gebhart/patrepeval huggingface dataset:
ACE2 X-Ray Structures Reveal a Large Hinge-bending Motion Important for Inhibitor Binding and Catalysis (2004)

The angiotensin-converting enzyme (ACE)-related carboxypeptidase, ACE2, is a type I integral membrane protein of 805 amino acids that contains one HEXXH + E zinc-binding consensus sequence. ACE2 has been implicated in the regulation of heart function and also as a functional receptor for the coronavirus that causes the severe acute respiratory syndrome (SARS). To gain further insights into this enzyme, the first crystal structures of the native and inhibitor-bound forms of the ACE2 extracellular domains were solved to 2.2- and 3.0-A resolution, respectively. Comparison of these structures revealed a large inhibitor-dependent hinge-bending movement of one catalytic subdomain relative to the other ( approximately 16 degrees ) that brings important residues into position for catalysis. The potent inhibitor MLN-4760 ((S,S)-2-[1-carboxy-2-[3-(3,5-dichlorobenzyl)-3H-imidazol4-yl]-ethylamino]-4-methylpentanoic acid) makes key binding interactions within the active site and offers insights regarding the action of residues involved in catalysis and substrate specificity. A few active site residue substitutions in ACE2 relative to ACE appear to eliminate the S(2)' substrate-binding subsite and account for the observed reactivity change from the peptidyl dipeptidase activity of ACE to the carboxypeptidase activity of ACE2.
Conventional and microwave‐assisted SPPS approach: a comparative synthesis of PTHrP(1–34)NH2 (2011)

Attracted by the possibility to optimize time and yield of the synthesis of difficult peptide sequences by MW irradiation, we compared Fmoc/tBu MW-assisted SPPS of 1-34 N-terminal fragment of parathyroid hormone-related peptide (PTHrP) with its conventional SPPS carried out at RT. MWs were applied in both coupling and deprotection steps of SPPS protocol. During the stepwise elongation of the resin-bound peptide, monitoring was conducted by performing MW-assisted mini-cleavages and analyzing them by UPLC-ESI-MS. Identification of some deletion sequences was helpful to recognize critical couplings and as such helped to guide the introduction of MW irradiations to these stages.
Nicking and joining activity of banana bunchy top virus replication protein in vitro. (1997)

The major open reading frame of banana bunchy top virus (BBTV) DNA-1 encodes a putative replication initiation protein (Rep). In vitro, a fusion protein of BBTV Rep linked to a maltose-binding protein exhibited both site-specific nicking and joining activities. These activities were dependent on the presence of Mg2+ or Mn2+, but did not require ATP. The fusion protein specifically cleaved ssDNA between bases +7 and +8 of a conserved nonanucleotide loop sequence which is present in the virion-strand of the stem-loop common region of each BBTV component. During this reaction, the fusion protein became covalently attached to the 5' end of the 3'cleavage product. After the nicking reactions, the fusion protein was also capable of catalysing the joining of two nicked ssDNA fragments in a site-specific manner. Based on these activities, BBTV Rep would appear to be very similar to the Rep proteins of the geminiviruses.
New design concept for a narrowband wavelength-selective optical tap and combiner (1987)

A novel design is proposed for a four-port optical tap that extracts efficiently from a fibre in which light containing several discrete wavelength bands is propagating only that light within one such band. The same device can be used simultaneously to combine light of the same wavelength as the extracted light with the other, unselected, wavelength bands.
Heterotrophic Growth of Blue-Green Algae in Dim Light (1971)

A unicellular blue-green alga, Agmenellum quadruplicatum, and a filamentous blue-green alga, Lyngbya lagerheimíi, were grown heterotrophically in dim light with glucose as major source of carbon and possibly energy. The dim-light conditions did not support autotrophic growth. The two blue-green algae appeared to have the same metabolic block, namely an incomplete tricarboxylic acid cycle, as has been found in other obligately phototrophic blue-green algae. Under dim-light conditions, glucose made a greater contribution to cell constituents (amino acids) of A. quadruplicatum and L. lagerheimii than under high-light conditions.
Studies on the receptor mediating cyclic AMP‐independent enhancement by adenosine of IgE‐dependent mediator release from rat mast cells (1986)

