gebhart/patrepeval huggingface dataset:
Ab Initio Study of Doped Carbon Nanotube Sensors (2003)

Recently great advances have been made in demonstrating the viability of using carbon nanotubes (CNTs) to detect the presence of chemical gases such as NO2, NH3, and O2, and they have led to the design of a new breed of sensor devices. Based on intrinsic CNTs, the devices are capable of detecting small concentration of molecules with high sensitivity under ambient conditions. However, these devices have a limitation that only molecules binding to a carbon nanotube can be detected. They are currently limited to NH3, NO2, and O2, and a host of highly toxic gases (such as carbon monoxide), water molecules, and biomolecules cannot be detected using these intrinsic CNT devices. Recent efforts on externally functionalizing CNT surface and internal doping in CNT only result in temporary sensing capability due to the weak van der Waals interaction between CNT and doped materials. In this paper, we propose the concept of a new type of nanoscale sensor devices that can detect the presence of CO and water molecules. To overcome the reliability problem, these devices are developed by substitutional doping of impurity atoms (such as boron, nitrogen atoms) into intrinsic single-wall carbon nanotubes or by using composite BxCyNz nanotubes. Using first-principle calculations, we demonstrate that these sensor devices can not only detect the presence of CO and water molecules, but also the sensitivity of these devices can be controlled by the doping level of impurity atoms in a nanotube.
Clinical review: Scoring systems in the critically ill (2010)

General illness severity scores are widely used in the ICU to predict outcome, characterize disease severity and degree of organ dysfunction, and assess resource use. In this article we review the most commonly used scoring systems in each of these three groups. We examine the history of the development of the initial major systems in each group, discuss the construction of subsequent versions, and, when available, provide recent comparative data regarding their performance. Importantly, the different types of scores should be seen as complementary, rather than competitive and mutually exclusive. It is possible that their combined use could provide a more accurate indication of disease severity and prognosis. All these scoring systems will need to be updated with time as ICU populations change and new diagnostic, therapeutic and prognostic techniques become available.
Model for Antibiotic Optimization via Neoglycosylation:  Synthesis of Liponeoglycopeptides Active against VRE (2007)

The neoglycosylation of a methoxyamine-appended vancomycin aglycon with all possible N‘-decanoylglucopyranose and N‘-biphenoylglucopyranose regioisomers led to the production of a focused set of liponeoglycopeptide variants in good yields and with excellent stereoselectivity. High-throughput antibacterial assays employing a unique set of vancomycin-resistant Enterococci faecalis and Enterococci faecium clinical isolates revealed that the nature and regiochemistry of glycosyl lipidation modulated vancomycin-resistent Enterococci potency. In contrast to prior work with lipoglycopeptides, this study reveals the glucose C3‘ or C4‘ as the optimal position for neoglycopeptide lipidation. This purely chemical method for the diversification of the glycolipid portion of lipoglycopeptide antibiotics is simple to perform on a large scale, requires minimal synthetic effort in sugar donor preparation, and provides access to highly active antibiotics that are not easily prepared by other state-of-the-art methods.
Bioluminescence in Mesopelagic Squid: Diel Color Change During Counterillumination (1980)

Two species of mesopelagic squid greatly altered the color of their bio-luminescence during counterillumination. The color change was triggered by changes in water temperature corresponding to those normally encountered by these vertically migrating animals. These squid can probably conceal themselves under the different colors of downwelling light that they encounter in their day and night habitats.
Spectral reflectance study of the Hadley-Appenine (Apollo 15) region (1985)

Twenty-three near infrared spectra were obtained from the Mauna Kea Observatory 2.2 m telescope. Results of an analysis of near infrared spectra obtained for surface units in the Hadley-Apennine region were presented. Compositional trends from the interior to exterior of the Imbrium are discussed.
Dramatic increase in the numbers of functionally mature dendritic cells in Flt3 ligand-treated mice: multiple dendritic cell subpopulations identified. (1996)

