gebhart/patrepeval huggingface dataset:
De Novo Design of Selective Antibiotic Peptides by Incorporation of Unnatural Amino Acids (2007)

The evolution of drug-resistant bacteria is one of the most critical problems facing modern medicine and requires the development of new drugs that exhibit their antibacterial activity via novel mechanisms of action. One potential source of new drugs could be the naturally occurring peptides that exhibit antimicrobial activity via membrane disruption. To develop antimicrobial peptides exhibiting increased potency and selectivity against Gram positive, Gram negative, and Mycobacterium bacteria coupled with reduced hemolytic activity, peptides containing unnatural amino acids have been designed, synthesized, and evaluated. These compounds were designed on the basis of the electrostatic surface potential maps derived from the NMR determined SDS and DPC micelle-bound conformations of (Ala8,13,18)magainin-2 amide. Unnatural amino acids were incorporated into the polypeptide backbone to control the structural and physicochemical properties of the peptides to introduce organism selectivity and potency. The methods and results of this investigation are described below.
Service session security in TINA-dynamic role creation and management in TWA service environment (2002)

Telecommunication Information Network Architecture (TINA) is a software architecture, which provides a set of specifications for the development of high-speed multimedia applications. Security management in the TINA service environment is studied in detail. To cope with federation and composition of service sessions, a dynamic role creation scheme from role class hierarchy is proposed. In combination with security space representation, algebraic specification of roles creates a new, composite role. A strongly-rolled system and role mapping between federated domains are proposed, which, in combination with dynamic role creation and algebraic role specification, will enable static security analysis of a complex, dynamic service environment.
A Tandem Affinity Purification-based Technology Platform to Study the Cell Cycle Interactome in Arabidopsis thaliana (2007)

Defining protein complexes is critical to virtually all aspects of cell biology because many cellular processes are regulated by stable protein complexes, and their identification often provides insights into their function. We describe the development and application of a high throughput tandem affinity purification/mass spectrometry platform for cell suspension cultures to analyze cell cycle-related protein complexes in Arabidopsis thaliana. Elucidation of this protein-protein interaction network is essential to fully understand the functional differences between the highly redundant cyclin-dependent kinase/cyclin modules, which are generally accepted to play a central role in cell cycle control, in all eukaryotes. Cell suspension cultures were chosen because they provide an unlimited supply of protein extracts of actively dividing and undifferentiated cells, which is crucial for a systematic study of the cell cycle interactome in the absence of plant development. Here we report the mapping of a protein interaction network around six known core cell cycle proteins by an integrated approach comprising generic Gateway-based vectors with high cloning flexibility, the fast generation of transgenic suspension cultures, tandem affinity purification adapted for plant cells, matrix-assisted laser desorption ionization tandem mass spectrometry, data analysis, and functional assays. We identified 28 new molecular associations and confirmed 14 previously described interactions. This systemic approach provides new insights into the basic cell cycle control mechanisms and is generally applicable to other pathways in plants.
X‐Ray Lithography Mask Technology (1981)

A high yield process will be described for fabricating large area free‐standing membranes of thickness down to 0.5 μm for use as an x‐ray lithography mask substrate. The choice of material, method of preparation, and technique for separating the membrane from its substrate will be discussed. Techniques for generating x‐ray absorber patterns with submicron feature size are reported. These methods result in absorber geometries which are uniquely suited to x‐ray lithography mask applications. Measurements of the mask patterning distortion and the temporal dimensional stability of a completed x‐ray mask are reported.
Phyllanthoside-phyllanthostatin synthetic studies. 7. Total synthesis of (+)-phyllanthocin and (+)-phyllanthocindiol (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhyllanthoside-phyllanthostatin synthetic studies. 7. Total synthesis of (+)-phyllanthocin and (+)-phyllanthocindiolAmos B. Smith III, Mineo Fukui, Henry A. Vaccaro, and James R. EmpfieldCite this: J. Am. Chem. Soc. 1991, 113, 6, 2071–2092Publication Date (Print):March 1, 1991Publication History Published online1 May 2002Published inissue 1 March 1991https://pubs.acs.org/doi/10.1021/ja00006a029https://doi.org/10.1021/ja00006a029research-articleACS PublicationsRequest reuse permissionsArticle Views2794Altmetric-Citations49LEARN 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
STRAND SEPARATION AND SPECIFIC RECOMBINATION IN DEOXYRIBONUCLEIC ACIDS: PHYSICAL CHEMICAL STUDIES (1960)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Handbook of applied cryptography (1997)

