gebhart/patrepeval huggingface dataset:
Chemical Studies on Tobacco Smoke. XXXIII. N'-Nitrosonornicotine in Tobacco: Analysis of Possible Contributing Factors and Biologic Implications2 (1975)

A chemical analytic method to determine N'-nitrosonornicotine (NNN) and N' -nitrosoanabasine (NAB) in tobacco was developed. NNN was found in the unburned tobacco of commercial products at concentrations betweeen 0.3 and 88.6 mug/g. The highest levels were observed in highly fermented snuff (29.1 mug/g) and fine-cut chewing tobacco (88.6 mug/g). NAB was not detected (smaller than 0.5 ng/g) in any tobacco examined. Two new tobacco components, N' -carbomethoxynornicotine and N' -carbomethoxyanabasine,were found. Possible origins of NNN in tobacco were discussed, especially in relation to concentrations of nitrite, nitate, and alkaloids, and in relation to pH and curing. Biologic implications, including the possible function of NNN (the first organic carcinogen isolated from unburned tobacco) as a causative factor in cancer of the oral cavity in tobacco chewers and betel quid chewers, were also discussed.
Dissecting the complement pathway in hepatic injury and regeneration with a novel protective strategy (2014)

Liver resection is commonly performed under ischemic conditions, resulting in two types of insult to the remnant liver: ischemia reperfusion injury (IRI) and loss of liver mass. Complement inhibition is recognized as a potential therapeutic modality for IRI, but early complement activation products are also essential for liver regeneration. We describe a novel site-targeted murine complement inhibitor, CR2-CD59, which specifically inhibits the terminal membrane attack complex (MAC), and we use this protein to investigate the complement-dependent balance between liver injury and regeneration in a clinical setting of pharmacological inhibition. CR2-CD59 did not impact in vivo generation of C3 and C5 activation products but was as effective as the C3 activation inhibitor CR2-Crry at ameliorating hepatic IRI, indicating that the MAC is the principle mediator of hepatic IRI. Furthermore, unlike C3 or C5 inhibition, CR2-CD59 was not only protective but significantly enhanced hepatocyte proliferation after partial hepatectomy, including when combined with ischemia and reperfusion. Remarkably, CR2-CD59 also enhanced regeneration after 90% hepatectomy and improved long-term survival from 0 to 70%. CR2-CD59 functioned by increasing hepatic TNF and IL-6 levels with associated STAT3 and Akt activation, and by preventing mitochondrial depolarization and allowing recovery of ATP stores.
Amyloid diseases: Abnormal protein aggregation in neurodegeneration (1999)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
STAT:  A Saccharide Topology Analysis Tool Used in Combination with Tandem Mass Spectrometry (2000)

Sequential stages of mass spectrometry (MSn) have the potential to provide a great deal of structural information in glycan analysis. The saccharide topology analysis tool (STAT) presented here is a Web-based computational program that can quickly extract sequence information from a set of MSn spectra for an oligosaccharide of up to 10 residues. After information such as precursor ion mass, possible monosaccharide moieties, charge carrier, and product ion mass has been input, all possible connectivities are generated and evaluated against the MSn data. The list of possible structures is given a rating based on the likelihood that it is the correct sequence. Examples are given to demonstrate the feasibility of applying STAT to MSn data generated from bacterial lipooligosaccharides and an N-linked glycan. The major advantage of STAT is that the list of possible structures is generated quickly and the rating system pushes the more likely structures to the top of the list. Combining the data generated by STAT with data on the branching patterns of the glycan serves to eliminate all but a handful of structures. These remaining structures could then be used to guide further structural analysis.
Competitive randomized algorithms for non-uniform problems (1990)

Competitive analysis is concerned with comparing the performance of on-line algorithms with that of optimal off-line algorithms. In some cases randomization can lead to algorithms with improved performance ratios on worst-case sequences. In this paper we present new randomized on-line algorithms for snoopy caching and the spin-block problem. These algorithms achieve competitive ratios approachinge/(e−1) ≈ 1.58 against an oblivious adversary. These ratios are optimal and are a surprising improvement over the best possible ratio in the deterministic case, which is 2. We also consider the situation when the request sequences for these problems are generated according to an unknown probability distribution. In this case we show that deterministic algorithms that adapt to the observed request statistics also have competitive factors approachinge/(e−1). Finally, we obtain randomized algorithms for the 2-server problem on a class of isosceles triangles. These algorithms are optimal against an oblivious adversary and have competitive ratios that approache/(e−1). This compares with the ratio of 3/2 that can be achieved on an equilateral triangle.
The cells that knew too much (2000)