Dendritic cells (DC) are the most efficient APC for T cells. The clinical use of DC as vectors for anti-tumor and infectious disease immunotherapy has been limited by their trace levels and accessibility in normal tissue and terminal state of differentiation. In the present study, daily injection of human Flt3 ligand (Flt3L) into mice results in a dramatic numerical increase in cells co-expressing the characteristic DC markers-class II MHC, CD11c, DEC205, and CD86. In contrast, in mice treated with either GM-CSF, GM-CSF plus IL-4, c-kit ligand (c-kitL), or G-CSF, class II+ CD11c+ cells were not significantly increased. Five distinct DC subpopulations were identified in the spleen of Flt3L-treated mice using CD8 alpha and CD11b expression. These cells exhibited veiled and dendritic processes and were as efficient as rare, mature DC isolated from the spleens of untreated mice at presenting allo-Ag or soluble Ag to T cells, or in priming an Ag-specific T cell response in vivo. Dramatic numerical increases in DC were detected in the bone marrow, gastro-intestinal lymphoid tissue (GALT), liver, lymph nodes, lung, peripheral blood, peritoneal cavity, spleen, and thymus. These results suggest that Flt3L could be used to expand the numbers of functionally mature DC in vivo for use in clinical immunotherapy.
Comparison of cellular recovery rates and morphologic detail obtained using membrane filter and cytocentrifuge techniques. (1976)

Two methods commonly used for collecting cells from a large volume of fluid-membrane filters (Millipore, Gelman, and Nuclepore) and cytocentrifugation-were compared for percentage of cell recovery and degree of cell preservation. Twenty samples of body cavity fluid were centrifuged, and the buffy coat of each was resuspended in a balanced electrolyte solution. The cellularity of each suspension was determined using both Coulter Counter and hemocytometer. Exact aliquots of each sample were collected on Millipore, Gelman, and Nuclepore filters and on slides by cytocentrifugation (Shandon). The resultant material was fixed in alcohol (95% ethanol), stained by the Papanicolaou method, mounted, and then evaluated with respect to the number of cells present and the diagnostically significant morphologic detail of the cells. Cell recovery was estimated by counting cells in known areas of each preparation and then ascertaining the total area. The Millipore filter technique consistently recovered the highest percentage of cells and preserved the best morphologic detail.
Studies on the catalase of Histoplasma capsulatum (1983)

Factors which control the levels of catalase within yeast cells of Histoplasma capsulatum were studied. Only a small fraction of the total catalase activity could be detected in whole cells. The bulk of the activity was revealed in cell-free extracts or in cells permeabilized with acetone. The formation of the enzyme was regulated by glucose and by oxygen. There were large, consistent differences in the levels of catalase among strains of H. capsulatum. The sensitivity of the strains to H2O2 toxicity also varied remarkably. Peroxidase activity could not be detected in cell-free extracts of the strains. Resistance to H2O2 did not correspond to levels of catalase. There was no obvious correlation of H2O2 sensitivity and virulence among the strains.
Transcriptional analysis of rolling circle replicating plasmid pVT736-1: evidence for replication control by antisense RNA (1995)

Several plasmids have been described in Actinobacillus actinomycetemcomitans, a gram-negative coccobacillus. Recently, the nucleotide sequence of pVT736-1, a cryptic plasmid of A. actinomycetemcomitans VT736, was determined. This plasmid possesses all the features necessary for rolling circle replication. The present study involved a transcriptional analysis of pVT736-1. Results of Northern (RNA) blot analyses and primer extension studies indicated that the two open reading frames identified in pVT736-1 are each preceded by at least one promoter. Expression of these promoters varied with growth phase. In addition, an antisense RNA (Cop RNA) appeared to control the synthesis of the putative replication protein. To our knowledge, this is the first rolling circle replicating plasmid isolated from a gram-negative organism that has been subjected to such detailed analysis.
Amplified femtosecond pulses from an Er:fiber system: Nonlinear pulse shortening and selfreferencing detection of the carrier-envelope phase evolution (2003)

We present an improved design of an amplified Er:fiber laser system for the generation of intense femtosecond pulses. By properly controlling the influence of optical nonlinearities inside a stretched pulse amplifier, the spectrum is broadened to over 100 nm. The pulses are recompressed to 65 fs. A linearly polarized output of 110 mW is obtained at 67 MHz repetition rate. As a first application, we report the generation of an octave-spanning supercontinuum inside a short piece of a highly nonlinear fiber. Self-referencing detection of the carrier-envelope phase evolution with an f-to-2f interferometer is demonstrated.
Inhibition of Protein Kinase-A by Overexpression of the Cloned Human Protein Kinase Inhibitor (1991)

