gebhart/patrepeval huggingface dataset:
Activation of human B cell proliferation through surface Bp35 (CD20) polypeptides or immunoglobulin receptors. (1987)

Human B cells can be activated with monoclonal antibodies (mAb) to surface IgM receptors or mAb to a 35-kilodalton B cell differentiation antigen, Bp35 (CD20). We compared anti-Ig-induced B cell activation with B cell triggering by anti-Bp35. Both anti-Ig- and anti-Bp35-dependent proliferation were augmented by the same co-stimulants, including a partially purified BCGF, recombinant IL 1, TPA, or each other. When anti-Bp35 and anti-Ig were used together to induce proliferation of tonsillar B cells, the strongest response was observed when anti-Bp35 was added 12 to 24 hr before anti-Ig. Anti-Bp35 also was found to act most effectively when added before the BCGF. Blood and tonsillar B cells differed in their proliferative response to anti-Ig or anti-Bp35: unlike dense tonsillar B cells, which consistently proliferated in response to either stimulus, blood B cells from many donors proliferated in response to anti-Ig but not to anti-Bp35 even in the presence of other co-stimuli. Dense tonsillar B cells that proliferate in response to anti-Bp35 appeared to be at a more activated stage than unresponsive blood B cells because they expressed higher levels of HLA class II molecules than blood B cells. Pretreatment of blood B cells with anti-Bp35 converted them to an HLA-DR(bri) phenotype and made them more responsive to anti-Ig-induced proliferation. These results suggest that B cells at different stages of differentiation differ in their response to anti-Bp35 and anti-Ig. The Bp35 surface polypeptide may play an early role in the activation of B cells prior to antigen or other signals.
Heterogeneity of transcriptional activity of mutant p53 proteins and p53 DNA target sequences. (1993)

Transcriptional activity of p53 was monitored by cotransfection of pCMV expression vectors containing wild-type and mutant p53 cDNAs into the p53-null H1299 lung cancer cells along with luciferase reporter plasmids containing different p53 target sequences in the 5' regulatory region: fragment A of the ribosomal gene cluster (RGC); p53 consensus sequence (p53CON); or a tandemly linked RGC+p53CON sequence. Our results show: (1) wild-type p53 stimulates the transcription of reporter genes with p53CON and RGC in their 5' region while most p53 mutants occurring in human cancers have lost this activity; (2) the R273H mutant retains transcriptional activity for the p53CON sequence but not RGC; (3) some mutants are temperature-sensitive for the transcriptional activity with the p53CON but not the RGC sequence; (4) p53 mutants vary in their ability to inhibit wild-type p53 transactivation but there is no difference between p53CON and RGC sequences; (5) lung cancer cells with endogenous mutant p53 proteins (M246I in H23 cells and R248L in H322 cells) retain transcriptional activity for the p53CON but not the RGC sequence. We conclude that p53 DNA target sequences vary in their response to mutant p53 proteins, and that p53 mutants vary in several transactivation related functions.
Eph receptors discriminate specific ligand oligomers to determine alternative signaling complexes, attachment, and assembly responses (1998)

Eph family receptor tyrosine kinases (including EphA3, EphB4) direct pathfinding of neurons within migratory fields of cells expressing gradients of their membrane-bound ligands. Others (EphB1 and EphA2) direct vascular network assembly, affecting endothelial migration, capillary morphogenesis, and angiogenesis. To explore how ephrins could provide positional labels for cell targeting, we tested whether endogenous endothelial and P19 cell EphB1 (ELK) and EphB2 (Nuk) receptors discriminate between different oligomeric forms of an ephrin-B1/Fc fusion ligand. Receptor tyrosine phosphorylation was stimulated by both dimeric and clustered multimeric ephrin-B1, yet only ephrin-B1 multimers (tetramers) promoted endothelial capillary-like assembly, cell attachment, and the recruitment of low-molecular-weight phosphotyrosine phosphatase (LMW-PTP) to receptor complexes. Cell-cell contact among cells expressing both EphB1 and ephrin-B1 was required for EphB1 activation and recruitment of LMW-PTP to EphB1 complexes. The EphB1-binding site for LMW-PTP was mapped and shown to be required for tetrameric ephrin-B1 to recruit LMW-PTP and to promote attachment. Thus, distinct EphB1-signaling complexes are assembled and different cellular attachment responses are determined by a receptor switch mechanism responsive to distinct ephrin-B1 oligomers.
Metagenomics: Application of Genomics to Uncultured Microorganisms (2004)