In this issue of the JCI, Ikehara et al. (1) report a novel function for an unusual population of lymphocytes — natural killer T (NKT) cells. These cells were originally identified as CD4–CD8– (double negative, DN) T cells responsible for rapid production of large amounts of IL-4 (2, 3), a cytokine that plays a critical role in supporting immunoglobulin production and inhibiting some inflammatory responses. NKT cells are now usually identified either by the coexpression of the NK cell marker NKR-P1 (NK1.1 in mice) and the T-cell antigen receptor (TCR), or by the presence of unusually restricted TCRα chains (termed Vα24JαQ in humans and Vα14Jα281 in mice and rats; refs. 4, 5). Although these cells may either be DN or express intermediate levels of the CD4 accessory molecule (CD4int), the fact that most NKT cells in humans, mice, and rats use similar TCRα chains has led to the suggestion that they recognize a restricted range of targets (4). Consistent with this hypothesis, many NKT-cell clones appear to be stimulated by the MHC class I–like molecule CD1, and NKT cells are severely depleted in mice carrying a targeted deletion of CD1d (6, 7).
Percolation in Transparent and Conducting Carbon Nanotube Networks (2004)

Ultrathin, uniform single-walled carbon nanotube networks of varying densities have been fabricated at room temperature by a vacuum filtration method. Measurements of the sheet conductance as a function of nanotube network density show 2D percolation behavior. In addition, the network transparency in the visible spectral range was examined and the results are in agreement with a standard thin-film model: fits to the standard theory indicate σac = σdc for transmission measurements at 550 nm. Transmission measurements also indicate the usefulness of nanotube network films as a transparent, conductive coating. Avenues for improvement of the network conductance are discussed.
Synthesis, accumulation, and excretion of trehalose in osmotically stressed Escherichia coli K-12 strains: influence of amber suppressors and function of the periplasmic trehalase (1991)

It has been reported previously that Escherichia coli K-12 carries an amber mutation that prevents osmotic stress-dependent accumulation of trehalose (M. L. Rod, K. Y. Alam, P. R. Cunningham, and D. P. Clark, J. Bacteriol. 170:3601-3610, 1988). We report that E. coli K-12 and W1485 (sup0) accumulated trehalose but that they required a higher osmotic strength in the growth medium than that required by their sup+ derivatives. Furthermore, the sup+ derivatives displayed both strongly increased trehalose-6-phosphate synthase activity and expression of otsA-lacZ and otsB-lacZ operon fusions compared with their parental strains. It is suggested that the amber mutation in question may be in a gene system encoding a transcriptional activator of the ots genes which govern the synthase. The much-used sup0 strain MC4100 behaved like the sup+ derivatives of W1485 with respect to trehalose synthesis. treA mutants with a defective periplasmic trehalase accumulated trehalose extracellularly under osmotic stress. The amount of trehalose excreted correlated with their synthase activity. Strains with an intact trehalase did not display extracellular trehalose accumulation. Thus, stressed E. coli cells regulate the cytoplasmic level of trehalose by a futile cycle involving overproduction, excretion, and degradation to glucose, which is reutilized.
Creating superpositions that correspond to efficiently integrable probability distributions (2002)

We give a simple and efficient process for generating a quantum superposition of states which form a discrete approximation of any efficiently integrable (such as log concave) probability density functions.
Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate (2007)

We have generated the first marmoset-specific DNA microarray and demonstrated its use to characterise large-scale gene expression profiles of hippocampus but also of other neuronal and non-neuronal tissues. In addition, we have generated a large collection of ESTs of marmoset origin, which are now available in the public domain. These new tools will facilitate molecular genetic research into this non-human primate animal model.
Reducing correspondence ambiguity in loosely labeled training data (2007)

We develop an approach to reduce correspondence ambiguity in training data where data items are associated with sets of plausible labels. Our domain is images annotated with keywords where it is not known which part of the image a keyword refers to. In contrast to earlier approaches that build predictive models or classifiers despite the ambiguity, we argue that that it is better to first address the correspondence ambiguity, and then build more complex models from the improved training data. This addresses difficulties of fitting complex models in the face of ambiguity while exploiting all the constraints available from the training data. We contribute a simple and flexible formulation of the problem, and show results validated by a recently developed comprehensive evaluation data set and corresponding evaluation methodology.
Complementary apodized grating waveguides for tunable optical delay lines (2012)

