gebhart/patrepeval huggingface dataset:
Mars Exploration Entry, Descent, and Landing Challenges (2007)

The United States has successfully landed five robotic systems on the surface of Mars. These systems all had landed masses below 0.6 metric tons, had landed footprints on the order of hundreds of kilometers, and landed at sites below 1:4 kilometers elevation due the need to perform entry, descent, and landing operations in an environment with sufficient atmospheric density. At present, robotic exploration systems engineers are struggling with the challenges of increasing landed mass capability to 0.8 metric tons while improving landed accuracy to 10 kilometers and landing at a site as high as 2 kilometers elevation for the Mars science laboratory project. Meanwhile, current plans for human exploration of Mars call for the landing of 40–80 metric tons surface elements at scientifically interesting locations within close proximity (tens of meters) of pre-positioned robotic assets. This paper summarizes past successful entry, descent, and landing systems and approaches being developed by the robotic Mars exploration program to increase landed performance (mass, accuracy, and surface elevation). In addition, the entry, descent, and landing sequence for a human exploration system will be reviewed, highlighting the technology and systems advances required.
In Search of Cellular Immunophenotypes in the Blood of Children with Autism (2011)

These results support previous findings that immune dysfunction may occur in some children with autism. Further evaluation of the nature of the dysfunction and how it may play a role in the etiology of autism or in facets of autism neuropathology and/or behavior are needed.
Nick-initiated homologous recombination: Protecting the genome, one strand at a time (2016)

Homologous recombination (HR) is an essential, widely conserved mechanism that utilizes a template for accurate repair of DNA breaks. Some early HR models, developed over five decades ago, anticipated single-strand breaks (nicks) as initiating lesions. Subsequent studies favored a more double-strand break (DSB)-centered view of HR initiation and at present this pathway is primarily considered to be associated with DSB repair. However, mounting evidence suggests that nicks can indeed initiate HR directly, without first being converted to DSBs. Moreover, recent studies reported on novel branches of nick-initiated HR (<sup>nick</sup>HR) that rely on single-, rather than double-stranded repair templates and that are characterized by mechanistically and genetically unique properties. The physiological significance of <sup>nick</sup>HR is not well documented, but its high-fidelity nature and low mutagenic potential are relevant in recently developed, precise gene editing approaches. Here, we review the evidence for stimulation of HR by nicks, as well as the data on the interactions of <sup>nick</sup>HR with other DNA repair pathways and on its mechanistic properties. We conclude that <sup>nick</sup>HR is a bona-fide pathway for nick repair, sharing the molecular machinery with the canonical HR but nevertheless characterized by unique properties that secure its inclusion in DNA repair models and warrant future investigations.
Trafficking machinery of NKT cells: shared and differential chemokine receptor expression among Vα24+Vβ11+ NKT cell subsets with distinct cytokine-producing capacity (2002)

Natural killer T (NKT) cells are important regulators of the immune system, but their trafficking machinery, including expression of chemokine receptors, has been poorly defined. Unlike other conventional T-cell populations, we show that most NKT cells express receptors for extralymphoid tissue or inflammation-related chemokines (CCR2, CCR5, and CXCR3), while few NKT cells express lymphoid tissue-homing chemokine receptors (CCR7 and CXCR5). A population with homing potential for lymph nodes (L selectin(+) CCR7(+)) exists only within a small subset of CD4 NKT cells. We show differential expression of chemokine receptors among NKT cell subsets: CCR4 is mainly expressed by a high cytokine (interleukin-4/interleukin-2)-producing (CD4) NKT subset, while CCR1, CCR6, and CXCR6 are preferentially expressed by the low cytokine-producing CD8 and CD4(-)CD8(-) subsets. In line with this, TARC/CCL17 (a CCR4 ligand) induces preferential chemotaxis of the CD4 NKT subset, while chemotactic activities of LARC/CCL20 (a CCR6 ligand) and MIP-1 alpha/CCL3 (a CCR1 ligand) are focused on the CD8 and CD4(-)CD8(-) NKT cells. We conclude that, unlike conventional naive, memory, or effector T cells, the entire NKT cell population expresses nonlymphoid tissue homing chemokine receptors, yet NKT cell subsets differ considerably from each other by displaying distinct and reciprocal expression patterns of some chemokine receptors. Our results identify chemokine receptors that are potentially important for trafficking of human blood NKT cell subsets and reveal their function (cytokine production capacity)-dependent differential trafficking potentials.
High-density peptide arrays (2009)