From the Publisher:
A valuable reference for the novice as well as for the expert who needs a wider scope of coverage within the area of cryptography, this book provides easy and rapid access of information and includes more than 200 algorithms and protocols; more than 200 tables and figures; more than 1,000 numbered definitions, facts, examples, notes, and remarks; and over 1,250 significant references, including brief comments on each paper.
Palladium(II) Complexes of β-Ketoamines Derived from Acetylacetone and Amines (1965)

Abstract Numerous new palladium(II) complexes, Pd-(Aca.R)2, have been synthesized with β-ketoamines derived from acetylacetone and amines, where R represents methyl, ethyl, n-propyl, n-butyl, benzyl, phenyl, o-, m- and p-tolyl, and o, o′-xylidyl. It should be noted that when R denotes n-propyl or n-butyl, the palladium(II) complexes have been prepared successfully, although the free ligands can not be isolated in a pure form. This may be regarded as an example of the stabilization of a molecular configuration through co-ordination with a metal ion. The visible and ultraviolet spectra indicate that the palladium(II) complexes prepared in the present paper, which are considered to be square-planar in non-donor solvents as well as in the solid state, combine no additional pyridine molecules, even in pyridine. This is contrary to the previous observation that Ni(Aca.R)2 complexes combine two molecules of pyridine to form a sexaco-ordinated complex in pyridine.
Pendant Polymer:Amino-β-Cyclodextrin:siRNA Guest:Host Nanoparticles as Efficient Vectors for Gene Silencing (2012)

A novel siRNA delivery vector has been developed, based on the self-assembly of monosubstituted cationic β-CD derivatives with a poly(vinyl alcohol)MW27kD (PVA) main-chain polymer bearing poly(ethylene glycol)MW2000 (PEG) and acid-labile cholesterol-modified (Chol) grafts through an acid-sensitive benzylidene acetal linkage. These components were investigated for their ability to form nanoparticles with siRNA using two different assembly schemes, involving either precomplexation of the pendant Chol-PVA-PEG polymer with the cationic β-CD derivatives before siRNA condensation or siRNA condensation with the cationic β-CD derivatives prior to addition of Chol-PVA-PEG to engage host:guest complexation. The pendant polymer:amino-β-CD:siRNA complexes were shown to form nanoparticles in the size range of 120-170 nm, with a slightly negative zeta potential. Cell viability studies in CHO-GFP cells shows that these materials have 10(3)-fold lower cytotoxicities than 25 kD bPEI, while maintaining gene-silencing efficiencies that are comparable to those of benchmark transfection reagents such as bPEI and Lipofectamine 2000. These results suggest that the degradable Chol-PVA-PEG polymer is able to self-assemble in the presence of siRNA and cationic-β-CD to form nanoparticles that are an effective and low-toxicity vehicle for delivering siRNA cargo to target cells.
Aβ Oligomers – a decade of discovery (2007)

Converging lines of evidence suggest that progressive accumulation of the amyloid beta-protein (A beta) plays a central role in the genesis of Alzheimer's disease, but it was long assumed that A beta had to be assembled into extracellular amyloid fibrils to exert its cytotoxic effects. Over the past decade, data have emerged from the use of synthetic A beta peptides, cell culture models, beta-amyloid precursor protein transgenic mice and human brain to suggest that pre-fibrillar, diffusible assemblies of A beta are also deleterious. Although the precise molecular identity of these soluble toxins remains unsettled, accumulating evidence suggests that soluble forms of A beta are indeed the proximate effectors of synapse loss and neuronal injury. Here we review recent progress in understanding the role of soluble oligomers in Alzheimer's disease.
Transferrin receptor-1 and ferritin heavy and light chains in astrocytic brain tumors: Expression and prognostic value (2017)

