gebhart/patrepeval huggingface dataset:
A simple, low overhead data compression algorithm for converting lossy processes to lossless (1993)

In this thesis, a hybrid lossless compression model is tested which employs a combination of both a lossy compression method and one or more lossless image compression methods to produce an overall lossless image compression. The hybrid model decomposes the original image into a browse and a residual image. The hybrid model is tested and evaluated using various combinations of lossy and lossless image compression methods. The lossy compression method used in the model is JPEG (Joint Photographic Experts (Group) . The lossless compression methods used are Huffman, Arithmetic, LZW, lossless JPEG. and Diagonal coding. The compression results achieved using the hybrid compression model are compared to the compression achieved using the corresponding direct lossless compression. Additionally, the hybrid model is evaluated as to the advantages that the decomposition of the image into browse and residual images provide to the user.
The source of toxicity in CTAB and CTAB-stabilized gold nanorods (2013)

The use of nanoparticles for sensing, cell imaging, and therapy has seen an extraordinary increase, in recent years. But, one of the issues commonly encountered when using nanoparticles in bioapplications is their toxicity. Cetyltrimethylammonium bromide (CTAB) is a common surfactant used in nanoparticle synthesis. One of CTAB’s uses is to direct the growth and stabilize the shape of certain types of colloidal metallic nanoparticles, for example gold nanorods. The main drawback is that these metallic nanoparticles cannot be used in applications with cells because of their cytotoxicity. Despite many conjectures, it is not yet clear what the origin of this cytotoxicity is. Here we explore some possible reasons and mechanisms that could be accounted for to explain this cytotoxicity. Due to its molecular structure, CTAB is difficult to detect in solution using conventional methods. In this thesis work, electrospray ionization mass spectrometry (ESI-MS) was used as a means to detect CTAB in solution and in vitro and to study the source of its toxicity. From the data collected, we have evidence that there are two active mechanisms: 1) CTAB’s interaction with the phospholipid bilayer that destabilizes the cell membrane leading to cell death, and 2) the catalytic action of one of CTAB’s dissociation products, the CTA+ cation, which might cause the quenching of the enzyme ATPsynthase and thus lead to energy deprivation and death of the cell. Our results also indicate that it is this second mechanism, which depends on the concentration of CTA+, to be the most lethal. We have found that nanorods can be successfully formed with high concentrations of Br-, which is non-toxic, with limited amounts of CTAB, because CTA+ might be playing a more important role only for stability purposes. This will reduce the amount of CTAB in solution to below cytotoxic values. We have also found out that once the nanorods are formed using CTAB as the stabilizing surfactant, low concentrations of an iodine/iodide mixture are able to modify, post-fabrication, the aspect ratio of the nanorods and thus their optical properties. This discovery might lead to the development of a new category of gold nanorods, with decreased toxicity and tunable morphology that would be ideal for applications in conjunction to cells.
Angiogenic factors stimulate mast-cell migration (1995)

Mast cells accumulate at sites of angiogenesis. The factor(s) that control mast-cell recruitment at these sites have yet to be defined. We sought to determine if angiogenic factors result in mast-cell chemotaxis. In this study, we observed that platelet-derived growth factor-AB (PDGF-AB), vascular endothelial cell growth factor (VEGF), and basic fibroblast growth factor (bFGF) each cause directed migration of murine mast cells at picomolar concentrations, with a typical bell-shaped dose-response curve. Another potent angiogenic factor, platelet-derived endothelial cell growth factor (PD-ECGF), appears to promote chemokinesis of mast cells, whereas tumor necrosis factor-alpha, a weak angiogenic factor, is less robust but still functions as a mast cell chemotactic factor. Epidermal growth factor (EGF), a growth factor with minimal angiogenic properties, was ineffective as a mast cell chemotactic factor. A checkerboard analysis confirmed the directional chemotactic response of PDGF-AB, VEGF, and bFGF, while indicating the chemokinetic response induced by PD-ECGF. Cross-desensitization of growth-factor-induced directed migration was observed between PDGF-AB and bFGF, and also between PDGF-AB and PD-ECGF. Tyrosine kinase-inhibitor genistein effectively dampened the chemotactic responses, whereas pertussis toxin had no effect. In summary, our findings suggest that factors known to act on endothelial cells and stimulate neovascularization may simultaneously serve to recruit mast cells to these sites. The local accumulation of mast cells is believed to facilitate new vessel formation through complex cell:cell interactions.
A trie compaction algorithm for a large set of keys (1996)