Arrays promise to advance biology by allowing parallel screening for many different binding partners. Meanwhile, lithographic methods enable combinatorial synthesis of > 50,000 oligonucleotides per cm(2), an advance that has revolutionized the whole field of genomics. A similar development is expected for the field of proteomics, provided that affordable, very high-density peptide arrays are available. However, peptide arrays lag behind oligonucleotide arrays. This review discusses recent developments in the field with an emphasis on methods that lead to very high-density peptide arrays.
High-Level Recombinant Gene Expression in Rabbit Endothelial Cells Transduced by Retroviral Vectors (1989)

By virtue of its immediate contact with the circulating blood, the endothelium provides an attractive target for retroviral vector transduction for the purpose of gene therapy. To see whether efficient gene transfer and expression was feasible, rabbit aortic endothelial cells were infected with three Moloney murine leukemia virus-derived retroviral vectors. Two of these vectors carry genes encoding products that are not secreted: N2, containing only the selectable marker gene neoR, and SAX, containing both neoR gene and an SV40-promoted adenosine deaminase (ADA) gene. The third vector, G2N, contains a secretory rat growth hormone (rGH) gene and an SV40-promoted neoR gene. Infection with all three vectors resulted in expression of the respective genes. A high level of human ADA expression was observed in infected endothelial cell populations both before and after selection in G418. G2N-infected rabbit aortic endothelial cells that were grown on a synthetic vascular graft continued to secrete rGH into the culture medium. These studies suggest that endothelial cells may serve as vehicles for the introduction in vivo of functioning recombinant genes.
Expression and characterization of the human c-myc DNA-binding protein. (1985)

In an effort to study in detail the nature of the protein product of the human protooncogene c-myc, we have expressed the gene at high levels in Escherichia coli. The c-myc coding region was taken from a full-length cDNA clone and inserted into a vector designed to express foreign gene products efficiently in E. coli. Pulse-labeling experiments indicated that the rate of expression of c-myc in this thermoinducible expression system is very efficient. The product was relatively stable and accumulated to approximately 10% of total cellular protein. A purification protocol was devised which allowed the c-myc protein to be readily purified in quantities sufficient for detailed biochemical and physical analyses. A high-titer polyclonal antiserum was raised against the pure protein and shown to immunoprecipitate the p110gag-myc fusion protein of MC-29-infected quail cells. This antiserum also selectively detects a protein with an apparent molecular weight of 64,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis from a Burkitt lymphoma cell line. We conclude that this 64-kilodalton protein is the human c-myc gene product since the E. coli-made protein exhibits an equivalent molecular weight on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, even though its calculated molecular weight is 49,000. Furthermore, we demonstrate that the bacterially made human c-myc protein is a DNA-binding protein and that it exhibits a high nonspecific affinity for double-stranded DNA.
[Cloning of the tag7 gene expressed in metastatic mouse tumors]. (1996)

Gene expression was compared in a metastatic (VMR-Liv) neoplastic cell line and a related nonmetastatic (VMR-O) neoplastic cell line by means of the differential display method. A fragment of cDNA corresponding to the tag7 gene, differentially expressed in the metastatic cell line, was isolated. The full-length tag7 cDNA was cloned and its nucleotide sequence was determined. No homology between the tag7 gene and known sequences was revealed. tag7 gene transcription was studied in some tumors, cell lines, and normal mouse organs.
Functional Dissection of Eukaryotic Initiation Factor 4F: the 4A Subunit and the Central Domain of the 4G Subunit Are Sufficient To Mediate Internal Entry of 43S Preinitiation Complexes (1996)

