gebhart/patrepeval huggingface dataset:
Theoretical and Experimental Analysis of In Vivo Wheeled Mobility (2004)

Laparoscopy is abdominal surgery performed with long tools inserted through small incisions. The use of small incisions reduces patient trauma, but also eliminates the surgeon’s ability to directly view and touch the surgical environment. These limitations generally restrict the application of laparoscopy to less complex procedures. Large robots external to the patient have been used to aid in the manipulation of the tools and improve dexterity. This paper presents a theoretical and experimental analysis of miniature in vivo robots. The objective is to develop a wireless mobile imaging robot that can be placed inside the abdominal cavity during surgery. Such robots will allow the surgeon to view the surgical environment from multi-angles. The motion of these in vivo robots will not be constrained by the insertion incisions.
Acyl CoA (1998)

Acyl coenzyme A:cholesterol acyltransferase (ACAT) (EC 2.3.1.26) is an enzyme, located in the endoplasmic reticulum of many types of cells, that catalyzes cholesterol ester formation from cholesterol and fatty acyl CoA substrates. Sterol esterification by ACAT or homologous enzymes is conserved in evolution dating back to yeast. The recent cloning of a human cDNA for ACAT, together with genome sequencing projects, has led to the identification of an ACAT gene family and provided molecular tools for determining ACAT's functions in vivo. Summarized here is the current knowledge concerning the molecular genetics of ACAT.
Structural and Energetic Impact of Non-Natural 7-Deaza-8-Azaadenine and Its 7-Substituted Derivatives on H-Bonding Potential with Uracil in RNA Molecules (2015)

Non-natural (synthetic) nucleobases, including 7-ethynyl- and 7-triazolyl-8-aza-7-deazaadenine, have been introduced in RNA molecules for targeted applications, and have been characterized experimentally. However, no theoretical characterization of the impact of these modifications on the structure and energetics of the corresponding H-bonded base pair is available. To fill this gap, we performed quantum mechanics calculations, starting with the analysis of the impact of the 8-aza-7-deaza modification of the adenine skeleton, and we moved then to analyze the impact of the specific substituents on the modified 8-aza-7-deazaadenine. Our analysis indicates that, despite of these severe structural modifications, the H-bonding properties of the modified base pair gratifyingly replicate those of the unmodified base pair. Similar behavior is predicted when the same skeleton modifications are applied to guanine when paired to cytosine. To stress further the H-bonding pairing in the modified adenine-uracil base pair, we explored the impact of strong electron donor and electron withdrawing substituents on the C7 position. Also in this case we found minimal impact on the base pair geometry and energy, confirming the validity of this modification strategy to functionalize RNAs without perturbing its stability and biological functionality.
Chemical Vapor Deposition Based Synthesis of Carbon Nanotubes and Nanofibers Using a Template Method (1998)

We have developed a new approach for preparing graphitic carbon nanofiber and nanotube ensembles. This approach entails chemical vapor deposition (CVD) based synthesis of carbon within the pores of an alumina template membrane with or without a Ni catalyst. Ethylene or pyrene was used in the CVD process with reactor temperatures of 545 °C for Ni-catalyzed CVD and 900 °C for the uncatalyzed process. The resultant carbon nanostructures were uniform hollow tubes with open ends. Increasing the deposition time converted the carbon nanotubes into carbon nanofibers. Transmission electron microscopy and electron diffraction data show the as deposited graphitic carbon nanofibers synthesized with the Ni catalyst were not highly ordered. Heating the carbon-containing membrane at 500 °C for 36 h, however, converts the carbon nanofibers into highly ordered graphite. The electron diffraction data show a spotted diffraction pattern characteristic of single-crystal graphite with the graphitic planes parallel to the long axis of the nanofibers.
Constitutive and cell‐division‐inducible protein—DNA interactions in two maize histone gene promoters (1993)

