gebhart/patrepeval huggingface dataset:
Cell migration through biomimetic hydrogel scaffolds (2003)

Cell migration is an essential step during processes such as embryonic development, wound healing, angiogenesis, and cancer metastasis. Migration is a complex integration of cellular adhesion to its substratum, reorganization of the cytoskeleton, proteolysis and remodeling of surrounding extracellular matrix (ECM), and activation and regulation of chemical signaling by growth factors and other mitogenic cues. These cooperative mechanisms enable a cell to move to its target to perform its function, whether to repair injured tissue, fight infections, or build new blood vessels.\nThe main objective of this research is to study mechanisms of cell migration within a biomimetic hydrogel system. Because of the complexity of the ECM, studying cell migration in ECM derivatives or even single components of the ECM can make it difficult to decipher the importance of each factor involved. In addition, the ECM imposes a spatial barrier to cells. For migration, the cells must not only interact with matrix adhesive ligands for force generation, but also develop strategies to overcome biomechanical resistance imposed by the matrix. Thus, the biomimetic hydrogel system developed can provide the mechanical support, adhesion ligands, degradation sequences, and other signals, so that a cell can migrate. This system will provide tight control over many experimental parameters and minimize nonspecific cell-material interactions. Hence the aim of the hydrogel system is to stimulate an active interaction between the synthetic polymer and the biological environment.\nThe biomimetic hydrogels are photopolymerizable hydrogels based on acrylated derivates of polyethylene glycol. This material contains proteolytically degradable peptide sequences, targeted for specific enzymes involved in cell migration, in the polymer backbone. Cell adhesion peptides are also grafted into the hydrogels during photopolymerization to promote interaction with specific cell surface receptors. Other bioactive signals, such as growth factors, can also be grafted into the network during photopolymerization. Thus a single hydrogel material can contain several different proteolytically sensitive segments, many cell adhesion ligands and various growth factors, allowing for one to mimic many properties of the ECM. This hydrogel system is used to assess cell migration mechanisms by controlling the identity and availability of bioactive signals presented to the cells and studying their affects.
Site-directed recombination via bifunctional PNA–DNA conjugates (2002)

Site-specific DNA binding molecules offer the potential for genetic manipulation of mammalian cells. Peptide nucleic acids (PNAs) are a DNA mimic in which the purine and pyrimidine bases are attached to a polyamide backbone. PNAs bind with high affinity to single-stranded DNA via Watson-Crick base pairing and can form triple helices via Hoogsteen binding to DNAPNA duplexes. Dimeric bis-PNAs capable of both strand invasion and triplex formation can form clamp structures on target DNAs. As a strategy to promote site-directed recombination, a bis-PNA was coupled to a 40-nt donor DNA fragment homologous to an adjacent region in the target gene. The PNA-DNA conjugate was found to mediate site-directed recombination with a plasmid substrate in human cell-free extracts, resulting in correction of a mutation in a reporter gene at a frequency at least 60-fold above background. Induced site-specific recombination was also seen when the bis-PNA and the donor DNA were co-mixed without covalent linkage. In addition, the bis-PNA and the bis-PNA-DNA conjugate were found to induce DNA repair specifically in the target plasmid. Both the PNA-induced recombination and the PNA-induced repair were found to be dependent on the nucleotide excision repair factor, XPA (xeroderma pigmentosum complementation group A protein). These results suggest that the formation of a PNA clamp on duplex DNA creates a helical distortion that strongly provokes DNA repair and thereby sensitizes the target site to recombination. The ability to promote recombination in a site-directed manner using PNA-DNA conjugates may provide a useful strategy to achieve targeted correction of defective genes.
Adaptive critic designs (1997)