Human cDNA clones for a heat-stable protein kinase inhibitor (PKI) protein of the cAMP-dependent protein kinase (PKA) were isolated using a mouse PKI cDNA fragment. Two human cDNA clones of 1.7 and 2.0 kb were sequenced and shown to encode the entire open reading frame of 228 nucleotides. Together these clones comprised 2147 nucleotides of the mRNA. The deduced amino acid sequence of the human clones showed 100% identity to the rabbit skeletal muscle PKI protein and 97% identity to the mouse brain PKI. The mouse and human PKI cDNAs shared nucleotide homology in their 3' untranslated regions as well as in the 32 nucleotides immediately 5' of the translation initiation site. Northern blot analysis of human skeletal muscle RNA with a human cRNA probe detected a major mRNA of approximately 4.0 kb. Transient overexpression in COS cells verified that a heat-stable inhibitor of protein kinase was produced by he human PKI cDNA, and protein extracts from the transfected COS cells inhibited both the C alpha and C beta isoforms of the PKA catalytic subunit with equal efficacy. Functional expression of the human PKI protein was further studied by assaying the ability of PKI expression vectors to inhibit PKA catalytic subunit stimulation of transcription from the human enkephalin promoter. In these studies, elimination of a conserved alternative translation start site in the 5' untranslated region of PKI was shown to potentiate the inhibitory activity of the PKI expression vector.
Role of cytokines in the early stages of chronic colitis in TCR alpha-mutant mice. (1997)

Chronic colitis develops spontaneously in mice mutant for T-cell receptor alpha (TCR alpha) genes maintained in pathogen-free conditions. Our previous studies indicate that the cytokine imbalance caused by a lack of TCR alpha beta + T cells may be associated with the development of chronic colitis in TCR alpha-mutant (TCR alpha -/-) mice. The histologic changes of chronic colitis are recognizable by 3 to 4 months of age and are characterized by marked crypt cell hyperplasia and the presence of an inflammatory cell infiltrate. Because early events in the development of chronic colitis may be important in the pathogenesis of the disorder, we investigated the changes in the colon at a time when chronic colitis was not yet histologically recognizable. In vivo labeling with 5-bromo-2'-deoxyuridine revealed increased epithelial proliferation in the crypts by 6 to 8 weeks of age. There was an increase in number of T cells in the colon of TCR alpha -/- mice compared with that in TCR alpha +/- (heterozygous TCR alpha-mutant) mice after 6 weeks of age. The predominant T-cell subsets were CD4+, TCR alpha- beta +, and TCR gamma delta + cells. Reverse transcription-PCR and immunohistochemistry of the colonic mucosa obtained from TCR alpha -/- mice (> 6 weeks old) showed a marked increase of IL-1 alpha and IL-1 beta but not of TNF alpha or transforming growth factor beta-1 compared with TCR alpha +/- mice. In vivo neutralization of IL-1 alpha or IL-1 beta by specific mAb suppressed colonic epithelial proliferation and decreased colonic mucosal T-cell infiltration in 8-week-old TCR alpha -/- mice. These results provide direct evidence that overproduction of IL-1 alpha and IL-1 beta in the colonic mucosa may play an important role in the early stages of development of chronic colitis in TCR alpha -/- mice.
Molecular analysis of the interaction of calcineurin with drug-immunophilin complexes (1994)

The calcium/calmodulin-regulated phosphatase calcineurin (CN) is the site of action of the immunosuppressive drugs cyclosporin A (CsA) and FK506. CN has recently been established as a key signaling enzyme in the T cell signal transduction cascade and an important regulator of transcription factors such as NF-AT and OAP/Oct-1, which are involved in the expression of a number of important T cell early genes. CsA and FK506 act by forming complexes with their respective intracellular receptors cyclophilin and FKBP (immunophilins), which can then bind to CN, inhibiting its enzymatic activity and thereby preventing early gene expression. CN is comprised of two subunits: a 59-kDa catalytic subunit (CNA), which contains a calmodulin binding domain and autoinhibitory region, and a 19-kDa intrinsic calcium binding regulatory subunit (CNB). In this study, we have utilized a series of deletion mutants of the CNA subunit to investigate the subunit and molecular requirements that govern the interaction of CN with drug-immunophilin complexes. The calmodulin binding and autoinhibitory domains of the CNA subunit were found to be dispensable for the binding of CN to drug-immunophilin complexes. In contrast, we found that the regulatory CNB subunit appears to play an obligatory role in this interaction and have defined an amino acid sequence of the CNA subunit which forms the binding site for CNB. Although necessary, the CNB subunit per se is not sufficient to mediate an interaction with drug-immunophilin complexes; amino acid residues of the CNA subunit, specifically a region located within the putative catalytic domain, are also required for the interaction of CN with both FKBP-FK506 and cyclophilin A-CsA.
Biological Activities of Melanotropic Peptide Fatty Acid Conjugates (1991)

