gebhart/patrepeval huggingface dataset:
Insight into the Mechanism of Serpin−Proteinase Inhibition from 2D [1H-15N] NMR Studies of the 69 kDa α1-Proteinase Inhibitor Pittsburgh−Trypsin Covalent Complex (2001)

We have used [(1)H-(15)N]-HSQC NMR to investigate the structural changes that occur in both serpin and proteinase in forming the kinetically trapped covalent protein-protein complex that is the basis for serpin inhibition of serine proteinases. By alternately using (15)N-alanine specifically-labeled alpha(1)-proteinase inhibitor (alpha(1)PI) Pittsburgh (serpin) and bovine trypsin (proteinase), we were able to selectively monitor structural changes in each component of the 69 kDa complex. Residue-specific assignments of four alanines in the reactive center loop and seven other alanines aided interpretation of the spectral changes in the serpin. We found that the majority of the alanine resonances, including those from reactive center loop residues P12, P11, and P9, were at identical positions in covalent complex and in cleaved alpha(1)PI. Five alanines that are close to the contact region with proteinase showed some chemical shift perturbation compared with cleaved alpha(1)PI, indicating some degree of structural deformation. With (15)N label in the proteinase, an HSQC spectrum was obtained that more closely resembled that of a molten globule, suggesting that the structure of the proteinase had been significantly altered as a result of complex formation. Large increases in line width for all alpha(1)PI resonances in the covalent complex, with the sole exception of two residues in the flexible N-terminal tail, indicate that, unlike the noncovalent alpha(1)PI-anhydroproteinase complex, the covalent complex is a rigid body of effectively increased molecular weight. We conclude that the mutual perturbations of serpin and proteinase result from steric compression and distortion, rather than simple contact effects. This distortion provides a structural basis for the greatly reduced catalytic efficiency of the proteinase in the complex and hence kinetic trapping of the covalent reaction intermediate.
Stereoselective Conjugate Addition Reactions Using In Situ Metallated Terminal Alkynes and the Development of Novel Chiral P,N-Ligands (2007)

Abstract In this account, new methods for the catalytic and stereoselective conjugate addition of terminal alkynes are described. Our laboratories have disclosed asymmetric addition reactions to aldehydes and imines using a combination of a zinc or copper salt and a terminal alkyne. Under these conditions, terminal alkyne is transformed in situ into an alkynyl metal species. Recently, it was found that these in situ generated alkynyl metal species can undergo conjugate additions to alkylidene malonate-type acceptors. In the zinc(II) triflate-catalyzed system, a highly diastereoselective conjugate addition has been realized using a chiral oxazepene acceptor. Subsequently, alternative conjugate addition protocols have been developed which employ a terminal alkyne, substoichiometric amounts of copper and a highly eletrophilic Meldrum’s acid derived acceptor. This reaction can be made enantioselective using a novel atropisomeric P,N-ligand (PINAP). With this ligand, excellent enantioselectivities can be achieved for the conjugate addition of aromatic alkynes to various Meldrum’s acid derived acceptors.
Determination of depth of in vivo bioluminescent signals using spectral imaging techniques (2003)

A spectral imaging technique applied to in vivo bioluminescent imaging is presented that provides an estimate of the depth of bioluminescent reporters inside living animals. The model, based on the standard diffusion approximation of light propagating in a slab sample, is described in this paper. Validation experiments performed on phantom and tissue models, as well as preliminary <i>in vivo</i> mouse images, demonstrate the ability of spectral imaging to provide a correct estimate of depth based upon a single view imaging system.
Solution Structure and Backbone Dynamics of the Functional Cytoplasmic Subdomain of Human Ephrin B2, a Cell-Surface Ligand with Bidirectional Signaling Properties (2002)

