gebhart/patrepeval huggingface dataset:
Abstract 765: Costimulatory SA-4-1BBL and monophosphoryl lipid A as novel adjuvant system for the development of cancer vaccines with robust therapeutic efficacy (2011)

Abstract Subunit vaccines based on tumor-associated antigens (TAAs) represent an attractive alternative to conventional treatments for cancer due to their safety profile and ability to control recurrences by establishing long-term immunological memory. However, the efficacy of TAA-based therapeutic vaccines is limited by weak immunogenic nature of these antigens and various immune evasion mechanisms employed by the progressing tumor. To overcome these limitations, we herein used SA-4-1BBL costimulatory molecule and toll-like receptor 4 agonist monophosphoryl lipid A (MPL) as two immunomodulators with distinct mechanisms of action as a novel adjuvant system for the development of HPV16 E7 and survivin TAA-based therapeutic vaccines against TC-1 cervical and 3LL pulmonary carcinoma mouse models, respectively. A single immunization with a vaccine formulation containing E7 protein plus SA-4-1BBL and MPL resulted in the eradication of established E7 expressing TC-1 tumors in 100% of mice. Similarly, a single vaccination with survivin, as a bona fide self-TAA, resulted in control and/or eradication of established 3LL pulmonary metastases and the efficacy of the vaccine was further improved by a booster injection. Combined adjuvants had better therapeutic efficacy over the individual agents while SA-4-1BBL significantly performed better than MPL. The therapeutic efficacy achieved with the combinatorial use of both adjuvants and SA-4-1BBL as monotherapy was correlated with elevated levels of IFN-γ+TNF-α+IL-2+ triple positive antigen-specific CD8+ T cells, cytotoxic response, long-term immune memory, and most importantly an increase in the intratumoral number of CD8+ T effector cells with simultaneous decrease in the number of CD4+FoxP3+ T regulatory cells, resulting in a favorable T effector/T regulatory cell ratio. In marked contrast, although MPL as monotherpay improved the effector function of CD8+ T cells, it did not increase the infiltration of these cells into the tumor. Surprisingly, MPL as monotherapy increased the number of CD4+FoxP3+ T regulatory cells infiltrating into the tumor, resulting in an unfavorable T effector/T regulatory cell ratio. Taken together, these data demonstrate the utility of using SA-4-1BBL and MPL as a novel adjuvant system for the development of therapeutic TAA-based subunit cancer vaccines with strong clinical implications. Work is in part funded by NIH 2R44 AI071618-02, R43 AI074176, R41 CA121665, KLCP, the W.M. Keck Foundation, and the Commonwealth of Kentucky Research Challenge Trust Fund. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 765. doi:10.1158/1538-7445.AM2011-765
Differential cutaneous wound healing in thermally injured MRL/MPJ mice (2007)

Adult wound repair occurs with an initial inflammatory response, reepithelialization, and the formation of a permanent scar. MRL/MpJ mice following ear-hole punch biopsies display accelerated healing and tissue regeneration. In this study, we characterized the healing responses in both MRL/MpJ and BALB/c mice following a 15% total body surface area full-thickness cutaneous burn injury. Macroscopic and histological observations show that delayed wound closure in MRL/MpJ mice is accompanied by an increase in edema, reduced neutrophil infiltration, and more prominent eschar. In vivo bromodeoxyuridine labeling showed no defect in keratinocyte proliferation and migration (reepithelialization). In comparison with BALB/c mice, MRL/MpJ wounds had greater collagen deposition, less granulation tissue formation, and contained fewer alpha-smooth muscle actin-positive myofibroblasts. An observed reduction in dermal neutrophil infiltration and myofibroblast development correlated with enhanced angiogenesis. Overall, BALB/c wounds contracted sooner and to a larger degree, resulting in a significant decrease in scar formation. Interestingly, MRL/MpJ mice showed overt abnormalities in hair follicle proliferation, morphogenesis, and subsequent hair regrowth postburn injury. No substantial evidence of tissue regeneration was observed in either BALB/c or MRL/MpJ wounds. Our results convincingly demonstrate that MRL/MpJ skin burn wounds heal with scar formation with delays in two critical wound healing events: wound closure, and myofibroblast development.
Image-Based BRDF Measurement Including Human Skin (1999)