Adenosine produced a concentration-related enhancement of antigen-induced 5-hydroxytryptamine (5-HT) release from rat serosal mast cells. This potentiation was maximal following the simultaneous addition of adenosine with antigen. Enhancement of 5-HT release was accompanied by potentiation of the adenosine 3':5'-cyclic monophosphate (cyclic AMP) response to challenge. The cyclic AMP response, which was antagonized by 8-phenyltheophylline, was characterized as an A2-purinoceptor-mediated effect by the use of 5'-N-ethylcarboxamideadenosine (NECA) and L-N6-phenylisopropyladenosine (L-PIA). Enhancement of 5-HT release, conversely, was not blocked by 8-phenyltheophylline suggesting it to be mediated by a cyclic AMP-independent mechanism. The effect of adenosine on 5-HT release was not reduced by the inhibition of the facilitated uptake of adenosine with dipyridamole, hexobendine or p-nitrobenzylthioguanosine, therefore, suggesting it to be mediated by a cell surface receptor. The receptor mediating enhancement of 5-HT does not appear to belong to the P2-purinoceptor subtype as adenosine was more potent than both adenosine monophosphate (AMP) and adenosine diphosphate (ADP) and alpha, beta-methylene ATP was inactive. Furthermore, the effects of AMP were blocked by alpha, beta-methylene ADP, which inhibits the conversion of AMP to adenosine. Adenosine, NECA, L- and D-PIA were all of equal potency in enhancing 5-HT release. Inosine and 3-deazaadenosine were also active. The rank order of potency of these adenosine analogues is not consistent with an effect at A1- or A2-purinoceptors. There appear to be two adenosine receptors on rat mast cells, an A2-purinoceptor which stimulates adenylate cyclase and a separate purinoceptor, stimulation of which produces enhancement of mediator release by an unknown mechanism. The effects mediated by these receptors appear to be independent of each other.
Applications of Genetic Engineering to the Pharmaceutical Industry (1983)

A frequent motive for genetic engineering is to transfer the gene for the desired protein from a cell that is difficult or impossible to grow into a cell which is easy and inexpensive to handle. In the pharmaceutical field this usually means isolation of a gene coding for a protein secreted by human cells, the protein often being glycosylated. While bacterial cells are an inexpensive host in which to express genes, they do not produce proteins which are glycosylated, nor necessarily properly processed. Thus while there are examples of successful bacterial systems, there is also an intense interest in expression in animal cells. The situation is often complicated by our lack of knowledge of the function, or even the necessity, of glycosylation. Examples of successes and problems in production of insulin and interferons in several hosts have been presented.
Controlled patterning of peptide nanotubes and nanospheres using inkjet printing technology (2007)

Peptide nanostructures are expected to serve as a major tool in future nanotechnological applications owing to their excellent self-assembly properties, biological and chemical flexibility and structural simplicity. Yet one of the limiting factors for the integration of peptide assemblies into functional electro-organic hybrid devices is the controlled patterning of their assemblies. Here we report the use of inkjet technology for the application of peptide nanostructures on nonbiological surfaces. The aromatic dipeptides nanotubes (ADNT) which readily self-assemble in solution were used as an 'ink' and patterned on transparency foil and ITO plastic surfaces using a commercial inkjet printer. While inkjet technology was used in the past for the patterning of carbon nanotubes, it was not used for the deposition of biomolecular nanostructures. Furthermore, during the development of the application we were able to produce two types of nanostructures, i.e. nanotubes and nanospheres by the self-assembly of the same aromatic dipeptide, tertbutoxycarbonyl-Phe-Phe-OH (Boc-Phe-Phe-OH), under different conditions. Both spherical and tubular structures could be efficiently patterned on surfaces into predesigned patterns. The applications of such technology are discussed.
Protective effect of antilipopolysaccharide monoclonal antibody in experimental Klebsiella infection (1997)

An O-antigen-specific murine monoclonal antibody (MAb) directed against an immunodominant epitope expressed on Klebsiella O1, O6, and O8 lipopolysaccharides (LPS) was examined with respect to its binding to nonencapsulated and encapsulated bacterial cells and its ability to protect against lethal murine Klebsiella sepsis. While the MAb (clone Ru-O1, mouse immunoglobulin G2b) bound well to nonencapsulated organisms of the O1 serogroup, binding was significantly, but not completely, abolished by the presence of the K2 capsule. In a model of experimental Klebsiella peritonitis and sepsis induced by a virulent O1:K2 serogroup strain, higher doses of anti-LPS MAb Ru-O1 than of a previously described anticapsular MAb specific for the K2 capsular polysaccharide were needed to provide protection. However, high-dose (40 microg/g of body weight) pretreatment with anti-LPS MAb Ru-O1 significantly reduced bacterial dissemination to various organs as well as macroscopic and histologic pulmonary alterations. Thus, since the number of Klebsiella capsular antigens occurring in clinical material is too large to be completely "covered" by a K-antigen-specific hyperimmunoglobulin preparation, O-antigen-specific antibodies may supplement K-antigen-specific immunoprophylaxis and -therapy of clinical Klebsiella infection.
Content-based transcoding of images in the Internet (2002)

