gebhart/patrepeval huggingface dataset:
Personalized Management of Chronic Obstructive Pulmonary Disease via Transcriptomic Profiling of the Airway and Lung (2013)

Chronic obstructive pulmonary disease (COPD) is a clinically heterogeneous disease composed of variable degrees of airflow obstruction, emphysematous destruction, and small airway wall thickening. The natural history of this disease, although generally characterized by continued decline in lung function, is also highly variable. Novel transcriptomic approaches to study the airway and lung tissue in COPD hold the potential to improve our understanding of the molecular mechanisms underlying this heterogeneity and identify molecular subtypes of disease that have similar clinical manifestations. This new understanding can be leveraged to develop targeted COPD therapies and ultimately personalize treatment of COPD based on each patient's specific molecular subphenotype.
用空气喷射水力旋流器（ASH）回收氰化物 (2006)

可移动的空气喷射水力旋流器系统（ASH）被用来从金提取厂废水中连续汽提和回收氰化物（即AVR法）.ASH单元更大的作用在于它可作为吸收装置.在一次通过ASH时,HCN气体的吸收率超过99%,在排放的废气中的HCN的浓度低于10·10^-6,这可提供一个比较安全的工作环境.一次通过ASH时,由亨利定律常数控制的汽提效率大于40%.
Rab GDP dissociation inhibitor as a general regulator for the membrane association of rab proteins. (1993)

Rab proteins comprise a family of small GTPases that serve a regulatory role in membrane traffic. These proteins are in part cytosolic and in part associated with the membranes of specific exocytic and endocytic organelles. Smg p25A/rab3A GDI, a cytosolic protein which inhibits the dissociation of GDP from smg p25A/rab3A, Sec4p, and rab11, has also been found to prevent association of rab3A with the membrane. In this study, we have used Madin-Darby canine kidney cells permeabilized with the bacterial toxin streptolysin O to test the general activity of rab3A GDI in modulating the membrane association of various small GTP-binding proteins. Rab3A GDP dissociation inhibitor (GDI) removed from the membrane all rab proteins we have tested and inhibited the membrane binding of in vitro translated rab proteins. However, rab3A GDI had a limited effect on the membrane association of a mutant rab5 protein which contained a farnesylated cysteine motif. Finally, we found that, although rab3A GDI resides primarily in the cytosol, it is also associated with compartments of the exocytic and endocytic pathways. Since rab3A GDI can modulate the membrane association of various rab proteins, we propose to rename it rab GDI.
A point mutation in the seventh hydrophobic domain of the alpha 2 adrenergic receptor increases its affinity for a family of beta receptor antagonists (1991)

Previous studies have shown that differences in subtype-specific ligand binding between alpha 2 and beta 2 adrenergic receptors are largely determined by the seventh hydrophobic domain. Here, we report that a single amino acid substitution (Phe412----Asn) in the seventh hydrophobic domain of the alpha 2 adrenergic receptor reduces affinity for the alpha 2 antagonist yohimbine by 350-fold and increases affinity for beta antagonist alprenolol by 3000-fold. The affinity of this mutant receptor alpha 2F----N for several alpha and beta adrenergic receptor agonists and antagonists was determined. Beta adrenergic receptor antagonists containing an oxygen atom linking the amino side chain with the aromatic ring bound to alpha 2F----N with high affinity, while the beta receptor antagonist sotalol, which lacks this oxygen, bound with low affinity. These data suggest that the Asn residue is involved in conferring specificity for binding to a specific class of beta receptor antagonists.
A two level mode decision algorithm for H.264 high profile intra encoding (2012)

A two level mode decision algorithm considering edge information for H.264 high profile intra encoding is proposed to reduce the computational complexity. In level one mode decision, the edge information is used to decide the appropriate intra coding block size according to the observations that a smooth macroblock usually chooses the large intra coding block size, and that a complex macroblock usually chooses the small one. In level two mode decision, we use the correlation between adjacent blocks to decide the appropriate prediction modes. The proposed method achieves 34%~59% reduction of computational complexity when compared to JM14 and the PSNR only drops 0.09 db in average.
The NK-1.1(-) mouse: a model to study differentiation of murine NK cells. (1986)