A trie structure is frequently used for various applications, such as natural language dictionaries, database systems and compilers. However, the total number of states of a trie (and transitions between them) becomes large, so that the space cost may not be acceptable for a huge key set. In order to resolve this disadvantage, this paper presents a new scheme, called a "two-trie", that enables us to perform efficient retrievals, insertions and deletions for the key sets. The essential idea is to construct two tries for both front and rear compressions of keys, which is similar to a DAWG (directed acyclic word-graph). The approach differs from a DAWG in that the two-trie approach presented can uniquely determine information corresponding to keys while a DAWG cannot. For an efficient implementation of the two-trie, two types of data structures are introduced. Theoretical and experimental observations show that the method presented is more practical than existing ones considering the use of dynamic key sets, information storage of keys and compression of transitions.
Molecular analysis of dengue virus attenuation after serial passage in primary dog kidney cells. (1997)

The complete nucleotide sequences of the genomes of dengue-1 virus virulent 45AZ5 PDK-O and attenuated vaccine candidate strain 45AZ5 PDK-27 have been determined and compared with the dengue-1 virus Western Pacific (West Pac) 74 parent strain from which 45AZ5 PDK-O was derived. Twenty-five (0.23%) nucleotide and 10 (0.29%) amino acid substitutions occurred between parent strain dengue-1 virus West Pac 74 and virulent strain 45AZ5 PDK-O, which was derived from the parent by serial passage in diploid foetal rhesus lung (FRhL-2) and mutagenized with 5-azacytidine. These substitutions were preserved in the 45AZ5 PDK-27 vaccine. 45AZ5 PDK-O and PDK-27 strains, which differ by 27 passages in primary dog kidney (PDK) cells, show 25 (0.23%) nucleotide and 11 (0.32%) amino acid divergences. These comparative studies suggest that the changes which occurred between the West Pac 74 and 45AZ5 PDK-O strains may alter the biological properties of the virus but may not be important for attenuation. Important nucleotide base changes responsible for attenuation accumulated between 45AZ5 PDK-O and 27.
Interferon‐α Treatment Induces Delayed CD4 Proliferative Responses to the Hepatitis C Virus Nonstructural Protein 3 Regardless of the Outcome of Therapy (1997)

The proliferative responses to a hepatitis C virus (HCV) recombinant nonstructural protein 3 (rNS3) were analyzed in 9 patients with chronic HCV infection before, during, and after 24 weeks of treatment with interferon-alpha (IFN-alpha) alone or in combination with ribavirin. Regardless of the therapy and the subsequent outcome, all patients showed an increased rNS3-specific proliferative response in peripheral blood mononuclear cells in vitro within 48 weeks from the start of therapy (P < .01). The proliferating cell phenotype was CD4 and was dependent on HLA-DP/DQ/DR class II antigen presentation. rNS3 induced in vitro detectable interleukin (IL)-2, IL-10, and IFN-gamma production in some patients before or after therapy (or both). No significant differences existed between responders and relapsed responders plus nonresponders with respect to the NS3-specific CD4 T helper (Th) cell responses. Thus, IFN-alpha therapy induces HCV NS3-specific CD4 Th cell proliferation regardless of the outcome of therapy.
Clostridium botulinum C2 Toxin Delays Entry into Mitosis and Activation of p34 cdc2 Kinase and cdc25-C Phosphatase in HeLa cells (1999)

The Clostridium botulinum C2 toxin ADP-ribosylates monomeric actin, thereby inducing disassembly of actin filaments, alteration of focal adhesions, and rounding of cells. After treatment with C2 toxin, cells stop to proliferate but remain viable for about 2 days. In view of reported correlations between the structure of the actin cytoskeleton and cell cycle transition, the effects of C2 toxin on the G(2)/M phase transition of the cell division cycle were studied. Since C2 toxin delayed entry into mitosis in HeLa cells, those enzymes which control entry into mitosis, the cyclin-dependent protein kinase mitosis-promoting factor (MPF) and the phosphatase cdc25-C were examined after treatment of synchronized cells with C2 toxin. MPF is composed of the regulatory cyclin B and the enzymatic p34cdc2 kinase subunits. For its activation at the G2/M border, p34cdc2 needs to be associated with cyclin B and additionally dephosphorylated at Tyr-15 by the specific phosphatase cdc25-C. Treatment of synchronized cells in S or G2 phase with C. botulinum C2 toxin prevented p34cdc2 protein kinase activation by inhibiting its tyrosine dephosphorylation at the G2/M border. Furthermore, the activity of cdc25-C phosphatase was decreased after treatment of cells with C2 toxin. Our results suggest that the prevented activation of the mitotic inducers p34cdc2 kinase and cdc25-C phosphatase represents the final downstream events in the action of C2 toxin resulting in a G(2) phase cell cycle delay in synchronized HeLa cells.
A High Accuracy Three-Dimensional Coordinate Digitizing System for Reconstructing the Geometry of Diarthrodial Joints (1997)

