gebhart/patrepeval huggingface dataset:
Binding of random copolymers of three amino acids to class II MHC molecules (1999)

Copolymer 1 [Cop 1, poly(Y,E,A,K)] is a random synthetic amino acid copolymer of L-tyrosine, L-glutamic acid, L-alanine and L-lysine, effective both in suppression of experimental allergic encephalomyelitis and in the treatment of relapsing forms of multiple sclerosis. Cop 1 binds promiscuously and very efficiently to purified human HLA-DR molecules within the peptide-binding groove. In the present study the binding of copolymers composed of three of the four amino acids found in poly(Y,E,A,K) to purified class II MHC molecules was examined. Poly(Y,A,K) and poly(Y,E,A,K) bound to purified human HLA-DR1 or -DR4 molecules with affinity higher than poly(Y,E,A), poly(E,A,K) or poly(Y,E,K), whereas poly(Y,E,A,K) and poly(E,A,K) were the better binders of HLA-DR2 molecules. On the other hand, poly(Y,E,A) and poly(Y,A,K) inhibited the binding of biotinylated poly(Y,E,A,K) to these molecules 10-fold more efficiently than poly(Y,E,K). Finally, poly(Y,E,A), poly(Y,A,K) and poly(E,A,K) were cross-reactive with poly(Y,E,A,K) using YEAK-specific T cell lines and clones of mouse or human origin.
Transcranial magnetic stimulation in patients with bipolar depression: a double blind, controlled study (2002)

Dolberg OT, Dannon PN, Schreiber S, Grunhaus L. Transcranial magnetic stimulation in patients with bipolar depression: a double blind, controlled study. Bipolar Disord 2002: 4(Suppl. 1): 94–95. © Blackwell Munksgaard, 2002
Dendritic Cells Express Multiple Chemokine Receptors Used as Coreceptors for HIV Entry (1998)

Cells of the dendritic lineage are thought to be among the first cells infected after mucosal exposure to HIV. In this study, we have identified the presence of multiple chemokine receptors on dendritic cells (DC) that may function as coreceptors for HIV entry. DC effectively used CCR5 for entry of macrophage (M)-tropic isolates. CCR3, the eotaxin receptor, initially identified on eosinophils, is expressed on DC and may be used as an entry coreceptor by certain dual-tropic strains. CXCR4 was not expressed on DC, although SDF-1 induced a calcium flux and DC could be infected by T cell line (T)-tropic HIV. Our findings provide evidence for the presence of a non-CXCR4 SDF-1 receptor on DC that is used mainly by T-tropic strains of HIV. DC from individuals homozygous for a 32-bp deletion of the CCR5 gene are also infectable with M-tropic strains of HIV-1, and this infection is inhibited by stromal cell-derived factor (SDF)1, suggesting that this receptor can also be used by M-tropic HIV for entry. Delineation of the spectrum of coreceptor usage on DC may offer new approaches to interfere with the initiation and propagation of HIV infection.
Custom Knock-Outs with Hairpin RNA-Mediated Gene Silencing (2003)

Hairpin (hpRNA)-mediated gene silencing exploits a cellular mechanism that recognizes double-stranded RNA (dsRNA) and subjects it and its corresponding mRNA to a sequence-specific degradation. This phenomenon is known as posttranscriptional gene silencing (PTGS) in plants and RNA interference (RNAi) in animals. dsRNA, when introduced into plant cells through hpRNA constructs, results in severe reduction of the target mRNA-the silencing effect being stably inherited over many generations. While hpRNA constructs can be made using conventional plasmids, use of generic vectors such as pHANNIBAL makes it more convenient to silence a number of genes simultaneously. Vectors, such as pHELLSGATE, that are based on the Gateway(R) technology are suitable for high-throughput gene silencing. The specificity of dsRNA silencing, it's ability to simultaneously silence multiple genes combined with the availability of high-throughput silencing vectors enables the researcher to generate custom knockout plants.
Emerging role of myeloperoxidase and oxidant stress markers in cardiovascular risk assessment (2003)

