute sulfuric acid pretreatment followed by enzymatic hydrolysis gave the highest sugar yields in cardboard and ADC final fractions at enzyme loadings of 100 mg enzyme protein/g sugars of raw materials. Treatment with our non-catalytic protein detoxification technology before adding enzymes improved sugar yields at low enzyme loading of 10 mg enzyme protein/g (glucan plus xylan) of raw materials. Pretreatment with 1% dilute sulfuric acid for 40 min followed by bovine serum albumin (BSA) supplemented enzymatic hydrolysis at an enzyme loading of 10 mg enzyme protein/g glucan recovered 79.1% of potential glucan and 88.2% of potential xylan in solution from ADC final, and 83.3% of potential glucan and 89.1% of potential xylan from ADC green. Experimental results were incorporated into an economic model to determine the economic feasibility of converting MSW to ethanol and identify opportunities for improving the economics. The minimum ethanol selling price for ADC final and ADC green was estimated as $0.6 per gallon and $0.91 per gallon, respectively.
Specificities of IgE and IgG Antibodies in Patients with Birch Pollen Allergy (1989)

58 sera from patients with established birch pollen allergy showed characteristic antibody-binding patterns in immunoblotting experiments. Regarding IgE, 56/58 patients recognized a protein of molecular weight (MW) 17 kilodaltons (kD), previously defined as Bet v I. 23/58 patients in addition reacted with a variety of 11 minor allergens with MWs ranging from 13 to 68 kD. A 13-kD protein was proved to represent an independent minor allergen. IgG binding in patients and healthy individuals was more pronounced on the minor allergens than on Bet v I. 3 different allergens were not detected by IgG of healthy individuals. In two-dimensional electrophoresis/immunoblot, a monoclonal antibody and human IgE (in both cases directed against Bet v I) detected a very similar cluster of spots, probably representing isoallergens of Bet v I.
Development of a Rare Cell Fractionation Device: Application for Cancer Detection (2004)

Isolating rare cells from biological fluids including whole blood or bone marrow is an interesting biological problem. Characterization of a few metastatic cells from cancer patients for further study is desirable for prognosis/diagnosis. Traditional methods have not proven adequate, due to the compositional complexity of blood, with its large numbers of cell types. To separate individual cells based on their mechanical characteristics, we have developed a series of massively parallel microfabricated sieving device. These devices were constructed with four successively narrower regions of channels numbering approximately 1800 per region. As cells traversed the device, they encountered each region and stopped at a gap width that prohibited passage due to their size. Cultured neuroblastoma cells, when mixed with whole blood and applied to the device, were retained in the 10-microm-wide by 20-microm-deep channels. All other cells migrated to the output. A derivative of the same device was utilized to characterize migration of whole blood. Adult white blood cells were retained at the 2.5-microm-wide by 5-microm-deep channels, while red blood cells passed through these channels. Devices designed to capture rare cells in peripheral circulation for downstream analysis will provide an important tool for diagnosis and treatment.
Material Handling System for Robotic Natural Orifice Surgery (2013)

Natural orifice translumenal endoscopic surgery (NOTES) is a relatively new surgical approach that uses no external incisions, thereby improving cosmetic outcomes, decreasing overall recovery time, and reducing the risk of external infection. In standard NOTES, flexible endoscopic tools have been used to carry out a variety of surgical procedures in the abdomen. As an alternative, miniature in vivo robots can be fully inserted into the peritoneal cavity and utilized to perform various surgical procedures. These in vivo robots eliminate tool triangulation issues, improve multitasking capabilities, and greatly increase freedom and dexterity when compared to standard endoscopic and laparoscopic tools. One major limitation is that once inserted, the in vivo robots are isolated within the abdomen and cannot send or receive materials to the external environment. The topic of this paper is a material handling system that has been developed to bridge this deficiency. This system features a flexible silicone overtube and an open-loop control system with manual and automatic operation capabilities. The system utilizes the helix of a spring to advance a payload (staples, robotic tool tips, etc.) along the length of the overtube. The system functioned as intended in benchtop and in vivo testing. Minimum bend radius was identified, and a payload was successfully advanced and retrieved through the shuttling system in porcine surgical procedures. NOTES access was achieved via a custom built transvaginal trocar. This paper presents the design and rationale, control strategy, and in vivo testing results for the NOTES material handling system. The system performs as intended based on functional requirements as demonstrated in benchtop and porcine in vivo testing. The control method is robust even when pushed beyond the physical constraints of the system. Collectively, the material handling system provides a simple, repeatable way for an operator to interface with miniature in vivo robots, improving surgical system flexibility while minimizing impact on the duration of an abdominal surgical procedure.
Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes (2010)

