gebhart/patrepeval huggingface dataset:
Human/mouse radiation chimera are capable of mounting a human primary humoral response (1995)

Lubin et al recently described a new approach that enables the generation of human/mouse chimera by adoptive transfer of human peripheral blood mononuclear cells (PBMC) into lethally irradiated normal strains of mice, radioprotected with bone marrow (BM) from donors with severe combined immune deficiency (SCID). In the present study, we demonstrate in such human/mouse chimera a marked humoral response to recall antigen, such as tetanus toxoid (TT) or hepatitis B surface antigen (HBsAg), as well as a significant primary response to keyhole limpet hemocyanin (KLH). Maximal anti-KLH response in human/Balb chimera was attained 2 to 4 weeks after the immunization and declined thereafter. One week after transplantation, the predominant anti-KLH subtype was IgM, while after 2 weeks, the dominance had shifted to IgG. Similar primary antibody response was also demonstrated against the human immunodeficiency virus (HIV) Nef protein. Comparison between human/Balb and human/SCID chimera showed a major difference in their ability to mount a primary response against KLH. In Balb/c recipients, more than half of the mice exhibited marked IgM titers against KLH, while there was hardly any anti-KLH IgM response in the SCID recipients. From the earliest time point onwards, when anti-KLH antibodies were found in the latter chimera, they were predominantly of the IgG type. We have previously shown that in human/Balb chimera, unlike in SCID recipients, dissemination of transplanted PBMC into the spleen and other internal organs occurs within 24 hours. Therefore, it is likely that the early seeding in the appropriate microenvironment of the lymphoid tissues, is crucial for the maintenance of virgin human B cells.
A Dictionary-Based Approach for Estimating Shape and Spatially-Varying Reflectance (2015)

We present a technique for estimating the shape and reflectance of an object in terms of its surface normals and spatially-varying BRDF. We assume that multiple images of the object are obtained under fixed view-point and varying illumination, i.e, the setting of photometric stereo. Assuming that the BRDF at each pixel lies in the non-negative span of a known BRDF dictionary, we derive a per-pixel surface normal and BRDF estimation framework that requires neither iterative optimization techniques nor careful initialization, both of which are endemic to most state-of the-art techniques. We showcase the performance of our technique on a wide range of simulated and real scenes where we outperform competing methods.
Noonan syndrome. (1987)

Noonan syndrome was first described over 20 years ago by Noonan and Ehmkel; they defined a specific group of nine patients with valvular pulmonary stenosis who, in addition, had short stature, mild mental retardation, hypertelorism, and unusual facies. In retrospect, the first case was probably described by Kobylinski in 1883.2 Since that time, over 300 cases have been reported in medical publications. The incidence of Noonan syndrome has been estimated to be between 1 in 1000 and 1 in 2500 live births.3 The cardinal features of Noonan syndrome are short stature, congenital heart defect, broad or webbed neck, a peculiar chest deformity with pectus carinatum superiorly and pectus excava- tum inferiorly, and characteristic facies, which alter predictably with age to produce a discrete but changing phenotype which is described and illus- trated below. Good reviews of Noonan syndrome are to be found by Mendez and Opitz,4 Nora et al,5 Char et al,6 and Pearl.7
Thermal stability of ultrathin ZrO2 films prepared by chemical vapor deposition on Si(100) (2001)

As a function of thermal treatment, the chemical stability of ultrathin ZrO2 films prepared by chemical vapor deposition on a silicon substrate is investigated by x-ray photoelectron spectroscopy. The chemical structure is stable up to 800 °C in both vacuum and N2 ambient, but a reaction forming zirconium silicide occurs above 900 °C in vacuum. The formation of silicide is accounted for by a reaction mechanism involving a reaction of ZrO2 with SiO, the latter formed above 900 °C at the interface between Si(100) and the thin layer of SiO2 formed during growth of the ZrO2.
Nuclear translocation of the Y‐box binding protein by ultraviolet irradiation (1997)

