gebhart/patrepeval huggingface dataset:
Open and closed loop control of complex molecules with shaped fs pulses (2004)

Summary form only given. Quantum control of photo induced reactions exploits molecular interferences by adjusting the phases of multiple quantum pathways to different product channels via adapted excitation light. The approach features general applicability but an accurate theoretical prediction of the optimal laserfield to drive a specific chemical reaction is possible only for very basic systems. Moreover, the experimental realization of such a predicted complex field at the site of the interaction volume is extremely difficult or even impossible. If the molecular system under study comprises more than two atoms, a closed loop experiment may bypass such complications since it identifies the optimal pulse shapes in a trial and error fashion, without any specific a priori knowledge. Such a loop is established by a tunable modulator to shape the fs Pulses at will, and a learning algorithm which reads and interprets a relevant response signal to compute a corrective input and return it to the shaper. Many successful demonstrations of this approach on a multitude of atomic and molecular systems have been presented in the last few years. However, in spite of these demonstrations, it was still uncertain whether this approach can be applied to highly complex systems, or even biological samples. The demonstrations illustrate that coherent control effected by a combination of open and closed loop experiments is well suited to uncover the structure and dynamics of complex molecules.
The Myf fibrillae of Yersinia enterocolitica (1993)

The Myf antigen produced by Yersinia enterocolitica appeared as a proteic polymer composed of 21 kDa subunits. By transposon mutagenesis we isolated Myf-defective mutants. Those allowed us to clone and sequence a 4.4 kb chromosomal locus involved in Myf production. This region was found to contain three genes that we called myfA, myfB and myfC. Genes myfB and myfC encode an assembly machine related to those involved in the synthesis of many fimbriae: MyfB, the putative chaperone, possesses the consensus residues of the PapD family and myfC encodes a putative outer-membrane protein. MyfA, the major subunit, was found to be 44% identical to the pH 6 antigen of Y. pestis. Myf is thus the Y. enterocolitica counterpart of this antigen, but it is by far not so well conserved as the other virulence determinants such as the Yops, suggesting that Myf and pH 6 antigen do not necessarily play the same role in Y. enterocolitica and Y. pestis. The study of the prevalence of myfA in various species of Yersinia revealed that, like the yst enterotoxin gene, its presence is restricted to the pathogenic serotypes of Y. enterocolitica. By immunogold labelling, Myf appeared as a layer of extracellular material extending locally 2 microns from the bacterial surface, indicative of a fibrillar structure.
Theoretical studies of the interaction between aluminum and poly(p-phenylenevinylene) and derivatives (1994)

We report the results of a theoretical study of the interaction between aluminum and poly(p-phenylenevinylene) and derivatives of poly(p-phenylenevinylene). This allows us to investigate the initial stages of formation of the metal/conjugated polymer interface. Applying the semiempirical Austin model 1 method, we find that aluminum reacts preferentially by forming covalent bonds with the vinylene linkages in both poly(p-phenylenevinylene) and poly(2,5-dimethoxy-p-phenylenevinylene). When carbonyl groups replace the methoxy groups, i.e., to form poly(2,5-dialdehyde-p-phenylenevinylene), new reactive sites are induced, leading to structures involving aluminum–oxygen bonds, with stabilities comparable to those involving reaction with the vinylene groups. In all of the three systems investigated, the interaction with aluminum induces major modifications of the polymer chains with interruptions of the π system caused by formation of sp3 sites. Charge distribution analysis indicates that electron charge transfer takes place from the aluminum atoms to the polymer chains.
α-Helix folding in the presence of structural constraints (2008)

We have investigated the site-specific folding kinetics of a photoswitchable cross-linked alpha-helical peptide by using single (13)C = (18)O isotope labeling together with time-resolved IR spectroscopy. We observe that the folding times differ from site to site by a factor of eight at low temperatures (6 degrees C), whereas at high temperatures (45 degrees C), the spread is considerably smaller. The trivial sum of the site signals coincides with the overall folding signal of the unlabeled peptide, and different sites fold in a noncooperative manner. Moreover, one of the sites exhibits a decrease of hydrogen bonding upon folding, implying that the unfolded state at low temperature is not unstructured. Molecular dynamics simulations at low temperature reveal a stretched-exponential behavior which originates from parallel folding routes that start from a kinetically partitioned unfolded ensemble. Different metastable structures (i.e., traps) in the unfolded ensemble have a different ratio of loop and helical content. Control simulations of the peptide at high temperature, as well as without the cross-linker at low temperature, show faster and simpler (i.e., single-exponential) folding kinetics. The experimental and simulation results together provide strong evidence that the rate-limiting step in formation of a structurally constrained alpha-helix is the escape from heterogeneous traps rather than the nucleation rate. This conclusion has important implications for an alpha-helical segment within a protein, rather than an isolated alpha-helix, because the cross-linker is a structural constraint similar to those present during the folding of a globular protein.
Improving online incremental speaker adaptation with eigen feature space MLLR (2009)