The inflammatory protein myeloperoxidase is present, active and mechanistically poised to participate in the initiation and progression of cardiovascular disease. The many links between myeloperoxidase, oxidation and cardiovascular disease suggest this leukocyte protein may have clinical utility in risk stratification for cardiovascular disease status and outcomes.
Nanoparticle-mediated drug delivery to tumor vasculature suppresses metastasis (2008)

Integrin alphanubeta3 is found on a subset of tumor blood vessels where it is associated with angiogenesis and malignant tumor growth. We designed an alphanubeta3-targeted nanoparticle (NP) encapsulating the cytotoxic drug doxorubicin (Dox) for targeted drug delivery to the alphanubeta3-expressing tumor vasculature. We observed real-time targeting of this NP to tumor vessels and noted selective apoptosis in regions of the alphanubeta3-expressing tumor vasculature. In clinically relevant pancreatic and renal cell orthotopic models of spontaneous metastasis, targeted delivery of Dox produced an antimetastatic effect. In fact, alphanubeta3-mediated delivery of this drug to the tumor vasculature resulted in a 15-fold increase in antimetastatic activity without producing drug-associated weight loss as observed with systemic administration of the free drug. These findings reveal that NP-based delivery of cytotoxic drugs to the alphanubeta3-positive tumor vasculature represents an approach for treating metastatic disease.
Role of flagellin in the pathogenesis of shock and acute respiratory distress syndrome: Therapeutic opportunities (2003)

Recognition of the flagellin-toll-like receptor 5 pathway offers novel opportunities for the experimental therapy of various forms of shock, sepsis, and acute respiratory distress syndrome.
The structure of the pseudorabies virus genome at the end of the inverted repeat sequences proximal to the junction with the short unique region (1990)

The complete nucleotide sequence is presented of the 2 x 67 kbp BamHI-EcoRV portion of the BamHI 10 fragment of the pseudorabies virus (PRV) genome (strain Ka) containing sequences upstream of the previously reported protein kinase gene, and completing the sequence of this 4008 bp fragment. It is predicted to contain a gene designated RSp40, homologous to gene US1 of herpes simplex virus type 1 (HSV-1), with the potential to encode a protein of 364 amino acids. Analysis of PRV mRNA synthesized in the presence and absence of cycloheximide indicated that, in contrast to its HSV-1 homologue, the PRV gene RSp40 does not specify an immediate-early mRNA. Between the RSp40 gene and the protein kinase gene are two reiterated sequences: one containing 11 tandem copies of a 35 nucleotide sequence and the other containing nine tandem copies of a 10 nucleotide sequence. The BamHI 10 and the BamHI 12 fragments of PRV contain the junctions between the short unique (US) and short repeat (RS) regions of the PRV genome. The nucleotide sequence of that portion of the BamHI 12 fragment containing US sequences was determined so that, by comparison with the nucleotide sequence of the BamHI 10 fragment, the junction between the US and RS regions could be defined. In BamHI 10 this was found to be at a point between the two reiterated sequences (which are in the RS region) and the protein kinase gene (which is in the US region). The organization of this region of the PRV genome is compared to that of other alphaherpesviruses.
Nickel-Cathoded Perovskite Solar Cells (2014)

Current lead halide perovskite solar cells use high work function (φ) precious metals, such as gold (φ = 5.1 eV), as the back cathode to maximize the attainable photovoltage. We report herein a set of perovskite-type solar cells that use nickel (φ = 5.04 eV), an earth-abundant element and non-precious metal, as back cathode and achieve the same open-circuit voltage as gold and an efficiency of 10.4%. This work opens a “nickel”-and-dimed (low-cost) way toward high-efficient perovskite solar cells.
A new method for the synthesis of a structural gene (1990)

A novel method of synthesizing a structural gene or gene fragment, consisting of the first synthesis of a single-stranded DNA (ssDNA), has been developed. As a preliminary test of this method, four synthetic genes or gene fragments have been synthesized. The first one with 396 base pairs (b.p.) codes for the mature rbcS from wheat, the next two with 370 and 342 b.p. respectively, for two half molecules of a gene for trichosanthin and the last one with 315 b.p. for the N-terminal 1-102 residues of human prourokinase. In all these syntheses, a plus-stranded DNA of the target gene was generally assembled by a stepwise or one step T4 DNA ligase reaction of six oligonucleotides (A, *pB, *pC, *pD, *pE and *pF) of 30-71 nucleotides long in the presence of two terminal complementary oligonucleotides (Ab' and eF') and three short inter-fragment complementary oligonucleotides (bc, cd and de). After purification, the synthetic ssDNA was inserted into a cloning vector, pWR13. The resulting product was directly used to transform a host cell. The structure of the cloned synthetic gene was confirmed by DNA sequence analysis.
Parasite polymorphism present within minimal T cell epitopes of Plasmodium falciparum circumsporozoite protein. (1988)