Protein-DNA interactions in the promoter regions of two maize histone genes have been analyzed by DNase I and DMS in vivo footprinting combined with LMPCR amplification. Both promoters present a bimodular structure characterized by a proximal cell division-specific set of interactions and a distal region which displays constitutive footprints but enhancement of these footprints upon cell proliferation. The inducible region contains two cis-elements common to all replication-dependent plant histone genes, one of them having previously been shown to be a target for the wheat nuclear protein HBP-2. In the constitutive region, the first demonstration for the existence of a transcription factor binding to the highly conserved plant histone-specific octamer CGCGGATC is provided. Exchange of cell-type-specific factors is postulated to occur at that site. Additional immediate upstream constitutive elements binding regulatory proteins include a degenerate octameric sequence, a CCAAT-box, a CACCC sequence and composite ACGTCA/ACGTGG hexameric sequences binding HBP-1-related trans-acting factors. The close proximity of these elements within the constitutive region and the redundancy of some of them suggest complex cooperation and competition mechanisms contributing to achieve the final expression level and likely also to mediate the interplay between constitutive and inducible factors.
Reactivity and Regulatory Properties of Human Anti-Idiotypic Antibodies Induced by T Cell Vaccination (2000)

Immunization with irradiated autoreactive T cells (T cell vaccination) induces anti-idiotypic T cell responses that preferentially recognize complementarity-determining region 3 sequences, contributing to clonal depletion of autoreactive T cells. However, it remains unknown whether T cell vaccination elicits anti-idiotypic humoral responses and whether the anti-idiotypic Abs play a similar role in the regulatory mechanism induced by T cell vaccination. In this study we examined the occurrence, the reactivity pattern, and the regulatory role of anti-idiotypic Abs elicited by T cell vaccination in patients with multiple sclerosis. We demonstrated for the first time that B cells producing anti-idiotypic Abs could be isolated from vaccinated patients. These EBV-transformed B cell lines were selected for specific reactivity to a 20-mer TCR peptide incorporating a common complementarity-determining region 3 sequence of the immunizing T cell clones. The resulting anti-idiotypic Abs were found to react with the original immunizing T cell clones and exhibit an inhibitory effect on their proliferation. The findings suggest that anti-idiotypic Ab responses can be induced by T cell vaccination in humans and that their regulatory properties are likely to contribute to the suppression of myelin basic protein-reactive T cells in vaccinated patients. The study has important implications in our understanding of the regulatory role of the anti-idiotypic humoral responses induced by T cell vaccination.
Control of the ratio of functional and non-functional ligands in clusters of the type Zr6O4(OH)4(carboxylate)12for their use as building blocks for inorganic–organic hybrid polymers (2004)

The methacrylate ligands of the cluster Zr6O4(OH)4(methacrylate)12 undergo degenerate exchange with methacrylic acid in solution. Addition of propionic or isobutyric acid allows partial or complete exchange of the methacrylate ligands for propionate or isobutyrate. The mixed-carboxylate cluster Zr6O4(OH)4(OMc)8(isobutyrate)4(BuOH) was independently prepared by reaction of Zr(OnBu)4 with a mixture of methacrylic acid and isobutyric acid. The structures of Zr6O4(OH)4(OMc)8(isobutyrate)4(BuOH) and Zr6O4(OH)4(isobutyrate)12(H2O) consist of an octahedral Zr6(μ3-O)4(μ3-OH)4 core with one of the carboxylate ligands being monodentate. The H2O or ROH molecule is coordinated to the neighbouring zirconium atom and, at the same time, hydrogen bonded to the monodentate carboxylate. A mechanism for the carboxylate exchange is suggested based on the structural observations.
Optical properties of metallic films for vertical-cavity optoelectronic devices (1998)

We present models for the optical functions of 11 metals used as mirrors and contacts in optoelectronic and optical devices: noble metals (Ag, Au, Cu), aluminum, beryllium, and transition metals (Cr, Ni, Pd, Pt, Ti, W). We used two simple phenomenological models, the Lorentz-Drude (LD) and the Brendel-Bormann (BB), to interpret both the free-electron and the interband parts of the dielectric response of metals in a wide spectral range from 0.1 to 6 eV. Our results show that the BB model was needed to describe appropriately the interband absorption in noble metals, while for Al, Be, and the transition metals both models exhibit good agreement with the experimental data. A comparison with measurements on surface normal structures confirmed that the reflectance and the phase change on reflection from semiconductor-metal interfaces (including the case of metallic multilayers) can be accurately described by use of the proposed models for the optical functions of metallic films and the matrix method for multilayer calculations.
Mechanism of action of IVIG in ITP (2002)