Eukaryotic translation is initiated following binding of ribosomes either to the capped 5' end of an mRNA or to an internal ribosomal entry site (IRES) within its 5' nontranslated region. These processes are both mediated by eukaryotic initiation factor 4F (eIF4F), which consists of eIF4A (helicase), eIF4E (cap-binding protein), and eIF4G subunits. Here we present a functional analysis of eIF4F which defines the subunits and subunit domains necessary for its function in initiation mediated by the prototypical IRES element of encephalomyocarditis virus. In an initiation reaction reconstituted in vitro from purified translation components and lacking eIF4A and -4F, IRES-mediated initiation did not require the cap-binding protein eIF4E but was absolutely dependent on eIF4A and the central third of eIF4G. This central domain of eIF4G bound strongly and specifically to a structural element within the encephalomyocarditis virus IRES upstream of the initiation codon in an ATP-independent manner and with the same specificity as eIF4F. The carboxy-terminal third of eIF4G did not bind to the IRES. The central domain of eIF4G was itself UV cross-linked to the IRES and strongly stimulated UV cross-linking of eIF4A to the IRES in conjunction with either eIF4B or with the carboxy-terminal third of eIF4G.
Review: Systemic treatment of advanced colorectal cancer: Tailoring therapy to the tumor (2008)

Colorectal cancer is a prevalent disease in Western countries. While prevention through screening is the best approach to combat the development of colorectal cancer through the removal of precursor adenomas, many patients present with advanced disease that will require surgery and systemic therapy to improve survival. With reference to systemic therapy, the median survival of patients with metastatic colorectal cancer (those with tumor spread to lymph nodes or distant sites) has improved over the past three decades due to the introduction of 5-fluorouracil (5-FU), its subsequent biomodulation, and the addition other chemotherapeutic agents. There is now evidence that the biology of the colorectal tumor, in addition to the stage of colorectal cancer, may predict response to 5-FU-based therapy. More recently, systemic biological therapies that target signaling processes for tumor growth, such as epidermal growth factor receptor, and vascular endothelial growth factor, are also effective in improving patient survival with metastatic colorectal cancer. The use of a combination of systemic therapies that include chemotherapy and biologic therapy should continue to increase patient survival with metastatic colorectal cancer through appropriately designed clinical trials. Treatments based on the biology of the colorectal tumor also need to be examined through clinical trials.
Peripheral Blood Stem Cell Collection in Elderly Patients (2008)

Abstract Introduction Intensive treatments like autologous stem cells transplantations are final standard treatment in lymphoma and myeloma for young people (1,2). In the context of population’s ageing, those treatments should be eligible for older patients. One of the major causes which did not allowed these procedures in elderly patients is the reports of the impact of the age on the process of mobilisation of peripheral stem cell (3). We proceed a retrospective study to explore the feasibility of stem cells collection in patients older than 65 years, compared to younger people. Material and patients During the period of 1999–2006, we identified all the patients older than 65 years, with myeloma and lymphoma, who performed peripheral stem cells collection in Brest’s blood collection centre. We excluded patients for bone marrow collection. Patients were eligible if they achieved more than 2.106 CD34/kg. Then we compared the results obtained in older patients with the results obtained in younger people. Results We identified 100 patients older than 65 years between the 359 patients who underwent peripheral stem cell harvest in Brest’s harvest centre. We excluded 37 others patients for non-conformity. The elderly patients were significantly older (age 68.9 vs. 49.3 y, p&amp;lt;10−6). No differences were seen for the number of collection between the older and the younger patients (1.59 vs. 1.50, p&amp;gt;0.05). The number of CD34/kg per patient was sufficient to realise more than one autologous transplantation in both groups of patients (5.3 vs. 6.67, p=0.004). Samples were sufficiently rich for CD34/kg (4.36 vs. 5.54, p=0.02). Patients were harvested in one (60), two (25) or more than 2 collections (15). Among the older patients, 71% achieved a sufficient collection of more than 2.106 CD34/kg in one sample only. Conclusion We identified one hundred patients older than 65 years, during a period of 8 years, who performed peripheral stem cells collection, with sufficient wealth (&amp;gt;2.106 CD34/kg). The majority of patients, 60%, need only one stem cells harvesting. The study confirmed that old patients could be harvested like young people, and eligible for stem cells autologous transplantation.
Vaccination of high-risk breast cancer patients with mucin-1 (MUC1) keyhole limpet hemocyanin conjugate plus QS-21. (2000)

