gebhart/patrepeval huggingface dataset:
Clonal analysis of astrocyte diversity in neonatal rat spinal cord cultures (1991)

Within the mammalian CNS, astrocytes appear to be a heterogeneous class of cells. To assay the number of distinct types of astrocytes in the rat spinal cord, cell lineage and phenotypic analyses were carried out on cultures from newborn rat spinal cord and five distinct types of astrocytes were observed. Proliferating precursors for each class of astrocyte were isolated by low density culture and shown to give rise to 5 distinct and morphologically homogeneous clusters of GFAP + astrocytes. Immunocytochemical analysis with antibodies A2B5 and Ran-2, which identify different glial lineages in optic nerve cultures, demonstrated that many clusters included both A2B5+ and A2B5- cells. Similarly, many clusters also possessed a mixture of Ran-2+ and Ran-2-cells, suggesting that in spinal cord cultures, in contrast to optic nerve cultures, expression of these antigens is regulated by individual cells rather than by cell lineage. Single-cell cloning studies, revealed that the abundance and proliferative capacity of individual astrocyte precursors differed depending on the type of astrocyte. To assay the effects of a complex cellular environment on the composition of astrocyte clones, lineage analysis was performed in complete spinal cord cultures using a replication deficient retrovirus. Although similar morphologically homogeneous clones of cells to those seen with single-cell clones were observed, the proliferative capacity and relative abundance of the distinct astrocyte precursors differed from that seen in single-cell cloning studies. Together these observations suggest that in spinal cord, gliogenesis is considerably more complex than in the optic nerve and that cultures of newborn rat spinal cord contain multiple, distinct populations of astrocytes.
Highly frequent single amino acid substitution in mammalian elongation factor 2 (EF-2) results in expression of resistance to EF-2-ADP-ribosylating toxins. (1987)

Toxin-resistant polypeptide chain elongation factor 2 cDNA has been cloned from a mutant hamster cell line with only non-ADP-ribosylatable elongation factor 2. The mutation conferring resistance to diphtheria toxin and Pseudomonas aeruginosa exotoxin A is a G-to-A transition in the first nucleotide of codon 717. Codon 715 encodes a histidine residue that is modified post-translationally to diphthamide, which is the target amino acid for ADP-ribosylation by both toxins. Transfection of mouse L cells with a recombinant elongation factor 2 cDNA differing from the wild-type only by this G-to-A transition confers resistance to P. aeruginosa exotoxin A. The degrees of toxin-resistant protein synthesis of stable transfectants are dependent on the ratio of non-ADP-ribosylated elongation factor 2 to wild-type elongation factor 2, not the amount of non-ADP-ribosylated elongation factor 2. The mutation creates a new Mbo II restriction site in the elongation factor 2 gene. Several independently isolated diphtheria toxin-resistant Chinese hamster ovary cell lines show the same alteration in the Mbo II restriction pattern.
Th17 responses and natural IgM antibodies are related to gut microbiota composition in systemic lupus erythematosus patients (2016)

Intestinal dysbiosis, characterized by a reduced Firmicutes/Bacteroidetes ratio, has been reported in systemic lupus erythematosus (SLE) patients. In this study, in vitro cultures revealed that microbiota isolated from SLE patient stool samples (SLE-M) promoted lymphocyte activation and Th17 differentiation from naïve CD4(+) lymphocytes to a greater extent than healthy control-microbiota. Enrichment of SLE-M with Treg-inducing bacteria showed that a mixture of two Clostridia strains significantly reduced the Th17/Th1 balance, whereas Bifidobacterium bifidum supplementation prevented CD4(+) lymphocyte over-activation, thus supporting a possible therapeutic benefit of probiotics containing Treg-inducer strains in order to restore the Treg/Th17/Th1 imbalance present in SLE. In fact, ex vivo analyses of patient samples showed enlarged Th17 and Foxp3(+) IL-17(+) populations, suggesting a possible Treg-Th17 trans-differentiation. Moreover, analyses of fecal microbiota revealed a negative correlation between IL-17(+) populations and Firmicutes in healthy controls, whereas in SLE this phylum correlated directly with serum levels of IFNγ, a Th1 cytokine slightly reduced in patients. Finally, the frequency of Synergistetes, positively correlated with the Firmicutes/Bacteroidetes ratio in healthy controls, tended to be reduced in patients when anti-dsDNA titers were increased and showed a strong negative correlation with IL-6 serum levels and correlated positively with protective natural IgM antibodies against phosphorylcholine.
Combination of Low-Index Quantum Barrier and Super Large Optical Cavity Designs for Ultranarrow Vertical Far-Fields From High-Power Broad-Area Lasers (2011)