IVIG is prepared from large pools of plasma from healthy donors and the IgG is present predominantly in monomeric form. It was first reported in 1981 by Dr. Paul Imbach that high doses of IVIG promote fast recovery of ITP in children. Despite extensive clinical use in a variety of autoimmune and inflammatory states, the mechanism of action of IVIG remains as yet incompletely understood. Several theories have been proposed to explain how administration of IVIG to individuals with ITP increases the platelet count. Following is an overview of some of the major theories.
Physicians' attitudes about quality-of-life issues in hematopoietic stem cell transplantation (2004)

Studies investigating quality of life (QOL) after hematopoietic stem cell transplantation demonstrate the spectrum of QOL outcomes awaiting survivors. Nevertheless, how transplantation physicians interpret and apply QOL information to clinical practice is poorly understood. We conducted a cross-sectional survey of transplantation physicians to address these issues and received 180 (24%) responses from physicians in 29 countries. Seventy-two percent reported that their patients are willing to accept poor QOL for a small chance of cure. Only 28% said that QOL considerations "often" or "almost all the time" enter into patients' decisions about transplantation. This contrasted with physicians' reported attention to QOL in their discussions with patients. Although 53% of physicians reported using QOL results to modify practice, 55% would be more likely to use these data if they were more understandable. To ensure generalizability of the results, a validation sample was randomly selected, and these 85 physicians (response rate, 76%) confirmed the findings of the original survey. Given the extensive data regarding posttransplantation QOL, resources should be devoted to exploring how patients and physicians use these data in clinical care and in devising methods to ensure that QOL results are interpretable and relevant to patients and physicians.
Rapid Prototyping in Copper Substrates for Digital Microfluidics (2006)

Two rapid prototyping techniques for digital microfluidics (see figure) are presented. In the first method, actuation electrodes are patterned on printed circuit board substrates by using photolithography. In the second technique, actuation electrodes are patterned directly onto substrates using a desktop laser printer. These techniques reduce the time, complexity, and cost required to produce devices, which makes this technology accessible to any research lab.
Exome and deep sequencing of clinically aggressive neuroblastoma reveal somatic mutations that affect key pathways involved in cancer progression (2016)

The spectrum of somatic mutation of the most aggressive forms of neuroblastoma is not completely determined. We sought to identify potential cancer drivers in clinically aggressive neuroblastoma.Whole exome sequencing was conducted on 17 germline and tumor DNA samples from high-risk patients with adverse events within 36 months from diagnosis (HR-Event3) to identify somatic mutations and deep targeted sequencing of 134 genes selected from the initial screening in additional 48 germline and tumor pairs (62.5% HR-Event3 and high-risk patients), 17 HR-Event3 tumors and 17 human-derived neuroblastoma cell lines.We revealed 22 significantly mutated genes, many of which implicated in cancer progression. Fifteen genes (68.2%) were highly expressed in neuroblastoma supporting their involvement in the disease. CHD9, a cancer driver gene, was the most significantly altered (4.0% of cases) after ALK.Other genes (PTK2, NAV3, NAV1, FZD1 and ATRX), expressed in neuroblastoma and involved in cell invasion and migration were mutated at frequency ranged from 4% to 2%.Focal adhesion and regulation of actin cytoskeleton pathways, were frequently disrupted (14.1% of cases) thus suggesting potential novel therapeutic strategies to prevent disease progression.Notably BARD1, CHEK2 and AXIN2 were enriched in rare, potentially pathogenic, germline variants.In summary, whole exome and deep targeted sequencing identified novel cancer genes of clinically aggressive neuroblastoma. Our analyses show pathway-level implications of infrequently mutated genes in leading neuroblastoma progression.
Complete dynamic repopulation of decellularized heart valves by application of defined physical signals—an in vitro study (2003)

This study demonstrated the superiority of the hydrodynamic approach of cellular reseeding to replace decellularized porcine heart valves with ovine cells with almost complete preservation of extracellular matrix integrity.
Seed loss through the urinary tract after prostate brachytherapy: examining the role of cystoscopy and urine straining post implant (2003)