We present a new image-based process for measuring the bidirectional reflectance of homogeneous surfaces rapidly, completely, and accurately. For simple sample shapes (spheres and cylinders) the method requires only a digital camera and a stable light source. Adding a 3D scanner allows a wide class of curved near-convex objects to be measured. With measurements for a variety of materials from paints to human skin, we demonstrate the new methods ability to achieve high resolution and accuracy over a large domain of illumination and reflection directions. We verify our measurements by tests of internal consistency and by comparison against measurements made using a gonioreflectometer.
Mitochondrial pathways in sarcopenia of aging and disuse muscle atrophy (2012)

Muscle loss during aging and disuse is a highly prevalent and disabling condition, but knowledge about cellular pathways mediating muscle atrophy is still limited. Given the postmitotic nature of skeletal myocytes, the maintenance of cellular homeostasis relies on the efficiency of cellular quality control mechanisms. In this scenario, alterations in mitochondrial function are considered a major factor underlying sarcopenia and muscle atrophy. Damaged mitochondria are not only less bioenergetically efficient, but also generate increased amounts of reactive oxygen species, interfere with cellular quality control mechanisms, and display a greater propensity to trigger apoptosis. Thus, mitochondria stand at the crossroad of signaling pathways that regulate skeletal myocyte function and viability. Studies on these pathways have sometimes provided unexpected and counterintuitive results, which suggests that they are organized into a complex, heterarchical network that is currently insufficiently understood. Untangling the complexity of such a network will likely provide clinicians with novel and highly effective therapeutics to counter the muscle loss associated with aging and disuse. In this review, we summarize the current knowledge on the mechanisms whereby mitochondrial dysfunction intervenes in the pathogenesis of sarcopenia and disuse atrophy, and highlight the prospect of targeting specific processes to treat these conditions.
Cambridge Crystallographic Data Centre. II. Structural Data File (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCambridge Crystallographic Data Centre. II. Structural Data FileF. H. Allen, Olga Kennard, W. D. S. Motherwell, W. G. Town, and D. G. WatsonCite this: J. Chem. Doc. 1973, 13, 3, 119–123Publication Date (Print):August 1, 1973Publication History Published online1 May 2002Published inissue 1 August 1973https://doi.org/10.1021/c160050a006RIGHTS & PERMISSIONSArticle Views110Altmetric-Citations27LEARN 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 InReddit PDF (553 KB) Get e-Alerts
The National Computer Security Survey (NCSS): Final Methodology (2008)

In 2006, RAND conducted the National Computer Security Survey (NCSS), the first nationally representative cybersecurity survey of businesses within the United States on behalf of the Bureau of Justice Statistics and the U.S. Department of Homeland Security. This report documents the methodology used to develop and field the NCSS, as well as the sampling design and weighting methodology used.
Molecular Mechanisms Deployed by Virally Encoded G Protein–Coupled Receptors in Human Diseases (2011)

G protein-coupled receptors (GPCRs) represent the largest family of cell surface molecules involved in signal transduction. Surprisingly, open reading frames for multiple GPCRs were hijacked in the process of coevolution between Herpesviridae family viruses and their human and mammalian hosts. Virally encoded GPCRs (vGPCRs) evolved as parts of viral genomes, and this evolution allowed the power of host GPCR signaling circuitries to be harnessed in order to ensure viral replicative success. Phylogenetically, vGPCRs are distantly related to human chemokine receptors, although they feature several unique characteristics. Here, we describe the molecular mechanisms underlying vGPCR-mediated viral pathogenesis. These mechanisms include constitutive activity, aberrant coupling to human G proteins and β-arrestins, binding and activation by human chemokines, and dimerization with other GPCRs expressed in infected cells. The likely structural basis for these molecular events is described for the two closest viral homologs of human GPCRs. This information may aid in the development of novel targeted therapeutic strategies against viral diseases.
Packed red cells versus whole blood transfusion for severe paediatric anaemia, pregnancy‐related anaemia and obstetric bleeding: an analysis of clinical practice guidelines from sub‐Saharan Africa and evidence underpinning recommendations (2018)