Astrocytic brain tumors are the most frequent primary brain tumors. Treatment with radio- and chemotherapy has increased survival making prognostic biomarkers increasingly important. The aim of the present study was to investigate the expression and prognostic value of transferrin receptor-1 (TfR1) as well as ferritin heavy (FTH) and light (FTL) chain in astrocytic brain tumors. A cohort of 111 astrocytic brain tumors (grade II-IV) was stained immunohistochemically with antibodies against TfR1, FTH, and FTL and scored semi-quantitatively. Double-immunofluorescence stainings were established to determine the phenotype of cells expressing these markers. We found that TfR1, FTH, and FTL were expressed by tumor cells in all grades. TfR1 increased with grade (p<0.001), but was not associated with prognosis in the individual grades. FTH and FTL were expressed by tumor cells and cells with microglial/macrophage morphology. Neither FTH nor FTL increased with malignancy grade, but low FTH expression by both tumor cells (p = 0.03) and microglia/macrophages (p = 0.01) correlated with shorter survival in patients anaplastic astrocytoma. FTL-positive microglia/macrophages were frequent in glioblastomas, and high FTL levels correlated with shorter survival in the whole cohort (p = 0.01) and in patients with anaplastic astrocytoma (p = 0.02). Double-immunofluorescence showed that TfR1, FTH, and FTL were co-expressed to a limited extent with the stem cell-related marker CD133. FTH and FTL were also co-expressed by IBA-1-positive microglia/macrophages. In conclusion, TfR1 was highly expressed in glioblastomas and associated with shorter survival in the whole cohort, but not in the individual malignancy grades. Low levels of FTH-positive tumor cells and microglia/macrophages were associated with poor survival in anaplastic astrocytomas, while high amounts of FTL-positive microglia/macrophages had a negative prognostic value. The results suggest that regulation of the iron metabolism in astrocytic brain tumors is complex involving both autocrine and paracrine signaling.
Mask topography effects in projection printing of phase-shifting masks (1994)

Topography effects of glass edges in phase-shifting masks (PSM's) on image quality are assessed using the rigorous electromagnetic simulation program TEMPEST on three different optical systems for four PSM technologies including alternating, rim, attenuated, and chromeless. The scalar and thin mask approximations used in simulation programs such as SPLAT can be in error by as much as 20% for certain classes of shifter edges. A feature size independent bias of 0.021 /spl lambda//NA per edge is recommended for alternating masks with vertical edges because light is lost near the etched glass edges. No direct electromagnetic interaction between chromium edges and shifter edges was found for rim phase-shifting masks. The rim dimension can thus be designed solely on the basis of the sidelobe level and peak intensity. For attenuated PSM, edge effects are less severe but sidelobe problems occur. For a center to sidelobe contrast of 0.6 over a DOF of 3 RU, a lower transmission of 4% is recommended. For chromeless PSM, the imbalance in image peaks is shown to be affected by the optical stepper parameters. In any PSM technology, it appears that a 360/spl deg/ glass protrusion may produce a drastic drop in intensity due to resonant effects.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Tumor cell bystander killing in colonic carcinoma utilizing the Escherichia coli DeoD gene to generate toxic purines. (1994)

Inefficiency of gene delivery, together with inadequate bystander killing, represent two major hurdles in the development of a toxin-mediated gene therapy for human malignancy. The product of the Escherischia coli DeoD gene (purine nucleoside phosphorylase, PNP) differs from the mammalian enzyme in its substrate specificity and is capable of catalyzing the conversion of several non-toxic deoxyadenosine analogs to highly toxic adenine analogs. We have found that expression of E. coli PNP in < 1% of a human colonic carcinoma cell line leads to the death of virtually all bystander cells after treatment with 6-methyl-purine-2'-deoxyribonucleoside, a deoxyadenosine analog that is a substrate for E. coli PNP but not human PNP. Minimal toxicity was observed in non-transfected or E. coli LacZ transfected cells that were treated with this compound. These results establish a rational approach to achieve significant bystander killing, even after gene transfer to only a small fraction of tumor cells.
Heparin-Like Structures on Respiratory Syncytial Virus Are Involved in Its Infectivity In Vitro (1998)

Addition of heparin to the virus culture inhibited syncytial plaque formation due to respiratory syncytial virus (RSV). Moreover, pretreatment of the virus with heparinase or an inhibitor of heparin, protamine, greatly reduced virus infectivity. Two anti-heparan sulfate antibodies stained RSV-infected cells, but not noninfected cells, by immunofluorescence. One of the antibodies was capable of neutralizing RSV infection in vitro. These results prove that heparin-like structures identified on RSV play a major role in early stages of infection. The RSV G protein is the attachment protein. Both anti-heparan sulfate antibodies specifically bound to this protein. Enzymatic digestion of polysaccharides in the G protein reduced the binding, which indicates that heparin-like structures are on the G protein. Such oligosaccharides may therefore participate in the attachment of the virus.
Remarks on some dynamical problems of controlling redundant manipulators (1990)