This paper investigates an eigen feature space maximum likelihood linear regression (fMLLR) scheme to improve the performance of online speaker adaptation in automatic speech recognition systems. In this stochastic-approximation-like framework, the traditional incremental fMLLR estimation is considered as a slowly changing mean of the eigen fMLLR. It helps the adaptation when only a limited amount of data is available at the beginning of the conversation. The scheme is shown to be able to balance the transformation estimation given the data and yields reasonable improvements for online systems.
Pegylated-liposomal doxorubicin versus doxorubicin, bleomycin, and vincristine in the treatment of AIDS-related Kaposi's sarcoma: results of a randomized phase III clinical trial. (1998)

PURPOSE Kaposi's sarcoma (KS), the most common neoplasm in patients with AIDS, is a significant clinical problem for which current therapies are frequently unsatisfactory. We conducted a randomized phase III clinical trial to compare the efficacy and toxicities of a new form of therapy, pegylated-liposomal doxorubicin, with standard combination chemotherapy in patients with advanced AIDS-related KS (AIDS-KS). PATIENTS AND METHODS Two hundred fifty-eight patients with advanced AIDS-KS were randomly assigned to receive either pegylated-liposomal doxorubicin (20 mg/m2) or the combination of doxorubicin (20 mg/m2), bleomycin (10 mg/m2) and vincristine (1 mg) (ABV) every 14 days for six cycles. Standard response criteria, toxicity criteria, and predefined indicators of clinical benefit were examined to evaluate outcomes. RESULTS Among 133 patients randomized to receive pegylated-liposomal doxorubicin, one achieved a complete clinical response and 60 achieved a partial response for an overall response rate of 45.9% (95% confidence interval [CI], 37% to 54%). Among 125 patients randomized to receive ABV, 31 achieved a partial response (24.8%; 95% confidence interval [CI], 17% to 32%). This difference was statistically significant (P &lt; .001). In addition to objective responses, prospectively defined clinical benefits and toxicity outcomes also favored pegylated-liposomal doxorubicin. CONCLUSION Pegylated-liposomal doxorubicin is more effective and less toxic than the standard combination chemotherapy regimen ABV for treatment of AIDS-KS.
A Four Amino Acid Deletion Polymorphism in the Third Intracellular Loop of the Human α2C-Adrenergic Receptor Confers Impaired Coupling to Multiple Effectors (2000)

The alpha(2)-adrenergic receptors (alpha(2)ARs) play a critical role in modulating neurotransmitter release in the central and peripheral sympathetic nervous systems. A polymorphism of the alpha(2)AR subtype localized to human chromosome 4 (the pharmacologic alpha(2C)AR subtype) within an intracellular domain has been identified in normal individuals. The polymorphism (denoted Del322-325) is because of an in-frame 12-nucleic acid deletion encoding a receptor lacking Gly-Ala-Gly-Pro in the third intracellular loop. To delineate the functional consequences of this structural alteration, Chinese hamster ovary cells were permanently transfected with constructs encoding wild-type human alpha(2C)AR and the polymorphic receptor. The Del322-325 variant had decreased high affinity agonist binding (K(H) = 7.3 +/- 0.95 versus 3.7 +/- 0.43 nm; %R(H) = 31 +/- 4 versus 49 +/- 4) compared with wild-type indicating impaired formation of the agonist-receptor-G protein complex. The polymorphic receptor displayed markedly depressed epinephrine-promoted coupling to G(i), inhibiting adenylyl cyclase by 10 +/- 4.3% compared with 73 +/- 2.4% for wild-type alpha(2C)AR. This also was so for the endogenous ligand norepinephrine and full and partial synthetic agonists. Depressed agonist-promoted coupling to the stimulation of MAP kinase ( approximately 71% impaired) and inositol phosphate production ( approximately 60% impaired) was also found with the polymorphic receptor. The Del322-325 receptor was approximately 10 times more frequent in African-Americans compared with Caucasians (allele frequencies 0.381 versus 0.040). Given this significant loss of function phenotype in several signal transduction cascades and the skewed ethnic prevalence, Del322-325 represents a pharmacoethnogenetic locus and may also be the basis for interindividual variation in cardiovascular or central nervous system pathophysiology.
Positioning accuracy when tracking UMTS mobiles in delay and angular dispersive channels (2002)

