gebhart/patrepeval huggingface dataset:
Productive and non‐productive binding of botulinum neurotoxin A to motor nerve endings are distinguished by its heavy chain (1996)

Botulinum neurotoxin type A, a di-chain protein produced by Clostridium botulinum and responsible for botulism, blocks acetylcholine release from peripheral nerves by binding to the terminals, undergoing internalization and proteolyzing a protein essential for exocytosis. As botulinum neurotoxin is being used clinically for the treatment of dystonias and certain spasticities, deciphering the details of its specific targeting to cholinergic nerve endings has assumed great importance. Thus, interaction of butolinum neurotoxin type A with murine motor nerve terminals—a prime target in vivo—was investigated. Autoradiographic analysis revealed saturable, high-affinity interaction of radioiodinated toxin (0.4 nM) with two ecto-acceptor types, distinguished by an excess of the toxin's heavy chain which prevented only a fraction of this binding. Botulinum neurotoxin was also biotinylated through its free sulfhydryl groups, known not to be essential for neurotoxicity. Similar binding of this active derivative was, likewise, partially blocked by heavy chain, confirming the above results. This binding that is resistant to heavy chain equates to botulinum neurotoxin interacting with productive ecto-acceptors, leading to delivery to its cytosolic site of action, because heavy chain proved unable to antagonize toxin-induced neuromuscular paralysis. In contrast, it is deduced that botulinum neurotoxin bound to heavy chain-susceptible sites has a different fate, presumably due to trafficking via another route, and thus would be inefficient in causing neuroparalysis. © 1996 Wiley-Liss, Inc.
Reduction of Electrical Crosstalk in Hybrid Backside Illuminated CMOS Imagers using Deep Trench Isolation (2008)

Hybrid backside illuminated CMOS imagers with zero pixel-to-pixel electrical crosstalk were developed. The application of highly doped polysilicon filled high aspect ratio trenches between pixels to reduce crosstalk is unique. These 1μm wide 50μm deep trenches enforce a lateral drift field between pixels, which counteracts diffusion and drastically reduces electrical crosstalk. Quantitative crosstalk characterization of trenched and non-trenched imagers is presented.
Endogenous monocyte chemoattractant protein-1 recruits monocytes in the zymosan peritonitis model (1998)

The role of monocyte chemoattractant protein-1 (MCP-1) in the recruitment of blood-derived monocytes in a model of zymosan peritoneal inflammation was investigated. After zymosan injection (1 mg) a rapid influx of polymorphonuclear leukocytes (PMN) and monocytes into the peritoneal cavity associated with mouse MCP-1 (JE) gene activation and protein secretion in the exudates occurred. MCP-1 production (maximal at 4 h) preceded the accumulation of monocytes (F4/80-positive cells, maximally recovered between 16 and 24 h). Treatment of mice with a single injection of anti-mouse MCP-1 antibody inhibited 16-h monocyte accumulation by approximately 40%, however, a significant decrease in the number of PMN was also measured. Finally, intraperitoneal injection of murine recombinant MCP-1 (1 microg) produced a selective accumulation of monocytes (F4/80-positive cells) into the peritoneal cavity. In conclusion, we show the novel existence of a strict relationship between MCP-1 production and leukocyte accumulation in this model of acute inflammation.
Secure Web Browsing with the OP Web Browser (2008)