A novel class of high-speed and tunable integrated photonic delay lines that compromise between loss and size is proposed. The devices consist of two cascaded apodized grating waveguides and with complementary (positively and negatively modulated) refractive index profiles for dispersion compensation. It is shown that the compact tunable delay lines are low-loss and offer long true-time delays and tuning ranges and high operation bit rates.
A solution for linearity, stability and frequency bandwidth in PAM electrocutaneous stimulators' isolation interface (1996)

This paper introduces a novel method to isolate low-level from high-voltage circuits and/or channels of PAM electrocutaneous stimulators in neuromuscular electrical stimulation (NMES). The method avoids problems of linearity and polarization stability of optocouplers and narrow bandwidth of isolation amplifiers. Its main parameters are: carrier frequency of rectangular pulses up to 1 MHz and maximum modulating signal (elliptical or triangular envelopes) of 50 kHz. The circuit has low drift, high-voltage isolation, low-power consumption, requires few components, is battery-operated and ideal for microcomputer interface-based applications.
TONE RECOGNITION OF CONTINUOUS MANDARIN SPEECH BASED ON HIDDEN MARKOV MODEL (1994)

In this paper, several tone recognition schemes for continuous Mandarin speech are discussed. First, an SCHMM is used to model the acoustic features of a syllable for tone discrimination. Parameters extracted from the F0 and energy contours of the syllable by discrete Legendre orthonormal transform are used as the recognition features. Then, a scheme using two-layer network is proposed to cope with the difficulty resulting from the declination effect on the F0 contour of the declarative sentential utterance. The declination effect is modeled by a sentence-level HMM on the upper layer and the acoustic features of each tone are modeled by a state-dependent SCHMM on the lower layer. Lastly, the coarticulation effect coming from neighboring syllables is considered in the scheme using context-dependent model. Performance of these recognition schemes was examined by simulations. A recognition rate of 86.34% was achieved.
Real-Time Streaming Data Delivery over Named Data Networking (2016)

Named Data Networking (NDN) is a proposed future Internet architecture that shifts the fundamental abstraction of the network from host-to-host communication to request-response for named, signed data-an information dissemination focused approach. This paper describes a general design for receiver-driven, real-time streaming data (RTSD) applications over the current NDN implementation that aims to take advantage of the architecture's unique affordances. It is based on experimental development and testing of running code for real-time video conferencing, a positional tracking system for interactive multimedia, and a distributed control system for live performance. The design includes initial approaches to minimizing latency, managing buffer size and Interest retransmission, and adapting retrieval to maximize bandwidth and control congestion. Initial implementations of these approaches are evaluated for functionality and performance results, and the potential for future research in this area, and improved performance as new features of the architecture become available, is discussed.
p63 expression profile in normal and malignant prostate epithelial cells. (2003)

p63 expression was evaluated in a tissue microarray of prostate tissues including benign glands, prostatic intraepithelial neoplasia and prostatic carcinoma. Immunostaining with anti-p63 antibody was restricted to basal cell nuclei. Detectable p63 was found in immortalized and early passage cell cultures, but not in senescent cultures or metastatic tumor-derived cell lines. The selective presence of p63 in basal cells of the prostate suggests that p63 can be used as a marker of basal cells and in vitro typing cell cultures of prostate cancer (CaP). The basal cell association underscores its critical functions in the biology of basal cells.
Distinctive gene expression profiles of CD34 cells from patients with myelodysplastic syndrome characterized by specific chromosomal abnormalities (2004)

Aneuploidy, especially monosomy 7 and trisomy 8, is a frequent cytogenetic abnormality in the myelodysplastic syndromes (MDSs). Patients with monosomy 7 and trisomy 8 have distinctly different clinical courses, responses to therapy, and survival probabilities. To determine disease-specific molecular characteristics, we analyzed the gene expression pattern in purified CD34 hematopoietic progenitor cells obtained from MDS patients with monosomy 7 and trisomy 8 using Affymetrix GeneChips. Two methods were employed: standard hybridization and a small-sample RNA amplification protocol for the limited amounts of RNA available from individual cases; results were comparable between these 2 techniques. Microarray data were confirmed by gene amplification and flow cytometry using individual patient samples. Genes related to hematopoietic progenitor cell proliferation and blood cell function were dysregulated in CD34 cells of both monosomy 7 and trisomy 8 MDS. In trisomy 8, up-regulated genes were primarily involved in immune and inflammatory responses, and down-regulated genes have been implicated in apoptosis inhibition. CD34 cells in monosomy 7 showed up-regulation of genes inducing leukemia transformation and tumorigenesis and apoptosis and down-regulation of genes controlling cell growth and differentiation. These results imply distinct molecular mechanisms for monosomy 7 and trisomy 8 MDS and implicate specific pathogenic pathways.
Human dendritic cells express neuronal Eph receptor tyrosine kinases: role of EphA2 in regulating adhesion to fibronectin (2003)