The Y-box binding protein, YB-1, is a member of a DNA binding protein family with a structurally and functionally conserved cold shock domain. Using Western blotting and immunohistochemical methods, larger amounts of YB-1 were detected in the cytosol, particularly at the perinuclear region, than in the nucleus of human cancer cells. UV irradiation increased accumulation of YB-1 in the nucleus at 20 min and thereafter. This translocation of YB-1 into the nucleus by UV irradiation was blocked by the protein kinase inhibitor H-7, but not HA-1004. Both green fluorescent protein (GFP)-YB-1 and GFP-YB-1C with the C-terminus (248-317) of YB-1 were located mainly in the cytosol, but GFP-YB-1deltaC with a deletion at the C-terminus of YB-1 was located in the nucleus. YB-1 is translocated into the nucleus by UV irradiation, possibly through a protein kinase C-mediated signal transduction pathway, and the C-terminal region of YB-1 might be important for cytoplasmic retention of YB-1.
The Role of the Sca‐1 + /CD31 − Cardiac Progenitor Cell Population in Postinfarction Left Ventricular Remodeling (2006)

Cardiac stem cell-like populations exist in adult hearts, and their roles in cardiac repair remain to be defined. Sca-1 is an important surface marker for cardiac and other somatic stem cells. We hypothesized that heart-derived Sca-1 / CD31 cells may play a role in myocardial infarction-induced cardiac repair/remodeling. Mouse heart-derived Sca-1 /CD31 cells cultured in vitro could be induced to express both endothelial cell and cardiomyocyte markers. Immunofluorescence staining and fluorescence-activated cell sorting analysis indicated that endogenous Sca-1 /CD31 cells were significantly increased in the mouse heart 7 days after myocardial infarction (MI). Western blotting confirmed elevated Sca-1 protein expression in myocardium 7 days after MI. Transplantation of Sca-1 /CD31 cells into the acutely infarcted mouse heart attenuated the functional decline and adverse structural remodeling initiated by MI as evidenced by an increased left ventricular (LV) ejection fraction, a decreased LV end-diastolic dimension, a decreased LV endsystolic dimension, a significant increase of myocardial neovascularization, and modest cardiomyocyte regeneration. Attenuation of LV remodeling was accompanied by remarkably improved myocardial bioenergetic characteristics. The beneficial effects of cell transplantation appear to primarily depend on paracrine effects of the transplanted cells on new vessel formation and native cardiomyocyte function. Sca-1 / CD31 cells may hold therapeutic possibilities with regard to the treatment of ischemic heart disease.
Keynote Address: Liquefaction-induced Lateral Flow and Its Effects on Foundation Piles (2003)

Characteristic features of lateral spreading in liquefied deposits of sandy soils are addressed with reference to the damage during the Kobe Earthquake in 1995. The cases of injury to foundation piles due to the lateral spreading are then introduced along with the results of in-situ soil investigations. The back analysis was made by modelling the pile-soil interaction by way of the beam connected with several springs. The spring constants were reduced at varying levels so as to yield the observed difference in horizontal displacements between the ground surface and pile top at the time of the earthquake. The degree of stiffness degradation which is compatible with the observed difference in displacements was obtained with the result that the stiffness of liquefied soil deposits is drastically reduced by a factor of 10-2 to 10-3.
A vaccinia serine protease inhibitor which prevents virus-induced cell fusion (1992)

A deletion mutant lacking the non-essential vaccinia virus gene K2L, a member of the serine protease inhibitor superfamily, was constructed. This virus replicates in vitro in all cell types tested and its virulence and immunogenicity in vivo are comparable to those of the parent virus in intranasally inoculated mice. However, in a variety of cell lines the cytopathic effect of the deletion mutant (vKL4) is markedly different from that caused by the parent virus: the absence of K2L in infected cells results in extensive polykaryocytosis. Reinsertion of the K2L gene into vKL4 abolishes this fusion activity, thus confirming that the polykaryocytosis is the result of the deletion of K2L rather than of spontaneous mutations elsewhere in the genome, and that in cells infected with the WR strain of vaccinia virus the K2L gene product prevents fusion. The cell type-specific polykaryocytosis induced by vKL4 is apparent at late times post-infection, occurs from within and requires the synthesis of at least one late virus protein. Other vaccinia virus proteins known to be involved in fusion of infected cells are a 14K membrane protein which is required for fusion, and the haemagglutinin which prevents fusion. The haemadsorption properties of cells infected with the parent virus and the deletion mutant were indistinguishable: both haemadsorbed chicken erythrocytes. A monoclonal antibody against the 14K protein inhibited fusion of vKL4-infected cells, thus demonstrating that in addition to the absence of the K2L gene product, the 14K protein is required for fusion to occur.
The Th17 pathway in the peripheral lung microenvironment interacts with expression of collagen V in the late state of experimental pulmonary fibrosis (2014)