When active regions that use low refractive index quantum barriers (LIQB) are combined with super large optical cavity (SLOC) designs in GaAs-based diode lasers, high-power operation with extremely narrow vertical far-fields is observed. However, LIQB designs are found to have lower slope efficiency and increased operation voltage. Comparison of experiment and finite element device simulation shows that this is due to hole accumulation at the edge of the active region. Example devices using an 8.6-μm thick SLOC deliver 30 W at 1065 nm with vertical divergence of 15.6° (95% power).
Glutamate dehydrogenase isoenzymes in the bovine retina and human leukocyte. (1994)

In the present study, we investigated the enzymatical properties of the heat-labile and heat-stable glutamate dehydrogenases (GDHs) from the bovine retina and human leukocytes. Retinal GDHs were mitochondrial enzymes with an optimal pH of 7.5. Heat-labile (membrane-associated form) and heat-stable (soluble form) GDHs were found in the bovine retina as well as in the human leukocytes. At least 5 GDH isoenzymes were found in the retina and leukocytes by nondenaturing polyacrylamide gel electrophoresis. After heat treatment, the high-speed pellet obtained from centrifugation of the human leukocytes at 100,000 x g retained the 3 smaller isoenzymes but had lost the 2 larger isoenzymes. Both heat-labile and heat-stable GDH were found in the neuroretina, retinal pigment epithelium and optic nerve with high activities. Our results suggest that these tissues may be the main active sites of the GDH deficiency.
INHIBITION OF ANTI-HLA-B7 ALLOREACTIVE CTL BY AFFINITY-PURIFIED SOLUBLE HLA (1991)

The objective of this study was to elucidate the interaction of naturally occurring soluble MHC class I molecules with alloreactive CTL and to discuss its possible relevance to graft acceptance. An anti-HLA-B7 specific CTL-line, BV.B7, was generated in vitro. On phenotyping the cells after 6 weeks, 80% were found to be CD8+, 14% CD4+ and 6% CD8+CD4+. CD4+ CTL were depleted using immunomagnetic beads precoated with an anti-CD4 antibody. Of the recovered CTL greater than 96% were CD8+. A total of 12 HLA-B7 target cell lines and PHA blasts tested were specifically lysed in a 51Cr-release assay. Soluble HLA class I molecules were isolated on affinity chromatography columns using the anti-HLA-B7 ME 1 and the anti-heavy chain W6/32 monoclonal antibodies. Antigen purity was confirmed by analysis on SDS-PAGE gels. CTL were preincubated with 0.1-1.8 micrograms/ml soluble HLA for 30 min at 37 degrees C and subsequently tested for cytotoxicity in the 51Cr-release assay; 1.1 micrograms/ml HLA-B7 molecules reduced CTL cytotoxicity by 50% whereas non-B7 HLA had no effect. Further, CTL cytotoxicity was reduced by preincubation with anti-CD8, anti-TcR, and anti-CD3 antibodies. We anticipate a possible down-regulatory role of soluble HLA on CTL in allogeneic transplantation.
Prevention of Second Primary Tumors with Isotretinoin in Squamous-Cell Carcinoma of the Head and Neck (1990)

Daily treatment with high doses of isotretinoin is effective in preventing second primary tumors in patients who have been treated for squamous-cell carcinoma of the head and neck, although it does not prevent recurrences of the original tumor.
Adducts of Carbenes with Group II and XII Metallocenes† (1998)

