gebhart/patrepeval huggingface dataset:
Adaptive Genetic Algorithm Observer and its Application to a Trailer Truck Control System (2006)

In this paper, we present an adaptive observer for nonlinear systems using a genetic algorithm (GA). It is considered that the GA has a superior performance for solution searching of multivariable systems. We utilize the GA searching ability to determine unobtainable variables in the control system. We extended the role of the GA observer to that of a parameter estimator for unknown systems and constructed an adaptive GA observer. The adaptive GA observer has a searching ability to estimate unobtainable variables and parameters simultaneously. In this paper, we use the estimated values of the system variables and parameters to design a neurocontroller (NC) using a GA. We applied the adaptive GA observer and NC design method to the backward movement control of a trailer truck. A simulation shows the effectiveness of the proposed method
Orai, STIM1 and iPLA2β: a view from a different perspective (2008)

The mechanism of store‐operated Ca 2+ entry (SOCE) remains one of the intriguing mysteries in the field of Ca 2+ signalling. Recent discoveries have resulted in the molecular identification of STIM1 as a Ca 2+ sensor in endoplasmic reticulum, Orai1 (CRACM1) as a plasma membrane channel that is activated by the store‐operated pathway, and iPLA 2 β as an essential component of signal transduction from the stores to the plasma membrane channels. Numerous studies have confirmed that molecular knock‐down of any one of these three molecules impair SOCE in a wide variety of cell types, but their mutual relations are far from being understood. This report will focus on the functional roles of Orai1, STIM1 and iPLA 2 β, and will address some specific questions about Orai1 and TRPC1, and their relation to SOC channels in excitable and non‐excitable cells. Also, it will analyse the novel role of STIM1 as a trigger for CIF production, and the complex relationship between STIM1 and Orai1 expression, puncta formation and SOCE activation. It will highlight some of the most recent findings that may challenge simple conformational coupling models of SOCE, and will offer some new perspectives on the complex relationships between Orai1, STIM1 and iPLA 2 β in the SOCE pathway.
The gomberg‐bachmann reaction of purines (1987)

Abstract The reaction of adenine derivatives with isoamyl nitrite in anisole solution was re‐investigated. The arylated products are a mixture of ortho, meta , and para ‐methoxyphenyl isomers with the ortho predominating. It is concluded that this is a typical free‐radical arylation and that the 6‐purinyl radical is a normal, well behaved aromatic radical.
Recent Progress of Synthetic Studies to Peptide and Peptidomimetic Cyclization (2008)

A large number of cyclic peptides, which exhibit a range of biological activities, have been found in nature. The reason of cyclic peptides that attracted world wide attention and made them extensively studied, is their enhanced metabolic stabilities, biological specificities, bioavailability, and conformational constrained structural feature, which make them important leads for drug discovery, and as actual drugs. Many cyclic peptides show very promising biological activities, including anticancer, antibacterial, antiviral, antifungal, anti-inflammatory, and anti-clotting or anti-atherogenic properties. Peptide cyclization becomes an effective and commonly employed strategy for peptide modifications. During the past several decades, great efforts have been made to develop more efficient methods for the synthesis of cyclic peptides and peptidomimetics. This review will be focused on the major progress of the novel recently developed peptide cyclization approaches and the profitable applications since 2002. Keywords: Peptidomimetic Cyclization, Macrolactamization, biological activities, cyclic peptides, metabolic stabilities, antibacterial, anticancer, anti-inflammatory
Stimulation over the human supplementary motor area interferes with the organization of future elements in complex motor sequences (1997)

