gebhart/patrepeval huggingface dataset:
A novel low-temperature preparation of several ferrimagnetic spinels and their magnetic and Mössbauer characterization (1988)

Ultrafine subdomain particles of NiFe2O4, Ni0.5Zn0.5Fe2O4, and CoFe2O4 were prepared under mild hydrothermal conditions by precipitating from metal nitrates. Magnetic and Mössbauer effect measurements revealed the superparamagnetic nature of these ferrite particles. The crystallite sizes were in the range 5.0–20.0 nm with a very narrow particle size distribution. The magnetic properties and Mössbauer hyperfine parameters of these subdomain ferrite particles are somewhat different from those reported for multidomain bulk materials. The hydrothermal ferrite powders were found to sinter to almost theoretical density with little or no intergranular porosity.
Hepatitis A virus cDNA and its RNA transcripts are infectious in cell culture (1987)

A full-length cDNA copy of an attenuated, cell culture-adapted hepatitis A virus (HAV HM-175/7 MK-5) genome was constructed in the PstI site of plasmid vector pBR322. Transfection of monkey kidney cells with this plasmid failed to induce the production of hepatitis A virus (HAV). The HAV cDNA was excised from pBR322 and inserted, without the oligo(dG) X oligo(dC) tails, into an RNA transcription vector to yield plasmid pHAV/7. Transfection of monkey kidney cells with pHAV/7 DNA induced HAV infection. Transfection with RNA transcripts produced in vitro from pHAV/7 yielded about 10-fold more HAV than did transfection with pHAV/7 DNA. Marmosets inoculated with transfection-derived virus developed anti-HAV antibodies and had liver enzyme patterns that closely resembled the liver enzyme patterns seen in animals inoculated with virus from a comparable level of cell culture passage. Infectious RNA transcripts from HAV cDNA should be useful for studying the molecular basis of cell culture adaptation and attenuation as well as for studying specific viral functions.
STRUCTURE AND FUNCTION OF BACTERIAL SIGMA FACTORS (1988)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Activation of the insulin receptor (IR) by insulin and a synthetic peptide has different effects on gene expression in IR-transfected L6 myoblasts (2008)

Single-chain peptides have been recently produced that display either mimetic or antagonistic properties against the insulin and IGF-1 (insulin-like growth factor 1) receptors. We have shown previously that the insulin mimetic peptide S597 leads to significant differences in receptor activation and initiation of downstream signalling cascades despite similar binding affinity and in vivo hypoglycaemic potency. It is still unclear how two ligands can initiate different signalling responses through the IR (insulin receptor). To investigate further how the activation of the IR by insulin and S597 differentially activates post-receptor signalling, we studied the gene expression profile in response to IR activation by either insulin or S597 using microarray technology. We found striking differences between the patterns induced by these two ligands. Most remarkable was that almost half of the genes differentially regulated by insulin and S597 were involved in cell proliferation and growth. Insulin either selectively regulated the expression of these genes or was a more potent regulator. Furthermore, we found that half of the differentially regulated genes interact with the genes involved with the MAPK (mitogen-activated protein kinase) pathway. These findings support our signalling results obtained previously and confirm that the main difference between S597 and insulin stimulation resides in the activation of the MAPK pathway. In conclusion, we show that insulin and S597 acting via the same receptor differentially affect gene expression in cells, resulting in a different mitogenicity of the two ligands, a finding which has critical therapeutic implications.
Isolation and characterization of an IgNAR variable domain specific for the human mitochondrial translocase receptor Tom70 (2003)