The author establishes the mutual effects of dynamical constraints on redundant manipulators, the type of behavior they produce, and the various kinds of controlling algorithms. The various methods for controlling the robot are analyzed and compared for their dynamical behavior. This is done via a geometric viewpoint where each method induces a geometrical structure on the joint space. This sheds some light on the global dynamical advantages and disadvantages of each method, some of which were previously overlooked.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Changing the Amino Acid Specificity of Yeast Tyrosyl-tRNA Synthetase by Genetic Engineering (2001)

In an attempt to generate mutant aminoacyl-tRNA synthetases capable of charging non-canonical amino acids, a series of yeast tyrosyl-tRNA synthetase (TyrRS) mutants was constructed by site-specific mutagenesis of putative active site residues, which were deduced by analogy with those of Bacillus stearothermophilus TyrRS. Among these mutants, one with the replacement of tyrosine at position 43 by glycine, “Y43G,” was found to be able to utilize several 3-substituted tyrosine analogues as substrates for aminoacy-lation. The catalytic efficiency (kcat/Km) of mutant Y43G for aminoacylation with L-tyro-sine was about 400-fold decreased as compared to that of the wild-type TyrRS. On the other hand, the ability to utilize 3-iodo-L-tyrosine was newly generated in this mutant TyrRS, since the wild-type TyrRS could not accept 3-iodo-L-tyrosine at all under physiological conditions. This mutant TyrRS should serve as a new tool for site-specific incorporation of non-canonical amino acids, such as those in 3-substituted tyrosine analogues, into proteins in an appropriate translation system in vivo or in vitro.
Implementation of a Localization System for Sensor Networks (2006)

Localization is very important for self-configuring wireless sensor networks. There are two main tasks to performing localization. Assuming availability of reference points, first the relationships to the reference points are established; in this thesis this relationship is the distance to the reference point. Second, using the reference point positions and the relations to these points, an algorithmic computation is carried out to compute the position. In the existing body of research on sensor network localization, the algorithmic aspects of this final position calculation have received the most attention. However there remain significant implementation issues related to both distance measurements and algorithmic computations. In this thesis the implementation issues regarding a sensor network localization system is studied along with some examples. In the first half, the implementation of a distributed, least-squares-based localization algorithm is presented. Low power and energy dissipation are key requirements for sensor networks. An ultra-low-power and dedicated hardware implementation of the localization system is presented. The cost of fixed-point implementation is also investigated. The design is implemented in a 0.13u CMOS process. It dissipates 1.7mW of active power and 0.122nJ/op of active energy with a silicon area of 0.55mm2. The mean calculated location error due to fixed-point implementation is shown to be 6%. In the second part, a radio frequency(RF) signal based Time of Flight (ToF) measuring ranging system for wireless sensor networks is proposed, designed and prototyped. The prototype measurement error is within -0.5m to 2m while operating at 100Msps sampling rate and using a 50MHz signal in the 2.4GHz ISM band. The system accuracy is limited by the sampling rate and can be linearly improved with increasing rates. This RF method is more cost effective than acoustic signal based ranging schemes, as it does not require ultrasonic transducers. The system is multipath resilient and can coexist with 2.4GHz band devices such as 802.11b/g networks. The estimated power consumption for the digital baseband is 2.35mW and its estimated area 0.25mm2 in a 90nm CMOS process
New functional roles for non-collagenous domains of basement membrane collagens (2002)

Collagens IV, XV and XVIII are major components of various basement membranes. In addition to the collagen-specific triple helix, these collagens are characterized by the presence of several non-collagenous domains. It is clear now that these ubiquitous collagen molecules are involved in more subtle and sophisticated functions than just the molecular architecture of basement membranes, particularly in the context of extracellular matrix degradation. Degradation of the basement membrane collagens occurs during numerous physiological and pathological processes such as embryonic development or tumorigenesis and generates collagen fragments. These fragments are involved in the regulation of functions differing from those of their original intact molecules. The non-collagenous C-terminal fragment NC1 of collagen IV, XV and XVIII have been recently highlighted in the literature because of their potential in reducing angiogenesis and tumorigenesis, but it is clear that their biological functions are not limited to these processes. Proteolytic release of soluble NC1 fragments stimulates migration, proliferation, apoptosis or survival of different cell types and suppresses various morphogenetic events.
Adeno‐associated virus‐mediated gene transfer into human retinal pigment epithelium cells (1998)

Adeno-associated virus-based vectors are able to efficiently transduce and stably persist in RPE cells.