The cytoplasmic domain of B ephrins plays a central role in bidirectional signal transduction processes controlling pattern formation and morphogenesis, such as axon guidance, cell migration, segmentation, and angiogensis. In particular, the extremely conserved last 33-residue cytoplasmic subdomain was shown to bind to both a PDZ domain for one signaling pathway [Lu et al. (2001) Cell 105, 69-79] and an SH2 domain from an alternative signaling network [Cowan and Henkemeyer (2001) Nature 413, 174-179]. To date, no structural information is available for the cytoplasmic domain of ephrin B proteins. We report here a detailed NMR study on the structural and dynamic properties of the cytoplasmic domain of human ephrin B2. Our results reveal the following: (1) the N-terminal region of the cytoplasmic domain from residues 253 to 300 lacks the ability for structure formation and is particularly prone to aggregation; and (2) the C-terminal functional subdomain from residues 301 to 333 assumes two distinctive structural elements with residues 301-322 adopting a well-packed hairpin structure followed by a flexible C-terminal tail. Furthermore, the backbone (15)N relaxation data demonstrate that the hairpin structure has significantly limited backbone motions, indicating a high conformational stability for the folded structure. Therefore, while the flexible C-terminal tail is suitable for binding to the PDZ domain, the folded hairpin may represent a latent structure requiring phosphorylation-induced conformational changes for high-affinity interactions with the SH2 domain.
Real-time statistical process control using tool data (semiconductor manufacturing) (1992)

A process monitoring scheme that takes advantage of real-time information in order to generate malfunction alarms is described. This is accomplished with the application of time-series filtering and multivariate statistical process control. This scheme is capable of generating alarms on a true real-time basis, while the wafer is still in the processing chamber. Several examples are presented with tool data collected from the SECSII port of single-wafer plasma etchers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
XCS based hidden firmware modification on embedded devices (2011)

Abstract—Most contemporary embedded devices, such as wireless routers, digital cameras, and digital photo frames, have Web based management interfaces that allow an administrator to perform management tasks on the device from a Web browser connecting to the device’s Web server. It has been shown earlier that many of these devices are vulnerable to Cross Site Scripting type attacks whereby some malicious JavaScript code can be injected in the Web pages stored on the device. When such infected pages are opened by the administrator, the malicious script is executed with admin privileges, and it can potentially fully compromise the embedded device. In this paper, we demonstrate that such full compromise of embedded devices is indeed possible in practice by showing how the injected malicious script can install an arbitrarily modified firmware on the device. We present the general framework of this kind of hidden firmware modification attacks, and report on our proof-of-concept implementation that targets Planex MZK-W04NU wireless routers. In addition, we also show how this vulnerability can be exploited to install botnet clients on embedded devices, and by doing so, to create embedded botnets. Our work proves that the risk of this type of attacks on embedded systems is considerable, and it will further increase in the future. Keywords-Embedded systems; security; Cross Site Scripting; Cross Channel Scripting; hidden firmware modification; malicious
Purification and partial biologic characterization of a human lymphocyte-derived peptide with potent neutrophil-stimulating activity. (1988)

A novel neutrophil-activating peptide is detected in supernatants from mitogen-stimulated human T lymphocyte preparations. This chemotaxin was purified to apparent homogeneity by sequential Gel G-75 permeation chromatography, wide pore reversed phase (RP-8) HPLC, size exclusion HPLC, and reversed phase (RP-18) HPLC. Additional characterization of this lymphocyte-derived neutrophil-activating peptide (LYNAP) resulted in a single peak upon reversed phase HPLC and size exclusion HPLC. SDS-PAGE under nonreducing conditions revealed a single line at 10 kDa. LYNAP stimulated neutrophil chemotaxis (ED50 of 3 +/- 3 ng/ml), chemokinesis (ED50 of 2 +/- 2 ng/ml), and caused degranulation of cytochalasin B pretreated human neutrophils (ED50 of 20 ng/ml). In purified human monocytes, chemotactic responses to LYNAP at doses up to 100 ng/ml were absent, indicating nonidentity with a lymphocyte-derived monocyte chemotactic factor previously described by other workers. LYNAP shows biochemical and biologic similarities to a recently detected monocyte-derived neutrophil-activating peptide (MONAP). Moreover, desensitization experiments revealed cross-deactivation between LYNAP and MONAP, not, however, between these two chemotactic peptides and other well characterized polymorphonuclear leukocyte chemotaxins, e.g., C5a, FMLP, leukotriene B4, or platelet-activating factor. This finding points toward structure identity or homology of both chemotaxins, MONAP and LYNAP.
Agrin Binding to α-Dystroglycan (1996)