Metagenomics (also referred to as environmental and community genomics) is the genomic analysis of microorganisms by direct extraction and cloning of DNA from an assemblage of microorganisms. The development of metagenomics stemmed from the ineluctable evidence that as-yet-uncultured microorganisms represent the vast majority of organisms in most environments on earth. This evidence was derived from analyses of 16S rRNA gene sequences amplified directly from the environment, an approach that avoided the bias imposed by culturing and led to the discovery of vast new lineages of microbial life. Although the portrait of the microbial world was revolutionized by analysis of 16S rRNA genes, such studies yielded only a phylogenetic description of community membership, providing little insight into the genetics, physiology, and biochemistry of the members. Metagenomics provides a second tier of technical innovation that facilitates study of the physiology and ecology of environmental microorganisms. Novel genes and gene products discovered through metagenomics include the first bacteriorhodopsin of bacterial origin; novel small molecules with antimicrobial activity; and new members of families of known proteins, such as an Na(+)(Li(+))/H(+) antiporter, RecA, DNA polymerase, and antibiotic resistance determinants. Reassembly of multiple genomes has provided insight into energy and nutrient cycling within the community, genome structure, gene function, population genetics and microheterogeneity, and lateral gene transfer among members of an uncultured community. The application of metagenomic sequence information will facilitate the design of better culturing strategies to link genomic analysis with pure culture studies.
Expression of neuroendocrine cell markers L-dopa decarboxylase, chromogranin A, and dense core granules in human tumors of endocrine and nonendocrine origin. (1988)

We evaluated the usefulness of L-dopa decarboxylase (DDC) as a tumor marker of neuroendocrine (NE) cell differentiation by measuring its expression in 432 human tumors of diverse types and origins. A subset of these tumors and cell lines derived from them also were studied for expression of two other general NE cell markers, chromogranin A (CgA) and dense core granules (DCG). High concentrations of DDC were present in 96 of 117 (82%) tumors recognized to be of NE or neural origin. As expected, endocrine tumors not recognized to be of NE cell origin, as well as leukemias, lymphomas, sarcomas, melanomas, and germ cell tumors, lacked DDC expression. Of interest, modest concentrations of DDC were present in 46 of 220 (21%) nonendocrine carcinomas, especially non-small cell lung and colorectal carcinomas. We studied concordant expression of the three NE cell markers in lung and colorectal tumors and cell lines. In both tumor types there was nearly 100% concordance between CgA and DCG expression. There was an excellent correlation between DDC and CgA expression in lung cancers, both small cell and non-small cell, but DDC positive colorectal carcinomas usually lacked CgA expression. We conclude: (a) DDC is an excellent cellular marker for tumors of the NE cell system; (b) about 20% of carcinomas not of NE cell origin, especially non-small cell lung and colorectal carcinomas, express DDC, suggesting a common endodermal origin of all of the respiratory and gastrointestinal mucosal cells; and (c) CgA and DCG are expressed concordantly, indicating that CgA expression may be used as a substitute for ultrastructural examination of tumors for DCG expression.
Thermal poling of silica in air and under vacuum: The influence of charge transport on second harmonic generation (1999)

A comparison between thermal poling of silica in air and in vacuum is reported. It is shown that the second-order susceptibility and thickness of the nonlinear layer as well as their time evolution are highly dependent on the surrounding poling atmosphere. In the vacuum case a charge distribution (under the anode) more complex and broader than that for the air case has also been revealed by laser induced pressure pulse measurements. A multiple charge carrier model can explain the formation and evolution of the depletion region under the anode. The findings are relevant to achieve improved nonlinearities in fiber and waveguide devices.
MgO-based tunnel junction material for high-speed toggle magnetic random access memory (2006)