Evidence comparing whole blood and packed red cell transfusion for common paediatric and maternal indications is virtually absent in SSA. Therefore, it is unclear whether policies promoting red cells over whole blood transfusion are clinically appropriate. Building a relevant evidence base will help develop effective policies promoting the most appropriate use of blood in African settings.
A 3D Organotypic Melanoma Spheroid Skin Model (2018)

Malignant transformation of melanocytes, the pigment cells of human skin, causes formation of melanoma, a highly aggressive cancer with increased metastatic potential. Recently, mono-chemotherapies continue to improve by melanoma specific combination therapies with targeted kinase inhibitors. Still, metastatic melanoma remains a life-threatening disease because tumors exhibit primary resistance or develop resistance to novel therapies, thereby regaining tumorigenic capacity. In order to improve the therapeutic success of malignant melanoma, the determination of molecular mechanisms conferring resistance against conventional treatment approaches is necessary; however, it requires innovative cellular in vitro models. Here, we introduce an in vitro three-dimensional (3D) organotypic melanoma spheroid model that can portray the in vivo architecture of malignant melanoma and may warrant new insights into intra-tumoral as well as tumor-host interactions. The model incorporates defined numbers of mature and differentiated melanoma spheroids in a 3D human full skin reconstruction model consisting of primary skin cells. The cellular composition and differentiation status of the embedded melanoma spheroids is similar to the one of cutaneous melanoma metastasis in vivo. Using this organotypic melanoma spheroid model as a drug screening platform may support the identification of responders to selected combination therapies, while sparing the unnecessary treatment burden for non-responders, thereby increasing the benefit of therapeutic interventions.
Cloning, characterization and expression of complete coding sequences of three IgE binding Malassezia furfur allergens, Mal f 7, Mal f 8 and Mal f 9 (2000)

Malassezia furfur, formerly known as Pityrosporum orbiculare or P. ovale, is a yeast that colonizes human skin. Normally, this yeast is nonpathogenic but under the influence of predisposing factors it may induce IgE reactivity in patients with atopic dermatitis. Approximately 40-65% of atopic dermatitis patients have IgE antibodies and/or skin reactivity against M. furfur and a higher T-cell response against this yeast is found in atopic dermatitis patients than in healthy individuals. By making a cDNA library displayed on a phage surface, we previously cloned five different IgE-binding proteins, Mal f 5, Mal f 6, MF 7, MF 8 and MF 9, from this yeast. The cDNAs encoding these allergens were sequenced and expressed in Escherichia coli. The sequences of MF 7, MF 8 and MF 9 were not full length (missing their 5'-ends) giving only partial gene products. To obtain complete cDNA sequences, we performed RACE-PCR to amplify the 5'-ends of each cDNA. These PCR products were sequenced and analyzed. The coding sequences of Mal f 7, Mal f 8 and Mal f 9 encode proteins with ORFs of 141 (16.2 kDa), 179 (19.2 kDa) and 126 (14.0 kDa) amino-acid residues, respectively. None of the putative proteins showed significant sequence homology with other known proteins in the searched database. The proteins encoded by the complete cDNA sequences were expressed in E. coli as recombinant proteins. Immunoblotting and radioallergosorbant test data showed that all of the expressed recombinant proteins have the ability to bind serum IgE from atopic dermatitis patients and furthermore, the M. furfur extract could specifically inhibit this IgE binding.
Wafer bonding technology and its applications in optoelectronic devices and materials (1997)