Abstract Finite element modeling (FEM) in orthopaedic biomechanics requires a measurement technique to obtain accurate, three-dimensional (3-D) representations of diarthrodial joints [5], Accurate representations of joints, including soft tissue, articular cartilage, and bone are needed for FEM to be useful in the study of joint behavior and orthopaedic implants. Based on measuring the thickness of articular cartilage, the accuracy requirement for the measurement technique is 20 μm for a relative error of 1 percent.
Bcl-XL Protects BimEL-induced Bax Conformational Change and Cytochrome c Release Independent of Interacting with Bax or BimEL (2002)

The Bcl-2 homology (BH) 3-only pro-apoptotic Bcl-2 family protein Bim plays an essential role in the mitochondrial pathway of apoptosis through activation of the BH1-3 multidomain protein Bax or Bak. To further understand how the BH3-only protein activates Bax, we provide evidence here that BimEL induces Bax conformational change and apoptosis through a Bcl-XL-suppressible but heterodimerization-independent mechanism. Substitution of the conserved leucine residue in the BH3 domain of BimEL for alanine (M1) inhibits the interaction of BimEL with Bcl-XL but does not abolish the ability of BimEL to induce Bax conformational change and apoptosis. However, removal of the C-terminal hydrophobic region from the M1 mutant (M1DeltaC) abolishes its ability to activate Bax and to induce apoptosis, although deletion of the C-terminal domain (DeltaC) alone has little if any effect on the pro-apoptotic activity of BimEL. Subcellular fractionation experiments show that the Bim mutant M1DeltaC is localized in the cytosol, indicating that both the C-terminal hydrophobic region and the BH3 domain are required for the mitochondrial targeting and pro-apoptotic activity of BimEL. Moreover, the Bcl-XL mutant (mt1), which is unable to interact with Bax and BimEL, blocks Bax conformational change and cytochrome c release induced by BimEL in intact cells and isolated mitochondria. BimEL or Bak-BH3 peptide induces Bax conformational change in vitro only under the presence of mitochondria, and the outer mitochondrial membrane fraction is sufficient for induction of Bax conformational change. Interestingly, native Bax is attached loosely on the surface of isolated mitochondria, which undergoes conformational change and insertion into mitochondrial membrane upon stimulation by BimEL, Bak-BH3 peptide, or freeze/thaw damage. Taken together, these findings indicate that BimEL may activate Bax by damaging the mitochondrial membrane structure directly, in addition to its binding and antagonizing Bcl-2/Bcl-XL function.
STAT3 Activation in Th17 and Th22 Cells Controls IL-22–Mediated Epithelial Host Defense during Infectious Colitis (2014)

The Citrobacter rodentium model mimics the pathogenesis of infectious colitis and requires sequential contributions from different immune cell populations, including innate lymphoid cells (ILCs) and CD4(+) lymphocytes. In this study, we addressed the role of STAT3 activation in CD4(+) cells during host defense in mice against C. rodentium. In mice with defective STAT3 in CD4(+) cells (Stat3(ΔCD4)), the course of infection was unchanged during the innate lymphoid cell-dependent early phase, but significantly altered during the lymphocyte-dependent later phase. Stat3(ΔCD4) mice exhibited intestinal epithelial barrier defects, including downregulation of antimicrobial peptides, increased systemic distribution of bacteria, and prolonged reduction in the overall burden of C. rodentium infection. Immunomonitoring of lamina propria cells revealed loss of virtually all IL-22-producing CD4(+) lymphocytes, suggesting that STAT3 activation was required for IL-22 production not only in Th17 cells, but also in Th22 cells. Notably, the defective host defense against C. rodentium in Stat3(∆CD4) mice could be fully restored by specific overexpression of IL-22 through a minicircle vector-based technology. Moreover, expression of a constitutive active STAT3 in CD4(+) cells shaped strong intestinal epithelial barrier function in vitro and in vivo through IL-22, and it promoted protection from enteropathogenic bacteria. Thus, our work indicates a critical role of STAT3 activation in Th17 and Th22 cells for control of the IL-22-mediated host defense, and strategies expanding STAT3-activated CD4(+) lymphocytes may be considered as future therapeutic options for improving intestinal barrier function in infectious colitis.
[Mitochondria transfer from self-granular cells to improve embryos' quality]. (2004)