The NK-1.1(-) mouse was constructed by weekly injections of monoclonal anti-NK-1.1 antibody from birth through adulthood. Spleen cells from these mice have decreased NK-1.1+ cells and null (Thy-1- and B220-) cells. Their splenic NK activity to YAC targets was low and was not enhanced by IFN-alpha or IFN-beta. Bone marrow (BM) of these NK-1.1(-) mice have normal precursors to NK cells: 1) NK activity could be generated from NK-1.1(-) BM cells cultured in rIL 2 for 5 to 6 days. These cultured BM cells expressed Qa-5, Thy-1, AsGm-1, and NK-1.1 antigens. The precursor cells of these BM cytotoxic cells are NK-1.1-; 2) transfer of BM cells from the NK-1.1(-) mice reconstituted the NK activity of irradiated, NK-depleted recipients. Lymphokine-activated killer cells could also be generated from spleens of these NK-1.1(-) mice. Therefore, the NK-1.1(-) mice were specifically depleted of mature cytotoxic NK cells, but not the NK-1.1- precursors of NK cells. This mouse model is valuable to study ontogeny and physiologic relevance of NK cells.
Measuring Tissue-Based Biomarkers by Immunochromatography Coupled with Reverse-Phase Lysate Microarray (2006)

I-RPM is a promising technology for quantitative grading of tissue biomarkers; however, antigen-dependent correlations are noted.
Feature Selection Using Principal Component Analysis (2010)

Principal component analysis (PCA) has been widely applied in the area of computer science. It is well-known that PCA is a popular transform method and the transform result is not directly related to a sole feature component of the original sample. However, in this paper, we try to apply principal components analysis (PCA) to feature selection. The proposed method well addresses the feature selection issue, from a viewpoint of numerical analysis. The analysis clearly shows that PCA has the potential to perform feature selection and is able to select a number of important individuals from all the feature components. Our method assumes that different feature components of original samples have different effects on feature extraction result and exploits the eigenvectors of the covariance matrix of PCA to evaluate the significance of each feature component of the original sample. When evaluating the significance of the feature components, the proposed method takes a number of eigenvectors into account. Then it uses a reasonable scheme to perform feature selection. The devised algorithm is not only subject to the nature of PCA but also computationally efficient. The experimental results on face recognition show that when the proposed method is able to greatly reduce the dimensionality of the original samples, it also does not bring the decrease in the recognition accuracy.
Electrical method for detection of endothelial cell shape change in real time: assessment of endothelial barrier function. (1992)

We have developed an electrical method to study endothelial cell shape changes in real time in order to examine the mechanisms of alterations in the endothelial barrier function. Endothelial shape changes were quantified by using a monolayer of endothelial cells grown on a small (10(-3) cm2) evaporated gold electrode and measuring the changes in electrical impedance. Bovine pulmonary microvessel endothelial cells and bovine pulmonary artery endothelial cells were used to study the effects of alpha-thrombin on cell-shape dynamics by the impedance measurement. alpha-Thrombin produced a dose-dependent decrease in impedance that occurred within 0.5 min in both cell types, indicative of retraction of endothelial cells and widening of interendothelial junctions because of "rounding up" of the cells. The alpha-thrombin-induced decrease in impedance persisted for approximately 2 hr, after which the value recovered to basal levels. Pretreatment of endothelial cells with the protein kinase C inhibitor, calphostin C, or with 8-bromoadenosine 3',5'-cyclic monophosphate prevented the decreased impedance, suggesting that the endothelial cell change is modulated by activation of second-messenger pathways. The alpha-thrombin-induced decrease in impedance was in agreement with the previously observed increases in transendothelial albumin permeability and evidence of formation of intercellular gaps after alpha-thrombin challenge. The impedance measurement may be a valuable in vitro method for the assessment of mechanisms of decreased endothelial barrier function occurring with inflammatory mediators. Since the rapidly occurring changes in endothelial cell shape in response to mediators such as thrombin are mediated activation of second-messenger pathways, the ability to monitor endothelial cell dynamics in real time may provide insights into the signal-transduction events mediating the increased endothelial permeability.
Hepatitis B virus DNA in Kaposi sarcoma. (1983)