The reactions and adducts of 1,3,4,5-tetramethylimidazol-2-ylidene with bis(pentamethylcyclopentadienyl)magnesium, -calcium, -strontium, -barium, or -zinc are described. A consistent tend in the spectroscopic properties and structures of the alkaline earth metallocenes is observed. The adduct between 1,3,4,5-tetramethylimidazol-2-ylidene and bis(pentamethylcyclopentadienyl)zinc shows a structure in which the zinc is only σ-bonded to the three ligating groups. Among the alkaline earth adducts, the σ-bonded interaction to the former carbene center of the 1,3,4,5-tetramethylimidazol-2-ylidene shows the shortest metal−carbon distances in each of the structures but the difference between the carbene−metal and pentamethylcyclopentadienyl−metal distances decreases as the atomic number of the metal increases.
Security versus energy tradeoffs in host-based mobile malware detection (2011)

The rapid growth of mobile malware necessitates the presence of robust malware detectors on mobile devices. However, running malware detectors on mobile devices may drain their battery, causing users to disable these protection mechanisms to save power. This paper studies the security versus energy tradeoffs for a particularly challenging class of malware detectors, namely rootkit detectors. We investigate the security versus energy tradeoffs along two axes: attack surface and malware scanning frequency, for both code and data based rootkit detectors. Our findings, based on a real implementation on a mobile handheld device, reveal that protecting against code-driven attacks is relatively cheap, while protecting against all data-driven attacks is prohibitively expensive. Based on our findings, we determine a sweet spot in the security versus energy tradeoff, called the balanced profile, which protects a mobile device against a vast majority of known attacks, while consuming a limited amount of extra battery power.
Electrical responses of neural units in the anteroventral cochlear nucleus of the cat. (1976)

Thesis. 1976. Ph.D.--Massachusetts Institute of Technology. Dept. of Electrical Engineering and Computer Science.
Proteins with Altered Levels in Plasma from Glioblastoma Patients as Revealed by iTRAQ-Based Quantitative Proteomic Analysis (2012)

Glioblastomas (GBMs) are the most common and lethal primary tumors of the central nervous system with high level of recurrence despite aggressive therapy. Tumor-associated proteins/peptides may appear in the plasma of these patients as a result of disruption of the blood-brain barrier in them, raising the scope for development of plasma-based tests for diagnosis and monitoring the disease. With this objective, we analyzed the levels of proteins present in the plasma from GBM patients using an iTRAQ based LC-MS/MS approach. Analysis with pooled plasma specimens from the patient and healthy control samples revealed high confidence identification of 296 proteins, of which 61 exhibited a fold-change ≥1.5 in the patient group. Forty-eight of them contained signal sequence. A majority have been reported in the differentially expressed transcript or protein profile of GBM tissues; 6 have been previously studied as plasma biomarkers for GBM and 16 for other types of cancers. Altered levels of three representative proteins-ferritin light chain (FTL), S100A9, and carnosinase 1 (CNDP1)-were verified by ELISA in a test set of ten individual plasma specimens. FTL is an inflammation marker also implicated in cancer, S100A9 is an important member of the Ca(2+) signaling cascade reported to be altered in GBM tissue, and CNDP1 has been reported for its role in the regulation of the levels of carnosine, implicated as a potential drug for GBM. These and other proteins in the dataset may form useful starting points for further clinical investigations for the development of plasma-based biomarker panels for GBM.
Detection of luminosity profiles of elongated shapes (2002)

A novel technique for identifying elongated shapes in grey-scale images is presented. The method provides the detection and identification of elongated shapes not only modelling their principal direction, but also reconstructing the transversal luminosity profile. The approach is proposed starting from the gradient-weighted Hough transform, endowing the Hough space with more complete information about the luminance gradient of the image. This paper presents and discusses the algorithm devised to implement the method on discretized data. As an example of application, we present results on images from mechanical pieces, where real and false defects are discriminated through effective reconstruction of their luminosity profile.
The enigmatic contribution of mitochondrial function in photosynthesis (2007)