Four fatty acids (FA, palmitic, myristic, decanoic, hexanoic) were individually conjugated to the N-terminus of the alpha-MSH fragment analog, H-Asp5-His6-D-Phe7-Arg8-Trp9-Lys10-NH2. This resulted in enhanced potency of the conjugates (compared to the unconjugated melanotropin analog) as determined in the lizard skin bioassay and in the mouse melanoma cell tyrosinase bioassay. The shorter conjugates of hexanoic and decanoic acid were at least equipotent to alpha-MSH in the lizard skin bioassay, whereas the longer myristoyl and palmitoyl analogs were 100 times less active. The myristoyl and palmitoyl conjugates exhibited a "creeping" potency in the lizard skin bioassay-that is, potency of the peptides increased with time in contact with the skins. These observations may be related to the more lipid nature of these FA-conjugates. In the tyrosinase assay, the conjugates were 10-100 times more active than alpha-MSH or the unconjugated analog. Each of the FA-melanotropic peptide conjugates exhibited prolonged (residual) melanotropic activity in both the lizard skin and melanoma cell bioassays. In other words, after removal of the melanotropin conjugates from contact with the skins or cells, responses were still manifested for hours or days thereafter. As little as 1 hr of contact with melanoma cells resulted in enhanced enzyme activity as measured 48 hr later. Since the conjugates, but not H-[Asp5, D-Phe7, Lys10]alpha-MSH5-10-NH2, exhibited prolonged activity, the conversion of reversible agonists to irreversible agonists was demonstrated.
Gene therapy with sodium/iodide symporter in hepatocarcinoma (2001)

The ability of thyroid cells to accumulate iodide is a prerequisite for successful radioiodide therapy of benign thyroid diseases and differentiated thyroid carcinoma. The transport of iodide across the cell membrane is mediated by the sodium iodide symporter (hNIS). Employing a bicistronic retroviral vector for the transfer of the hNIS coding sequence and the hygromycin resistance gene stable hNIS expressing rat Morris hepatoma (MH3924A) cell lines were generated by hygromycin selection. Genetically modified MH3924A cell lines accumulated up to 235 times more iodide when compared to non-infected hepatoma cells with a maximal iodide uptake after 60 minutes incubation. Competition experiments in the presence of sodium perchlorate revealed a dose dependent decrease of the iodide uptake, FCCP led to a loss of accumulated I(-), whereas DIDS increased the I(-) uptake into the cells. However, a rapid efflux of the radioactivity (80%) was observed during the first 10 minutes after the 125I(-) containing medium had been replaced by non-radioactive medium. In rats, the hNIS-expressing tumors accumulated six times more iodide as compared to the contralateral wild type tumor as monitored by scintigraphy. An ex vivo quantitation of the iodide content performed 1 hour after tracer administration in 1g tumor tissue revealed a 17-fold higher iodide accumulation in the genetically modified tumors. In vivo also a rapid efflux of the radioactivity out of the tumor was observed. Therefore, the transduction of the hNIS gene per se is sufficient to induce 125I(-) transport in Morris hepatoma cells in vitro and in vivo. For a therapeutic application of the hNIS gene, however, additional conditions need to be defined which inhibit the iodide efflux.
Trapidil Inhibits Endothelial Cell Proliferation and Angiogenesis in the Chick Chorioallantoic Membrane and in the Rat Cornea (1995)