We report the first demonstration of a magnetoresistive random access memory (MRAM) circuit incorporating MgO-based magnetic tunnel junction (MTJ) material for higher performance. We compare our results to those of AlOx-based devices, and we discuss the MTJ process optimization and material changes that made the demonstration possible.We present data on key MTJ material attributes for different oxidation processes and free-layer alloys, including resistance distributions, bias dependence, free-layer magnetic properties, interlayer coupling, breakdown voltage, and thermal endurance. A tunneling magnetoresistance (TMR) greater than 230% was achieved with CoFeB free layers and greater than 85% with NiFe free layers. Although the TMR with NiFe is at the low end of our MgO comparison, even this MTJ material enables faster access times, since its TMR is almost double that of a similar structure with an AlOx barrier. Bit-to-bit resistance distributions are somewhat wider for MgO barriers, with sigma about 1.5% compared to about 0.9% for AlOx. The read access time of our 4 Mb toggle MRAM circuit was reduced from 21 ns with AlOx to a circuit-limited 17 ns with MgO.
Wavelength-dependent penetration depths of ultraviolet radiation in human skin (2008)

The wavelength-dependent penetration depth of ultraviolet radiation in human skin is a fundamental parameter for the estimation of the possible photobiological impact of ultraviolet (UV) radiation. We have determined the absorption spectra of human skin in vivo in the wavelength range from 290 to 341 nm in 3-nm steps using laser optoacoustics and calculated the respective penetration depths. Data were analyzed with respect to different skin regions and skin phototype of the 20 subjects in the study (phototype I: n=3; II: n=7; III: n=5; IV: n=5), revealing large variability between individuals. The penetration depth of UV radiation in human skin is highly dependent on wavelength and skin area, but no significant dependence on skin phototype could be found.
Parasite: mining the structural information on the world-wide web (1998)

The World-Wide Web is potentially the world&amp;apos;s largest knowledge base but only if new information retrieval techniques are developed to take advantage of its unique characteristics, particularly the semi-structured information within pages, across pages, and in page names. Because these types of structure are represented in such different ways, a large number of specialized tools have been required to gather structural information. I provide a relational database interface to the Web called Squeal, which encapsulates these different types of structure in a uniform manner, allowing the user to query the Web in Structured Query Language (SQL) as if it were a database. A novel &amp;quot;just-in-time&amp;quot; interpreter automatically retrieves information from the Web as implicitly demanded by user queries, a technique which could be applied not just to the Internet but to other sources of data too large to be precomputed into a database. The level of abstraction provided by Squeal allows the user to easily ...
Fabrication of periodic domain grating in LiNbO 3 by electron beam writing for application of nonlinear optical processes (1991)

A novel technique for the fabrication of domain reversed gratings in LiNbO3 by means of direct electron beam writing at room temperature without any static bias is reported. The domain grating has been achieved not only at the – c surface of the crystal, but also for the entire region of the crystal. Such a structure should be useful for various nonlinear optic applications. A preliminary study on the second harmonic generation has also been demonstrated under the quasiphasematched condition with high efficiency.
Characterization of Human Brain S100 Protein Fraction: Amino Acid Sequence of S100β (1985)

Two major components of human brain S100 fraction were purified by HPLC and an amino acid sequence was elucidated for the S100 beta component. Human S100 proteins showed absorption spectra and amino acid compositions similar to S100 alpha and S100 beta from bovine brain. However, the relative amounts of the human proteins were 4% S100 alpha and 96% S100 beta by weight, while the bovine protein distribution was 47% S100 alpha and 53% S100 beta by weight. An amino acid sequence of human S100 beta was established by analysis of overlapping fragments generated by cyanogen bromide and trypsin cleavage. Three amino acid sequence differences between the human and bovine S100 beta were found at residues 7, 62, and 80. These differences were chemically conservative and compatible with minimum single base changes in the codon structures. These results document that S100 beta is a conserved protein among mammals and provide the necessary foundation for current clinical studies.
Diagnosis of Acute Renal Allograft Rejection by Analyzing Whole Blood mRNA Expression of Lymphocyte Marker Molecules (2007)

