gebhart/patrepeval huggingface dataset:
Sequences Homologous to 5′ Splice Sites Are Required for the Inhibitory Activity of Papillomavirus Late 3′ Untranslated Regions (1994)

Expression of bovine papillomavirus type 1 (BPV-1) late genes is limited to terminally differentiated keratinocytes in an infected epithelium. We have previously shown that although the BPV-1 late polyadenylation site is functional in nonpermissive cells, a 53-nucleotide (nt) fragment of the late 3' untranslated region acts posttranscriptionally to reduce polyadenylated cytoplasmic RNA levels. This 53-nt fragment does not appear to function by destabilizing polyadenylated cytoplasmic RNA (P. A. Furth and C. C. Baker, J. Virol. 65:5806-5812, 1991). In this study, we used site-directed mutagenesis and deletion analysis to demonstrate that the sequence AAG/GUAAGU, which is identical to the consensus 5' splice site sequence, was both necessary and sufficient for the inhibitory activity of the 53-nt fragment. Furthermore, base pairing between the 5' end of the U1 small nuclear RNA and this 5' splice site-like sequence was shown to be required for the inhibitory activity in vivo. We have also further mapped the human papillomavirus type 16 late 3' inhibitory element (I. M. Kennedy, J. K. Haddow, and J. B. Clements, J. Virol. 65:2093-2097, 1991) to a 51-nt region containing four overlapping sequence motifs with partial homology to 5' splice sites. Mutation of each of these motifs demonstrated that only one of these motifs is required for the inhibitory activity. However, the presence of the other motifs may contribute to the full inhibitory activity of the element. No BPV-1 or human papillomavirus type 16 mRNAs which are spliced by using the potential 5' splice sites present in the viral late 3' untranslated regions have been identified. This suggests that the primary function of these 5' splice site-like sequences is the inhibition of late gene expression. The most likely mechanism of action of these elements is reduction of polyadenylation efficiency, perhaps through interference with 3'-terminal exon definition.
Ultralarge complexes of PF4 and heparin are central to the pathogenesis of heparin-induced thrombocytopenia (2004)

Abstract Heparin-induced thrombocytopenia and thrombosis (HITT) is a severe complication of heparin therapy caused by antibodies to complexes between unfractionated heparin (UFH) and platelet factor 4 (PF4) that form over a narrow molar range of reactants and initiate antibody-induced platelet activation. We observed that UFH and tetrameric PF4 formed ultralarge (&amp;gt; 670 kDa) complexes (ULCs) only over a narrow molar range with an optimal ratio of PF4 to heparin of approximately 1:1. These ULCs were stable and visible by electron microscopy, but they could be dissociated into smaller complexes upon addition of heparin. ULCs formed inefficiently when PF4 was incubated with low-molecular-weight heparin, and none formed with the pentasaccharide fondaparinux sodium. In addition, mutation studies showed that formation of ULCs depended on the presence of PF4 tetramers. The ULCs were more reactive as determined by their capacity to bind to a HITT-like monoclonal antibody and showed greater capacity to promote platelet activation in an antibody- and FcγRIIA-dependent manner than were the smaller complexes. The capacity of PF4 to form ULCs composed of multiple PF4 tetramers arrayed in a lattice with several molecules of UFH may play a fundamental role in autoantibody formation, antibody-dependent platelet activation, and the propensity for thrombosis in patients with HITT.
Direct Immobilization of Glutamate Dehydrogenase on Optical Fiber Probes for Ultrasensitive Glutamate Detection (1999)