Current Web browsers are plagued with vulnerabilities, providing hackers with easy access to computer systems via browser-based attacks. Browser security efforts that retrofit existing browsers have had limited success because the design of modern browsers is fundamentally flawed. To enable more secure web browsing, we design and implement a new browser, called the OP Web browser, that attempts to improve the state-of-the-art in browser security. Our overall design approach is to combine operating system design principles with formal methods to design a more secure Web browser by drawing on the expertise of both communities. Our overall design philosophy is to partition the browser into smaller subsystems and make all communication between subsystems simple and explicit. At the core of our design is a small browser kernel that manages the browser subsystems and interposes on all communications between them to enforce our new browser security features. To show the utility of our browser architecture, we design and implement three novel security features. First, we develop novel and flexible security policies that allows us to include plugins within our security framework. Our policy removes the burden of security from plugin writers, and gives plugins the flexibility to use innovative network architectures to deliver content while still maintaining the confidentiality and integrity of our browser, even if attackers compromise the plugin. Second, we use formal methods to prove that the address bar displayed within our browser user interface always shows the correct address for the current Web page. Third, we design and implement a browser-level information-flow tracking system to enable post-mortem analysis of browser-based attacks. If an attacker is able to compromise our browser, we highlight the subset of total activity that is causally related to the attack, thus allowing users and system administrators to determine easily which Web site lead to the compromise and to assess the damage of a successful attack. To evaluate our design, we implemented OP and tested both performance and filesystem impact. To test performance, we measure latency to verify OP's performance penalty from security features are be minimal from a users perspective. Our experiments show that on average the speed of the OP browser is comparable to Firefox and the audit log occupies around 80 KB per page on average.
Basic secretagogues activate protein tyrosine phosphorylation and release of arachidonic acid in mast cells via a novel protein kinase C and phosphatidylinositol 3-kinase-dependent mechanism (1998)

Mast cells play a central role in inflammatory and immediate-type allergic reactions. These granulated cells release by a process of regulated exocytosis a variety of biologically active substances which are either preformed (e.g. histamine), or synthesized de novo following activation [e. g. metabolites of arachidonic acid (AA) and multifunctional cytokines]. Exocytosis in mast cells is activated either in response to aggregation of the receptors for immunoglobulin E (FcepsilonRI) or by the direct activation of pertussis toxin-sensitive G-proteins by a class of receptor mimetic agents, collectively known as basic secretagogues of mast cells. In the present study we show that compound 48/80 (c48/80), a synthetic member of the class of basic secretagogues, stimulates protein tyrosine phosphorylation of a number of as yet unidentified cellular substrates. These phosphorylations were inhibited by the tyrphostin AG-18, by the phosphatidylinositol 3-kinase inhibitor wortmannin and by the protein kinase C inhibitors K252a and GF1 09203X. These inhibitors also inhibited the release of AA induced by c48/80 but had no effect on exocytosis. Taken together, our findings suggest that basic secretagogues induce protein tyrosine phosphorylation as part of their parallel multiple signaling pathways which are presumably mediated by more than one G-protein. Both protein kinase C and phosphatidylinositol 3-kinase serve as intermediates in this signaling pathway. The protein tyrosine kinase signaling pathway, which mediates the activation of AA release, does not contribute to secretion of the preformed mediators such as histamine, but it might largely contribute to the de novo production of inflammatory mediators like leukotrienes and prostaglandins.
Catalytic Enantioselective Oxidative Cross‐Coupling of Benzylic Ethers with Aldehydes (2013)

The first one-pot enantioselective oxidative coupling of cyclic benzylic ethers with aldehydes has been developed. A variety of benzylic ethers were transformed into the corresponding oxygen heterocycles with high enantioselectivity. Mechanistic experiments were conducted to determine the nature of the reaction intermediates. The application of this strategy to coupling reactions with other nucleophiles besides aldehydes was also explored.
Adenovirus early region 4 encodes functions required for efficient DNA replication, late gene expression, and host cell shutoff (1985)

To delineate the function of adenovirus early region 4 (E4) gene products, we constructed a set of mutant viruses which carry defined lesions within this coding region. Deletion and insertion mutations within six of seven known E4 coding regions had no measurable effect on virus growth in cultured cells. A variant carrying a deletion within the last coding region (encoding a 34,000-molecular-weight polypeptide) was modestly defective, and a mutant lacking the majority of the E4 region was severely defective for growth. The phenotypes of the two defective mutants are similar and complex. Both display perturbations in DNA replication, translation of the E2A mRNA, accumulation of late viral mRNAs, and host cell shutoff.
Vertical nanowire array-based field effect transistors for ultimate scaling (2013)