We used high-frequency repetitive transcranial magnetic stimulation (rTMS) to study the role of the mesial frontocentral cortex (including the supplementary motor area) in the organization of sequential finger movements of different complexity in humans. In 15 subjects, rTMS was randomly applied to the scalp overlying the region of the supplementary motor area and over other positions, including the contralateral primary motor cortex (hand area) during the performance of three overlearned finger sequences on an electronic piano. In all trials, rTMS (frequency 15-20 Hz) started 2 s after the first key press and lasted for approximately 2 s. All sequences were metronome-paced at 2 Hz and retrieved from memory. The 'simple' sequence consisted of 16 repeated index finger key presses, the 'scale' sequence of four times four sequential key presses of the little, ring, middle and index fingers, and the 'complex' sequence of a much less systematic and, therefore, more difficult series of 16 key presses. To measure the effects of rTMS interference with regional cortical function, we analysed rTMS-induced accuracy errors in the movement sequences. Stimulation over the supplementary motor area induced accuracy errors only in the complex sequence, while stimulation over the primary motor cortex induced errors in both the complex and scale sequences, and stimulation over other positions (e.g. F3, F4, FCz, P3, P4) did not interfere with sequence performance at all. Stimulation over the supplementary motor area interfered with the organization of subsequent elements in the complex sequence of movements, with error induction occurring approximately 1 s later than with stimulation over the primary motor cortex. Our findings are in keeping with recent results in non-human primates (Tanji J, Shima K. Nature, 1994; 371: 413-6) indicating a critical role of the supplementary motor area in the organization of forthcoming movements in complex motor sequences that are rehearsed from memory and fit into a precise timing plan.
Is alopecia areata an autoimmune-response against melanogenesis-related proteins, exposed by abnormal MHC class I expression in the anagen hair bulb? (1995)

The etiology of alopecia areata (AA), a putative autoimmune disease characterized by sudden hair loss, has remained obscure. It is not understood, how the characteristic inflammatory infiltrate that selectively attacks anagen hair follicles in AA is generated. We hypothesize that this reflects an unexplored form of autoimmunity, a cytotoxic T cell attack on rhythmically synthesized autoantigens normally sequestered by a lack or very low level of MHC class I (MHC I)-expression, and suggest the following mechanism of AA pathogenesis: Microtrauma, neurogenic inflammation, or microbial antigens cause a localized breakdown of MHC I-"negativity" in the proximal anagen hair bulb via proinflammatory cytokines. This exposes autoantigens derived from melanogenesis-related proteins (MRP-DP), which are only generated during anagen, and triggers two successive waves of autoimmune responses: CD8+ cytotoxic T cells initiate AA after recognizing MRP-DP abnormally presented by MHC I molecules on hair matrix melanocytes and/or keratinocytes; a secondary attack, carried by CD4+ T cells and antigen presenting cells, is then mounted against MHC class II--presented additional autoantigens exposed by damaged melanocytes and keratinocytes. The latter causes most of the follicular damage, and extrafollicular disease, and depends greatly on the immunogenetic background of affected individuals. This unifying hypothesis explains the clinical heterogeneity and all salient features of AA, and argues that only the unlikely coincidence of multiple predisposing events triggers AA. The suppression of MHC I--expression and synthesis of MRP in the hair bulb, and the "tolerization" of MRP-DP autoreactive CD8+ T cells may be promising strategies for treating AA.
Texture synthesis on surfaces (2001)

Many natural and man-made surface patterns are created by interactions between texture elements and surface geometry. We believe that the best way to create such patterns is to synthesize a texture directly on the surface of the model. Given a texture sample in the form of an image, we create a similar texture over an irregular mesh hierarchy that has been placed on a given surface.
Rare protein-altering variants in ANGPTL7 lower intraocular pressure and protect against glaucoma (2019)

Protein-altering variants that are protective against human disease provide in vivo validation of therapeutic targets. Here we use genotyping data in UK Biobank and FinnGen to conduct a search for protein-altering variants conferring lower intraocular pressure (IOP) and protection against glaucoma. Through protein-altering variant association analysis we find a missense variant in UK Biobank (rs28991009 (MAF=0.8%) genotyped in 81,527 individuals with measured IOP and an independent set of 4,269 glaucoma patients and 251,355 controls) that significantly lowers IOP (β = −0.73 mmHg for heterozygotes, −2.96 mmHg for homozygotes, P = 1 × 10 −13 ) and is associated with 34% reduced risk of glaucoma ( P = 0.005). In FinnGen, we identify an ANGPTL7 missense variant at a greater than 50-fold increased frequency in Finland compared with other populations (rs147660927, p.Arg220Cys, MAF Finland = 4.1%), which was genotyped in 5,177 glaucoma patients and 130,461 controls and is associated with 30% lower glaucoma risk ( P = 1 × 10 −9 ). We further find three rarer variants in UK Biobank, including a protein-truncating variant, which confer a strong composite lowering of IOP ( P = 0.002), suggesting the protective mechanism likely resides in the loss of an interaction or function. Our results support inhibition or down-regulation of ANGPTL7 as a therapeutic strategy for glaucoma
Th17 Cell Frequency and IL-17 Concentration Correlate With Pre- and Postoperative Pain Sensation in Patients With Intervertebral Disk Degeneration (2014)