The new antigen receptor (IgNAR) from sharks is a disulphide bonded dimer of two protein chains, each containing one variable and five constant domains, and functions as an antibody. In order to assess the antigen-binding capabilities of isolated IgNAR variable domains (VNAR), we have constructed an in vitro library incorporating synthetic CDR3 regions of 15-18 residues in length. Screening of this library against the 60 kDa cytosolic domain of the 70 kDa outer membrane translocase receptor from human mitochondria (Tom70) resulted in one dominant antigen-specific clone (VNAR 12F-11) after four rounds of in vitro selection. VNAR 12F-11 was expressed into the Escherichia coli periplasm and purified by anti-FLAG affinity chromatography at yields of 3 mg x L(-1). Purified protein eluted from gel filtration columns as a single monomeric protein and CD spectrum analysis indicated correct folding into the expected beta-sheet conformation. Specific binding to Tom70 was demonstrated by ELISA and BIAcore (Kd = 2.2 +/- 0.31 x 10(-9) m-1) indicating that these VNAR domains can be efficiently displayed as bacteriophage libraries, and selected against target antigens with an affinity and stability equivalent to that obtained for other single domain antibodies. As an initial step in producing 'intrabody' variants of 12F-11, the impact of modifying or removing the conserved immunoglobulin intradomain disulphide bond was assessed. High affinity binding was only retained in the wild-type protein, which combined with our inability to affinity mature 12F-11, suggests that this particular VNAR is critically dependent upon precise CDR loop conformations for its binding affinity.
Clinical pretreatment risk factors and Ga‐67 scintigraphy early during treatment for prediction of outcome of patients with aggressive non‐Hodgkin lymphoma (2002)

BACKGROUND Clinical pretreatment risk factors indicate the severity of disease in patients with aggressive non-Hodgkin lymphoma (NHL). Ga-67 scintigraphy during treatment is an early indicator of treatment-related features of lymphoma cells. The ability of risk factors and Ga-67 to predict disease outcome was compared in 139 patients with aggressive NHL. METHODS Pretreatment clinical risk factors and Ga-67 scintigraphy performed after one cycle and at mid-treatment were evaluated for their correlation with response rate and as predictors of 5-year failure-free survival (FFS). Univariate analysis was performed to determine the ability of pretreatment risk factors and Ga-67 early during treatment to predict FFS. Subsequently, multivariate analysis was performed on the variables with significant univariate results using the Cox proportional hazards method. The predictive value of risk factors and Ga-67 scintigraphy was calculated to determine their suitability in selecting patients with poor outcome. RESULTS Response rate correlated with stage of disease (P < 0.01) and the international prognostic index (IPI) score (P < 0.05). Five-year FFS was predicted by stage of disease (P < 0.004), performance status (P < 0.02), and the IPI score (P < 0.01). Response rate correlated with results of Ga-67 scintigraphy after one cycle of chemotherapy (P < 0.001) and at mid-treatment (P < 0.001). Five-year FFS was predicted by Ga-67 after one cycle of chemotherapy (P < 0.0004) and at mid-treatment (P < 0.0001). Positive Ga-67 after the first cycle of treatment predicted 64% of patients who had failure of treatment. A positive study at mid-treatment predicted 77% of patients who had treatment failure. Cox analysis showed Ga-67 after one course (P < 0.0012) and at mid-treatment (P < 0.0002) as being the most significant variables in predicting FFS. CONCLUSIONS Ga-67 scintigraphy demonstrates early the effect of treatment in patients with aggressive NHL. It is a better predictor than pretreatment risk factors of both response rate and FFS. Positive Ga-67 early during treatment may be used as an independent test in selecting patients who will not respond favorably to current protocol treatment for early therapeutic modifications. Cancer 2002;94:873–8. © 2002 American Cancer Society. DOI 10.1002/cncr.10344
Four different forms of interferon-induced 2',5'-oligo(A) synthetase identified by immunoblotting in human cells. (1987)

Antibodies against synthetic peptides derived from the cDNA sequence of interferon-induced 2',5'-oligo(A) synthetase, and which immunoprecipitate the native enzyme activity, were found to detect multiple enzyme forms in denaturing electrophoretic immunoblots. In some human cell lines, four different interferon-induced proteins of 40, 46, 67, and 100 kDa were found to react with the same peptide antibodies. Each isolated form was shown to have 2',5'-oligo(A) synthetase activity, but the dependence on double-stranded RNA was markedly different for activation of the individual enzymes. The four enzyme forms also differ in their intracellular localization, on microsomes (100 kDa), in nuclei (67, 46, 40 kDa), and on membrane structures (67 kDa). Plasma membranes from interferon-treated Daudi lymphoblastoid cells are highly enriched in the 67-kDa 2',5'-oligo(A) synthetase form. The 2',5'-oligo(A) synthetase activity induced by interferons in human cells appears, therefore, as a complex multienzyme system.
Liposomal doxorubicin‐induced toxicity: Depletion and impairment of phagocytic activity of liver macrophages (1995)