Nanowire-based field-effect transistors are among the most promising means of overcoming the limits of today's planar silicon electronic devices, in part because of their suitability for gate-all-around architectures, which provide perfect electrostatic control and facilitate further reductions in "ultimate" transistor size while maintaining low leakage currents. However, an architecture combining a scalable and reproducible structure with good electrical performance has yet to be demonstrated. Here, we report a high performance field-effect transistor implemented on massively parallel dense vertical nanowire arrays with silicided source/drain contacts and scaled metallic gate length fabricated using a simple process. The proposed architecture offers several advantages including better immunity to short channel effects, reduction of device-to-device variability, and nanometer gate length patterning without the need for high-resolution lithography. These benefits are important in the large-scale manufacture of low-power transistors and memory devices.
Nanocrystal nonvolatile memory devices (2002)

In this paper we present an overview of nanocrystal memories - a nascent nonvolatile memory technology that promises to extend the scaling of more conventional charge storage devices to nanometer-scale dimensions.
Steady-State Kinetic Characterization of RB69 DNA Polymerase Mutants Τhat Affect dNTP Incorporation (1999)

The function of six highly conserved residues (Arg482, Lys483, Lys486, Lys560, Asn564, and Tyr567) in the fingers domain of bacteriophage RB69 DNA polymerase (RB69 gp43) were analyzed by kinetic studies with mutants in which each of these residues was replaced with Ala. Our results suggest that Arg482, Lys486, Lys560, and Asn564 contact the incoming dNTP during the nucleotidyl transfer reaction as judged by variations in apparent Km and kcat values for dNTP incorporation by these mutants compared to those for the exonuclease deficient parental polymerase under steady-state conditions. On the basis of our studies, as well as on the basis of the crystal structure of RB69 gp43, we propose that a conformational change in the fingers domain, which presumably occurs prior to polymerization, brings the side chains of Arg482, Lys486, Lys560, and Asn564 into the vicinity of the primer-template terminus where they can contact the triphosphate moiety of the incoming dNTP. In particular, on the basis of structural studies reported for the "closed" forms of two other DNA polymerases and from the kinetic studies reported here, we suggest that (i) Lys560 and Asn564 contact the nonbonding oxygens of the alpha and beta phosphates, respectively, and (ii) both Arg482 and Lys486 contact the gamma phosphate oxygens of the incoming dNTP of RB69 gp43 prior to the nucleotidyl transfer reaction. We also found that Ala substitutions at each of these four RB69 gp43 sites could incorporate dGDP as a substrate, although with markedly reduced efficiency compared to that with dGTP. In contrast in the parental exo- background, the K483A and Y567A substituted enzymes could not use dGDP as a substrate for primer extension. These results, taken together, are consistent with the putative roles of the four conserved residues in RB69 gp43 as stated above.
The HMG-1 box protein family: classification and functional relationships (1995)

The abundant and highly-conserved nucleoproteins comprising the high mobility group-1/2 (HMG-1/2) family contains two homologous basic domains of about 75 amino acids. These basic domains, termed HMG-1 boxes, are highly structured and facilitate HMG-DNA interactions. Many proteins that regulate various cellular functions involving DNA binding and whose target DNA sequences share common structural characteristics have been identified as having an HMG-1 box; these proteins include the RNA polymerase I transcription factor UBF, the mammalian testis-determining factor SRY and the mitochondrial transcription factors ABF2 and mtTF1, among others. The sequences of 121 HMG-1 boxes have been compiled and aligned in accordance with thermodynamic results from homology model building (threading) experiments, basing the alignment on structure rather than by using traditional sequence homology methods. The classification of a representative subset of these proteins was then determined using standard least-squares distance methods. The proteins segregate into two groups, the first consisting of HMG-1/2 proteins and the second consisting of proteins containing the HMG-1 box but which are not canonical HMG proteins. The proteins in the second group further segregate based on their function, their ability to bind specific sequences of DNA, or their ability to recognize discrete non-B-DNA structures. The HMG-1 box provides an excellent example of how a specific protein motif, with slight alteration, can be used to recognize DNA in a variety of functional contexts.
Acute Effects of Different Atrial Pacing Sites in Patients with Atrial Fibrillation: Comparison of Single Site and Biatrial Pacing (2001)