Numerous studies have revealed the presence of T helper 17 (Th17) cells in pathologic intervertebral disk (IVD) tissues and the contribution of Th17-associated cytokines to the development of this disease. However, the pre- and postoperative changes in the proportion of Th17 cells and the concentration of IL-17 in the peripheral blood of patients with IVD degeneration are not clear. The levels of Th17 frequency and the interleukin-17 (IL-17) concentration in peripheral blood from patients and volunteers were examined by flow cytometry and by enzyme-linked immunosorbent assay (ELISA), respectively. The clinical results were evaluated using the visual analogue scale (VAS). These results were subjected to a correlation analysis. Compared with the normal controls, the proportion of Th17 cells and the concentration of IL-17 were significantly increased preoperatively in patients with IVD degeneration. Postoperatively, the levels of Th17 cells and the expression of IL-17 were dramatically decreased. The correlation analysis of the VAS pain scores, Th17 cell frequency, and IL-17 concentration, including the pre- and postoperative levels and the changes induced by the surgery, revealed a positive correlation. The authors' results explain the contribution of Th17 cells and IL-17 to the pain sensation experienced by patients with IVD degeneration. These 2 factors may be good indicators for the evaluation of the surgical outcome of patients with lumbar disk herniation.
The effectiveness of acupuncture research across components of the trauma spectrum response (tsr): a systematic review of reviews (2012)

Based on the results of our review, acupuncture appears to be effective for treating headaches and, although more research is needed, seems to be a promising treatment option for anxiety, sleep disturbances, depression and chronic pain. It does not, however, demonstrate any substantial treatment benefit for substance abuse. Because there were no reviews on PTSD or sexual function that met our pre-defined inclusion criteria, we cannot comment on acupuncture's effectiveness in treating these conditions. More quality data are also needed to determine whether acupuncture is appropriate for treating fatigue or cognitive difficulties. Further, while acupuncture has been shown to be generally safe, safety was not described in the majority of studies, making it difficult to provide any strong recommendations. Future research should address safety reporting in detail in order to increase our confidence in acupuncture's efficacy across the identified TSR components.
High Performance n-Type Organic Field-Effect Transistors Based on π-Electronic Systems with Trifluoromethylphenyl Groups (2005)

Novel pi-electron systems with trifluoromethylphenyl groups and/or a thiazolothiazole unit were developed as n-type semiconductors for OFETs. They showed excellent n-type performances with high electron mobilities. The trifluoromethylphenyl group was found to be very effective in inducing n-type behavior. The thiazolothiazole unit was favorable for forming stacking structures leading to efficient intermolecular pi-pi interactions.
Coverage Control for Mobile Sensing Networks (2004)

This paper presents control and coordination algorithms for groups of vehicles. The focus is on autonomous vehicle networks performing distributed sensing tasks, where each vehicle plays the role of a mobile tunable sensor. The paper proposes gradient descent algorithms for a class of utility functions which encode optimal coverage and sensing policies. The resulting closed-loop behavior is adaptive, distributed, asynchronous, and verifiably correct.
Mutations in motif II of Escherichia coli DNA helicase II render the enzyme nonfunctional in both mismatch repair and excision repair with differential effects on the unwinding reaction (1995)