Doxorubicin entrapped within conventional liposomes (200 nm in diameter; lip-Dox) has major toxic effects on liver macrophages of the rat for a considerable period of time following i.v. administration, with respect to both specific phagocytic capacity and cell numbers. At different time-points after injection of lip-Dox or free doxorubicin, radiolabeled, negatively charged, "empty" test liposomes were injected. Phagocytic capacity was determined by isolating the liver macrophages and measuring the amount of macrophage-associated radioactivity. Four subfractions of liver macrophages of different cell-size and with intrinsically different phagocytic capacity were isolated. Twenty-four hours after injection of lip-Dox, the phagocytic capacity of the larger-sized liver macrophages was strongly decreased. The relatively low intrinsic phagocytic capacity of the smaller-sized macrophages was only slightly impaired. Phagocytic capacity after injection of lip-Dox was nearly restored to control values after 14 days. Blood clearance of Klebsiella pneumoniae bacteria after pre-treatment with lip-Dox was strongly decreased. Pre-treatment with the free drug and/or placebo liposomes had no effect on phagocytic and bacterial blood-clearance capacity. A major depletion of the liver macrophage population was observed, as revealed by both macrophage isolation and histology. Only 2 weeks after injection of lip-Dox, the number of cells had returned to that seen in control animals. In view of the important host-defense functions of the liver macrophages, especially in the control of tumor growth and infection, the findings reported here should be taken into consideration when lip-Dox is to be administered in anti-tumor therapy.
Clinical Significance of Alterations of Chromosome 8 in High-Grade, Advanced, Nonmetastatic Prostate Carcinoma (1999)

Genetic alterations of chromosome 8 appear to accumulate in parallel with the progression of prostate carcinomas. AI of the c-myc gene, especially with loss of 8p22, appears to be associated with poor patient prognosis.
Quantitative staging of embryonic development of the grasshopper,Schistocerca nitens (1979)

During development of the grasshopper embryo, it is feasible to examine the structure, pharmacology, and physiology of uniquely identified cells. These experiments require a fast, accurate staging system suitable for live embryos. We present a system comprising (1) subdivision of embryogenesis into equal periods, (2) expression of stage in percent of complete embryogenesis time, (3) characterization of stages by light micrographs (and descriptive test), and (4) illustration of stages at the egg, embryo, and limb levels of resolution. Advantages of a percent-system include communicability, flexibility in temporal resolution, accurate assignment of elapsed time in developmental processes, and uniform coverage of the period of embryogenesis. The stages described are at 5% intervals with an estimated error of +/- 1%.
Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. (1990)

A target nucleic acid sequence can be replicated (amplified) exponentially in vitro under isothermal conditions by using three enzymatic activities essential to retroviral replication: reverse transcriptase, RNase H, and a DNA-dependent RNA polymerase. By mimicking the retroviral strategy of RNA replication by means of cDNA intermediates, this reaction accumulates cDNA and RNA copies of the original target. Product accumulation is exponential with respect to time, indicating that newly synthesized cDNAs and RNAs function as templates for a continuous series of transcription and reverse transcription reactions. Ten million-fold amplification occurs after a 1- to 2-hr incubation, with an initial rate of amplification of 10-fold every 2.5 min. This self-sustained sequence replication system is useful for the detection and nucleotide sequence analysis of rare RNAs and DNAs. The analogy to aspects of retroviral replication is discussed.
Synthesis and evaluation of 2-pyridinone derivatives as HIV-1-specific reverse transcriptase inhibitors. 2. Analogs of 3-aminopyridin-2(1H)-one (1992)

A series of nonnucleoside 3-aminopyridin-2(1H)-one derivatives was synthesized and evaluated for HIV-1 RT inhibitory properties. Several analogs proved to be potent and highly selective antagonists with in vitro IC50 values as low as 19 nM in the enzyme assay using rC.dG as template-primer. Two compounds from this series, 3-[[(4,7-dimethylbenzoxazol-2-yl)methyl]-amino]-5-ethyl-6-methy lpyridin-2(1H)-one (34, L-697,639) and the corresponding 4,7-dichloro analogue (37, L-697,661) inhibited the spread of HIV-1 IIIb infection by 95% in MT4 cell culture at concentrations of 25-50 nM and were selected for clinical trials as antiviral agents.
Whole‐genome Sequencing of an Aggressive BRAF Wild‐type Papillary Thyroid Cancer Identified EML4–ALK Translocation as a Therapeutic Target (2014)