A positive feedback loop between the expression patterns of collagen V and IL-17 may coordinate the maintenance of peripheral collagen I in the absence of IL-17 receptor A in fibrosis-susceptible strains in a site-specific manner.
Quantity of dietary protein intake, but not pattern of intake, affects net protein balance primarily through differences in protein synthesis in older adults (2014)

To examine whole body protein turnover and muscle protein fractional synthesis rate (MPS) following ingestions of protein in mixed meals at two doses of protein and two intake patterns, 20 healthy older adult subjects (52-75 yr) participated in one of four groups in a randomized clinical trial: a level of protein intake of 0.8 g (1RDA) or 1.5 g·kg(-1)·day(-1) (∼2RDA) with uneven (U: 15/20/65%) or even distribution (E: 33/33/33%) patterns of intake for breakfast, lunch, and dinner over the day (1RDA-U, 1RDA-E, 2RDA-U, or 2RDA-E). Subjects were studied with primed continuous infusions of L-[(2)H5]phenylalanine and L-[(2)H2]tyrosine on day 4 following 3 days of diet habituation. Whole body protein kinetics [protein synthesis (PS), breakdown, and net balance (NB)] were expressed as changes from the fasted to the fed states. Positive NB was achieved at both protein levels, but NB was greater in 2RDA vs. 1RDA (94.8 ± 6.0 vs. 58.9 ± 4.9 g protein/750 min; P = 0.0001), without effects of distribution on NB. The greater NB was due to the higher PS with 2RDA vs. 1RDA (15.4 ± 4.8 vs. -18.0 ± 8.4 g protein/750 min; P = 0.0018). Consistent with PS, MPS was greater with 2RDA vs. 1RDA, regardless of distribution patterns. In conclusion, whole body net protein balance was greater with protein intake above recommended dietary allowance (0.8 g protein·kg(-1)·day(-1)) in the context of mixed meals, without demonstrated effects of protein intake pattern, primarily through higher rates of protein synthesis at whole body and muscle levels.
Verbal and visuospatial working memory development and deficits in children and adolescents with schizophrenia (2010)

Our findings support disruptions in shared verbal and visuospatial working memory networks, such as those supporting encoding processes, in children and adolescents with schizophrenia. We also found specific deficits in non-shared verbal working memory performance in childhood-onset schizophrenia.
Antibody Uptake into Neurons Occurs Primarily via Clathrin-dependent Fcγ Receptor Endocytosis and Is a Prerequisite for Acute Tau Protein Clearance (2013)

Tau immunotherapy is effective in transgenic mice, but the mechanisms of Tau clearance are not well known. To this end, Tau antibody uptake was analyzed in brain slice cultures and primary neurons. Internalization was rapid (<1 h), saturable, and substantial compared with control mouse IgG. Furthermore, temperature reduction to 4 °C, an excess of unlabeled mouse IgG, or an excess of Tau antibodies reduced uptake in slices by 63, 41, and 62%, respectively (p = 0.002, 0.04, and 0.005). Uptake strongly correlated with total and insoluble Tau levels (r(2) = 0.77 and 0.87 and p = 0.002 and 0.0002), suggesting that Tau aggregates influence antibody internalization and/or retention within neurons. Inhibiting phagocytosis did not reduce uptake in slices or neuronal cultures, indicating limited microglial involvement. In contrast, clathrin-specific inhibitors reduced uptake in neurons (≤ 78%, p < 0.0001) and slices (≤ 35%, p = 0.03), demonstrating receptor-mediated endocytosis as the primary uptake pathway. Fluid phase endocytosis accounted for the remainder of antibody uptake in primary neurons, based on co-staining with internalized dextran. The receptor-mediated uptake is to a large extent via low affinity FcγII/III receptors and can be blocked in slices (43%, p = 0.04) and neurons (53%, p = 0.008) with an antibody against these receptors. Importantly, antibody internalization appears to be necessary for Tau reduction in primary neurons. Overall, these findings clarify that Tau antibody uptake is primarily receptor-mediated, that these antibodies are mainly found in neurons with Tau aggregates, and that their intracellular interaction leads to clearance of Tau pathology, all of which have major implications for therapeutic development of this approach.
Promoter analysis of the Xanthomonas campestris pv. campestris gum operon directing biosynthesis of the xanthan polysaccharide (1996)