Site-directed mutagenesis has been employed to address the functional significance of the highly conserved aspartic and glutamic acid residues present in the Walker B (also called motif II) sequence in Escherichia coli DNA helicase II. Two mutant proteins, UvrDE221Q and UvrDD220NE221Q, were expressed and purified to apparent homogeneity. Biochemical characterization of the DNA-dependent ATPase activity of each mutant protein demonstrated a kcat that was < 0.5% of that of the wild-type protein, with no significant change in the apparent Km for ATP. The E221Q mutant protein exhibited no detectable unwinding of either partial duplex or blunt duplex DNA substrates. The D220NE221Q mutant, however, catalyzed unwinding of both partial duplex and blunt duplex substrates, but at a greatly reduced rate compared with that of the wild-type enzyme. Both mutants were able to bind DNA. Thus, the motif II mutants E221Q and D220NE221Q were able to bind ATP and DNA to the same extent as wild-type helicase II but demonstrate a significant reduction in ATP hydrolysis and helicase functions. The mutant uvrD alleles were also characterized by examining their abilities to complement the mutator and UV light-sensitive phenotypes of a uvrD deletion mutant. Neither the uvrDE221Q nor the uvrDD220NE221Q allele, supplied on a plasmid, was able to complement either phenotype. Further genetic characterization of the mutant uvrD alleles demonstrated that uvrDE221Q confers a dominant negative growth phenotype; the uvrDD220NE221Q allele does not exhibit this effect. The observed difference in effect on viability may reflect the gene products' dissimilar kinetics for unwinding duplex DNA substrates in vitro.
pH Clock-Operated Mechanized Nanoparticles (2009)

Mechanized nanoparticles (MNPs) consisting of supramolecular machines attached to the surface of mesoporous silica nanoparticles are designed to release encapsulated guest molecules controllably under pH activation. The molecular machines are comprised of cucurbit[6]uril (CB[6]) rings that encircle tethered trisammonium stalks and can be tuned to respond under specific pH conditions through chemical modification of the stalks. Luminescence spectroscopy demonstrates that the MNPs are able to contain guest molecules within nanopores at neutral pH levels and then release them once the pH is lowered or raised.
Generation and Characterization of Recombinant Vascular Targeting Agents from Hybridoma Cell Lines (2001)

Vascular targeting agents (VTAs) can be produced by linking antibodies or antibody fragments directed against endothelial cell markers to effector moieties. So far, it has been necessary to produce the components of VTAs (antibody, antibody fragment, linker, and effector) separately and, subsequently, to conjugate them by biochemical reactions. We devised a cloning and expression system to allow rapid generation of recombinant VTAs from hybridoma cell lines. The VTAs consist of a single chain Fv antibody fragment as a targeting moiety and either truncated Pseudomonas exotoxin (resulting in immunotoxins) or truncated human tissue factor (resulting in coaguligands) as effectors. The system was applied to generate recombinant immunotoxins and coaguligands directed against endoglin, vascular endothelial growth factor (VEGF):VEGF receptor (VEGFR) complex and vascular cell adhesion molecule 1 (VCAM-1). The fusion proteins exhibited similar functional activity to analogous biochemical constructs. This is the first report to describe the generation and characterization of recombinant coaguligands.
Positive Selection of Natural Autoreactive B Cells (1999)

Lymphocyte development is critically influenced by self-antigens. T cells are subject to both positive and negative selection, depending on their degree of self-reactivity. Although B cells are subject to negative selection, it has been difficult to test whether self-antigen plays any positive role in B cell development. A murine model system of naturally generated autoreactive B cells with a germ line gene-encoded specificity for the Thy-1 (CD90) glycoprotein was developed, in which the presence of self-antigen promotes B cell accumulation and serum autoantibody secretion. Thus, B cells can be subject to positive selection, generated, and maintained on the basis of their autoreactivity.
Acrosomal Status Evaluation in Human Ejaculated Sperm with Monoclonal Antibodies (1985)

An important question in mammalian gamete physiology concerns how capacitation and the occurrence of acrosome reactions in motile sperm relate to fertility. Evaluation of these relationships has been restricted by practical limitations because rapid, quantitative assays are unavailable. We have developed a rapid, reproducible assay for the evaluation of acrosomal status utilizing monoclonal antibodies specific to antigens localized in the acrosomal cap region of the sperm head. Mice were immunized with human ejaculated sperm preparations and the resultant hybridomas producing antisperm antibody were selected by solid-phase radioimmunoassay and indirect immunofluorescence (IIF). Two monoclonal antibodies (HS-19, HS-21) recognized target antigens restricted to the acrosomal cap by IIF, and 87 +/- 8.5% of the sperm in fresh ejaculates from 10 different sperm donors showed positive cap fluorescence with these reagents. Loss of HS-21 binding as measured by IIF was correlated with disappearance of the acrosomal cap as observed directly by transmission electron microscopy. Acrosomal disappearance, artificially induced in vitro using the calcium ionophore A23187, also resulted in a loss of HS-21 binding. The induction of acrosomal loss by ionophore was dependent upon extracellular calcium. The data presented suggest that specific monoclonal antibodies can be used for the rapid evaluation of acrosomal status in mammalian sperm.
Structural studies on the full‐length LysR‐type regulator TsaR from Comamonas testosteroni T‐2 reveal a novel open conformation of the tetrameric LTTR fold (2010)