A potentiality of the location problem in wireless networks that has not been explored enough is the mobility of the user equipment. The use of a Kalman tracker helps in reducing the variability of the positioning by optimally averaging in time. We compare the location accuracy obtained in comparison to the least-square solution with no tracking. The performance comparison is done in a UMTS scenario, using uplink and downlink measurements in realistic propagation conditions.
Protein sequencing by tandem mass spectrometry. (1986)

Methodology for determining amino acid sequences of proteins by tandem mass spectrometry is described. The approach involves enzymatic and/or chemical degradation of the protein to a collection of peptides which are then fractionated by high-performance liquid chromatography. Each fraction, containing as many as 10-15 peptides, is then analyzed directly, without further purification, by a combination of liquid secondary-ion/collision-activated dissociation mass spectrometry on a multianalyzer instrument. Interpretation of collision-activated dissociation mass spectra is described, and results are presented from a study of soluble peptides produced by treatment of apolipoprotein B with cyanogen bromide and trypsin.
A two-step adhesion cascade for T cell/endothelial cell interactions under flow conditions. (1994)

Neutrophil adherence to endothelial cells (ECs) under conditions of flow occurs in successive steps, including selectin-dependent primary adhesion and CD18-dependent secondary adhesion. We used a parallel-plate flow chamber to assess the steps in T cell adherence in vitro. On monolayers of L cells transfected with the EC adhesion molecules E-selectin, vascular cell adhesion molecule-1 (VCAM-1), or intercellular adhesion molecule-1 (ICAM-1), E-selectin was capable of mediating only primary adhesion, ICAM-1 was capable of mediating only secondary adhesion, and VCAM-1 was capable of mediating both primary and secondary adhesion. Studies using human umbilical vein EC monolayers stimulated for 24 h with IL-1 also revealed distinct primary and secondary steps in T cell adhesion under flow, and the secondary adhesion was inhibited > 90% by blocking both VCAM-1/alpha 4 beta 1 integrin and ICAM-1/CD18 integrin pathways. However, the primary adhesion under conditions of flow could not be attributed to any of the mechanisms known to support adhesion of leukocytes to ECs. Alone, this pathway was shown to mediate T cell rolling and was a necessary prerequisite for engagement of the two integrin pathways in this system. Thus, T cell adherence to 24-h IL-1-stimulated human umbilical vein ECs at venular wall shear stresses involves at least two successive steps, with clear molecular distinctions from the mechanisms accounting for neutrophil/EC adhesion.
A variant of Chlamydia trachomatis with deletion in cryptic plasmid: implications for use of PCR diagnostic tests (2006)

A new variant of Chlamydia trachomatis with a deletion in the cryptic plasmid has been detected in Sweden, following an unexpected 25% decrease in
Collagen fibrillogenesis in vitro: interaction of types I and V collagen regulates fibril diameter (1990)