It has been reported that a trial single site or biatrial pacing can suppress the occurrence of AF. However, its mechanism remains unclear. The study population included 32 patients with AF (n = 20: AF group), or without paroxysmal AF (n = 12: control group). The mechanism and efficacy of atrial pacing were investigated by electrophysiological studies to determine which was more effective for suppressing AF induction; single site pacing of the right atrial appendage (RAA) or distal coronary sinus (CS-d), or biatrial (simultaneous BAA and CS-d) pacing. In the AF group, AF inducibility was significantly higher with BAA extrastimulus during RAA (12/20; P < 0.0001) or biatrial paced drive (7/20; P < 0.01) than during CS-d paced drive (0/20). In the control group, AF was not induced at any site paced. In the AF group, the conduction delay and other parameters of atrial vulnerability significantly improved during CS-d paced drive. The atrial recovery time (ART) at RAA and CS-d was measured during each basic pacing mode. ART was defined as the sum of the activation time and refractory period, and the difference between ARTs at RAA and CS-d was calculated as the ART difference (ARTD). The ARTD was significantly longer during BAA pacing in the AF group than in control group (155.0 +/- 32.8 vs 128.8 +/- 32.9 ms, P < 0.05). In the AFgroup, ARTDs during biatrial (52.0 +/- 24.2 ms) and CS-d pacing (51.7 +/- 26.0 ms) were significantly shorter than ARTD during RAA pacing. The CS-d paced drive was more effective for suppressing AF induction than biatrial or RAA paced drive by alleviating conduction delay. CS-d and biatrial pacing significantly reduced ARTD compared with RAA pacing.
Conduction studies in peripheral cat nerve using implanted electrodes: I. Methods and findings in controls (1988)

Silicone rubber cuff and patch electrodes with multiple contacts were implanted along the sciatic-tibial-plantar nerves in cat for repeated studies of conduction properties of normal peripheral nerve over periods of time. The contacts were used in various combinations for precise localization of changes in conduction velocities and excitability along the extent of normal nerves. In this paper the particular characteristics and limitations associated with cuff-electrode recordings of neural activity are discussed. The nerve action potential was recorded using a tripolar configuration with a central lead flanked by two shunted leads at symmetrical distances. This configuration records the spatial derivative of the action potential and rejects potentials from sources outside the cuff. The voltage changes are restricted by the silicone cuff, and the dynamic range is therefore very high, allowing detection from single myelinated fibers to whole nerve responses. The electrodes are well suited for following the development of regeneration and degeneration following experimental lesions.
Monophosphoryl lipid A obtained from lipopolysaccharides of Salmonella minnesota R595. Purification of the dimethyl derivative by high performance liquid chromatography and complete structural determination. (1985)

The monophosphoryl lipid A (MLA) obtained from the lipopolysaccharides of Salmonella minnesota R595 was fractionated on a silicic acid column to yield the heptaacyl, hexaacyl, and pentaacyl MLA. Each of these MLAs was methylated with diazomethane to yield the dimethyl derivative and purified to homogeneity by reverse-phase high performance liquid chromatography. The molecular ions obtained by positive ion fast atom bombardment mass spectrometry of purified dimethyl heptaacyl MLA allowed us to establish the molecular formula and Mr of C112H211N2O23P and 1983.3, respectively. Cleavage at the glycosidic linkage yielded an oxonium ion of mass 1115, which showed that the distal sugar unit contained one phosphate (dimethyl), two hydroxymyristates, one laurate, and one myristate, while the reducing sugar unit contained two hydroxymyristates and one palmitate. By utilizing two-dimensional NMR spectroscopy, we were able to assign all of the protons of dimethyl heptaacyl MLA. This assignment included the beta protons of the three acyloxyacyl groups. A substantial downfield shift of the protons at the 3- and 3' -carbons was observed, which indicated that these two positions are occupied by ester groups. Fast atom bombardment mass spectral analysis of the hexaacyl and pentaacyl MLAs showed that these structures were identical to the previously designated TLC-3 and TLC-5 fractions, respectively, from Salmonella typhimurium. From this study, the complete structures of the MLA series found in the LPS of S. minnesota can now be described.
A Chemically Functionalizable Nanoporous Material [Cu 3 (TMA) 2 (H 2 O) 3 ] n (1999)