Considerable cumulative evidence has accrued suggesting a vital role for mitochondrial function in optimizing photosynthesis. Both pharmacological approaches using respiratory inhibitors and reverse genetic approaches have recently underscored the high degree of interconnection between photosynthesis and respiration--the major pathways of energy production which are largely confined to the plastid and mitochondria, respectively. Here recent studies into the nature of these interactions are reviewed, with particular focus on (i) the recently described link between the mitochondrial electron transport chain activity, ascorbate biosynthesis, and photosynthesis; and (ii) the contribution of mitochondrial metabolism to the photorespiratory process. Whilst there is increasing evidence of a role for ascorbate in co-ordinating the rates of respiration and photosynthesis, some data are presented here for plants grown under extreme environmental conditions that suggest that this relationship is not absolute. It thus seems likely that interactions between these compartments are perhaps more numerous and complicated than previously thought. This observation suggests that although the elucidation of the genetic bases of both photorespiration and the Wheeler-Smirnoff pathway of ascorbate biosynthesis has recently been completed, much further research is probably necessary in order to understand fully how energy metabolism is co-ordinated in the illuminated leaf.
Infection with Borna Disease Virus: Molecular and Immunobiological Characterization of the Agent (1992)

Borna disease virus (BDV), which seems to be distinct from all other known viruses, exhibits a unique mechanism of pathogenesis. This review highlights several aspects of the biology of infection with this virus and summarizes the preliminary characterization of the agent. Studies on BDV may help to illuminate several important areas of neurobiology, including the mechanisms regulating the replication of a new type of RNA virus in the nuclei of neural cells, the neuroinvasiveness and neurotropism of such viruses, their T cell-mediated immunopathology, tolerance in newborn animals to persistent viral infection of the central nervous system, and behavioral diseases and eating disorders induced by such agents.
Proteolysis in Cultured Liver Epithelial Cells during Oxidative Stress (1995)

Exposure to various forms of mild oxidative stress significantly increased the intracellular degradation of both "short-lived" and "long-lived," metabolically radiolabeled, cell proteins in cultures of Clone 9 liver cells (normal liver epithelia). The oxidative stresses employed were bolus H2O2 addition; continuous H2O2 flux; the redox cycling quinones, menadione and paraquat; and the aldehydic products of lipid peroxidation, 4-hydroxynonenal, malonyldialdehyde, and hexenal. In general, exposure to more severe oxidative stress produced a concentration-dependent decline in intracellular proteolysis, in some cases to below baseline levels. Oxidatively modified "foreign" proteins (superoxide dismutase and hemoglobin) were also selectively degraded, in comparison with untreated foreign proteins, when added to lysates of Clone 9 liver cells. As with intracellular proteolysis, the degradation of foreign proteins added to cell lysates was greatly increased by mild oxidative modification, but depressed by more severe oxidative modification. The proteinase activity was recovered in > 300-kDa cell fractions, and inhibitor profiles and immunoprecipitation studies indicated that the multicatalytic proteinase complex, proteasome, was responsible for most of the selective degradation observed with mild oxidative stress; up to approximately 95% for intracellular proteolysis and 65-80% for degradation of foreign modified proteins. Seven days of daily treatment with an antisense oligodeoxynucleotide, directed against the initiation codon region of the proteasome C2 subunit gene, severely depressed the intracellular levels of several proteasome subunit polypeptides (by Western blot analysis), and also depressed the H2O2 induced increase in intracellular proteolysis by approximately 95%, without significantly affecting baseline proteolytic rates. Extensive studies revealed only small or no increases in the overall capacity of oxidatively stressed cells to degrade oxidatively modified protein substrates; a finding supported by both Western blot and Northern blot analyses which revealed no significant increase in the levels of proteasome subunit polypeptides or mRNA transcripts. We conclude that mild oxidative stress increases intracellular proteolysis by modifying cellular proteins, thus increasing their proteolytic susceptibility. In contrast, severe oxidative stress diminishes intracellular proteolysis, probably by generating severely damaged cell proteins that cannot be easily degraded (e.g. cross-linked/aggregated proteins), and by damaging proteolytic enzymes. We further conclude that the multicatalytic proteinase complex proteasome is responsible for most of the recognition and selective degradation of oxidatively modified proteins in Clone 9 liver cells.
A systems biology approach for pathway level analysis (2007)