DNA extracted from Kaposi sarcoma biopsies was analyzed for the presence of hepatitis B viral (HBV) DNA sequences by Southern blot hybridization. The probes used were (i) molecularly cloned subgenomic fragments of HBV DNA and (ii) HBV DNA extracted from Dane particles that included DNA sequences that encode hepatitis B surface antigen and core antigen. The limited study reported here demonstrates that HBV DNA exists mainly in an episomal state in the Kaposi sarcoma tissue and that these DNA forms are different from those found in hepatitis B virion. The presence of various DNA forms suggests that HBV DNA is engaged in DNA replication, which implies that the tissue is infected with HBV.
Cellobiose Dehydrogenase and a Copper-Dependent Polysaccharide Monooxygenase Potentiate Cellulose Degradation by Neurospora crassa (2011)

The high cost of enzymes for saccharification of lignocellulosic biomass is a major barrier to the production of second generation biofuels. Using a combination of genetic and biochemical techniques, we report that filamentous fungi use oxidative enzymes to cleave glycosidic bonds in cellulose. Deletion of cdh-1, the gene encoding the major cellobiose dehydrogenase of Neurospora crassa, reduced cellulase activity substantially, and addition of purified cellobiose dehydrogenases from M. thermophila to the Δcdh-1 strain resulted in a 1.6- to 2.0-fold stimulation in cellulase activity. Addition of cellobiose dehydrogenase to a mixture of purified cellulases showed no stimulatory effect. We show that cellobiose dehydrogenase enhances cellulose degradation by coupling the oxidation of cellobiose to the reductive activation of copper-dependent polysaccharide monooxygenases (PMOs) that catalyze the insertion of oxygen into C-H bonds adjacent to the glycosidic linkage. Three of these PMOs were characterized and shown to have different regiospecifities resulting in oxidized products modified at either the reducing or nonreducing end of a glucan chain. In contrast to previous models where oxidative enzymes were thought to produce reactive oxygen species that randomly attacked the substrate, the data here support a direct, enzyme-catalyzed oxidation of cellulose. Cellobiose dehydrogenases and proteins related to the polysaccharide monooxygenases described here are found throughout both ascomycete and basidiomycete fungi, suggesting that this model for oxidative cellulose degradation may be widespread throughout the fungal kingdom. When added to mixtures of cellulases, these proteins enhance cellulose saccharification, suggesting that they could be used to reduce the cost of biofuel production.
A multi-objective genetic local search algorithm and its application to flowshop scheduling (1998)

We propose a hybrid algorithm for finding a set of nondominated solutions of a multi objective optimization problem. In the proposed algorithm, a local search procedure is applied to each solution (i.e., each individual) generated by genetic operations. Our algorithm uses a weighted sum of multiple objectives as a fitness function. The fitness function is utilized when a pair of parent solutions are selected for generating a new solution by crossover and mutation operations. A local search procedure is applied to the new solution to maximize its fitness value. One characteristic feature of our algorithm is to randomly specify weight values whenever a pair of parent solutions are selected. That is, each selection (i.e., the selection of two parent solutions) is performed by a different weight vector. Another characteristic feature of our algorithm is not to examine all neighborhood solutions of a current solution in the local search procedure. Only a small number of neighborhood solutions are examined to prevent the local search procedure from spending almost all available computation time in our algorithm. High performance of our algorithm is demonstrated by applying it to multi objective flowshop scheduling problems.
Exotendons for assistance of human locomotion (2003)

It is concluded that unpowered passive elastic devices can substantially reduce the muscle forces and the metabolic energy needed for walking, without requiring a change in movement. When optimally designed, such devices may allow independent locomotion in patients with large deficits in muscle function.
Small dsRNAs induce transcriptional activation in human cells (2006)