The small-diameter fibrils of the chick corneal stroma are heterotypic, composed of both collagen types I and V. This tissue has a high concentration of type V collagen relative to other type I-containing tissues with larger-diameter fibrils, suggesting that heterotypic interactions may have a regulatory role in the control of fibril diameter. The interactions of collagen types I and V were studied using an in vitro self-assembly system. Collagens were purified from lathyritic chick embryos in the presence of protease inhibitors. The type V collagen preparations contained higher molecular weight forms of the alpha 1(V) and alpha 2(V) chains constituting 60-70% of the total. Rotary-shadow electron micrographs showed a persistence of a small, pepsin-sensitive terminal region in an amount consistent with that seen by electrophoresis. In vitro, this purified type V collagen formed thin fibrils with no apparent periodicity, while type I collagen fibrils had a broad distribution of large diameters. However, when type I collagen was mixed with increasing amounts of type V collagen a progressive and significant decrease in both the mean fibril diameter and the variance was observed for D periodic fibrils. The amino-terminal domain of the type V collagen molecule was required for this regulatory effect and in its absence little diameter reducing activity was observed. Electron microscopy using collagen type-specific monoclonal antibodies demonstrated that the fibrils formed were heterotypic, containing both collagen types I and V. These data indicate that the interaction of type V with type I collagen is one mechanism modulating fibril diameter and is at least partially responsible for the regulation of collagen fibril formation.
Central role of liver in anticancer and radioprotective activities of Toll-like receptor 5 agonist (2013)

Vertebrate Toll-like receptor 5 (TLR5) recognizes bacterial flagellin proteins and activates innate immune responses to motile bacteria. In addition, activation of TLR5 signaling can inhibit growth of TLR5-expressing tumors and protect normal tissues from radiation and ischemia-reperfusion injuries. To understand the mechanisms behind these phenomena at the organismal level, we assessed nuclear factor kappa B (NF-κB) activation (indicative of TLR5 signaling) in tissues and cells of mice treated with CBLB502, a pharmacologically optimized flagellin derivative. This identified the liver and gastrointestinal tract as primary CBLB502 target organs. In particular, liver hepatocytes were the main cell type directly and specifically responding to systemic administration of CBLB502 but not to that of the TLR4 agonist LPS. To assess CBLB502 impact on other pathways, we created multireporter mice with hepatocytes transduced in vivo with reporters for 46 inducible transcription factor families and found that along with NF-κB, CBLB502 strongly activated STAT3-, phenobarbital-responsive enhancer module (PREM), and activator protein 1 (AP-1-) -driven pathways. Livers of CBLB502-treated mice displayed induction of numerous immunomodulatory factors and massive recruitment of various types of immune cells. This led to inhibition of growth of liver metastases of multiple tumors regardless of their TLR5 status. The changed liver microenvironment was not, however, hepatotoxic, because CBLB502 induced resistance to Fas-mediated apoptosis in normal liver cells. Temporary occlusion of liver blood circulation prevented CBLB502 from protecting hematopoietic progenitors in lethally irradiated mice, indicating involvement of a factor secreted by responding liver cells. These results define the liver as the key mediator of TLR5-dependent effects in vivo and suggest clinical applications for TLR5 agonists as hepatoprotective and antimetastatic agents.
Effect of Cross-Linking Reagents for Hyaluronic Acid Hydrogel Dermal Fillers on Tissue Augmentation and Regeneration (2010)

A novel, biocompatible, and nontoxic dermal filler using hyaluronic acid (HA) hydrogels was successfully developed for tissue augmentation applications. Instead of using highly reactive cross-linkers such as divinyl sulfone (DVS) for Hylaform, 1,4-butanediol diglycidyl ether (BDDE) for Restylane, and 1,2,7,8-diepoxyoctane (DEO) for Puragen, HA hydrogels were prepared by direct amide bond formation between the carboxyl groups of HA and hexamethylenediamine (HMDA) with an optimized carboxyl group modification for effective tissue augmentation. The HA-HMDA hydrogels could be prepared within 5 min by the addition of HMDA to HA solution activated with 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide (EDC) and 1-hydroxybenzotriazole monohydrate (HOBt). Five kinds of samples, a normal control, a negative control, a positive control of Restylane, adipic acid dihydrazide grafted HA (HA-ADH) hydrogels, and HA-HMDA hydrogels, were subcutaneously injected to wrinkled model mice. According to the image analysis on dorsal skin augmentation, the HA-HMDA hydrogels exhibited the best tissue augmentation effect being stable longer than 3 months. Furthermore, histological analyses after hematoxylin-eosin (H&E) and Masson's trichrome staining revealed the excellent biocompatibility and safety of HA-HMDA hydrogels. The dermal thickness and the dermal collagen density in wrinkled mice after treatment with HA-HMDA hydrogels for 12 weeks were comparable to those of normal mice. Compared with HA-DVS hydrogels and Restylane, the excellent tissue augmentation by HA-HMDA hydrogels might be ascribed to the biocompatible residues of amine groups in the cross-linker of HMDA. The HA-HMDA hydrogels will be investigated further as a novel dermal filler for clinical applications.
Price-taker bidding strategy under price uncertainty (2002)