Our objective was to determine whether an immune response can be generated against MUC1 peptide and against tumor cell MUC1 after vaccination with MUC1-keyhole limpet hemocyanin (KLH) conjugate plus QS-21 in breast cancer patients. Nine patients with a history of breast cancer but without evidence of disease were treated with MUC1-KLH conjugate plus QS-21, containing 100 microg of MUC1 and 100 microg of QS-21. s.c. vaccinations were administered at weeks 1, 2, 3, 7, and 19. Peripheral blood was drawn at frequent intervals to assess antibody titers. Skin tests were placed at weeks 1, 3, 9, and 21 to determine delayed type hypersensitivity reactions. Common toxicities included a local skin reaction at the site of the vaccine, usually of 4-5 days' duration, and mild flu-like symptoms usually of 1-2 days' duration. High IgM and IgG antibody titers against synthetic MUC1 were detected. IgG antibody titers remain elevated from a minimum of 106-137 weeks after the first vaccination. Binding of IgM antibody to MCF-7 tumor cells was observed in seven patients, although there was minimal binding of IgG antibody. Two patients developed significant antibody titers post-high-dose chemotherapy and stem cell reinfusion. There was no evidence of T cell activation. This MUC1-KLH conjugate plus QS-21 was immunogenic and well tolerated in breast cancer patients. Additional trials are ongoing to determine the optimal MUC1 peptide for use in larger clinical trials. Further investigation of vaccine therapy in high-risk breast cancer is warranted.
(Co‐)Polyesters Derived from Isosorbide and 1,4‐Cyclohexane Dicarboxylic Acid and Succinic Acid (2010)

Abstract The homopolyester of isosorbide and cis – trans 1,4‐cyclohexane dicarboxylic acid (CHDA) was prepared by three different methods, but only polycondensation of isosorbide and CHDA dichloride yielded a satisfactory molecular weight (corrected $\overline M _{\rm n} $ = 11 000 Da). For the best sample the MALDI‐TOF mass spectrum revealed a high content of cycles. The homopolyester of CHDA and isomannide or isoidide was prepared analogously. For the homopolyesters of CHDA high glass transition temperatures were found ( T g = 146 °C for isosorbide, 133 °C for isomannide, and 115 °C for isoidide), whereas the polyester of isosorbide and succinic acid (SuA) has a T g around 77 °C. Copolyester of isosorbide and various molar ratios of CHDA and SuA were prepared by two different methods, but only rather low molecular weights were obtained. SEC measurements with and without “universal calibration” revealed that the normal calibration with polystyrene overestimates the real molecular weights by 30–45%. magnified image
Some observations on the penetration of antibiotics through mucus in vitro (1966)

A study has been made on the penetration values in vitro of antibiotics through hog gastric mucin at pH 7.4. Determinations have also been done on the binding of antibiotics to mucus and human plasma. The mucolytic agent N-acetyl cysteine has been studied in regard to its effect on antibiotics penetrating mucus and for any possible inactivation of antibiotics.
Partial Purification and Characterization of Nuclear Ribonuclease P from Wheat (1997)

Ribonuclease P (RNase P) from wheat nuclei has been purified over 1000-fold, using wheat germ extract as starting material and a combination of poly(ethylenglycol) precipitation and column chromatography. The enzyme was shown to be of nuclear origin by its characteristic ionic requirements; for optimum activity it requires 0.5-1.5 mM Mg2+, which can be partly replaced by Mn2+. With about 100 kDa, wheat nuclear RNase P has the lowest molecular mass reported so far for a eukaryotic RNase P. The enzyme has an isoelectric point of 5.0 and a buoyant density of 1.34 g/ml in CsCl, suggesting the presence of a nucleic acid component; it is, however, insensitive against treatment with micrococcal nuclease. Wheat germ RNase P requires an intact tertiary structure of the pre-tRNA substrate; its cleavage efficiency is also influenced by the presence of an intron, and by the nature of the 3' terminus of the substrate. The apparent Km and Vmax for an intronless plant pre-tRNA(Tyr) are 10.3 nM and 1.12 fmol/min, respectively.
Efficient and reproducible generation of tumour-infiltrating lymphocytes for renal cell carcinoma (2015)