We present a system for transcoding images in the Internet in order to improve their delivery to client devices with a wide range of communication, processing, storage and display capabilities. The content-based image transcoder analyzes the images in order to classify them into image type and image purpose classes. The system then utilizes transcoding policies based on the content classes to manipulate and transcode the images. We describe the image transcoding process for a variety of client devices, including PDAs, hand-held computers (HHCs), TV browsers and color PCs, and demonstrate improvements in delivery speed and accessibility of the images in the Internet.
Neurovascular complications of cocaine abuse (1991)

A 3-year prospective study of 31,081 admissions to an inner-city, emergency trauma hospital revealed 33 patients less than or equal to 45 years of age who had a total of 35 acute neurovascular events (infarction or hemorrhage) related to cocaine abuse (3% of the total 979 cocaine-related admissions). Fifty-four percent of the events were ischemic, and 46% were hemorrhagic. Six patients died. The majority (63%) of ischemic events were hemispheric and subcortical in distribution. Eleven of 13 angiograms were abnormal (five aneurysms and two arteriovenous malformations were identified). No case of "vasculitis" was seen. Seventy percent of the patients exclusively abused crack cocaine, and 94% of the neurovascular events were related to its use. No first-time cocaine users were identified. During the last year of the study, 29% of the 558 cocaine-related admissions were psychiatric admissions, and most (58%) were for treatment of depressive illness (34 patients were admitted for attempted suicide).
Characterization of the Yersinia pestis Yfu ABC Inorganic Iron Transport System (2001)

In Yersinia pestis, the causative agent of plague, two inorganic iron transport systems have been partially characterized. The yersiniabactin (Ybt) system is a siderophore-dependent transport system required for full virulence. Yfe is an ABC transport system that accumulates both iron and manganese. We have identified and cloned a Y. pestis yfuABC operon. The YfuABC system is a member of the cluster of bacterial ABC iron transporters that include Sfu of Serratia, Hit of Haemophilus, and Yfu of Yersinia enterocolitica. The Y. pestis KIM6+ system is most homologous to that in Y. enterocolitica, showing identities of 84% for YfuA (periplasmic binding protein), 87% for YfuB (inner membrane permease), and 75% for YfuC (ATP hydrolase). We constructed a yfuABC promoter-lacZ fusion to examine regulation of transcription. This promoter contains a potential Fur binding sequence and is iron and Fur regulated. Significant expression from the yfuABC promoter occurred during iron-deficient growth conditions. In vitro transcription and translation of a recombinant plasmid encoding yfuABC indicates that YfuABC proteins are expressed. Escherichia coli 1017 (an enterobactin-deficient mutant) carrying this plasmid was able to grow in an iron-restrictive complex medium. We constructed a deletion encompassing the yfuABC promoter and most of yfuA. This mutation was introduced into strains with mutations in Ybt, Yfe, or both systems to examine the role of Yfu in iron acquisition in Y. pestis. Growth of the yfu mutants in a deferrated, defined medium (PMH2) at 26 and 37 degrees C failed to identify a growth or iron transport defect due to the yfu mutation. Fifty percent lethal dose studies in mice did not demonstrate a role for the Yfu system in mammalian virulence.
Effects of Sex Steroids on Prolactin Secreting Rat Pituitary Cells in Culture (1976)