LysR-type transcriptional regulators (LTTRs) constitute the largest family of regulators in prokaryotes. The full-length structures of the LTTR TsaR from Comamonas testosteroni T-2 and its complex with the natural inducer para-toluensulfonate have been characterized by X-ray diffraction. Both ligand-free and complexed forms reveal a dramatically different quaternary structure from that of CbnR from Ralstonia eutropha, or a putative LysR-type regulator from Pseudomonas aeruginosa, the only other determined full-length structures of tetrameric LTTRs. Although all three show a head-to-head tetrameric ring, TsaR displays an open conformation, whereas CbnR and PA01-PR present additional contacts in opposing C-terminal domains that close the ring. Such large differences may be due to a broader structural versatility than previously assumed or either, reflect the intrinsic flexibility of tetrameric LTTRs. On the grounds of the sliding dimer hypothesis of LTTR activation, we propose a structural model in which the closed structures could reflect the conformation of a ligand-free LTTR, whereas inducer binding would bring about local changes to disrupt the interface linking the two compact C-terminal domains. This could lead to a TsaR-like, open structure, where the pairs of recognition helices are closer to each other by more than 10 A.
Electron centers in single-crystalAl2O3 (1977)

The two prominent absorption bands centered at 6.1 and 4.8 eV in neutron-bombarded ${\mathrm{Al}}_{2}$${\mathrm{O}}_{3}$ single crystals have been investigated. Optical excitation into the 6.1 eV causes growth of bands at 5.4, 4.8, and 4.1 eV, whereas excitation into these latter bands causes growth of the 6.1-eV band. The oscillator strength of the 4.8-eV band was found to be in the range 0.5-1 as compared to a value nearly twice that for the 6.1-eV band. Excitation with 4.8-eV light produces an emission band at 3.75 eV and the yield and polarization of this emission as a function of the polarization of the exciting light was studied. This polarization behavior together with previous theoretical calculations is consistent with an assignment of the 4.8-eV band to the transition of the ${F}^{+}$ center. The oscillator strength ratio and the reciprocal relationship between the 4.8-eV band and the 6.1-eV band strongly indicate that the latter is associated with the $F$ center.
Neutrophils Activate Plasmacytoid Dendritic Cells by Releasing Self-DNA–Peptide Complexes in Systemic Lupus Erythematosus (2011)

Systemic lupus erythematosus (SLE) is a severe and incurable autoimmune disease characterized by chronic activation of plasmacytoid dendritic cells (pDCs) and production of autoantibodies against nuclear self-antigens by hyperreactive B cells. Neutrophils are also implicated in disease pathogenesis; however, the mechanisms involved are unknown. Here, we identified in the sera of SLE patients immunogenic complexes composed of neutrophil-derived antimicrobial peptides and self-DNA. These complexes were produced by activated neutrophils in the form of web-like structures known as neutrophil extracellular traps (NETs) and efficiently triggered innate pDC activation via Toll-like receptor 9 (TLR9). SLE patients were found to develop autoantibodies to both the self-DNA and antimicrobial peptides in NETs, indicating that these complexes could also serve as autoantigens to trigger B cell activation. Circulating neutrophils from SLE patients released more NETs than those from healthy donors; this was further stimulated by the antimicrobial autoantibodies, suggesting a mechanism for the chronic release of immunogenic complexes in SLE. Our data establish a link between neutrophils, pDC activation, and autoimmunity in SLE, providing new potential targets for the treatment of this devastating disease.
Giant photoresistivity and optically controlled switching in self-assembled nanowires (2001)

We report the observation of giant photoresistivity in electrochemically self-assembled CdS and ZnSe nanowires electrodeposited in a porous alumina film. The resistance of these nanowires increases by one to two orders of magnitude when exposed to infrared radiation, possibly because of real-space transfer of electrons from the nanowires into the surrounding alumina by photon absorption. This phenomenon has potential applications in “normally on” infrared photodetectors and optically controlled switches.