The synaptic basal membrane protein agrin initiates the aggregation of acetylcholine receptors at the postsynaptic membrane of the developing neuromuscular junction. Recently, alpha-dystroglycan was found to be a major agrin-binding protein on the muscle cell surface and was therefore considered a candidate agrin receptor. Employing different truncation fragments of agrin, we determined regions of the protein involved in binding to alpha-dystroglycan and to heparin, an inhibitor of alpha-dystroglycan binding. Deletion of a 15-kDa fragment from the C terminus of agrin had no effect on its binding to alpha-dystroglycan from rabbit muscle membranes, even though this deletion completely abolishes its acetylcholine receptor aggregating activity. Conversely, deletion of a central region does not affect agrin's clustering activity, but reduced its affinity for alpha-dystroglycan. Combination of these two deletions resulted in a fragment of approximately 35 kDa that weakly bound to alpha-dystroglycan, but displayed no clustering activity. All of these fragments bound to heparin with high affinity. Thus, alpha-dystroglycan does not show the binding specificity expected for an agrin receptor. Our data suggest the existence of an additional component on the muscle cell surface that generates the observed ligand specificity.
Impromptu (2004)

This paper discusses the software architecture of Impromptu, a mobile IP-based audio computing platform, with an associated set of network-based applications and services. Impromptu merges the communication properties and universal mobility of the telephone with the multi-tasking and open protocol world of the handheld PC. Its supporting architecture handles multiple streaming audio applications, provides speech services for consistent audio user interfaces across applications, and enables user management of these varied applications running simultaneously.
Clinical and pathological observations on pigs with postweaning multisystemic wasting syndrome (2001)

The aim of this work was to characterise the lesions and agents present in clinically normal and clinically affected pigs on a farm during an outbreak of postweaning multisystemic wasting syndrome (PMWS), and to evaluate the diagnostic techniques for detecting porcine circovirus type 2 (PCV-2) and other microorganisms. Four pigs in the early stage and 11 pigs in the late stage of the disease, and eight clinically normal pigs were necropsied. Samples of lymphoid tissue and serum were also obtained from 12 slaughter pigs from the same farm. The tissues were examined histopathologically, and in situ hybridisation, serology and PCR were used to detect porcine circovirus type 1 (PCV-1) and/or PCV-2 in tissues and/or sera. The presence of porcine reproductive and respiratory syndrome virus (PRRSV), Aujeszky's disease virus (ADV) and porcine parvovirus (PPV) were also investigated. Characteristic microscopical lesions of PMWS were observed in the lymphoid tissues of the pigs in all three necropsied groups; the lesions were most common and severe in the pigs in the early stage of the disease, less so in the pigs in the late stage of the disease, and least in the clinically normal pigs. PCV-2 infection was detected in all the necropsied pigs by in situ hybridisation and PCR. Only three pigs had the PCV-1 genome in serum or lymph node tissue. In contrast, the slaughter pigs had no microscopical lesions and no PCV-2 nucleic acid in their serum or tissues, and only one of them had the pCV-1 genome in its serum. Immunohistochemical, serological and PCR studies revealed that PRRSV and ADV were also present on the farm during the outbreak.
Development of Natural Protein Microarrays for Diagnosing Cancer Based on an Antibody Response to Tumor Antigens (2004)

The detection of autoantibodies to tumor antigens has potential utility for the early diagnosis of cancers. In previous studies, we have identified tumor antigens based on Western blot analysis of tumor cell lysates that were incubated with subject sera to identify proteins that elicit specific reactivity in sera from patients with the corresponding tumor type. More recently, we have explored the use of microarrays spotted with tumor proteins as an alternative to Western blots. Microarrays provide a high throughput, high sensitivity alternative to the use of Western blots for tumor antigen profiling. In this study, we have assessed the reproducibility of natural protein microarrays and their ability to distinguish between lung cancer sera and controls. Protein lysates from the A549 human lung adenocarcinoma cell line were separated into 1840 fractions that were spotted in duplicate, along with various controls, on nitrocellulose coated slides. Sera from 18 newly diagnosed patients with lung cancer and from 15 healthy controls were each hybridized to an individual microarray. The reactivity of arrayed proteins with Ig was determined by incubation with biotinylated goat-anti-human-Ig followed by phycoerythrin-conjugated streptavidin. The intensity measures of duplicate spots (within-slide) and duplicate slides (between-slides) were highly reproducible, exhibiting correlation values >0.9. A total of 63 of the 1840 arrayed fractions demonstrated increased reactivity in cancer patients relative to controls as measured by a rank-based statistic (p < 0.008). Microarrays of tumor-derived proteins provide the means for uncovering a repertoire of tumor antigens that have induced an antibody response in patients with specific cancers.
Programmable nanophotonics for quantum information processing and artificial intelligence (2017)