A clonal strain of rat pituitary tumor cells (GH3) was used to study the effects of different sex steroids on the production of prolactin (PRL). Hormone production was measured by radioimmunoassay and expressed as the amount of hormone which accumulated in the medium of monolayer cultures during 24 h. The stimulatory effect of 17beta-estradiol (10(-11)M-10(-6)M) on PRL production was significant after 4 days and the maximum effect (300% of control cultures) was observed at 10(-8)M after 10 days of treatment. After removal of added 17beta-estradiol, the production of PRL returned to control levels in 5 days. Progesterone (10(-11)M-10(-6)M) caused a dose-related decrease in PRL production reaching 60% of control values at 10(-6)M. Testerone (10(-6)M) stimulated the production of PRL (130% of controls), whereas 5alpha-dihydrotestosterone (10(-6)M) had a small effect (107% of controls) which was not always reproducible. None of the sex steroids affected cell growth. Progesterone (10(-6)M) inhibited the stimulatory effect of 17beta-estradiol (10(-8)M) on PRL production. The effect of 17beta-estradiol (10(-8)M) and thyrotropin releasing hormone (TRH) (3 X 10(-7) M) was addititive, while no additional stimulatory effect was observed when 17beta-estradiol (10(-8)M) was combined with testosterone (10(-6)M). If the properties of the GH3 cells are analogous to those of normal lactotropes, the sex steroids may alter PRL production at the pituitary level, an influence that may be further modulated by TRH.
Industrial pyrolysis of cellulosic materials. [Chemical reactions occurring during pyrolysis and analysis of volatile fractions] (1975)

Industrial pyrolysis of cellulosic materials to various fuels and chemicals requires an understanding of the complex reactions involved and how they can be controlled to provide acceptable yields. Investigation of a variety of model compounds and cellulosic substrates by modern methods of thermal and chemical analysis has shown that initial pyrolysis of glycosidically linked compounds takes place through transglycosylation to provide a mixture of anhydro sugars and randomly linked oligosaccharides. At higher temperatures, dehydration, fission and rearrangement of the sugar units provide a volatile fraction containing water and various carbonyl compounds. These reactions are also accompanied by evolution of carbon dioxide and carbon monoxide. The residues which could not escape the heated zone are carbonized by further dehydration, condensation of the unsaturated products, elimination of the substituent and crosslinking of the resulting free radicals. Since the initial pyrolytic reactions are heterolytic, the course of the pyrolysis and the yield of various products could be substantially changed by addition of acidic or alkaline catalysts. (auth)
Macroporous Nanowire Nanoelectronic Scaffolds for Synthetic Tissues (2012)

The development of three-dimensional (3D) synthetic biomaterials as structural and bioactive scaffolds is central to fields ranging from cellular biophysics to regenerative medicine. As of yet, these scaffolds cannot electrically probe the physicochemical and biological microenvironments throughout their 3D and macroporous interior, although this capability could have a marked impact in both electronics and biomaterials. Here, we address this challenge using macroporous, flexible and free-standing nanowire nanoelectronic scaffolds (nanoES), and their hybrids with synthetic or natural biomaterials. 3D macroporous nanoES mimic the structure of natural tissue scaffolds, and they were formed by self-organization of coplanar reticular networks with built-in strain and by manipulation of 2D mesh matrices. NanoES exhibited robust electronic properties and have been used alone or combined with other biomaterials as biocompatible extracellular scaffolds for 3D culture of neurons, cardiomyocytes and smooth muscle cells. Furthermore, we show the integrated sensory capability of the nanoES by real-time monitoring of the local electrical activity within 3D nanoES/cardiomyocyte constructs, the response of 3D-nanoES-based neural and cardiac tissue models to drugs, and distinct pH changes inside and outside tubular vascular smooth muscle constructs.
Solution mapping of T cell receptor docking footprints on peptide-MHC (2007)

T cell receptor (TCR) recognition of peptide-MHC (pMHC) is central to the cellular immune response. A large database of TCR-pMHC structures is needed to reveal general structural principles, such as whether the repertoire of TCR/MHC docking modes is dictated by a "recognition code" between conserved elements of the TCR and MHC genes. Although approximately 17 cocrystal structures of unique TCR-pMHC complexes have been determined, cocrystallization of soluble TCR and pMHC remains a major technical obstacle in the field. Here we demonstrate a strategy, based on NMR chemical shift mapping, that permits rapid and reliable analysis of the solution footprint made by a TCR when binding onto the pMHC surface. We mapped the 2C TCR binding interaction with its allogeneic ligand H-2Ld-QL9 and identified a group of NMR-shifted residues that delineated a clear surface of the MHC that we defined as the TCR footprint. We subsequently found that the docking footprint described by NMR shifts was highly accurate compared with a recently determined high-resolution crystal structure of the same complex. The same NMR footprint analysis was done on a high-affinity mutant of the TCR. The current work serves as a foundation to explore the molecular dynamics of pMHC complexes and to rapidly determine the footprints of many Ld-specific TCRs.
Multimodal Probabilistic Model-Based Planning for Human-Robot Interaction (2018)