We discuss a variety of adaptive critic designs (ACDs) for neurocontrol. These are suitable for learning in noisy, nonlinear, and nonstationary environments. They have common roots as generalizations of dynamic programming for neural reinforcement learning approaches. Our discussion of these origins leads to an explanation of three design families: heuristic dynamic programming, dual heuristic programming, and globalized dual heuristic programming (GDHP). The main emphasis is on DHP and GDHP as advanced ACDs. We suggest two new modifications of the original GDHP design that are currently the only working implementations of GDHP. They promise to be useful for many engineering applications in the areas of optimization and optimal control. Based on one of these modifications, we present a unified approach to all ACDs. This leads to a generalized training procedure for ACDs.
The primary structure of the variable region of an immunoglobin IV light-chain amyloid-fibril protein (AL GIL) (1988)

The primary structure of the variable region of an amyloid-fibril protein GIL of immunoglobulin lambda-light-chain origin (AL) was determined. The AL protein obtained from the fibrils in the spleen of a 54-year-old man with primary systemic amyloidosis could be assigned to subgroup IV of the lambda variable-region sequence. About 50% of the protein was found to be truncated in the N-terminus and lacked the first six amino acid residues. The polypeptides consisted of about 146 amino acid residues and contained traces of carbohydrate. An acceptor site for N-glycosylation was found in positions 90-93, but no glycopeptide could be isolated. Comparison of the amino acid sequence of AL protein GIL with that of the only Bence-Jones protein of subgroup IV previously studied revealed a sequence homology of 89%. A similar comparison made with other AL proteins gave sequence homologies below 66%.
Protective Role of CXC Receptor 4/CXC Ligand 12 Unveils the Importance of Neutrophils in Atherosclerosis (2007)

The CXC ligand (CXCL)12/CXC receptor (CXCR)4 chemokine-receptor axis controls hematopoiesis, organ development, and angiogenesis, but its role in the inflammatory pathogenesis of atherosclerosis is unknown. Here we show that interference with Cxcl12/Cxcr4 by a small-molecule antagonist, genetic Cxcr4 deficiency, or lentiviral transduction with Cxcr4 degrakine in bone marrow chimeras aggravated diet-induced atherosclerosis in apolipoprotein E-deficient (Apoe-/-) or LDL receptor-deficient (Ldlr-/-) mice. Chronic blockade of Cxcr4 caused leukocytosis and an expansion of neutrophils and increased neutrophil content in plaques, associated with apoptosis and a proinflammatory phenotype. Whereas circulating neutrophils were recruited to atherosclerotic lesions, depletion of neutrophils reduced plaque formation and prevented its exacerbation after blocking Cxcr4. Disrupting Cxcl12/Cxcr4 thus promotes lesion formation through deranged neutrophil homeostasis, indicating that Cxcl12/Cxcr4 controls the important contribution of neutrophils to atherogenesis in mice.
Self-blinding citizen science to explore psychedelic microdosing (2021)

Microdosing is the practice of regularly using low doses of psychedelic drugs. Anecdotal reports suggest that microdosing enhances well-being and cognition; however, such accounts are potentially biased by the placebo effect. This study used a 'self-blinding' citizen science initiative, where participants were given online instructions on how to incorporate placebo control into their microdosing routine without clinical supervision. The study was completed by 191 participants, making it the largest placebo-controlled trial on psychedelics to-date. All psychological outcomes improved significantly from baseline to after the 4 weeks long dose period for the microdose group; however, the placebo group also improved and no significant between-groups differences were observed. Acute (emotional state, drug intensity, mood, energy, and creativity) and post-acute (anxiety) scales showed small, but significant microdose vs. placebo differences; however, these results can be explained by participants breaking blind. The findings suggest that anecdotal benefits of microdosing can be explained by the placebo effect.
A Self-Optimizing Control System for Hard Rock Percussive Drilling (2008)

The derivation and application of a self-optimizing control system for percussive drilling of hard rock is presented. The control system superimposes an oscillating force signal onto the drill feed force and demodulates the signal from the drill rotational torque. The resultant demodulated signal is then used to control the drill, allowing real-time maximization of penetration rate, minimum hole deviation, and measurement of rock characteristics regardless of drilling conditions. The control system allows the drill to adapt to changing rock conditions. Testing has proven the control to be reliable and to increase drilling efficiency.
Propagating surface plasmons on nanoporous gold (2012)