This is the first report of the whole genomic sequencing of a papillary thyroid cancer in which we identified an EML4-ALK translocation of a TRAPP oncogene mutation. These findings suggest that this tumor has a more distinct oncogenesis than BRAF mutant papillary thyroid cancer. Whole genome sequencing can elucidate an oncogenic context and expose potential therapeutic vulnerabilities in rare cancers.
Molecular Features of the Broadly Neutralizing Immunoglobulin G1 b12 Required for Recognition of Human Immunodeficiency Virus Type 1 gp120 (2003)

IgG1 b12 is a broadly neutralizing antibody against human immunodeficiency virus type 1 (HIV-1). The epitope recognized by b12 overlaps the CD4 receptor-binding site (CD4bs) on gp120 and has been a target for vaccine design. Determination of the three-dimensional structure of immunoglobulin G1 (IgG1) b12 allowed modeling of the b12-gp120 interaction in which the protruding third complementarity-determining region (CDR) of the heavy chain (H3) was crucial for antibody binding. In the present study, extensive mutational analysis of the antigen-binding site of Fab b12 was carried out to investigate the validity of the model and to identify residues important for gp120 recognition and, by inference, key to the anti-HIV-1 activity of IgG1 b12. In all, 50 mutations were tested: 40 in H3, 4 each in H2 and L1, and 2 in L3. The results suggest that the interaction of gp120 with H3 of b12 is crucially dependent not only on a Trp residue at the apex of the H3 loop but also on a number of residues at the base of the loop. The arrangement of these residues, including aromatic side chains and side chains that hydrogen bond across the base of the loop, may rigidify H3 for penetration of the recessed CD4-binding cavity. The results further emphasize the importance to gp120 binding of a Tyr residue at the apex of the H2 loop that forms a second finger-like structure and a number of Arg residues in L1 that form a positively charged, shelf-like structure. In general, the data are consistent with the b12-gp120 interaction model previously proposed. At the gene level, somatic mutation is seen to be crucial for the generation of many of the structural features described. The Fab b12 mutants were also tested against the b12 epitope-mimic peptide B2.1, and the reactivity profile had many similarities but also significant differences from that observed for gp120. The paratope map of b12 may facilitate the design of molecules that are able to elicit b12-like activities.
RAID-II: a high-bandwidth network file server (1994)

In 1989, the RAID (Redundant Arrays of Inexpensive Disks) group at U. C. Berkeley built a prototype disk array called RAID-I. The bandwidth delivered to clients by RAID-I was severely limited by the memory system bandwidth of the disk array' s host workstation. We designed our second prototype, RAID-H, to deliver more of the disk array bandwidth to file server clients. A custom-built crossbar memory system called the XBUS board connects the disks directly to the high-speed network, allowing data for large requests to bypass the server workstation. RAID-II runs Log-Structured File System (LFS) software to optimize performance for bandwidth-intensive applications.The RAID-II hardware with a single XBUS controller board delivers 20 megabytes/second for large, random read operations and up to 31 megabytes/second for sequential read operations. A preliminary implementation of LFS on RAID-II delivers 21 megabytes/second on large read requests and 15 megabytes/second on large write operations.
Protective and Harmful Immunity to RSV Infection (2017)

Respiratory syncytial virus (RSV) is an exceptional mucosal pathogen. It specializes in infection of the ciliated respiratory epithelium, causing disease of variable severity with little or no direct systemic effects. It infects virtually all children by the age of three years and then repeatedly infects throughout life; this it does despite relatively slight variations in antigenicity, apparently by inducing selective immunological amnesia. Inappropriate or dysregulated responses to RSV can be pathogenic, causing disease-enhancing inflammation that contributes to short- and long-term effects. In addition, RSV's importance as a largely unrecognized pathogen of debilitated older people is increasingly evident. Vaccines that induce nonpathogenic protective immunity may soon be available, and it is possible that different vaccines will be optimal for infants; older children; young to middle-age adults (including pregnant women); and elderly persons. At the dawn of RSV vaccination, it is timely to review what is known (and unknown) about immune responses to this fascinating virus.
Rapid and Sensitive Detection of Respiratory Virus Molecular Signatures Using a Silver Nanorod Array SERS Substrate (2006)