This paper presents a method for constructing human-robot interaction policies in settings where multimodality, i.e., the possibility of multiple highly distinct futures, plays a critical role in decision making. We are motivated in this work by the example of traffic weaving, e.g., at highway on-ramps/off-ramps, where entering and exiting cars must swap lanes in a short distance-a challenging negotiation even for experienced drivers due to the inherent multimodal uncertainty of who will pass whom. Our approach is to learn multimodal probability distributions over future human actions from a dataset of human-human exemplars and perform real-time robot policy construction in the resulting environment model through massively parallel sampling of human responses to candidate robot action sequences. Direct learning of these distributions is made possible by recent advances in the theory of conditional variational autoencoders (CVAEs), whereby we learn action distributions simultaneously conditioned on the present interaction history, as well as candidate future robot actions in order to take into account response dynamics. We demonstrate the efficacy of this approach with a human-in-the-loop simulation of a traffic weaving scenario.
DNA chip technolgy (1999)

A mini-revolution is sweeping the world of science and medicine. DNA chip or microarray technology will have a more profound impact than other recent major advances, including DNA sequencing and the polymerase chain reaction (PCR). This mini-review explains the technology, its scope, and impact on science and medicine, as well as its cost and possible limitations.
Optimum Design Procedure for Multi-Pinhole-Plate Ultrasonic Atomizer (1987)

An optimum design procedure of the vibrating system for a Multi-Pinhole-Plate ultrasonic atomizer has been studied. It is composed of a thin plate with many pinholes and a circular ring piezoelectric element. The greatest efficiency was achieved at under two conditions. One was the coincidence among the first resonance frequencies of the inner portion inside the element and the outer portion and the second resonance frequency of the entire system. The other was when the inner diameter of the element was equal to that of the second nodal circle of a circular plate.
Synthesis of Germanium Nanocrystals in High Temperature Supercritical Fluid Solvents (2004)

Crystalline germanium (Ge) nanocrystals were synthesized by arrested precipitation in supercritical hexane and octanol at 400∼550 °C and 20.7 MPa in a continuous flow reactor. Two Ge precursors were explored, diphenylgermane (DPG) and tetraethylgermane (TEG), which undergo thermolysis to crystalline Ge under these conditions. Octanol is added to control particle growth, which appears to serve as a capping ligand that binds to the particle surface through an alkoxide linkage. The nanocrystals were characterized by high-resolution transmission electron microscopy (HRTEM), energy-dispersive X-ray spectroscopy (EDS), FTIR spectroscopy, and X-ray diffraction (XRD). The average nanocrystal diameter could be changed over a wide range, from ∼2 nm to ∼70 nm, by varying the reaction temperature and precursor concentration. Relatively size-monodisperse nanocrystals could be produced, with standard deviations about the mean diameter as low as ∼10%. UV−visible absorbance and photoluminescence (PL) spectra of Ge nanocrystals in the 3 to 4 nm diameter size range exhibit optical absorbance and PL spectra blue-shifted by approximately 1.7 eV relative to the band gap of bulk Ge, with quantum yields up to 6.6%.
Flavonoid genes in petunia: addition of a limited number of gene copies may lead to a suppression of gene expression. (1990)

To evaluate the effect of increased expression of genes involved in flower pigmentation, additional dihydroflavonol-4-reductase (DFR) or chalcone synthase (CHS) genes were transferred to petunia. In most transformants, the increased expression had no measurable effect on floral pigmentation. Surprisingly, however, in up to 25% of the transformants, a reduced floral pigmentation, accompanied by a dramatic reduction of DFR or CHS gene expression, respectively, was observed. This phenomenon was obtained with both chimeric gene constructs and intact CHS genomic clones. The reduction in gene expression was independent of the promoter driving transcription of the transgene and involved both the endogenous gene and the homologous transgene. The gene-specific collapse in expression was obtained even after introduction of only a single gene copy. The similarity between the sense transformants and regulatory CHS mutants suggests that this mechanism of gene silencing may operate in naturally occurring regulatory circuits.