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2017.
Fabrication of Highly Uniform Nanoparticles from Recombinant Silk-Elastin-like Protein Polymers for Therapeutic Agent Delivery (2011)

Here we generate silk-elastin-like protein (SELP) polymeric nanoparticles and demonstrate precise control over their dimensions using an electrospray differential mobility analyzer (ES-DMA). Electrospray produces droplets encompassing several polymer strands. Evaporation ensues, leading polymer strands to accumulate at the droplet interface, forming a hollow nanoparticle. The resulting nanoparticle size distributions, which govern particle yield, depend on buffer concentration to the -1/3 power, polymer concentration to the 1/3 power, and ratio of silk-to-elastin blocks. Three recombinantly tuned ratios of 8:16, 4:8, and 4:16, respectively named SELP-815K, SELP-47K, and SELP-415K, are employed, with the latter ratio resulting in a thinner shell and larger diameter for the nanoparticles than the former. The DMA narrows the size distribution by electrostatically classifying the aerosolized nanoparticles. These highly uniform nanoparticles have variations of 1.2 and 1.4 nm for 24.0 and 36.0 nm particles, respectively. Transmission electron microscopy reveals the nanoparticles to be faceted, as a buckling instability releases compression energy arising from evaporation after the shell has formed by bending it. A thermodynamic equilibrium exists between compression and bending energies, where the facet length is half the particle diameter, in agreement with experiments. Rod-like particles also formed from polymer-stabilized filaments when the viscous length exceeds the jet radius at higher solution viscosities. The unusual uniformity in composition and dimension indicates the potential of these nanoparticles to deliver bioactive and imaging agents.
Hydrophilic multi-walled carbon nanotubes decorated with magnetite nanoparticles as lymphatic targeted drug delivery vehicles (2009)

Hydrophilic multi-walled carbon nanotubes decorated with magnetite nanoparticles were readily taken up into lymph vessels and delivered gemcitabine to lymph nodes with high efficiency under the guidance of a magnetic field.
Synthetic use of lithium nitride, an unusual reducing agent. Formation of Ti4 and Ti6 complexes (1985)

Lithium nitride acts as a reducing agent in co-ordinating solvents librating dinitrogen, reducing TiCl4 to LiTiCl4(THF)4(THF = tetrahydrofuran), (η5-C5H5)2TiCl2 to [(η5-C5H5)2TiCl]2 and (C5H5)6Ti6(C5H4)2N, and (η5-C5H5)TiCl3 to (η5-C5H5)TiCl2(THF), [(η5-C5H5)TiCl2]n, and(C5H5)6(c5H4)2Ti6N3; in the presence of CO, Li3N reacts with (η5-C5H5)2TiCl2(2:3 molar ratio) to form (η5-C5H5)2Ti(CO)2.
Rapid Onset of Cutaneous Anesthesia with EMLA Cream After Pretreatment with a New Ultrasound-Emitting Device (2004)

A prospective, randomized, double-blinded, placebo-controlled clinical trial demonstrated rapid onset of cutaneous anesthesia by pretreatment of the skin with ultrasound before application of EMLA cream.
Microalbuminuria and the Risk for Early Progressive Renal Function Decline in Type 1 Diabetes (2007)