A spectroscopic assay based on surface enhanced Raman scattering (SERS) using silver nanorod array substrates has been developed that allows for rapid detection of trace levels of viruses with a high degree of sensitivity and specificity. This novel SERS assay can detect spectral differences between viruses, viral strains, and viruses with gene deletions in biological media. The method provides rapid diagnostics for detection and characterization of viruses generating reproducible spectra without viral manipulation.
Diagnostic protein discovery using proteolytic peptide targeting and identification (2004)

Plasma protein profiling with mass spectrometry is currently being evaluated as a diagnostic tool for cancer and other diseases. These experiments consist of three steps: plasma protein fractionation, analysis with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS), and comparisons of the MALDI profiles to develop diagnostic fingerprints using bioinformatic techniques. While preliminary results appear promising in small sample groups, the method is limited by the sensitivity of MALDI-MS for intact proteins, the limited mass range of MALDI-MS, and difficulties associated with isolating individual proteins for identification to validate the diagnostic fingerprint. Here we present an alternative and improved method directed toward diagnostic protein discovery, which incorporates proteolytic peptide profiling, bioinformatic targeting of ion signals, and MALDI tandem mass spectrometry (MS/MS) peptide sequencing, rather than fingerprinting. Pancreatic cancer patients, pancreatitis patients, and controls are used as the model system. Profiling peptides after enzymatic digestion improves sensitivity and extends the accessible protein molecular weight range when compared to intact protein profiling. The first step is to extract and fractionate the proteins from plasma. Each fraction is digested with trypsin and subsequently analyzed by MALDI-MS. Rather than using bioinformatic analysis as a pattern-matching technique, peptides are targeted based on the disease to control peak intensity ratios measured in the averages of all mass spectra in each group and t-tests of the intensity of each individual peak. The targeted peptide ion signals are subsequently identified using MALDI-MS/MS in quadrupole-TOF and tandem-TOF instruments. This study found not only the proteins targeted and identified by a previous protein profiling experiment, but also detected additional proteins. These initial results are consistent with the known biology of pancreatic cancer or pancreatitis, but are not specific to those diseases.
Effects of dietary quillaja saponin and curcumin on the performance and immune status of weaned piglets1 (2005)

The objective of this study was to determine whether dietary quillaja saponin and curcumin (extract of turmeric) can modify piglet immune status and performance immediately after weaning. Piglets (n = 192) were weaned at 29 +/- 0.1 d and allocated to treatment (six replicates of eight pig per treatment) accounting for weight, litter, and gender, using a 2 x 2 factorial arrangement. Factors were diets with or without (as-fed basis) quillaja saponin (750 mg/kg during wk 1, 300 mg/kg during wk 2 to 3) and with or without dietary curcumin (200 mg/kg). Diets were fed ad libitum for 20 d after weaning. Feed intake was measured daily. Piglets were weighed at weaning, d 7, 14, and 20 after weaning. On each of d 6 and 20 after weaning, eight pigs per treatment were sacrificed for blood and tissue collection. Treatment had no effect on piglet growth. The ADFI and G:F were similar for all treatments between d 0 and 14 of the trial. Between d 15 and 20, ADFI and G:F were lower in quillaja-supplemented piglets (ADFI = 621 vs. 572 g/d; G:F = 0.75 vs. 0.85; P < 0.05). Serum immunoglobulin (Ig) G, IgA, interferon-gamma, and C-reactive protein (CRP) did not differ among treatments on d 6 after weaning. On d 20, IgG and CRP were greater (P < 0.05) in saponin-supplemented pigs (IgG = 17.5 vs. 11.4 mg/mL; CRP = 26.98 vs. 12.5 mg/mL). Small intestine villus and crypt measurements did not differ among treatments on either d 6 or 20. Saponin supplementation during the postweaning period seemed to potentiate an immune response in the weaned piglet but had a detrimental effect on the utilization of feed. Dietary curcumin had no influence on any measured aspect of pig performance or immune status.