The Xanthomonas campestris gum gene cluster is composed of 12 genes designated gumB, -C, -D, -E, -F, -G, -H, -I, -J, -K, -L, and -M. The transcriptional organization of this gene cluster was analyzed by the construction of gum-lacZ transcriptional fusions in association with plasmid integration mutagenesis. This analysis, coupled with primer extension assays, indicated that the gum region was mainly expressed as an operon from a promoter located upstream of the first gene, gumB.
Cloning and expression of cDNA for anti-müllerian hormone. (1986)

Messenger RNA, prepared from fetal bovine testicular tissue, was used to construct a cDNA library in lambda gt11 phage. The library was screened with an antibody probe directed against bovine anti-Müllerian hormone and three positive clones were isolated. Cross-hybridizing cDNA inserts carried by clones 4 and 5 (1.2 and 0.08 kilobases long, respectively) code for a fragment of authentic anti-Müllerian hormone, as shown by the ability of the anti-epitope antibodies eluted from fusion protein 4 to bind strongly to anti-Müllerian hormone on immunoblots and by the capacity of anti-epitope antibodies 4 and 5 to precipitate radioiodinated bovine anti-Müllerian hormone. A probe prepared from insert 4 hybridizes with an mRNA present only in tissues that are known producers of anti-Müllerian hormone, such as the fetal testis and adult ovarian follicles. The amount of specific mRNA in tissues of males and females is related to the rate of their anti-Müllerian hormone production. The 2.1-kilobase size of this mRNA species is large enough to code for the Mr 62,000 anti-Müllerian hormone polypeptide chain. Insert 4 also hybridizes with an mRNA of similar size in human and rat fetal testicular tissue. The third isolated clone, clone 8, which does not cross-hybridize with the others, carries a cDNA insert coding for a ubiquitous protein, smaller than anti-Müllerian hormone, with which it apparently shares an epitope.
α,β-Unsaturated β-Silyl Imide Substrates for Catalytic, Enantioselective Conjugate Additions:  A Total Synthesis of (+)-Lactacystin and the Discovery of a New Proteasome Inhibitor (2006)

Chiral (salen)Al mu-oxo dimer 1 catalyzes the highly enantioselective conjugate addition of carbon-centered nucleophiles to alpha,beta-unsaturated silyl imides. Allyldimethylsilane-substituted imide 4 was identified as an optimal substrate, undergoing addition reactions with a variety of nitrile nucleophiles in high yield and enantiomeric excess. The silicon-containing products are synthetically useful chiral building blocks, as demonstrated by their application to an enantioselective total synthesis of the potent proteasome inhibitor (+)-lactacystin (2). Elaboration of lactam 5a to the natural product was effected in 12 steps and in 11% overall yield and proceeded through an unusual spiro beta-lactone intermediate (11). This compound was found to inhibit the chymotrypsin-like site of the 26S proteasome at similar levels to known inhibitor clasto-lactacystin beta-lactone (omuralide).
A method for accurate spatial registration of PET images and histopathology slices (2015)

We have developed a registration method to align PET images and histopathology slices with an accuracy comparable to the spatial resolution of the PET images.
Interleukin 2 and Psoriasis (1988)

Immunotherapy with interleukin 2 and lymphokine-activated killer cells can result in regression of metastatic cancer. Dermatologic complications associated with this therapy include erythema, pruritus, and a mild desquamation. Three patients with a history of psoriasis received high-dose interleukin 2 alone or in conjunction with lymphokine-activated killer cells for treatment of metastatic renal cell carcinoma. Two patients developed an erythrodermic exacerbation during therapy while the third patient experienced a localized flare. Topical treatment was effective in inducing remission in all three patients. Histologic analysis of serial skin biopsy specimens revealed psoriasiform changes in involved skin as well as epidermal spongiosis and a perivascular mononuclear cell infiltrate. The psoriatic exacerbation from interleukin 2 did not affect antitumor response to the therapy and should not be considered a contraindication to treatment.
Lipid Metabolism Genes in Contralateral Unaffected Breast and Estrogen Receptor Status of Breast Cancer (2013)