Ultrasensitive glutamate monitoring is important in a variety of areas of biochemical analysis. We have developed a glutamate sensor with micrometer to submicrometer diameter. Glutamate dehydrogenase (GDH) has been directly immobilized onto an optical fiber probe surface through covalent binding mechanisms. An optical fiber surface is initially activated by silanization, which adds amine groups (NH2) to the surface. We then affix functional groups CHO to the optical fiber surface by employing a bifunctional cross-linking agent, glutaraldehyde. The amino acids of GDH molecules (or other biomolecules) readily attach to these free CHO groups on the fiber surface. Optimal immobilization of GDH occurred between 20 and 25 h in the enzyme solution. The immobilized GDH enzyme molecules on the fiber surface have shown high enzymatic activity. The sensor is able to detect its substrate, glutamate, by monitoring the fluorescence of NADH, a product of the reaction between NAD+ and glutamate. The concentration detection limit of the sensor is 0.22 μM glutamate, and the absolute mass detection limit is 3 amol. Response times of the sensors are fast due to the direct GDH molecule immobilization. The glutamate sensor is selective and stable. A submicrometer glutamate sensor has been tested. Our glutamate probes could be applied to the study of subcellular level neurophysiological responses.
Salicylic acid attenuates virulence in endovascular infections by targeting global regulatory pathways in Staphylococcus aureus (2003)

Aspirin has been previously shown to reduce the in vivo virulence of Staphylococcus aureus in experimental endocarditis, through antiplatelet and antimicrobial mechanisms. In the present study, salicylic acid, the major in vivo metabolite of aspirin, mitigated two important virulence phenotypes in both clinical and laboratory S. aureus strains: α-hemolysin secretion and fibronectin binding in vitro. In addition, salicylic acid reduced the expression of the α-hemolysin gene promoter, hla, and the fibronectin gene promoter, fnbA. Transcriptional analysis, fluorometry, and flow cytometry revealed evidence of salicylic acid–mediated activation of the stress-response gene sigB. Expression of the sigB-repressible global regulon sarA and the global regulon agr were also mitigated by salicylic acid, corresponding to the reduced expression of the hla and fnbA genes in vitro. Studies in experimental endocarditis confirmed the key roles of both sarA and sigB in mediating the antistaphylococcal effects of salicylic acid in vivo. Therefore, aspirin has the potential to be an adjuvant therapeutic agent against endovascular infections that result from S. aureus, by downmodulating key staphylococcal global regulons and structural genes in vivo, thus abrogating relevant virulence phenotypes.
Overcoming Resistance to Natural Killer Cell Based Immunotherapies for Solid Tumors (2019)

Despite advances in the diagnostic and therapeutic modalities, the prognosis of several solid tumor malignancies remains poor. Different factors associated with solid tumors including a varied genetic signature, complex molecular signaling pathways, defective cross talk between the tumor cells and immune cells, hypoxic and immunosuppressive effects of tumor microenvironment result in a treatment resistant and metastatic phenotype. Over the past several years, immunotherapy has emerged as an attractive therapeutic option against multiple malignancies. The unique ability of natural killer (NK) cells to target cancer cells without antigen specificity makes them an ideal candidate for use against solid tumors. However, the outcomes of adoptive NK cell infusions into patients with solid tumors have been disappointing. Extensive studies have been done to investigate different strategies to improve the NK cell function, trafficking and tumor targeting. Use of cytokines and cytokine analogs has been well described and utilized to enhance the proliferation, stimulation and persistence of NK cells. Other techniques like blocking the human leukocyte antigen-killer cell receptors (KIR) interactions with anti-KIR monoclonal antibodies, preventing CD16 receptor shedding, increasing the expression of activating NK cell receptors like NKG2D, and use of immunocytokines and immune checkpoint inhibitors can enhance NK cell mediated cytotoxicity. Using genetically modified NK cells with chimeric antigen receptors and bispecific and trispecific NK cell engagers, NK cells can be effectively redirected to the tumor cells improving their cytotoxic potential. In this review, we have described these strategies and highlighted the need to further optimize these strategies to improve the clinical outcome of NK cell based immunotherapy against solid tumors.
Pathophysiology of Upper Airway Closure During Sleep (1991)