Self-mitochondria transfer can improve embryos' quality and pregnancy rate without influence on fertilization rate.
Ouabain, a steroid hormone that signals with slow calcium oscillations (2001)

The plant-derived steroid, digoxin, a specific inhibitor of Na,K-ATPase, has been used for centuries in the treatment of heart disease. Recent studies demonstrate the presence of a digoxin analog, ouabain, in mammalian tissue, but its biological role has not been elucidated. Here, we show in renal epithelial cells that ouabain, in doses causing only partial Na,K-ATPase inhibition, acts as a biological inducer of regular, low-frequency intracellular calcium ([Ca(2+)](i)) oscillations that elicit activation of the transcription factor, NF-kappa B. Partial inhibition of Na,K-ATPase using low extracellular K(+) and depolarization of cells did not have these effects. Incubation of cells in Ca(2+)-free media, inhibition of voltage-gated calcium channels, inositol triphosphate receptor antagonism, and redistribution of actin to a thick layer adjacent to the plasma membrane abolished [Ca(2+)](i) oscillations, indicating that they were caused by a concerted action of inositol triphosphate receptors and capacitative calcium entry via plasma membrane channels. Blockade of ouabain-induced [Ca(2+)](i) oscillations prevented activation of NF-kappa B. The results demonstrate a new mechanism for steroid signaling via plasma membrane receptors and underline a novel role for the steroid hormone, ouabain, as a physiological inducer of [Ca(2+)](i) oscillations involved in transcriptional regulation in mammalian cells.
Multifaceted Regioregular Oligo(thieno[3,4-b]thiophene)s Enabled by Tunable Quinoidization and Reduced Energy Band Gap (2015)

Thiophene-based materials have occupied a crucial position in the development of organic electronics. However, the energy band gaps of oligo- and polythiophenes are difficult to modulate without resorting to push-pull electronic effects. We describe herein a new series of monodisperse oligo(thieno[3,4-b]thiophene) derivatives with well-defined regioregular structures synthesized efficiently by direct C-H arylation. These compounds show a unique palette of colors and amphoteric redox properties with widely tunable energy band gaps. The capacity to stabilize both cations and anions results in both anodic and cathodic electrochromism. Under excitation, these compounds can produce photoionized states able to interconvert into neutral triplet or form these through singlet exciton fission or intersystem crossing. These features arise from a progressive increase in quinoidization on a fully planar platform making the largest effective conjugation length among hetero-oligomers. Oligo(thieno[3,4-b]thiophene)s might represent the more distinctive family of oligothiophenes of this decade.
Epidemiology and Outcome of Invasive Fungal Infection in Adult Hematopoietic Stem Cell Transplant Recipients: Analysis of Multicenter Prospective Antifungal Therapy (PATH) Alliance Registry (2008)

IA remains the most commonly identified IFI among HSCT recipients, but rates of survival in persons with IA appear to have improved, compared with previously reported data. Invasive candidiasis and IFI due to molds other than Aspergillus species remain a significant problem in HSCT recipients.
Systemic Therapeutic Gene Delivery for Cancer: Crafting Paris Arrow (2009)