The whole blood gene expression quantities of costimulatory molecules CD154 and ICOS reasonably robustly differentiated rejection patients from control patients. The clinical use of the analysis is limited by poor capability to differentiate patients with rejection from patients with other causes of graft dysfunction.
L-URIDINE: SYNTHESIS AND BEHAVIOR AS ENZYME SUBSTRATE (1969)

L-Uridine, the enantiomer of the normal RNA constituent D-uridine, was synthesized from L-ribose through coupling with bis(trimethylsilyl)-uracil. The synthetic product had the expected chemical and physical characteristics. When used as the acceptor for phosphate transfer by the nucleoside phosphotransferase of carrot, L-uridine is converted to 5'-L-uridylic acid. The Michaelis constants K(m) are 28 x 10(-3)M for L-uridine, 5 x 10(-3)M for D-uridine. The nucleoside phosphotransferase of human prostate, which phosphorylates D-uridine in the 5', 3', or 2' positions, fails to transfer phosphate to the 2' position of L-uridine, but does produce 5'-and 3'-L-uridylic acids.
<title>Flat panel detector for digital radiology using active matrix readout of amorphous selenium</title> (1997)

A large area, flat panel solid state detector is being investigated for both digital radiography and fluoroscopy. The detector employs amorphous selenium (a-Se) to detect x- rays. The charge image formed on the surface of the a-Se is read out in situ using an active matrix array. A theoretical analysis of the spatial frequency dependent detective quantum efficiency (DQE) is performed. Because of the very high intrinsic resolution of a-Se, the detector is inherently undersampled and aliasing is always present. An interpretation of DQE(f) for the undersampled a-Se detector will be given. The analysis shows that the main factors, besides the quantum efficiency of the a-Se layer, affecting DQE(f) are: (1) aliasing; (2) gain fluctuation noise of a- Se, i.e., the Swank factor of a-Se; (3) electronic noise which prevents quantum noise limited operation at low exposure levels such as those used in fluoroscopy and (4) temporal response which causes a reduction in noise by averaging. The validity of the theoretical model was confirmed experimentally using our prototype detector with the Swank factor being established using pulse height spectroscopy. The model was then applied to three important x-ray imaging applications: mammography, chest radiography and fluoroscopy. The results show that the most important strategy for maximizing DQE(f) is to increase the pixel fill factor which can be unity using specialized techniques Methods for reducing aliasing in the detector will be described.
Scalable Hardware Trojan Activation by Interleaving Concrete Simulation and Symbolic Execution (2018)

Intellectual Property (IP) based System-on-Chip (SoC) design is a widely used practice today. The IPs gathered from third-party vendors may not be trustworthy since they may contain malicious implants (hardware Trojans). To avoid the detection of the Trojan, adversaries usually hide it under rare branches or rare assignments triggered under extremely rare input sequences. Due to exponential input space complexity, state-of-the-art constrained-random test generation methods are not suitable for activating these rare scenarios. While existing model checking based directed test generation approaches are promising, they are not capable of generating tests for large RTL designs due to the capacity restrictions of formal methods. In this paper, we propose an automated and scalable test generation approach for activation of hardware Trojans in RTL designs. This paper makes three important contributions. First, it provides a scalable test generation framework by effective utilization of symbolic execution and concrete simulation. Next, it is a fully automated approach for generating directed tests for activating rare branches and rare assignments. Finally, our experimental results demonstrate that the generated tests are able to activate hard-to-cover Trojans in large and complex RTL benchmarks.
Reflections on network architecture (2006)

After a long period when networking research seemed to be focused mainly on making the existing Internet work better, interest in "clean slate" approaches to network architecture seems to be growing. Beginning with the DARPA program in the mid-1990's, researchers working on active networks explored such an approach, based on the idea of a programming interface as the basic interoperability mechanism of the network. This note draws on the author's experiences in that effort and attempts to extract some observations or "lessons learned" that may be relevant to more general network architecture research.
Simultaneous Molecular and Hypoxia Imaging of Brain Tumors In Vivo Using Spectroscopic Photoacoustic Tomography (2008)