Identification of T cell antigenic sites is critical for antisporozoite malarial vaccine design. Here, we present data that define two minimal functional T cell sites present in an immunogenic domain of the circumsporozoite protein of Plasmodium falciparum. These two sites overlap one another and correlate with polymorphic regions of the molecule. This suggests that these polymorphisms may be a result of pressure from immune T cells.
Ontogeny of the Heavy Chain Immunoglobulin Repertoire in Fetal Liver and Bone Marrow (1998)

We studied the kinetics of maturation of B cell progenitors in the mouse embryo, from day 15 of development to birth, both in liver and bone marrow. The analysis of Ig heavy chain rearrangements at different time points of late fetal development shows that oligoclonal patterns of V(H)-D-J(H) rearrangements are detected by day 15 in fetal liver. The pattern is polyclonal and diverse by day 17; however, 80% of the rearrangements are nonproductive. In bone marrow, the pattern of rearrangements is less diverse at birth, although the percentage of nonproductive rearrangements approaches adult bone marrow levels (35-40%). After day 17 in fetal liver, there is a sudden reversal in the percentage of nonproductive rearrangements that reaches 33% at day 19 (birth). Maturation of B cells, as measured by the fraction of surface Ig+ in total B220+ cells and the presence of N sequence additions in V(H)-D-J(H) joints, occurs in the marrow before fetal liver. These results demonstrate that the lymphopoietic environment in fetal liver and bone marrow of animals at the same stage of development is functionally distinct.
Neural Smithing: Supervised Learning in Feedforward Artificial Neural Networks (1999)

From the Publisher:
Artificial neural networks are nonlinear mapping systems whose structure is loosely based on principles observed in the nervous systems of humans and animals. The basic idea is that massive systems of simple units linked together in appropriate ways can generate many complex and interesting behaviors. This book focuses on the subset of feedforward artificial neural networks called multilayer perceptions (MLP). These are the most widely used neural networks, with applications as diverse as finance (forecasting), manufacturing (process control), and science (speech and image recognition). This book presents an extensive and practical overview of almost every aspect of MLP methodology, progressing from an initial discussion of what MLPs are and how they might be used to an in-depth examination of technical factors affecting performance. The book can be used as a tool kit by readers interested in applying networks to specific problems, yet it also presents theory and references outlining the last ten years of MLP research.
Multiple interactions of IgG with its core oligosaccharide can modulate recognition by complement and human Fc γ receptor I and influence the synthesis of its oligosaccharide chains (1996)

Glycosylation at Asn297 within the CH2 domains of IgG is important for recognition by the effector ligands Fc gammaR and C. Protein engineering has been used to replace amino acid residues within the extensive oligosaccharide interaction site that contact the core hexasaccharide (GlcNAc2Man3GlcNAc). Replacement of residues Phe241, Val264, or Asp265, in particular, results in reduced recognition of human chimeric anti-nitroiodophenacetyl IgG3 produced in Chinese hamster ovary cells, by guinea pig C and human C1q. Replacement of residues Val264 or Asp265, in particular, results in reduced superoxide production triggered through human Fc gammaRI expressed on U937 cells. These results suggest that noncovalent interactions of multiple amino acid residues of IgG with oligosaccharide residues that include the primary and secondary GlcNAc are necessary for optimal recognition of IgG by human Fc gammaRI and C1q. Replacement of residues 241, 243, 264, 265, or 301 with alanine in each case resulted in increased galactosylation and sialylation relative to the wild-type oligosaccharide chains. In particular, for the mutant FA243 there was much increased sialylation of its oligosaccharide chains (73%) relative to the wild-type (4%). Thus, even single residue replacements within the oligosaccharide interaction site of the C region can influence galactosylation and sialylation of its oligosaccharide chains. These data suggest a protein engineering route to the production of more homogeneously glycosylated IgG molecules with or without compromised biologic activities.
Intractable postherpetic itch and cutaneous deafferentation after facial shingles (2002)