A common challenge in the analysis of genomics data is trying to understand the underlying phenomenon in the context of all complex interactions taking place on various signaling pathways. A statistical approach using various models is universally used to identify the most relevant pathways in a given experiment. Here, we show that the existing pathway analysis methods fail to take into consideration important biological aspects and may provide incorrect results in certain situations. By using a systems biology approach, we developed an impact analysis that includes the classical statistics but also considers other crucial factors such as the magnitude of each gene's expression change, their type and position in the given pathways, their interactions, etc. The impact analysis is an attempt to a deeper level of statistical analysis, informed by more pathway-specific biology than the existing techniques. On several illustrative data sets, the classical analysis produces both false positives and false negatives, while the impact analysis provides biologically meaningful results. This analysis method has been implemented as a Web-based tool, Pathway-Express, freely available as part of the Onto-Tools (http://vortex.cs.wayne.edu).
The Use of Topographical Constraints In Receptor Mapping:  Investigation of the Topographical Requirements of the Tryptophan 30 Residue for Receptor Binding of Asp-Tyr-d-Phe-Gly-Trp-(N-Me)Nle-Asp-Phe-NH2(SNF 9007), a Cholecystokinin (26−33) Analogue That Binds to both CCK-B and δ-Opioid Receptors (1996)

The cholecystokinin (26-33) [CCK (26-33)] octapeptide analog Asp-Tyr-D-Phe-Gly-Trp(N-Me)-Nle-Asp-Phe-NH2 (SNF 9007) is a potent and selective ligand for both the CCK-B and delta-opioid receptors. Pharmacological studies of SNF 9007 suggest a relationship between the ligand requirements of CCK-B and delta-opioid receptors, which further implies a possible structural relationship between these receptors. We have utilized topographical constrainment of the important Trp30 residue to investigate structural features of SNF 9007 that would distinguish between binding requirements in this region for the CCK-B and delta-opioid receptors. Thus, the four optically pure isomers of beta-MeTrp were substituted for L-Trp30 of SNF 9007. Receptor binding results suggest that the preferred topography of the Trp30 residue for CCK-B receptor binding may be the 2S,3S (erythro-L) configuration whereas for the delta-opioid receptor it may be the 2S,3R (threo-L) configuration. Molecular modeling studies of these ligands further support the recently revised receptor-bound model for CCK-B octapeptide ligands (Kolodziej et al. J. Med. Chem. 1995, 38, 137-149) and are in good agreement with the DPDPE-delta opioid receptor "template" model (Nikiforovich et al. Biopolymers 1991, 31, 941-955).
Administration of a phorbol ester to patients with hematological malignancies: preliminary results from a phase I clinical trial of 12-O-tetradecanoylphorbol-13-acetate. (2002)

These studies confirm the feasibility of TPA administration to humans and establish the foundation for the development of phorbol esters as therapy for patients with a variety of malignant and nonmalignant disorders.
Visiting the State Capitals Yet Again (2002)

In the February 2002 Word Ways I explored trandeletions and transadditions of the names of the state capitals. How close could I get to finding 50 one-letter transdeletions? Where one-letter transdeletions could not be located, what were the fewest number of letters that needed to be deleted to effect a transdeletion? How close could I get to finding 50 one-letter transadditions? Where one-letter transadditions could not be located, what were the fewest number of letters that needed to be added to effect a transaddition? My previous article offered transdeletions for all 50 state capital names, involving deletion of a total of 71 letters. The article also offered transadditions for 43 of the state capital names, involving addition of 85 letters.
Solexa Ltd (2004)

Solexa Ltd is developing an integrated system, based on a breakthrough single molecule sequencing technology, to address a US$2 billion market that is expected to grow exponentially alongside and as a consequence of further technological enhancements. The system, software and consumables will initially be sold to research organizations, pharmaceutical companies and diagnostic companies that will sequence large regions of genomic DNA, including whole genomes, at costs several orders of magnitude below current levels. Solexa expects to launch its first product in 2006, and as it continues to make time and cost efficiencies, additional products will be launched into the expanding markets that will have broad applications in basic research through to healthcare management.