Recent studies have shown that small noncoding RNAs, such as microRNAs and siRNAs, regulate gene expression at multiple levels including chromatin architecture, transcription, RNA editing, RNA stability, and translation. Each form of RNA-dependent regulation has been generally found to silence homologous sequences and collectively called RNAi. To further study the regulatory role of small RNAs at the transcriptional level, we designed and synthesized 21-nt dsRNAs targeting selected promoter regions of human genes E-cadherin, p21(WAF1/CIP1) (p21), and VEGF. Surprisingly, transfection of these dsRNAs into human cell lines caused long-lasting and sequence-specific induction of targeted genes. dsRNA mutation studies reveal that the 5' end of the antisense strand, or "seed" sequence, is critical for activity. Mechanistically, the dsRNA-induced gene activation requires the Argonaute 2 (Ago2) protein and is associated with a loss of lysine-9 methylation on histone 3 at dsRNA-target sites. In conclusion, we have identified several dsRNAs that activate gene expression by targeting noncoding regulatory regions in gene promoters. These findings reveal a more diverse role for small RNA molecules in the regulation of gene expression than previously recognized and identify a potential therapeutic use for dsRNA in targeted gene activation.
The role of the COMT Val158Met polymorphism in the phenotypic expression of obsessive‐compulsive disorder (2009)

Obsessive-Compulsive Disorder (OCD) is characterized by the presence of obsessions and compulsions, and shows considerable phenotypic variability. Family and twin studies have indicated a genetic component in the etiology of OCD, and the catechol-O-methyl transferase (COMT) gene is an important candidate gene for OCD. This study investigates the influence of the functional COMT Val158Met polymorphism on the phenotypic expression of OCD, using an item-level factor-analytic approach in a large sample. The COMT Val158Met variant was genotyped in 373 patients and 462 controls. It was tested whether there was an association between the COMT Val158Met polymorphism and OCD or dimensional phenotypes such as YBOCS severity score, age of onset of obsessive-compulsive symptoms and six symptom dimensions recently found in a large item-level factor-analytic study [Katerberg et al., submitted]. We further investigated possible sex-specific associations between the COMT Val158Met polymorphism and OCD or dimensional phenotypes. There was a trend for an association of the COMT 158Met allele with OCD in males, and an interaction between the COMT Val158Met genotype and sex on the somatic and sensory phenomena symptom dimension, with females showing lower scores. In conclusion, a dimensional approach seems fruitful in detecting genes of importance for OCD.
The Pyrrolobenzodiazepine Dimer SJG-136 Forms Sequence-Dependent Intrastrand DNA Cross-Links and Monoalkylated Adducts in Addition to Interstrand Cross-Links (2009)

SJG-136 (1) is a sequence-selective DNA-interactive agent that is about to enter phase II clinical trials. Using a HPLC/MS-based methodology developed to evaluate the binding of DNA-interactive agents to oligonucleotides of varying length and sequence, we have demonstrated that, in addition to the previously known interstrand cross-link at Pu-GATC-Py sequences, 1 can form a longer interstrand cross-link at Pu-GAATC-Py sequences, an intrastrand cross-link at both shorter Pu-GATG-Py and longer Pu-GAATG-Py sequences, and, in addition, monoalkylated adducts at suitable PBD binding sites where neither intra- or interstrand cross-links are feasible because of the unavailability of two appropriately positioned guanines. Crucially, we have demonstrated a preference for the extended intrastrand cross-link with Pu-GAATG-Py, which forms more rapidly than the other cross-links (rank order: Pu-GAATG-Py > Pu-GATC-Py >> Pu-GATG-Py and Pu-GAATC-Py). However, thermal denaturation studies suggest that the originally reported Pu-GATC-Py interstrand cross-link is more stable, consistent with the covalent joining of both strands of the duplex and a lower overall distortion of the helix according to modeling studies. These observations impact on the proposed mechanism of action of SJG-136 (1) both in vitro and in vivo, the repair of its adducts and mechanism of resistance in cells, and potentially on the type of pharmacodynamic assay used in clinical trials.
Selecting informative genes using a multiobjective evolutionary algorithm (2003)