While the upper airway normally remains patent during quiet breathing in wakefulness and sleep, patients with obstructive sleep apnea have repetitive periods of upper airway closure during sleep. The upper airway closures usually occur at various sites in the pharynx. The patency of the potentially collapsible pharynx during inspiration depends on the balance between subatmospheric pressure in the pharyngeal airway and airway dilating forces generated by pharyngeal muscles. The pressure required to collapse the upper airway in the absence of upper airway muscle activity, ie, closing pressure, is normally subatmospheric. In obstructive sleep apnea, positive pressures are required to maintain patency of the passive upper airway. The pathophysiologic mechanisms underlying upper airway closures during sleep form the basis for the treatment of obstructive sleep apnea. In general, these treatment modalities attempt to (1) raise the pharyngeal pressure above the closing pressure, (2) decrease the closing pressure, or (3) increase upper airway muscle activity.
Bacterial Proliferation in Platelet Products Stored at Room Temperature (1971)

A theoretical objection to ambient-temperature platelet storage is the possibility of proliferation of micro-organisms introduced into the system during phlebotomy or component preparation. After gram-negative septicemia followed platelet infusion in two patients with cancer, a study was begun to determine the frequency of contamination in platelets stored at 25°C. Culture of 2188 U of platelets, pooled in groups of eight after storage, revealed bacteria in more than 20 per cent of pools; the minimal frequency of contamination in individual units was calculated to be 2.4 per cent. Bacteria including species of corynebacterium, staphylococcus, micrococcus, streptococcus, sarcina, bacillus, herellea, pseudomonas and flavobacterium were recovered; Enterobacter (Aerobacter) cloacae was isolated seven times and caused both septicemias. Twenty-five of 143 transfusions were later shown to have contained micro-organisms. The frequency of bacterial recovery progressively increased with increasing storage time. Such platelets should be used with caution, particularly in patients lacking normal host-defense mechanisms.
What Is the Role for the Circumferential Margin in the Modern Treatment of Rectal Cancer? (2008)

CRM involvement is one of the key factors in rectal cancer treatment.
Signal Enhancement in HPLC/Microcoil NMR Using Automated Column Trapping (2006)

A new HPLC NMR system is described that performs analytical separation, preconcentration, and NMR spectroscopy in rapid succession. The central component of our method is the online preconcentration sequence that improves the match between postcolumn analyte peak volume and microcoil NMR detection volume. Separated samples are collected on to a C18 guard column with a mobile phase composed of 90% D2O/10% acetonitrile-D3 and back-flushed to the NMR microcoil probe with 90% acetonitrile-D3/10% D2O. To assess the performance of our unit, we separated a standard mixture of 1 mM ibuprofen, naproxen, and phenylbutazone using a commercially available C18 analytical column. The S/N measurements from the NMR acquisitions indicated that we achieved signal enhancement factors up to 10.4 (+/-1.2)-fold. Furthermore, we observed that preconcentration factors increased as the injected amount of analyte decreased. The highest concentration enrichment of 14.7 (+/-2.2)-fold was attained injecting 100 microL of solution of 0.2 mM (approximately 4 microg) ibuprofen.
ChemInform Abstract: The Thermal Behavior of Sulfates. Part 16. The Chemical Vapor Transport of Ga2(SO4)3 with Cl2 and HCl. Experimental Results and Calculations. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Phospholipase A2 engineering: Design, synthesis, and expression of a gene for bovine (pro)phospholipase A2 (1989)

A gene coding for the (pro)phospholipase A2 (PLA2) from bovine pancreas has been designed, synthesized, and expressed in Escherichia coli. The gene was designed with a variety of restriction sites that will facilitate future mutagenesis studies. Codons occurring frequently in prokaryotic systems were chosen whenever possible. The total gene spans 404 base pairs and was divided into 33 oligonucleotides. The gene was constructed in two halves of 224 and 180 base pairs from the oligonucleotides by the shotgun ligation technique using pBSM13- as the cloning vehicle. The two fragments were then ligated and cloned into pBSM13- to complete the gene. The (pro)PLA2 gene was then verified by restriction site mapping and dideoxy sequencing. The gene was expressed to high levels from a high copy number vector, designated as pJPN, derived from the E. coli secretion vector pIN-III-ompA3. Although the protein failed to be excreted and was in the form of insoluble inclusion body, active PLA2 could be obtained by renaturation of the inclusion body pellet followed by tryptic activation, which removes the signal sequence and the pro-peptide of proPLA2. The PLA2 thus obtained reacted with the antisera raised against the natural PLA2 purified from bovine pancreas, and the specific activity of the expressed PLA2 was identical to that of the natural PLA2. The shotgun ligation and synthetic gene approaches are simple and inexpensive and can be adapted to express most of the enzymes in the phospholipase A2 family.
Polymer Light-Emitting Electrochemical Cells:  In Situ Formation of a Light-Emitting p−n Junction (1996)