Although zeolites and related materials combine nanoporosity with high thermal stability, they are difficult to modify or derivatize in a systematic way. A highly porous metal coordination polymer [Cu3(TMA)2(H2O)3]n (where TMA is benzene-1,3,5-tricarboxylate) was formed in 80 percent yield. It has interconnected [Cu2(O2CR)4] units (where R is an aromatic ring), which create a three-dimensional system of channels with a pore size of 1 nanometer and an accessible porosity of about 40 percent in the solid. Unlike zeolites, the channel linings can be chemically functionalized; for example, the aqua ligands can be replaced by pyridines. Thermal gravimetric analysis and high-temperature single-crystal diffractometry indicate that the framework is stable up to 240 degreesC.
In Silico Model-Driven Assessment of the Effects of Single Nucleotide Polymorphisms (SNPs) on Human Red Blood Cell Metabolism (2002)

The completion of the human genome project and the construction of single nucleotide polymorphism (SNP) maps have lead to significant efforts to find SNPs that can be linked to pathophysiology. In silico models of complete biochemical reaction networks relate a cell's individual reactions to the function of the entire network. Sequence variations can in turn be related to kinetic properties of individual enzymes, thus allowing an in silico model-driven assessment of the effects of defined SNPs on overall cellular functions. This process is applied to defined SNPs in two key enzymes of human red blood cell metabolism: glucose-6-phosphate dehydrogenase and pyruvate kinase. The results demonstrate the utility of in silico models in providing insight into differences between red cell function in patients with chronic and nonchronic anemia. In silico models of complex cellular processes are thus likely to aid in defining and understanding key SNPs in human pathophysiology.
Mitochondria in human offspring derived from ooplasmic transplantation: Brief communication (2001)

Ooplasmic transfer from fertile donor oocytes into potentially compromised recipient patient oocytes has led to the birth of nearly 30 babies worldwide. Cytoplasmic transplantation has caused apprehension, since the mixing of human ooplasm from two different maternal sources may generate mitochondrial (mt) heteroplasmy (both recipient and donor mtDNA) in offspring. This investigation traced the mitochondrial donor population both during the ooplasmic transfer technique and in the bloods of two 1 year old children using mtDNA fingerprinting. Donor ooplasm stained for active mitochondria was transferred into recipient ooplasm and the mitochondria were visualized by confocal microscopy after the microinjection procedure and fertilization. Heteroplasmy was found in the blood from each of the children. This report is the first case of human germline genetic modification resulting in normal healthy children.
Synthesis and structure-affinity of a series of 7.alpha.-undecylestradiol derivatives: a potential vector for therapy and imaging of estrogen-receptor-positive cancers (1990)

A series of 7 alpha-undecylestradiol derivatives, featuring various substituents at the end of the undecyl spacer chain, were synthesized and evaluated for their interaction with the estrogen receptor and nonreceptor sites. Their relative binding affinities (RBA) for calf uterine estrogen receptors were measured by competitive binding assays and varied between 0.5 and 8.4% of that of unlabeled 17 beta-estradiol. Enhanced lipophilicity and steric hindrance of the substituent on the end of the spacer chain resulted in decreased binding affinity for the estrogen receptor, while interactions with nonreceptor sites increased. RBA values were not affected by prolonged incubation times, suggesting a stable ligand-receptor complex. The potential to use the 7 alpha-undecylestradiol as a vector for site-selective delivery of diagnostic and therapeutic moieties to estrogen-receptor-positive human cancers is discussed.