Recent advances in biotechnology offer the ability to measure the levels of expression of thousands of genes in parallel. Analysis of such data can provide understanding and insight into gene function and regulatory mechanisms, and open a new opportunity to tissue classification. Since the first work of Golub et al. (1999, 2000) in cancer classification based on gene expression profile rather than on morphological appearance of the tumor, there have been several endeavors in this direction. However, these tasks are made more difficult due to the noisy nature of array data and the overwhelming number of genes. In this paper, we propose a solution to the problem of gene selection using a multiobjective evolutionary algorithm (MOEA). Results from experiments with benchmarking data sets are also given.
A Highly Selective and Sensitive Fluorescent Chemosensor for Hg2+ in Neutral Buffer Aqueous Solution (2004)

A selective and sensitive fluorescent chemosensor for Hg2+, which was composed of two aminonaphthalimide fluorophores and a receptor of 2,6-bis(aminomethyl)pyridine, was synthesized through the reaction of 2,6-bis(chloromethyl)pyridine and N-[2-(2-hydroxyethoxy)ethyl]-4-piperazino-1,8-naphthalimide. The chemosensor showed an about 17-fold increase in fluorescence quantum yield upon addition of 1 equiv of Hg2+ in neutral buffer aqueous solution, and the other common metal ions did not notably disturb the detection of Hg2+.
Group I Metabotropic Glutamate Receptor Signalling and its Implication in Neurological Disease (2010)

Stimulation of Group I metabotropic glutamate receptors (mGluR1 and mGluR5) leads to activation of a wide variety of signalling pathways. mGluRs couple to Gα(q/)₁₁ proteins, activating phospholipase Cβ1 resulting in both diacylglycerol and inositol-1,4,5-triphosphate formation followed by the activation of protein kinase C. In addition, mGluR activation can lead to modulation of a number of ion channels, such as different types of calcium and potassium channels. Group I mGluRs can also activate other downstream protein kinases, such as ERK1/2 and AKT, which are implicated in cellular growth, differentiation, and survival. Moreover, Group I mGluRs interact with a variety of different proteins that are important for the regulation of synaptic signalling, such as Homer and PDZ domain containing proteins, such as Tamalin. A role for mGluR1/5 in a number of disease states has also been proposed. As mGluR1/5 signal transduction is complex and involves multiple partners, a better understanding of alterations in mGluR signalling in brain disorders will be required in order to discern the molecular and cellular basis of these pathologies. This review will highlight recent findings concerning mGluR signaling alterations in brain pathologies, such as stroke, fragile X syndrome, Alzheimer's disease, Parkinson's disease, Huntington's disease, epilepsy, and drug addiction.
Pearls and pitfalls in experimental in vivo models of migraine: Dural trigeminovascular nociception (2013)

This review will summarize the history of the development of models of dural trigeminovascular nociception, including intravital microscopy and laser Doppler flowmetry at the level of the vasculature, and electrophysiology and Fos techniques used to observe neuronal activation at the trigeminal nucleus caudalis. It will also describe some of pitfalls of these assays and developments for the future.
Development in culture of the chick embryo from fertilized ovum to hatching (1990)

An experiment was carried out to investigate whether thick albumen is essential for the normal development of the chick embryo. Fertilized ova recovered from the oviducts of hens were cultured in vitro and transferred to recipient eggshells with (method A) or without (method B) replacement of the thick albumen by thin albumen. Embryos from freshly laid eggs were transferred to recipient eggshells with (method C) or without (method E) replacement of the thick albumen by thin albumen or with replacement of the thick albumen by thin albumen diluted with solution of salts (method D). Embryos were then incubated until hatching. The rates of hatching of the cultured embryos were 34.4%, 16.2%, 50.0%, 6.9-26.7%, and 47.5% for methods A, B, C, D, and E, respectively. Thus the rate of hatching of cultured fertilized ova was increased by replacement of the thick albumen by thin albumen at the blastoderm stage. Chicks obtained by method A reached maturity and produced viable offspring, and this technique provides an improved method for the culture of fertilized ova to hatching.
Combined Bezafibrate and Medroxyprogesterone Acetate: Potential Novel Therapy for Acute Myeloid Leukaemia (2009)

Collectively our data demonstrate that B/M treatment of AML cells elevated ROS and delivered the anti-neoplastic actions of 15d-PGJ(2). These observations provide the mechanistic rationale for the redeployment of B/M in elderly and relapsed AML.