Some patients develop chronic itch from neurological injuries, and shingles may be a common cause. Neuropathic itch can lead to self-injury from scratching desensate skin. A 39-year-old woman experienced severe postherpetic itch, but no postherpetic neuralgia, after ophthalmic zoster. Within 1 year, she had painlessly scratched through her frontal skull into her brain. Sensory testing and skin biopsies were performed on itchy and normal scalp to generate preliminary hypotheses about mechanisms of neuropathic itch. Quantitation of epidermal neurites in PGP9.5-immunolabeled skin biopsies demonstrated loss of 96% of epidermal innervation in the itchy area. Quantitative sensory testing indicated severe damage to most sensory modalities except itch. These data indicate that in this patient, severe postherpetic itch was associated with loss of peripheral sensory neurons. Possible mechanisms include electrical hyperactivity of hypo-afferented central itch-specific neurons, selective preservation of peripheral itch-fibers from neighboring unaffected dermatomes, and/or imbalance between excitation and inhibition of second-order sensory neurons.
p-Trifluoromethyldiazirinyl-etomidate: A Potent Photoreactive General Anesthetic Derivative of Etomidate That Is Selective for Ligand-Gated Cationic Ion Channels (2010)

We synthesized the R- and S-enantiomers of ethyl 1-(1-(4-(3-((trifluoromethyl)-3H-diazirin-3-yl)phenyl)ethyl)-1H-imidazole-5-carboxylate (trifluoromethyldiazirinyl-etomidate), or TFD-etomidate, a novel photoactivable derivative of the stereoselective general anesthetic etomidate (R-(2-ethyl 1-(phenylethyl)-1H-imidazole-5-carboxylate)). Anesthetic potency was similar to etomidate's, but stereoselectivity was reversed and attenuated. Relative to etomidate, TFD-etomidate was a more potent inhibitor of the excitatory receptors, nAChR (nicotinic acetylcholine receptor) ((alpha1)(2)beta1delta1gamma1) and 5-HT(3A)R (serotonin type 3A receptor), causing significant inhibition at anesthetic concentrations. S- but not R-TFD-etomidate enhanced currents elicited from inhibitory alpha1beta2gamma2L GABA(A)Rs by low concentrations of GABA, but with a lower efficacy than R-etomidate, and site-directed mutagenesis suggests they act at different sites. [(3)H]TFD-etomidate photolabeled the alpha-subunit of the nAChR in a manner allosterically regulated by agonists and noncompetitive inhibitors. TFD-etomidate's novel pharmacology is unlike that of etomidate derivatives with photoactivable groups in the ester position, which behave like etomidate, suggesting that it will further enhance our understanding of anesthetic mechanisms.
DNA Recognition by Peptide Complexes of Rhodium(III): Example of a Glutamate Switch (1994)

A family of metal-peptide complexes has been synthesized by coupling short oligopeptides (13 residues) onto the metallointercalating [Rh(phi)_2(phen’)]^(3+) (phi = 9,10-phenanthrenequinone diimine; phen’ = 5-(amidoglutaryl)-1,10-phenanthroline). These complexes were prepared to explore whether the side-chain functionalities of small peptides may be used to augment metal complex recognition. The metal-peptide complexes bind and, with photoactivation, cleave DNA. The DNA site-specificity is seen to depend on the peptide side-chain functional groups. In particular, a single glutamate at position 10 is found to be essential in directing DNA site-recognition to the sequence 5’-CCA-3’. Methylation of the glutamate side chain or direct substitution of glutamine for glutamate abolishes the 5’-CCA-3’ selectivity, while substitutions at other likely DNA-binding residues show no appreciable change in selectivity. Significantly, the 5’-CCA-3’ selectivity is even sensitive to a highly conservative E10D substitution. DNA photocleavage of oligonucleotides by the metal-peptide complexes and HPLC analysis of DNA products provide evidence for major groove chemistry. Circular dichroism indicates significant α-helical content in the peptide, which depends upon the presence of the glutamate. A model for the glutamate-dependent site-selectivity is presented using shape-selective intercalation of the metal complex and base-specific contacts of the ancillary peptide. These monomeric metal-peptide complexes appear to serve as particularly useful mimics for larger site-specific DNA-binding proteins and may provide a basis for the design of an array of small, sequence-specific DNA-binding metal complexes.
Regulation and Adaptive Evolution of Lactose Operon Expression in Lactobacillus delbrueckii (2002)

Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis are both used in the dairy industry as homofermentative lactic acid bacteria in the production of fermented milk products. After selective pressure for the fast fermentation of milk in the manufacture of yogurts, L. delbrueckii subsp. bulgaricus loses its ability to regulate lac operon expression. A series of mutations led to the constitutive expression of the lac genes. A complex of insertion sequence (IS) elements (ISL4 inside ISL5), inserted at the border of the lac promoter, induced the loss of the palindromic structure of one of the operators likely involved in the binding of regulatory factors. A lac repressor gene was discovered downstream of the beta-galactosidase gene of L. delbrueckii subsp. lactis and was shown to be inactivated by several mutations in L. delbrueckii subsp. bulgaricus. Regulatory mechanisms of the lac gene expression of L. delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis were compared by heterologous expression in Lactococcus lactis of the two lac promoters in front of a reporter gene (beta-glucuronidase) in the presence or absence of the lac repressor gene. Insertion of the complex of IS elements in the lac promoter of L. delbrueckii subsp. bulgaricus increased the promoter's activity but did not prevent repressor binding; rather, it increased the affinity of the repressor for the promoter. Inactivation of the lac repressor by mutations was then necessary to induce the constitutive expression of the lac genes in L. delbrueckii subsp. bulgaricus.
Varicella-zoster virus glycoprotein I is essential for growth of virus in Vero cells (1997)

Varicella-zoster virus (VZV) encodes at least six glycoproteins. Glycoprotein I (gI), the product of open reading frame 67, is a 58- to 62-kDa glycoprotein found in VZV-infected cells. We constructed two VZV gI deletion mutants. Immunoprecipitation of VZV gE from infected cells indicated that cells infected with VZV deleted for gI expressed a gE that was larger (100 kDa) than that expressed in cells infected with the parental virus (98 kDa). Cell-associated or cell-free VZV deleted for gI grew to lower titers in melanoma cells than did parental VZV. While VZV deleted for gI replicated in other human cells, the mutant virus replicated to very low titers in primary guinea pig and monkey cells and did not replicate in Vero cells. When compared with the parental virus, rescued viruses, in which the gI deletion was restored with a wild-type allele, showed a similarly sized gE and comparable growth patterns in melanoma and Vero cells. VZV deleted for gI entered Vero cells; however, viral DNA synthesis was impaired in these cells. The VZV gI mutant was slightly impaired for adsorption to human cells. Thus, VZV gI is required for replication of the virus in Vero cells, for efficient replication of the virus in nonhuman cells, and for normal processing of gE.
[The design of a fiber optic hygrometer using in patient monitor]. (1998)

Fiber optic sensor is a kind of newly developed sensory technology in recent ten years. With intrinsic security and wide application, it is superior to the traditional point sensors. This paper presents the design of a kind of fiber optic hygrometer using in patient monitor.
Silicon Chip Interfaced with a Geometrically Defined Net of Snail Neurons (2005)

Abstract We have successfully interfaced living neuronal networks with a defined geometry of synaptic connections to a semiconductor chip, enabling a non‐invasive supervision of network activity at a single‐cell level. Two networks of two and four neurons are presented and the signaling pathways are discussed. The outgrowth of neurons from the pond snail Lymnaea stagnalis and the formation of synapses are controlled by topographical structures processed from a polyester resist. Action potentials are evoked in individual neurons by capacitive stimulators integrated in the chip. They propagate along guided neurites, pass through electrical synapses, and trigger postsynaptic excitations that are recorded by field‐effect transistors. The networks represent proof‐of‐principle experiments for the development of complex hybrid neuroelectronic devices for applications in brain research, pharmacology, and information technology.