This paper provides a framework to obtain the optimal bidding strategy of a price-taker producer. An appropriate forecasting tool is used to estimate the probability density functions of next-day hourly market-clearing prices. This probabilistic information is used to formulate a self-scheduling profit maximization problem that is solved taking advantage of its particular structure. The solution of this problem allows deriving a simple yet informed bidding rule. Results from a realistic case study are discussed in detail.
Anandamide, an endogenous cannabimimetic eicosanoid, binds to the cloned human cannabinoid receptor and stimulates receptor-mediated signal transduction. (1993)

Arachidonylethanolamide (anandamide), a candidate endogenous cannabinoid ligand, has recently been isolated from porcine brain and displayed cannabinoid-like binding activity to synaptosomal membrane preparations and mimicked cannabinoid-induced inhibition of the twitch response in isolated murine vas deferens. In this study, anandamide and several congeners were evaluated as cannabinoid agonists by examining their ability to bind to the cloned cannabinoid receptor, inhibit forskolin-stimulated cAMP accumulation, inhibit N-type calcium channels, and stimulate one or more functional second messenger responses. Synthetic anandamide, and all but one congener, competed for [3H]CP55,940 binding to plasma membranes prepared from L cells expressing the rat cannabinoid receptor. The ability of anandamide to activate receptor-mediated signal transduction was evaluated in Chinese hamster ovary (CHO) cells expressing the human cannabinoid receptor (HCR, termed CHO-HCR cells) and compared to control CHO cells expressing the muscarinic m5 receptor (CHOm5 cells). Anandamide inhibited forskolin-stimulated cAMP accumulation in CHO-HCR cells, but not in CHOm5 cells, and this response was blocked with pertussis toxin. N-type calcium channels were inhibited by anandamide and several active congeners in N18 neuroblastoma cells. Anandamide stimulated arachidonic acid and intracellular calcium release in both CHOm5 and CHO-HCR cells and had no effect on the release of inositol phosphates or phosphatidylethanol, generated after activation of phospholipase C and D, respectively. Anandamide appears to exhibit the essential criteria required to be classified as a cannabinoid/anandamide receptor agonist and shares similar nonreceptor effects on arachidonic acid and intracellular calcium release as other cannabinoid agonists.
Facioscapulohumeral Dystrophy: Incomplete Suppression of a Retrotransposed Gene (2010)

Each unit of the D4Z4 macrosatellite repeat contains a retrotransposed gene encoding the DUX4 double-homeobox transcription factor. Facioscapulohumeral dystrophy (FSHD) is caused by deletion of a subset of the D4Z4 units in the subtelomeric region of chromosome 4. Although it has been reported that the deletion of D4Z4 units induces the pathological expression of DUX4 mRNA, the association of DUX4 mRNA expression with FSHD has not been rigorously investigated, nor has any human tissue been identified that normally expresses DUX4 mRNA or protein. We show that FSHD muscle expresses a different splice form of DUX4 mRNA compared to control muscle. Control muscle produces low amounts of a splice form of DUX4 encoding only the amino-terminal portion of DUX4. FSHD muscle produces low amounts of a DUX4 mRNA that encodes the full-length DUX4 protein. The low abundance of full-length DUX4 mRNA in FSHD muscle cells represents a small subset of nuclei producing a relatively high abundance of DUX4 mRNA and protein. In contrast to control skeletal muscle and most other somatic tissues, full-length DUX4 transcript and protein is expressed at relatively abundant levels in human testis, most likely in the germ-line cells. Induced pluripotent (iPS) cells also express full-length DUX4 and differentiation of control iPS cells to embryoid bodies suppresses expression of full-length DUX4, whereas expression of full-length DUX4 persists in differentiated FSHD iPS cells. Together, these findings indicate that full-length DUX4 is normally expressed at specific developmental stages and is suppressed in most somatic tissues. The contraction of the D4Z4 repeat in FSHD results in a less efficient suppression of the full-length DUX4 mRNA in skeletal muscle cells. Therefore, FSHD represents the first human disease to be associated with the incomplete developmental silencing of a retrogene array normally expressed early in development.