The effects of trapidil, a coronaro-active drug which has been shown to inhibit the mitogenic activity of platelet derived growth factor (PDGF), have been investigated on the proliferation of the human endothelial cells (HUV-EC-C), on the neovascularization in the chorioallantoic membrane of the chick embryo (CAM) as well as on the angiogenesis of rat cornea following chemical injury. The proliferation of HUV-EC-C in the presence of trapidil (25 and 250 micrograms/mL) was significantly inhibited by 19 and 25% respectively, compared to controls. On 2-days old CAMs, agarose disks containing 100-150 micrograms of trapidil produced an avascular zone indicating significant antiangiogenic activity, while control agarose disks were without effect. Corneal neovascularization was induced by applying a silver nitrate/potassium nitrate applicator to the rat eyes. A 6-day-treatment with eye drops of a solution of 10 mg/mL trapidil significantly decreased the rate of vessel growth compared with vehicle controls. The antiangiogenic activity of trapidil was markedly increased by the association with hydrocortisone (1.34 mg/mL). These results suggest that trapidil, alone or in combination with a steroid, could be a promising candidate for the therapy of corneal diseases in which alterations induced by neovascular growth play a substantial role.
Engineering a novel specificity in subtilisin BPN' (1993)

The specificity of subtilisin BPN' toward substrates with large hydrophobic P4 residues has been improved by single amino acid replacements at positions 104 and 107. Mutations were designed to (i) increase the size of the P4 binding pocket by replacing Ile107, which is at the bottom of the S4 pocket, by Val, Ala, and Gly and (ii) lose the hydrogen bond between Tyr104 and Ser130 at the entrance of the P4 binding pocket by changing Tyr104 to Phe and thus reduce interactions between small P4 side chains and residue 104. All mutant subtilisins, except for I107V, have increased specificity for residues with large side chains at P4 compared with wild type. Using the conventional definition of specificity as the competition of different substrates for the same enzyme, the I107G mutant subtilisin has one of the largest improvements in substrate specificity reported for subtilisin so far; kcat/KM is increased > 200-fold for Phe compared with Ala as the P4 residue. Further, the activity of I107G toward its specific substrate is comparable to that of the wild-type enzyme. Surprisingly, much of the increase in specificity on mutation of Ile107-->Gly appears to result from a lesion that is transmitted through the structure and effects catalysis. The value of kcat/KM for the small substrate acetyltyrosine ethyl ester, which binds to the S1 pocket, drops by 93% on mutation of Ile107-->Gly. The lesion in subtilisin I107G is complemented, however, on binding of longer substrates that have a large hydrophobic P4 amino acid side chain that can bind in the S4 pocket.
Semi-anthropomorphic 3D printed multigrasp hand for industrial and service robots (2013)

This paper presents the preliminary prototype design and implementation of the Nazarbayev University (NU) Hand, a new semi-anthropomorphic multigrasp robotic hand. The hand is designed to be an end effector for industrial and service robots. The main objective is to develop a low-cost, low-weight and easily manufacturable robotic hand with a sensor module allowing acquisition of data for autonomous intelligent object manipulation. 3D printing technologies were extensively used in the implementation of the hand. Specifically, the structure of the hand is printed using a 3D printer as a complete assembly voiding the need of using fasteners and bearings for the assembly of the hand and decreasing the total weight. The hand also incorporates a sensor module containing a LIDAR, digital camera and non-contact infrared temperature sensor for intelligent automation. As an alternative to teach pendants for the industrial manipulators, a teaching glove was developed, which acts as the primary human machine interface between the user and the NU Hand. The paper presents an extensive performance characterization of the robotic hand including finger forces, weight, audible noise level during operation and sensor data acquisition.
Rational development of a HIV‐1 gene therapy vector (2003)

Based on our results we have constructed a vector that is both more efficient, and has better safety characteristics, than the widely used pHR' HIV-1 vector construct.
Commensal-dependent expression of IL-25 regulates the IL-23–IL-17 axis in the intestine (2008)

Alterations in the composition of intestinal commensal bacteria are associated with enhanced susceptibility to multiple inflammatory diseases, including those conditions associated with interleukin (IL)-17-producing CD4(+) T helper (Th17) cells. However, the relationship between commensal bacteria and the expression of proinflammatory cytokines remains unclear. Using germ-free mice, we show that the frequency of Th17 cells in the large intestine is significantly elevated in the absence of commensal bacteria. Commensal-dependent expression of the IL-17 family member IL-25 (IL-17E) by intestinal epithelial cells limits the expansion of Th17 cells in the intestine by inhibiting expression of macrophage-derived IL-23. We propose that acquisition of, or alterations in, commensal bacteria influences intestinal immune homeostasis via direct regulation of the IL-25-IL-23-IL-17 axis.