TILs can be consistently produced from renal cell carcinoma biopsies maintaining autologous tumour recognition after expansion in vitro. While the method of disaggregation has little impact on the success of TIL growth, methods that preserve the cell surface architecture facilitate TIL recognition of an autologous tumour, which is important in terms of characterising the functionality of the expanded TIL population.
Surface‐Initiated Atom Transfer Radical Polymerization of Oligo(ethylene glycol) Methyl Methacrylate from a Mixed Self‐Assembled Monolayer on Gold (2006)

Abstract This paper describes the in‐situ synthesis of an oligo(ethylene glycol)‐functionalized polymer brush in which the oligo(ethylene glycol) chains are presented as side‐chains from a methacrylate backbone that is anchored to the surface. These polymer “bottlebrushes” have been synthesized by surface‐initiated atom transfer radical polymerization (SI‐ATRP) of oligo(ethylene glycol) methyl methacrylate (OEGMA) from a mixed self‐assembled monolayer (SAM) of an ATRP initiator‐functionalized alkanethiol and a diluent, methyl‐terminated thiol. The systematic control of the ATRP initiator surface density afforded by the mixed SAM on gold and the polymerization time enables the polymer chain length and surface density to be independently controlled. Surface plasmon resonance (SPR) spectroscopy of fibronectin (Fn) adsorption on poly(OEGMA) grown from the surface of the mixed SAMs on gold shows that above a threshold solution molar ratio of the ATRP‐initiator thiol to methyl‐terminated thiol of 0.2, and a dry film thickness of ∼ 4 nm, Fn adsorption on the surface‐initiated poly(OEGMA) coatings was below the detection limit of SPR. The relatively low surface density of the ATRP initiator required to confer protein resistance to the surface suggests that SI‐ATRP may be a viable strategy to create protein resistant polymer brushes on real‐world materials.
Recombinant human erythropoietin protects the myocardium from ischemia-reperfusion injury and promotes beneficial remodeling (2003)

Erythropoietin (EPO), originally identified for its critical hormonal role in promoting erythrocyte survival and differentiation, is a member of the large and diverse cytokine superfamily. Recent studies have identified multiple paracrineautocrine functions of EPO that coordinate local responses to injury by maintaining vascular autoregulation and attenuating both primary (apoptotic) and secondary (inflammatory) causes of cell death. Experimental evidence also supports a role for EPO in repair and regeneration after brain and spinal cord injury, including the recruitment of stem cells into the region of damage. Tissue expression of the EPO receptor is widespread, especially during development, and includes the heart. However, it is currently unknown as to whether EPO plays a physiological function in adult myocardial tissue. We have assessed the potential protective role of EPO in vitro with adult rat cardiomyocytes, and in vivo in a rat model of myocardial infarction with reperfusion. The results show that EPO markedly prevents the apoptosis of cultured adult rat myocardiocytes subjected to 28 h of hypoxia (approximately 3% normal oxygen). Additional studies employing a rat model of coronary ischemia-reperfusion showed that the administration of recombinant human EPO (5,000 units/kg of body weight; i.p. daily for 7 days) reduces cardiomyocyte loss by approximately 50%, an extent sufficient to normalize hemodynamic function within 1 week after reperfusion. These observations not only suggest a potential therapeutic role for recombinant human EPO in the treatment of myocardial ischemia and infarction by preventing apoptosis and attenuating postinfarct deterioration in hemodynamic function, but also predict that EPO is likely a tissue-protective cytokine in other organs as well.