Tremendous strides have been made in proteogenomics and RNA interference technologies. Hence "personalized" cancer gene therapy has become a foreseeable rather than a predictable reality. Currently, the lack of an optimized, systemic gene delivery vehicle remains a key limiting factor for developing effective treatment applications. Since their introduction by Felgner in 1987, cationic lipids have been an attractive consideration for gene delivery, in view of their biocompatibility, biodegradability, low toxicity, and low immunogenicity. Successful in vivo transgene expression by cationic lipid- or cationic polymer-based delivery depends critically on a long circulating half life (>48 h), a definable systemic biodistribution with target-specific cancer localization, and efficient cell entry and internalization. Ideally, the agent should have a hydrophobic, stabilized core that ensures integrity of the therapeutic entity in vivo, a biocompatible, neutrally charged shell (zeta potential of approximately +/-10 mv) for enhanced, "stealth" circulation, and a suitable size (approximately 50-200 nm in diameter) for access into the tumor neovasculature and reduced reticuloendothelial system (RES) uptake. "Smart" receptor-targeting moieties can redirect intracellular trafficking. Additional engineered features have also been incorporated to minimize lysosomal degradation (membrane fusogenic lipids or proton sponge), promote endosomal escape into cytoplasm (cell penetrating peptides, triblock copolymer construction), and enhance nuclear entry and activate the endogenous transcriptional machinery (inclusion of a nuclear localization signal). Improvements in each of these respective areas of study have converged to yield promising in vivo results.
Fabrication of hollow silica aerogel spheres by a droplet generation method and sol–gel processing (1989)

A system was designed to produce hollow silica aerogel spheres by combining a droplet generation method with sol–gel processing. Simultaneous passage of an alkoxide solution and a fill gas, through a dual-nozzle system, formed a continuous stream of hollow droplets in the fluid state. The spherical droplets were levitated in a basic atmosphere containing ammonia which converted the sol into a rigid gel state. Supercritical drying was used for the elimination of residual solvents without shrinkage and cracking.
MAPK/ERK Signaling in Osteosarcomas, Ewing Sarcomas and Chondrosarcomas: Therapeutic Implications and Future Directions (2012)

The introduction of cytotoxic chemotherapeutic drugs in the 1970's improved the survival rate of patients with bone sarcomas and allowed limb salvage surgeries. However, since the turn of the century, survival data has plateaued for a subset of metastatic, nonresponding osteo, and/or Ewing sarcomas. In addition, most high-grade chondrosarcoma does not respond to current chemotherapy. With an increased understanding of molecular pathways governing oncogenesis, modern targeted therapy regimens may enhance the efficacy of current therapeutic modalities. Mitogen-Activated Protein Kinases (MAPK)/Extracellular-Signal-Regulated Kinases (ERK) are key regulators of oncogenic phenotypes such as proliferation, invasion, angiogenesis, and inflammatory responses; which are the hallmarks of cancer. Consequently, MAPK/ERK inhibitors have emerged as promising therapeutic targets for certain types of cancers, but there have been sparse reports in bone sarcomas. Scattered papers suggest that MAPK targeting inhibits proliferation, local invasiveness, metastasis, and drug resistance in bone sarcomas. A recent clinical trial showed some clinical benefits in patients with unresectable or metastatic osteosarcomas following MAPK/ERK targeting therapy. Despite in vitro proof of therapeutic concept, there are no sufficient in vivo or clinical data available for Ewing sarcomas or chondrosarcomas. Further experimental and clinical trials are awaited in order to bring MAPK targeting into a clinical arena.
Function of the alpha 1 beta 2 gamma 2S gamma-aminobutyric acid type A receptor is modulated by protein kinase C via multiple phosphorylation sites. (1992)

Activation of protein kinase C (PKC) results in down-modulation of the gamma-aminobutyric acid type A (GABAA) receptor. In this study, the recombinant subunit combination alpha 1 beta 2 gamma 2S was expressed in Xenopus oocytes. The resulting channel was shown to be modulated by 2 microM oleoylacetylglycerol or, stereo-specifically, by low concentrations (10 nM) of the phorbol ester 4 beta-phorbol 12-myristate 13-acetate. By site-specific mutagenesis, we altered the serine or threonine residues of consensus phosphorylation sites for PKC in the large, intracellular domain of alpha 1, beta 2, and gamma 2S. Mutant subunits were co-expressed with wild type subunits to yield alpha 1 beta 2 gamma 2S combinations. All of the tested 14 mutations did not affect the level of expression of GABA current. Two of these mutations, Ser-410 in beta 2 and Ser-327 in gamma 2S, resulted in a significant reduction of the effect of the activator of PKC, 4 beta-phorbol 12-myristate 13-acetate, on the GABA current amplitude. Thus, we have identified two single serine residues, Ser-410 in the subunit beta 2 and Ser-327 in gamma 2S, as phosphorylation sites of a PKC endogenous to Xenopus oocytes. Co-expression of the mutant subunits suggests that phosphorylation of both sites is required for a full, PKC-mediated down-regulation of GABA currents.