Neutral nucleotide substitutions occur at varying rates along genomes, and it remains a major issue to unravel the mechanisms that cause these variations and to analyze their evolutionary consequences. Here, we study the role of replication in the neutral substitution pattern. We obtained a high-resolution replication timing profile of the whole human genome by massively parallel sequencing of nascent BrdU-labeled replicating DNA. These data were compared to the neutral substitution rates along the human genome, obtained by aligning human and chimpanzee genomes using macaque and orangutan as outgroups. All substitution rates increase monotonously with replication timing even after controlling for local or regional nucleotide composition, crossover rate, distance to telomeres, and chromatin compaction. The increase in non-CpG substitution rates might result from several mechanisms including the increase in mutation-prone activities or the decrease in efficiency of DNA repair during the S phase. In contrast, the rate of C --> T transitions in CpG dinucleotides increases in later-replicating regions due to increasing DNA methylation level that reflects a negative correlation between timing and gene expression. Similar results are observed in the mouse, which indicates that replication timing is a main factor affecting nucleotide substitution dynamics at non-CpG sites and constitutes a major neutral process driving mammalian genome evolution.
CALCIUM-DEPENDENT HISTAMINE RELEASE WITH DEGRANULATION FROM ISOLATED RAT MAST CELLS BY ADENOSINE 5’;-TRIPHOSPHATE (1971)

It has generally been recognized that histamine release from mast cells induced by antigen-antibody reaction, as well as by certain basic compounds, is dependent upon the cellular energy generating processes since these reactions are inhibited by anoxic conditions and by metabolic inhibitors which uncouples oxidative phosphorylation or block respiratory enzymes (1-7). A preliminary study was attempted in order to see whether adenosine 5'-triphosphatase (ATPase) is really activated in association with the release of histamine. However, it was unexpectedly found, at the beginning of such a work, that adenosine 5'-triphosphate (ATP) itself caused a marked histamine release and this was accompanied with conspicuous morphological changes characterized by the degranula tion of mast cells when the medium contained calcium ions.
Bulk optical properties of healthy female breast tissue (2002)

We have measured the bulk optical properties of healthy female breast tissues in vivo in the parallel plate, transmission geometry. Fifty-two volunteers were measured. Blood volume and blood oxygen saturation were derived from the optical property data using a novel method that employed a priori spectral information to overcome limitations associated with simple homogeneous tissue models. The measurements provide an estimate of the variation of normal breast tissue optical properties in a fairly large population. The mean blood volume was 34 +/- 9 microM and the mean blood oxygen saturation was 68 +/- 8%. We also investigated the correlation of these optical properties with demographic factors such as body mass index (BMI) and age. We observed a weak correlation of blood volume and reduced scattering coefficient with BMI: correlation with age, however, was not evident within the statistical error of these experiments. The new information on healthy breast tissue provides insight about the potential contrasts available for diffuse optical tomography of breast tumours.
Schnurri interacts with Mad in a Dpp‐dependent manner (2000)