Nanoporous gold films are prepared using a dealloying method and form a sponge type bicontinuous network. As the structure sizes are below 50&#xA0;nm, the material forms an effective medium with a negative dielectric constant for near infrared light. The dispersion relation of the propagating surface plasmons on the air/nanoporous gold interface is determined from reflection measurements in the Kretschmann configuration. A characteristic red-shift by ca. 0.85&#xA0;eV compared to surface plasmons on solid gold layers is observed. The results are compared with calculated dispersion relations applying the Bruggeman effective medium theory for the nanoporous gold films.
Crystal Structure of Human Antibody 2909 Reveals Conserved Features of Quaternary Structure-Specific Antibodies That Potently Neutralize HIV-1 (2010)

Monoclonal antibody 2909 belongs to a class of potently neutralizing antibodies that recognize quaternary epitopes on HIV-1. Some members of this class, such as 2909, are strain specific, while others, such as antibody PG16, are broadly neutralizing; all, however, recognize a region on the gp120 envelope glycoprotein that includes two loops (V2 and V3) and forms appropriately only in the oligomeric HIV-1 spike (gp120(3)/gp41(3)). Here we present the crystal structure of 2909 and report structure-function analysis with antibody chimeras composed of 2909 and other members of this antibody class. The 2909 structure was dominated by a heavy-chain third-complementarity-determining region (CDR H3) of 21 residues, which comprised 36% of the combining surface and formed a β-hairpin club extending ∼20 Å beyond the rest of the antibody. Sequence analysis and mass spectrometry identified sites of tyrosine sulfation at the middle and top of CDR H3; substitutions with phenylalanine either ablated (middle substitution) or substantially diminished (top substitution) neutralization. Chimeric antibodies composed of heavy and light chains, exchanged between 2909 and other members of the class, indicated a substantial lack of complementation. Comparison of 2909 to PG16 (which is tyrosine sulfated and the only other member of the class for which a structure has previously been reported) showed that both utilize protruding, anionic CDR H3s for recognition. Thus, despite some diversity, members of this class share structural and functional similarities, with conserved features of the CDR H3 subdomain likely reflecting prevalent solutions by the human immune system for recognition of a quaternary site of HIV-1 vulnerability.
Actividad antimicrobiana de extractos orgánicos aislados de Aplysina fistularis (Demospongiae: Aplysinidae) (2000)

Organic extracts of the sponge Aplysina fistularis (Pallas 1766) were tested for antimicrobial activity against Gram positive bacteria (Staphylococcus aureus) and Gram negative bacteria (Escherichia coli, Klebsiel­ la pneumoniae and Pseudomonas aeruginosa). The minimal inhibitory concentration (MI C) and toxic activity of extract were determined. Susceptibility trials of organic fractions obtained by V LC: Hexane, EtOAc and CHCl, showed that EtOAc fraction has antibacterial activity against E. coli, while CHCl, fraction inhibited E. coli and S. aureus growth. The later refractioning of EtOAc fraction and the biodirected assays showed that fractions FI2 and F 13 of EtOAclHex and EtOAc F 14 were bioactive against Gram positive and Gram negative bacteria. Only EtOAc/MeOH Sf2 from subfractionig of EtOAc FI4 produced inhibition for E. coli and S. aureus. In Sf2 EtOAc/MeOH , MIC was moderate for S. aureus (MIC > 256 g/ml). F4 CHCI3IMeOH produced a high inhibition in S. aureus (MIC = 0.125 g/ml) and for E. coli (MIC > 16 g/ml). F10 CHCl3/MeOH showed a moderate activi­ty against S. aureus(MIC > 128 g/ml) and low activity against E. coli (MIC = 512 g/ml). F10 CHCl3/MeOH did no present toxic activity against Artemia salina. The fractious F4 CHCl3/MeOH and Sf2 EtOAc/MeOH were toxic for this organism when the concentration was higher than 100 μglml. LC50 in both cases was 548.4 and 243.4 μg/ml respectively. Secondary metabolites of medium polarity obtained from A.fistularis have a wide spec­trum of anti bacterial activity. Toxicity analysis suggests that only F10 CHCl3/MeOH has potential as an antimi­crobial agent for clinical use.
Color image processing [basics and special issue overview] (2005)