This study describes one institution's experience with seed retrieval through the urinary tract and makes recommendations for cystoscopy and urine straining post prostate brachytherapy (PB). 1794 patients from two separate cohorts covering different time periods (early versus late) were analyzed. All patients were preplanned with a modified peripheral loading technique and implanted with preloaded needles (125I or 103Pd) under ultrasound guidance. A catheter was used to delineate the urethra during the volume study but was not used during the implant. All patients underwent post implant cystoscopy. All patients were instructed to strain their urine for seven days post implant and return any seeds to our center. In our experience, seed loss through the urinary tract is a common event after PB, occurring in 29.7% of patients and was more common in patients from the early cohort, those implanted with 125I seeds or those patients with prior transurethral resection of the prostate. Average seed loss per case, however, represents only 0.58% of total activity. We continue to recommend routine post implant cystoscopy for seed retrieval and periprocedural management. We no longer recommend that patients strain their urine at home after documenting a low rate of seed loss after discharge.
Kinetic Analysis of His-Tagged Protein Binding to Nickel-Chelating Nanolipoprotein Particles (2010)

Nanolipoprotein particles (NLPs) are discoidal self-assembling membrane mimetics that have been primarily used as a platform for the solubilization and stabilization of membrane proteins. Nickel-chelating nanolipoprotein particles (NiNLPs) containing nickel-chelating lipids (Ni-lipid) for the targeted immobilization of His-tagged proteins hold promise as carriers of hydrophilic biological molecules for a range of applications. The effect of protein loading (i.e., the number of proteins bound per NiNLP) and Ni-lipid content on the time scales and kinetics of binding are important to various applications such as vaccine development, diagnostic imaging, and drug delivery. We have immobilized hexa-His-tagged LsrB, a Yersinia pestis transport protein, onto NiNLPs to examine the effect of protein binding stoichiometry and Ni-lipid content on the time scales and kinetics of protein binding by surface plasmon resonance (SPR). Data indicate that the dissociation half-time increases with Ni-lipid content up to a molar concentration of 35% and decreases as the number of bound protein per NiNLP increases. These findings indicate that the kinetics of protein binding are highly dependent on both the number of bound protein per NiNLP and Ni-lipid content.
Clay Mineralogy of the Cretaceous-Tertiary Boundary Clay (1983)

Analyses of the clay mineralogy of samples from the Cretaceous-Tertiary boundary layer at four localities show that the boundary clay is neither mineralogically exotic nor distinct from locally derived clays above and below the boundary. The significant ejecta component in the clay that is predicted by the asteroid-impact scenario was not detected.
Altered Patterns of Cellular Gene Expression in Dermal Microvascular Endothelial Cells Infected with Kaposi's Sarcoma-Associated Herpesvirus (2002)

Kaposi's sarcoma (KS)-associated herpesvirus (KSHV; also called human herpesvirus 8) is believed to be the etiologic agent of Kaposi's sarcoma, multicentric Castleman's disease, and AIDS-associated primary effusion lymphoma. KSHV infection of human dermal microvascular endothelial cells (DMVEC) in culture results in the conversion of cobblestone-shaped cells to spindle-shaped cells, a characteristic morphological feature of cells in KS lesions. All spindle-shaped cells in KSHV-infected DMVEC cultures express the latency-associated nuclear protein LANA1, and a subfraction of these cells undergo spontaneous lytic cycle induction that can be enhanced by tetradecanoyl phorbol acetate (TPA) treatment. To study the cellular response to infection by KSHV, we used two different gene array screening systems to examine the expression profile of either 2,350 or 9,180 human genes in infected compared to uninfected DMVEC cultures in both the presence and absence of TPA. In both cases, between 1.4 and 2.5% of the genes tested were found to be significantly upregulated or downregulated. Further analysis by both standard and real-time reverse transcription-PCR procedures directly confirmed these results for 14 of the most highly upregulated and 13 of the most highly downregulated genes out of a total of 37 that were selected for testing. These included strong upregulation of interferon-responsive genes such as interferon response factor 7 (IRF7) and myxovirus resistance protein R1, plus upregulation of exodus 2 beta-chemokine, RDC1 alpha-chemokine receptor, and transforming growth factor beta3, together with strong downregulation of cell adhesion factors alpha(4)-integrin and fibronectin plus downregulation of bone morphogenesis protein 4, matrix metalloproteinase 2, endothelial plasminogen activator inhibitor 1, connective tissue growth factor, and interleukin-8. Significant dysregulation of several other cytokine-related genes or receptors, as well as endothelial cell and macrophage markers, and various other genes associated with angiogenesis or transformation was also detected. Western immunoblot and immunohistochemical analyses confirmed that the cellular IRF7 protein levels were strongly upregulated during the early lytic cycle both in KSHV-infected DMVEC and in the body cavity-based lymphoma BCBL1 PEL cell line.
Synovial fluid levels of tumor necrosis factor α and oncostatin M correlate with levels of markers of the degradation of crosslinked collagen and cartilage aggrecan in rheumatoid arthritis but not in osteoarthritis (2000)