Noninvasive molecular and functional imaging in vivo is promising for detecting and monitoring various physiological conditions in animals and ultimately humans. To this end, we present a novel noninvasive technology, spectroscopic photoacoustic tomography (SPAT), which offers both strong optical absorption contrast and high ultrasonic spatial resolution. Optical contrast allows spectroscopic separation of signal contributions from multiple optical absorbers (e.g., oxyhemoglobin, deoxyhemoglobin, and a molecular contrast agent), thus enabling simultaneous molecular and functional imaging. SPAT successfully imaged with high resolution the distribution of a molecular contrast agent targeting integrin overexpressed in human U87 glioblastomas in nude mouse brains. Simultaneously, SPAT also imaged the hemoglobin oxygen saturation and the total hemoglobin concentration of the vasculature, which revealed hypoxia in tumor neovasculature. Therefore, SPAT can potentially lead to better understanding of the interrelationships between hemodynamics and specific biomarkers associated with tumor progression.
Chromosomal organization of the human VH4 gene family. Location of individual gene segments (1993)

To investigate the organization and evolution of VH gene segments, we characterized the elements belonging to the VH4 gene family from the germline of a single subject. One hundred sixty VH4-carrying lambda-phage clones were isolated from a genomic library. A combination of hybridization and sequence analysis yielded 13 distinct VH4 clones. Six of these elements had one or more nucleotide substitutions that distinguished them from previously identified VH4 genes, whereas seven elements were identical to previously described VH4 genes. In four of the six new sequences, nucleotide substitutions resulted in amino acid replacements. One pseudogene was identified. On the basis of sequence-specific hybridization using oligonucleotide probes corresponding to these sequences, each of the elements could be assigned to a specific band in a BglII digest. Since the VH4-carrying BglII bands have been mapped in genomic DNA, it was also possible to assign chromosomal locations to the specific VH4 elements. The results indicate that the majority of VH4 elements are located in a region of approximately 500 kb, extending from approximately 500 to 1000 kb 5' of the JH locus. The distribution of shared structural motifs among the VH4 elements indicates that the VH4 gene family has evolved through repeated duplication and gene conversion events.
How thin is a thin bed? An alternative perspective (2009)

The resolution limit of seismic data is a complex issue that involves not only wavelet frequency, phase characters, and data quality (S/N), but also criteria on how to measure resolvability. In his classic 1973 paper “How thin is a thin bed?,” Widess discussed the effect of bed thickness on re-flection character and timing using a symmetrical wavelet and suggested that λ/8 be the resolution limit, or the minimum distance at which a composite waveform stabilized as the derivative of the waveform from an individual reflection. However, this definition has more theoretical than practical impact because of the difficulties in judging waveform stabilization. A more workable and widely accepted definition of resolution limit corresponds to Rayleigh's criterion of peak-to-trough separation at λ/4 (Kallweit and Wood, 1982). This point is also a “tuning point,” at which composite amplitude reaches a maximum if an opposite-polarity (at top and bottom) thin bed is involved.
Botswana - the feeding has started : Botswana focus : part 2 (2012)

China has a well-documented and undiminished appetite for miner resources in Africa. It now appears the Chinese focus is also shifting firmly to Botswana. 
Dr Willem Smuts takes a look at the implications for the juniors active there.
NAB 365 (clenbuterol) and salbutamol in asthmatics: a double-blind clinical trial. (1979)

A double-blind comparison between orally administered NAB 365 (clenbuterol) and salbutamol was conducted in 30 impatients with either asthma or chronic bronchitis with asthma who had at least 15% reversibility in airway obstruction following inhalation of 1,500 microgram of orciprenaline. NAB 365 (clenbuterol) was administered to 15 patients at 30 microgram b.i.d. for 3 days; then the dosage was reduced to 20 microgram b.i.d. Salbutamol was administered to the other 15 patients at 4 mg t.i.d. Both drugs were administered for an average of 13 days. NAB 365 (clenbuterol) was shown to be an effective bronchodilator, with more rapid activity than that of salbutamol, on the FVC, FEV1, PEFR, the differences being significant on the third and seventh day of treatment. These findings are briefly discussed. No significant cardiovascular effects were noted for either drug, nor were differences found in need for additional treatment or in side-effects.