The direct wafer bonding process has found broad applications in many critical areas including both commercial and state-of-the-art photonic devices and more recently, formation of semiconductor compliant substrates. Using the wafer bonding technology, we have demonstrated 1.3-/spl mu/m vertical-cavity surface-emitting lasers (VCSELs) with a 1-mA continuous-wave (CW) threshold current and 0.83-mA pulsed threshold current. Superior device performance has also been achieved with photodetectors and micromachined tunable devices. Applying the wafer bonding process in a novel way, we have fabricated compliant universal substrates on which largely mismatched (e.g., 15% mismatch) heteroepitaxial layers can be grown defect free.
DNA double-strand break repair in cell-free extracts from Ku80-deficient cells: implications for Ku serving as an alignment factor in non-homologous DNA end joining (2000)

Non-homologous DNA end joining (NHEJ) is considered the major pathway of double-strand break (DSB) repair in mammalian cells and depends, among other things, on the DNA end-binding Ku70/80 hetero-dimer. To investigate the function of Ku in NHEJ we have compared the ability of cell-free extracts from wild-type CHO-K1 cells, Ku80-deficient xrs6 cells and Ku80-cDNA-complemented xrs6 cells (xrs6-Ku80) to rejoin different types of DSB in vitro. While the two Ku80-proficient extracts were highly efficient and accurate in rejoining all types of DNA ends, the xrs6 extract displayed strongly decreased NHEJ efficiency and accuracy. The lack of accuracy is most evident in non-homologous terminus configurations containing 3'-overhangs that abut a 5'-overhang or blunt end. While the sequences of the 3'-overhangs are mostly preserved by fill-in DNA synthesis in the Ku80-proficient extracts, they are always completely lost in the xrs6 extract so that, instead, small deletions displaying microhomology patches at their breakpoints arise. In summary, our results are consistent with previous results from Ku-deficient yeast strains and indicate that Ku may serve as an alignment factor that not only increases NHEJ efficiency but also accuracy. Furthermore, a secondary NHEJ activity is present in the absence of Ku which is error-prone and possibly assisted by base pairing interactions.
Toxicological Profile for Radon (2002)

This public health statement tells you about radon and the effects of exposure to it.The Environmental Protection Agency (EPA) identifies the most serious hazardous waste sites in the nation. These sites are then placed on the National Priorities List (NPL) and are targeted for long-term federal clean-up activities. The presence of radon at any site could be a consequence of its natural occurrence in the environment; its production from substances in anthropogenic hazardous waste; or both. These sites may be sources of exposure and exposure to this substance may be harmful.When a substance is released from a large area, such as an industrial plant, or from a container, such as a drum or bottle, it enters the environment. This release does not always lead to exposure. You are exposed to a substance when you come in contact with it. You may be exposed by breathing, eating, or drinking the substance, or by skin contact. External exposure to radiation may occur from natural or man-made sources. Radon is a naturally-occurring radioactive gas that changes into other radioactive substances, called progeny. Since radon and its progeny are present together in rock, soil, water, air, and construction materials, you will be exposed to the low-level radiation they give off just by being near them. Naturally occurring sources of radiation include radon and other radioactive elements in air, water, soil, or building materials, as well as cosmic radiation from space. Man-made radioactive materials are found in consumer products, industrial equipment, nuclear medicine patients, and to a smaller extent from atomic bomb fallout, hospital waste, and nuclear reactors.The results of the 1992 EPA National Residential Radon Survey estimated that 1 in 15 homes had an elevated radon level (i.e., a level at or above the EPA action level of 4 picocuries per liter of air). At the time, an estimated 5.8 million homes had an elevated radon level. The source of radon in homes is from naturally occurring (geologic) sources.When you are exposed to radon many factors will determine whether you will be harmed. These factors include the dose (how much), the duration (how long), and how you come in contact with it. You must also consider any other chemicals you are exposed to and your age, sex, diet, family traits, lifestyle, and state of health.
Antibodies to human fetal erythroid cells from a nonimmune phage antibody library (2001)