Solid-state polymer light-emitting electrochemical cells have been fabricated using thin films of blends of poly(1,4-phenylenevinylene) and poly(ethylene oxide) complexed with lithium trifluoromethanesulfonate. The cells contain three layers: the polymer film (as the emissive layer) and indium-tin oxide and aluminum films as the two contact electrodes. When externally biased, the conjugated polymers are p-doped and n-doped on opposite sides of the polymer layer, and a light-emitting p-n junction is formed in between. The admixed polymer electrolyte provides the counterions and the ionic conductivity necessary for doping. The p-n junction is dynamic and reversible, with an internal built-in potential close to the band gap of the redox-active conjugated polymer (2.4 eV for PPV). Green light emitted from the p-n junction was observed with a turn-on voltage of about 2.4 V. The devices reached 8 cd/m(2) at 3 V and 100 cd/m(2) at 4 V, with an external quantum efficiency of 0.3-0.4% photons/electron. The response speed of these cells was around 1 s, depending on the diffusion of ions. Once the light-emitting junction had been formed, the subsequent operation had fast response (microsecond scale or faster) and was no longer diffusion-controlled.
Multi-fold MIL Training for Weakly Supervised Object Localization (2014)

Object category localization is a challenging problem in computer vision. Standard supervised training requires bounding box annotations of object instances. This time-consuming annotation process is sidestepped in weakly supervised learning. In this case, the supervised information is restricted to binary labels that indicate the absence/presence of object instances in the image, without their locations. We follow a multiple-instance learning approach that iteratively trains the detector and infers the object locations in the positive training images. Our main contribution is a multi-fold multiple instance learning procedure, which prevents training from prematurely locking onto erroneous object locations. This procedure is particularly important when high-dimensional representations, such as the Fisher vectors, are used. We present a detailed experimental evaluation using the PASCAL VOC 2007 dataset. Compared to state-of-the-art weakly supervised detectors, our approach better localizes objects in the training images, which translates into improved detection performance.
The Peterson Reaction (1984)

La reaction Peterson, l'equivalent silicie de la reaction Wittig, est utilisee pour preparer des alcenes et une grande variete d'alcenes substitues et fonctionnalises
Improving dynamic tomography, through Maximum a posteriori estimation (2014)

Direct study of pore-scale fluid displacements, and other dynamic (i.e. time-dependent) processes is not feasible with conventional X-ray micro computed tomography (&mu;CT). We have previously verified that a priori knowledge of the underlying physics can be used to conduct high-resolution, time-resolved imaging of continuous, complex processes, at existing X-ray &mu;CT facilities. In this paper we present a maximum a posteriori (MAP) model of the dynamic tomography problem, which allows us to easily adapt and generalise our previous dynamic &mu;CT approach to systems with more complex underlying physics.
EgMYB2, a new transcriptional activator from Eucalyptus xylem, regulates secondary cell wall formation and lignin biosynthesis (2005)

Summary EgMYB2, a member of a new subgroup of the R2R3 MYB family of transcription factors, was cloned from a library consisting of RNA from differentiating Eucalyptus xylem. EgMYB2 maps to a unique locus on the Eucalyptus grandis linkage map and co-localizes with a quantitative trait locus (QTL) for lignin content. Recombinant EgMYB2 protein was able to bind specifically the cis-regulatory regions of the promoters of two lignin biosynthetic genes, cinnamoyl-coenzyme A reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD), which contain MYB consensus binding sites. EgMYB2 was also able to regulate their transcription in both transient and stable expression assays. Transgenic tobacco plants over-expressing EgMYB2 displayed phenotypic changes relative to wild-type plants, among which were a dramatic increase in secondary cell wall thickness, and an alteration of the lignin profiles. Transcript abundance of genes encoding enzymes specific to lignin biosynthesis was increased to varying extents according to the position of individual genes in the pathway, whereas core phenylpropanoid genes were not significantly affected. Together these results suggest a role for EgMYB2 in the co-ordinated control of genes belonging to the monolignol-specific pathway, and therefore in the biosynthesis of lignin and the regulation of secondary cell wall formation.
Resilient Quantum Computation (1998)