The present results argue that Shn may act as a nuclear component of the Dpp signalling pathway through direct interaction with Mad.
Alkylation of amines. General exhaustive alkylation method for the synthesis of quaternary ammonium compounds (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAlkylation of amines. General exhaustive alkylation method for the synthesis of quaternary ammonium compoundsHarold Z. Sommer, Hayden I. Lipp, and Larry L. JacksonCite this: J. Org. Chem. 1971, 36, 6, 824–828Publication Date (Print):March 1, 1971Publication History Published online1 May 2002Published inissue 1 March 1971https://pubs.acs.org/doi/10.1021/jo00805a021https://doi.org/10.1021/jo00805a021research-articleACS PublicationsRequest reuse permissionsArticle Views3227Altmetric-Citations93LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Microcavities with highly dispersive materials (2004)

Our detailed theoretical studies show how inserting materials that support electro-magnetically induced transparency into microcavities enables design of microcavities with extraordinarily long lifetimes, and enables all-optical signal processing at single photon power levels.
Transforming growth factor-beta and the initiation of chondrogenesis and osteogenesis in the rat femur. (1990)

We have investigated the ability of exogenous transforming growth factor-beta (TGF-beta) to induce osteogenesis and chondrogenesis, critical events in both bone formation and fracture healing. Daily injections of TGF-beta 1 or 2 into the subperiosteal region of newborn rat femurs resulted in localized intramembranous bone formation and chondrogenesis. After cessation of the injections, endochondral ossification occurred, resulting in replacement of cartilage with bone. Gene expression of type II collagen and immunolocalization of types I and II collagen were detected within the TGF-beta-induced cartilage and bone. Moreover, injection of TGF-beta 2 stimulated synthesis of TGF-beta 1 in chondrocytes and osteoblasts within the newly induced bone and cartilage, suggesting positive autoregulation of TGF-beta. TGF-beta 2 was more active in vivo than TGF-beta 1, stimulating formation of a mass that was on the average 375% larger at a comparable dose (p less than 0.001). With either TGF-beta isoform, the dose of the growth factor determined which type of tissue formed, so that the ratio of cartilage formation to intramembranous bone formation decreased as the dose was lowered. For TGF-beta 1, reducing the daily dose from 200 to 20 ng decreased the cartilage/intramembranous bone formation ratio from 3.57 to zero (p less than 0.001). With TGF-beta 2, the same dose change decreased the ratio from 3.71 to 0.28 (p less than 0.001). These data demonstrate that mesenchymal precursor cells in the periosteum are stimulated by TGF-beta to proliferate and differentiate, as occurs in embryologic bone formation and early fracture healing.
Topological analysis of the Escherichia coli ferrichrome-iron receptor by using monoclonal antibodies (1995)

Ferrichrome-iron transport in Escherichia coli is initiated by the outer membrane receptor FhuA. Thirty-five anti-FhuA monoclonal antibodies (MAbs) were isolated to examine the surface accessibility of FhuA sequences and their contribution to ligand binding. The determinants of 32 of the MAbs were mapped to eight distinct regions in the primary sequence of FhuA by immunoblotting against (i) five internal deletion FhuA proteins and (ii) four FhuA peptides generated by cyanogen bromide cleavage. Two groups of MAbs bound to FhuA in outer membrane vesicles but not to intact cells, indicating that their determinants, located between residues 1 and 20 and 21 and 59, are exposed to the periplasm. One of the 28 strongly immunoblot-reactive MAbs bound to FhuA on intact cells in flow cytometry, indicating that its determinant, located between amino acids 321 and 381, is cell surface exposed. This MAb and four others which in flow cytometry bound to cells expressing FhuA were tested for the ability to block ligand binding. While no MAb inhibited growth promotion by ferrichrome or cell killing by microcin 25, some prevented killing by colicin M and were partially able to inhibit the inactivation of T5 phage. These data provide evidence for spatially distinct ligand binding sites on FhuA. The lack of surface reactivity of most of the immunoblot-reactive MAbs suggests that the majority of FhuA sequences which lie external to the outer membrane may adopt a tightly ordered organization with little accessible linear sequence.