The ability to isolate fetal nucleated red blood cells (NRBCs) from the maternal circulation makes possible prenatal genetic analysis without the need for diagnostic procedures that are invasive for the fetus. Such isolation requires antibodies specific to fetal NRBCs. To generate a panel of antibodies to antigens present on fetal NRBCs, a new type of nonimmune phage antibody library was generated in which multiple copies of antibody fragments are displayed on each phage. Antibody fragments specific for fetal NRBCs were isolated by extensive predepletion of the phage library on adult RBCs and white blood cells (WBCs) followed by positive selection and amplification on fetal liver erythroid cells. After two rounds of selection, 44% of the antibodies analyzed bound fetal NRBCs, with two-thirds of these showing no binding of WBCs. DNA fingerprint analysis revealed the presence of at least 16 unique antibodies. Antibody specificity was confirmed by flow cytometry, immunohistochemistry, and immunofluorescence of total fetal liver and adult RBCs and WBCs. Antibody profiling suggested the generation of antibodies to previously unknown fetal RBC antigens. We conclude that multivalent display of antibodies on phage leads to efficient selection of panels of specific antibodies to cell surface antigens. The antibodies generated to fetal RBC antigens may have clinical utility for isolating fetal NRBCs from maternal circulation for noninvasive prenatal genetic diagnosis. Some of the antibodies may also have possible therapeutic utility for erythroleukemia.
Methotrexate for the Treatment of Crohn's Disease (1995)

In a group of patients with chronically active Crohn's disease, methotrexate was more effective than placebo in improving symptoms and reducing requirements for prednisone.
Variation of Protein Corona Composition of Gold Nanoparticles Following Plasmonic Heating (2013)

It is well recognized that the primary interaction of most biological environments with nanoparticles (NPs) is strongly influenced by a long-lived ("hard") protein corona that surrounds the NP and remains strongly adsorbed to its surface. The amount and composition of associated proteins in the corona adsorbed onto the NPs is related to several important factors, including the physicochemical properties of the NPs and the composition of the protein solution. Here, for the first time, it is shown that plasmonic heat induction (by laser activation) leads to significant changes in the composition of the hard protein corona adsorbed on low aspect ratio gold nanorods. Using mass spectrometry, several proteins in the corona were identified whose concentrations change most substantially as a result of photoinduced (plasmonic) heating versus simple thermal heating. Molecular modeling suggests that the origin of these changes in protein adsorption may be the result of protein conformational changes in response to much higher local temperatures that occur near the gold nanorods during photoinduced, plasmonic heating. These results may define new applications in vivo for NPs with hyperthermia capability and better define the likely interactions of cells with NPs after plasmonic heating. Potential changes in the protein corona following hyperthermia treatment may influence the final biological fate of plasmonic NPs in clinical applications and help elucidate safety considerations for hyperthermia applications.
Structural and electrical properties of Ge nanocrystals embedded in SiO2 by ion implantation and annealing (2005)

Silicon dioxide (SiO2) on Si layers with embedded germanium nanocrystals (Ge-ncs) were fabricated using Ge+ implantation and subsequent annealing. Transmission electron microscopy and Rutherford backscattering spectrometry have been used to study the Ge redistribution in the SiO2 films as a function of annealing temperature. A monolayer of Ge-ncs near the Si∕SiO2 interface was formed under specific annealing conditions. This layer, with a nc density and mean size measured to be, respectively, 1.1×1012∕cm2 and 5nm, is located at approximately 4nm from the Si∕SiO2 interface. Capacitance–voltage measurements were performed on metal-oxide-semiconductor structures containing such implanted SiO2 layers in order to study their electrical properties. The results indicate a strong memory effect at relatively low programming voltages (&amp;lt;5V) due to the presence of Ge-ncs near the Si∕SiO2 interface.