Practical realization of quantum computers will require overcoming decoherence and operational errors, which lead to problems that are more severe than in classical computation. It is shown that arbitrarily accurate quantum computation is possible provided that the error per operation is below a threshold value.
Teaching practice and reform of Physical Chemistry of Inorganic Materials (2010)

Course of Physical Chemistry of Inorganic Materials starts from the basic common rules of the science and engin-eering of inorganic materials.This course clarifies the common laws among the composition,the structure and the properties of inorganic materials using the basic principles and methods of materials science.This course is the core course of the major of inorganic materials science and engineering in materials field.Well construction of the course has significant importance on the construction of the subject and the fostering of people with special ability.Continuous education reform on the course is the necessary direction to adapt with the current new development of the subject of inorganic materials.Based on more than decades educational practice experience,this paper discussed the education practice and reform of Physical Chemistry of Inorganic Materials course.
Hybrid polymer/lipid vesicles: state of the art and future perspectives (2013)

Hybrid vesicles resulting from the combined self-assembly of both amphiphilic copolymers and lipids have attracted particular interest from chemists and (bio)physicists over the last five years. Such assemblies may be viewed as an advanced vesicular structure compared to their liposome and polymersome forerunners as the best characteristics from the two different systems can be integrated in a new, single vesicle. To afford such a design, the different parameters controlling both self-assembly and membrane structure must be tuned. This highlight aims to present a comprehensive overview of the fundamental aspects related to these structures, and discuss emerging developments and future applications in this field of research.
Human Tumor-Released Microvesicles Promote the Differentiation of Myeloid Cells with Transforming Growth Factor-β–Mediated Suppressive Activity on T Lymphocytes (2006)

Human tumors constitutively release endosome-derived microvesicles, transporting a broad array of biologically active molecules with potential modulatory effects on different immune cells. Here, we report the first evidence that tumor-released microvesicles alter myeloid cell function by impairing monocyte differentiation into dendritic cells and promoting the generation of a myeloid immunosuppressive cell subset. CD14+ monocytes isolated from healthy donors and differentiated with interleukin (IL)-4 and granulocyte macrophage colony-stimulating factor in the presence of tumor-derived microvesicles turned into HLA-DR(-/low) cells, retaining CD14 expression and failing to up-regulate costimulatory molecules, such as CD80 and CD86. These phenotypic changes were paralleled by a significant release of different cytokines, including IL-6, tumor necrosis factor-alpha, and transforming growth factor-beta (TGF-beta), and a dose-dependent suppressive activity on activated T-cell-proliferation and cytolytic functions, which could be reversed by anti-TGF-beta-neutralizing antibodies. Microvesicles isolated from plasma of advanced melanoma patients, but not from healthy donors, mediated comparable effects on CD14+ monocytes, skewing their differentiation toward CD14+HLA-DR-/low cells with TGF-beta-mediated suppressive activity on T-cell-functions. Interestingly, a subset of TGF-beta-secreting CD14+HLA-DR- cells mediating suppressive activity on T lymphocytes was found to be significantly expanded in peripheral blood of melanoma patients compared with healthy donors. These data suggest the development in cancer patients of an immunosuppressive circuit by which tumors promote the generation of suppressive myeloid cells through the release of circulating microvesicles and without the need for cell-to-cell contact. Therapeutic interventions on the crucial steps of this pathway may contribute to restore tumor/immune system interactions favoring T-cell-mediated control of tumor growth in cancer patients.