Humans have always seen the world in color but only recently have we been able to generate vast quantities of color images with such ease. In the last three decades, we have seen a rapid and enormous transition from grayscale images to color ones. Today, we are exposed to color images on a daily basis in print, photographs, television, computer displays, and cinema movies, where color now plays a vital role in the advertising and dissemination of information throughout the world. Color monitors, printers, and copiers now dominate the office and home environments, with color becoming increasingly cheaper and easier to generate and reproduce. Color demands have soared in the marketplace and are projected to do so for years to come. With this rapid progression, color and multispectral properties of images are becoming increasingly crucial to the field of image processing, often extending and/or replacing previously known grayscale techniques. We have seen the birth of color algorithms that range from direct extensions of grayscale ones, where images are treated as three monochrome separations, to more sophisticated approaches that exploit the correlations among the color bands, yielding more accurate results. Hence, it is becoming increasingly necessary for the signal processing community to understand the fundamental differences between color and grayscale imaging. There are more than a few extensions of concepts and perceptions that must be understood in order to produce successful research and products in the color world.
Anions of protected cyanohydrins as acyl carbanion equivalents and their use in a new synthesis of ketones (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAnions of protected cyanohydrins as acyl carbanion equivalents and their use in a new synthesis of ketonesGilbert Stork and Luis MaldonadoCite this: J. Am. Chem. Soc. 1971, 93, 20, 5286–5287Publication Date (Print):October 1, 1971Publication History Published online1 May 2002Published inissue 1 October 1971https://pubs.acs.org/doi/10.1021/ja00749a069https://doi.org/10.1021/ja00749a069research-articleACS PublicationsRequest reuse permissionsArticle Views1289Altmetric-Citations162LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Gallium(III) corroles (2004)

Gallium(III) corroles are closed-shell analogs of zinc(II) porphyrins. These intensely fluorescent molecules can be modified readily to tune their solubility and photophysical properties. A water-soluble gallium corrole has been synthesized and investigated in depth; it binds tightly to human serum albumin, opening the possibility of using corroles as therapeutic agents as well as probes of biological structures.
RSK-B, a Novel Ribosomal S6 Kinase Family Member, Is a CREB Kinase under Dominant Control of p38α Mitogen-activated Protein Kinase (p38αMAPK) (1998)

A novel ribosomal S6 kinase (RSK) family member, RSK-B, was identified in a p38alphaMAPK-baited intracellular interaction screen. RSK-B presents two catalytic domains typical for the RSK family. The protein kinase C-like N-terminal and the calcium/calmodulin kinase-like C-terminal domains both contain conserved ATP-binding and activation consensus sequences. RSK-B is a p38alphaMAPK substrate, and activated by p38alphaMAPK and, more weakly, by ERK1. RSK-B phosphorylates the cAMP response element-binding protein (CREB) and c-Fos peptides. In intracellular assays, RSK-B drives cAMP response element- and AP1-dependent reporter expression. RSK-B locates to the cell nucleus and co-translocates p38alphaMAPK. In conclusion, RSK-B is a novel CREB kinase under dominant p38alphaMAPK control, also phosphorylating additional substrates.
In Vitro Processing of Human Tumor Necrosis Factor-α (1995)

Tumor necrosis factor (TNF)-alpha is initially synthesized as a membrane-bound, cell-associated 26-kDa protein that is further cleaved to yield the soluble 17-kDa form. By using a radiolabeled in vitro translated TNF-alpha precursor we detected a serine proteinase processing activity present in crude membrane preparations of monocytic cells able to generate a 17-kDa active protein. A similar processing pattern was obtained using purified neutral serine proteinase proteinase-3 (PR-3). Moreover, while a secretory leukocyte proteinase inhibitor (a natural serine anti-proteinase) did not affect the in vitro TNF-alpha processing, IgG preparations containing high titers of anti-PR-3 autoantibodies completely blocked this activity. The NH2-terminal sequencing of the reaction products obtained with either membrane preparations or PR-3 showed that cleavage occurs in both cases between Val77 and Arg78. These results together with cellular expression and localization of PR-3 suggest a potential role for this enzyme as an accessory TNF-alpha processing enzyme.
NSDHL, an enzyme involved in cholesterol biosynthesis, traffics through the Golgi and accumulates on ER membranes and on the surface of lipid droplets (2003)