This in vivo study suggests that TNFalpha and other proinflammatory cytokines are involved in the up-regulation of the coordinated degradation of cartilage aggrecan and collagen in RA. Further, OSM may act synergistically with other proinflammatory cytokines in up-regulating the production of metalloproteinases by chondrocytes in rheumatoid joints.
Isoforms p69 and p100 of 2′,5′-Oligoadenylate Synthetase Induced Differentially by Interferons In Vivo and In Vitro (1993)

Four isoforms of 2',5'-oligoadenylate (2-5A) synthetase have been identified (40, 44, 69, and 100 kD). The 40- and 44-kD enzymes are encoded by the same gene, probably different from the genes encoding the larger isoforms. In this study, induction of the 100- and 69-KD (p100, p69) isoforms in different individuals and in different cell types was investigated after treatment with recombinant human interferons (IFN): IFN-alpha 2, IFN-beta ser, or IFN-gamma. The p69 and p100 isoforms were quantitated in cell extracts on Western blots using specific polyclonal antibodies, or their activity was measured after purification of cell extracts on immunoaffinity columns. The p69 and p100 isoforms were differentially induced in Daudi, fibroblast, and colon adenocarcinoma cells treated with IFNs. Considerable individual variations in both basal and induced levels of p69 and p100 were observed in peripheral blood mononuclear cells from normal donors cultured with IFNs in vitro, and from cancer patients treated with IFN-alpha 2 or with IFN-beta ser. These results demonstrate that the p69 and p100 isoforms are present in vivo in peripheral blood mononuclear cells and their level is increased following IFN administration. Furthermore, both the in vivo and in vitro observations indicate that the expression of these enzymes is specific to each cell type and varies among individuals.
The calf reo-like virus (rotavirus) vaccine: an ineffective immunization agent for rotaviral diarrhea of piglets. (1979)

Rotavirus, in a commercially available calf vaccine, did not replicate in newborn colostrum-free piglets inoculated orally with one half of a calf dose. Gross and microscopic examination of these vaccinated piglets revealed no lesions consistent with rotaviral infection and vaccinated piglets were susceptible to challenge by porcine rotavirus. Challenged piglets vomited, had diarrhea and became severely dehydrated. Rotavirus was visualized in their gut fluid. Villi in the small intestines were shortened, blunted and fused. Rotaviral antigens were seen in enterocytes.
Ataxin-2 and its Drosophila homolog, ATX2, physically assemble with polyribosomes (2006)

Mutations resulting in the expansion of a polyglutamine tract in the protein ataxin-2 give rise to the neurodegenerative disorders spinocerebellar ataxia type 2 and Parkinson's disease. The normal cellular function of ataxin-2 and the mechanism by which polyglutamine expansion of ataxin-2 causes neurodegeneration are unknown. Here, we demonstrate that ataxin-2 and its Drosophila homolog, ATX2, assemble with polyribosomes and poly(A)-binding protein (PABP), a key regulator of mRNA translation. The assembly of ATX2 with polyribosomes is mediated independently by two distinct evolutionarily conserved regions of ATX2: an N-terminal Lsm/Lsm-associated domain (LsmAD), found in proteins that function in nuclear RNA processing and mRNA decay, and a PAM2 motif, found in proteins that interact physically with PABP. We further show that the PAM2 motif mediates a physical interaction of ATX2 with PABP in addition to promoting ATX2 assembly with polyribosomes. Our results suggest a model in which ATX2 binds mRNA directly through its Lsm/LsmAD domain and indirectly via binding PABP that is itself directly bound to mRNA. These findings, coupled with work on other ataxin-2 family members, suggest that ATX2 plays a direct role in translational regulation. Our results raise the possibility that polyglutamine expansions within ataxin-2 cause neurodegeneration by interfering with the translational regulation of particular mRNAs.