This study aimed to establish the time of initiation and the determinants of renal function decline in type 1 diabetes. Until now, such decline has been assumed to be a late-occurring event associated with proteinuria. A total of 267 patients with normoalbuminuria and 301 patients with microalbuminuria were followed for 8 to 12 yr. Linear trends (slopes) in GFR were estimated by serial measurement of serum cystatin C. Cases of early renal function decline were defined by loss in cystatin C GFR that exceeded -3.3%/yr, a threshold that corresponds to the 2.5th percentile of the distribution of GFR slopes in an independent nondiabetic normotensive population. Cases of early renal function decline occurred in 9% (mean slope -4.4; range -5.9 to -3.3%/yr) of the normoalbuminuria group and 31% (mean slope -7.1; range -23.8 to -3.3%/yr) of the microalbuminuria group (P < 0.001). Risk for early renal function decline depended on whether microalbuminuria regressed, remained stable, or progressed, rising from 16 to 32 and 68%, respectively (P < 0.001). In multivariate analysis, risk for decline was higher after age 35 yr or when glycosylated hemoglobin exceeded 9% but did not vary with diabetes duration, smoking, BP, or angiotensin-converting enzyme inhibitor treatment. Contrary to the existing paradigm of diabetic nephropathy, progressive renal function decline in type 1 diabetes is an early event that occurs in a large proportion of patients with microalbuminuria. Together with testing for microalbuminuria, clinical protocols using cystatin C to diagnose early renal function decline and track response to therapeutic interventions should be developed.
Morphological variation and classification of field-grown Stylosanthes seabrana and S. scabra (2010)

Seventy-eight Stylosanthes seabrana and S. scabra lines were grown at CSIRO Lansdown Research Station, north Queensland and 32 morphological and agronomic characteristics were measured and used as attributes to define simi larity groups using the numerical classification program PATN. At the 5-Group level, groups were mostly homogeneous by species. Terminal leaflet shape and terminal leaflet apex shape, the presence or absence of leaflet and stem hairs, the presence or absence of inflorescence bristles, the pres ence or absence of stipule horn lateral bristles and stipule horn terminal bristles were the most useful attributes defining groups.
Intercellular Communication and Cell-Cell Adhesio n (1992)

In developmental biology, binary cell-cell interactions often determine the fate of one or both cell partners. The two cells must adhere to one another to allow chemical signals to be transmitted in one or both directions across the regions of cell-cell contact. The molecular mechanisms of cell-cell adhesion and intercellular communication, even if they are mediated by different cell surface components, may be functionally integrated in several different ways. Studies of helper T cells with antigen-presenting B cells in culture have illuminated such binary interactions. The possible application of similar mechanisms to other binary developmental systems is briefly explored.
Continuous Sun-Pumped Room Temperature Glass Laser Operation (1964)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text G. R. Simpson, "Continuous Sun-Pumped Room Temperature Glass Laser Operation," Appl. Opt. 3, 783-784 (1964) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Organic Iodine(I, III, and V) Chemistry: 10 Years of Development at the Medical University of Warsaw, Poland (2000)

This review reports some novel (or considerably improved) methods for the synthesis of aromatic iodides, (dichloroiodo)arenes, (diacetoxyiodo)arenes, iodylarenes and diaryliodonium salts, as well as some facile, oxidative anion metatheses in crude diaryliodonium halides and, for comparison, potassium halides. All these new results were obtained in our laboratory over the past decade (1990-2000). A full list of our papers dealing with the organic iodine(I, III and V) chemistry, covering exlusively the aromatic derivatives, is also provided.
Increased epidermal cell proliferation in normal human skin in vivo following local administration of interferon-gamma. (1993)

Recombinant human interferon-gamma was administered intradermally (10 micrograms in 0.1 ml) to healthy adult human volunteers from day 1 to day 3, and epidermal cell proliferation was measured on whole skin biopsies at day 6. Three independent parameters were assessed, namely, a) epidermal keratin-16 expression, b) keratinocyte proliferating cell nuclear antigen expression, and c) keratinocyte silver nucleolar organizer region counts. Significantly increased scores for each parameter were observed after interferon-gamma injection (P < 0.01 in each case) compared to site-matched controls. Keratin-16 expression was confined to suprabasal epidermis, whereas proliferating cell nuclear antigen and silver nucleolar organizer region counts were particularly elevated in the basal epidermis. Taken together with previous findings, these studies indicate both proinflammatory and growth regulatory roles for interferon-gamma in human skin. These data are likely to be of particular importance to pathophysiological mechanisms of psoriasis and related cutaneous inflammatory diseases.