NSDHL, for NAD(P)H steroid dehydrogenase-like, encodes a sterol dehydrogenase or decarboxylase involved in the sequential removal of two C-4 methyl groups in post-squalene cholesterol biosynthesis. Mutations in this gene are associated with human CHILD syndrome (congenital hemidysplasia with ichthyosiform nevus and limb defects), an X-linked, male lethal disorder, as well as the mouse mutations bare patches and striated. In the present study, we have investigated the subcellular localization of tagged proteins encoded by wild-type and selected mutant murine Nsdhl alleles using confocal microscopy. In addition to an ER localization commonly found for enzymes of post-squalene cholesterol biosynthesis, we have identified a novel association of NSDHL with lipid droplets, which are endoplasmic reticulum (ER)-derived cytoplasmic structures that contain a neutral lipid core. We further demonstrate that trafficking through the Golgi is necessary for ER membrane localization of the protein and propose a model for the association of NSDHL with lipid droplets. The dual localization of NSDHL within ER membranes and on the surface of lipid droplets may provide another mechanism for regulation of the levels and sites of accumulation of intracellular cholesterol.
Optimal Induction of Hepatitis C Virus Envelope-Specific Immunity by Bicistronic Plasmid DNA Inoculation with the Granulocyte-Macrophage Colony-Stimulating Factor Gene (1998)

In this study, we have constructed various DNA vaccine vectors that carried hepatitis C virus (HCV) envelope genes without and with the granulocyte-macrophage colony-stimulating factor (GM-CSF) gene in several different ways. In Buffalo rats that received plasmids carrying the HCV envelope genes, which encode envelope proteins E1 and E2, both antibody and lymphoproliferative responses against these proteins were induced. These responses were greatly enhanced by the codelivery of the GM-CSF gene. In particular, inoculation with a bicistronic plasmid that independently expressed the GM-CSF gene and the envelope genes in the same construct generated the highest antibody titers and significantly increased lymphoproliferative responses against these proteins. Moreover, strong antibody responses to homologous and heterologous hypervariable region 1 peptides were elicited in the immunized rats.
Chimerism and cure: hematologic and pathologic correction of murine sickle cell disease (2003)

Bone marrow transplantation (BMT) is the only curative therapy for sickle cell disease (SCD). However, the morbidity and mortality related to pretransplantation myeloablative chemotherapy often outweighs the morbidity of SCD itself, thus severely limiting the number of patients eligible for transplantation. Although nonmyeloablative transplantation is expected to reduce the risk of BMT, it will likely result in mixed-chimerism rather than complete replacement with donor stem cells. Clinical application of nonmyeloablative transplantation thus requires knowledge of the effect of mixed chimerism on SCD pathophysiology. We have, therefore, created a panel of transplanted SCD mice that received transplants displaying an array of red blood cell (RBC) and white blood cell (WBC) chimerism. A significant enrichment of RBC over WBC chimerism occurred in these mice, because of the dramatic survival advantage of donor over sickle RBCs in the peripheral blood. Increasing levels of RBC chimerism provided progressive correction of hematologic and pathologic abnormalities. However, sickle bone marrow and splenic hematopoiesis was not corrected until peripheral blood sickle RBCs were fully replaced with donor RBCs. These results have important and unexpected implications for nonmyeloablative BMT for SCD. As the critical hematopoietic organs were not corrected without full RBC replacement, 100% peripheral blood RBC chimerism becomes the most important benchmark for cure after nonmyeloablative BMT.
Viral Respiratory Infections in the Institutionalized Elderly: Clinical and Epidemiologic Findings (1992)

Viruses are an important cause of acute respiratory infections in the institutionalized elderly during the winter months.