Risk biomarkers that are specific to estrogen receptor (ER) subtypes of breast cancer would aid the development and implementation of distinct prevention strategies. The contralateral unaffected breast of women with unilateral breast cancer (cases) is a good model for defining subtype-specific risk because women with ER-negative (ER-) index primaries are at high risk for subsequent ER-negative primary cancers. We conducted random fine needle aspiration of the unaffected breasts of cases. Samples from 30 subjects [15 ER-positive (ER+) and 15 ER- cases matched for age, race and menopausal status] were used for Illumina expression array analysis. Findings were confirmed using quantitative real-time PCR (qRT-PCR) in the same samples. A validation set consisting of 36 subjects (12 ER+, 12 ER- and 12 standard-risk healthy controls) was used to compare gene expression across groups. ER- case samples displayed significantly higher expression of 18 genes/transcripts, 8 of which were associated with lipid metabolism on gene ontology analysis (GO: 0006629). This pattern was confirmed by qRT-PCR in the same samples, and in the 24 cases of the validation set. When compared to the healthy controls in the validation set, significant overexpression of 4 genes (DHRS2, HMGCS2, HPGD and ACSL3) was observed in ER- cases, with significantly lower expression of UGT2B11 and APOD in ER+ cases, and decreased expression of UGT2B7 in both subtypes. These data suggest that differential expression of lipid metabolism genes may be involved in the risk for subtypes of breast cancer, and are potential biomarkers of ER-specific breast cancer risk.
A scFv Antibody-Based Immunoaffinity Chromatography Column for Clean-Up of Bisphenol A-Contaminated Water Samples (2008)

This is a report on the development of immunoaffinity chromatography using a column of silica gel with an immobilized single-chain variable fragment (scFv) antibody specific to bisphenol A (BPA) for cleanup of BPA-contaminated water samples. The BBA-2187 scFv antibody specific to BPA was purified from the periplasmic fractions of the recombinant Escherichia coli. After a sample of BPA-contaminated river water was applied to the immunoaffinity column, the background signal intensity observed in high-performance liquid chromatography (HPLC) analysis of the eluates was markedly lower than that observed in HPLC analysis of the eluates from an Oasis HLB cartridge treated with the same sample. The immunoaffinity column efficiently concentrated BPA from actual river water samples with different matrices. Our results demonstrate that the immunoaffinity column with immobilized BBA-2187 scFv antibody is efficient for the cleanup of BPA-contaminated water samples from different sources.
The preparation of nucleoside carbonates (1971)

The preparation of some di(nucleoside) carbonates by means of a simple transesterification reaction is described. The active 3′-O-βββ-trichloroethoxycarbonyl esters of suitably protected pyrimidine nucleosides were treated with the 5′-monosodio-derivatives of 2′,3′-O-isopropylidene-adenosine, -cytidine, -inosine, -guanosine, and -uridine. The method was extended to the preparation of the tri(nucleoside) dicarbonates, di(thymidinyl) adenosinyl dicarbonate and di(deoxyuridinyl) uridinyl dicarbonate.
Translation initiation factor eIF-4gamma is encoded by an amplified gene and induces an immune response in squamous cell lung carcinoma (1997)

Amplification of cellular oncogenes is an important mechanism of altered gene expression in human cancers. Using comparative genomic hybridization we recently identified an amplification at 3q26.1-q26.3 in 30% of squamous cell carcinomas of the lung. A variety of methods including microdissection-mediated procedures permit cloning of genes encoded within amplified domains but do not directly lead to the identification of biologically relevant genes. In this study, we have circumvented this problem by combining an immunological and molecular genetic approach to analyze squamous cell lung carcinoma. To identify both amplified and tumor relevant genes, we generated a cDNA expression library from a tumor with the 3q amplification and hybridized the expressed recombinant polypeptides with the autologous serum. Of 400000 cDNA clones we identified 17 antigens which induce an immune response in a patient with squamous cell lung carcinoma. While most clones represent individual genes sequence analysis revealed that four of the 17 cDNAs are nearly identical with the eukaryotic translation initiation factor (eIF)-4gamma recently assigned on 3q. We demonstrated that the gene for eIF-4gamma was amplified within 3q26-q27 in independent squamous cell lung carcinomas. In this study, we report the identification of several antigens which elicit an immune response in a squamous cell lung carcinoma patient including eIF-4gamma. eIF-4gamma is encoded by an amplified gene and possibly plays a crucial part in the development of squamous cell lung carcinoma.
Once daily fluticasone furoate nasal spray is effective in seasonal allergic rhinitis caused by grass pollen (2007)

Fluticasone furoate nasal spray 110 mug od was effective in improving the nasal symptoms of SAR. It also produced significant improvements in ocular symptoms.