Eph receptor tyrosine kinases and their ligands, the ephrins, have been primarily described in the nervous system for their roles in axon guidance, development, and cell intermingling. Here we address whether Eph receptors may also regulate dendritic cell (DC) trafficking. Reverse transcription-polymerase chain reaction (RT-PCR) analysis showed that DCs derived from CD34+ progenitors, but not from monocytes, expressed several receptors, in particular EphA2, EphA4, EphA7, EphB1, and EphB3 mRNA. EphB3 was specifically expressed by Langerhans cells, and EphA2 and EphA7 were expressed by both Langerhans- and interstitial-type DCs. EphA and EphB protein expression on DCs generated in vitro was confirmed by staining with ephrin-A3-Fc and ephrin-B3-Fc fusion proteins that bind to different Eph members, in particular EphA2 and EphB3. Immunostaining with anti-EphA2 antibodies demonstrated the expression of EphA2 by immature DCs and by skin Langerhans cells isolated ex vivo. Interestingly, ephrin expression was detected in epidermal keratinocytes and also in DCs. Adhesion of CD34+-derived DCs to fibronectin, but not to poly-l-lysine, was increased in the presence of ephrin-A3-Fc, a ligand of EphA2, through a beta1 integrin activation pathway. As such, EphA2/ephrin-A3 interactions may play a role in the localization and network of Langerhans cells in the epithelium and in the regulation of their trafficking.
Linear Algorithm for Data Compression via String Matching (1981)

A linear implementation of the optimal universal data compression methods of Lempel and Ziv is described. The main tool is McCreight's algorithm for constructing suffix trees. Both bounded and unbounded memory are considered.
Association of autism severity with a monoamine oxidase A functional polymorphism (2003)

A functional polymorphism (the upstream variable-number tandem repeat region, or uVNTR) in the monoamine oxidase A (MAOA) promoter region has been reported to be associated with behavioral abnormalities as well as increased serotonergic responsivity. We examined the relation between MAOA-uVNTR alleles and the phenotypic expression of autism in 41 males younger than 12.6 years of age. Children with the low-activity MAOA allele had both lower intelligence quotients (IQ) and more severe autistic behavior than children with the high-activity allele. In follow-up testing of 34 of the males at the 1-year time-point, those with the low-activity allele showed a worsening in IQ but no change in the severity of their autistic behavior. We conclude that functional MAOA-uVNTR alleles may act as a genetic modifier of the severity of autism in males.
Preserving integrity in remote file location and retrieval (2002)

We present a service for locating and retrieving files from an untrusted network such that the integrity of the retrieved files can be verified. This service enables groups of people in geographically remote locations to share files using an untrusted network. For example, distribution, of an organization's software to all the organization's sites can be accomplished using this service. Distribution of files in an untrusted network is complicated by two issues: (1) location of files and (2) verification of file integrity. ftp and World-wide Web (WWW) services require some user intervention to locate a file, so they cannot be embedded in automated systems. Distributed systems have mechanisms for automated file location and retrieval, but they require trust in all system principals and do not provide an appropriate balance between availability of files and retrieval cost for our applications. Verification of the integrity of a file retrieved from an untrusted network is necessary because the file is subject to malicious modification attacks. Our service provides the capability to automatically locate, retrieve, and verify files specified by a client using a single trusted principal. We demonstrate our service by building a system shell that automatically downloads remote software when needed.
Clinical Significance of CSF Glutamate Concentrations Following Severe Traumatic Brain Injury in Humans (1998)

Glutamate excitotoxicity is a putative mechanism of secondary damage after traumatic brain injury (TBI). No relationship between glutamate release and clinical status has been shown in humans, however. We hypothesize a dose-response relationship between CSF glutamate concentrations and severity of injury, electrophysiological deterioration as measured by somatosensory evoked potential amplitudes, and clinical outcome. From August 1991 to March 1996, intensive monitoring of 55 patients with severe TBI (GCS < or = 8 after resuscitation) included twice daily CSF glutamate levels and hourly somatosensory evoked potentials (SSEPs) for an average of 5 days. Clinical outcomes were survival/nonsurvival and Glasgow outcome score (GOS) at 3 months or more post-injury. Glutamate levels were not associated with severity of injury, electrophysiological deterioration, or clinical outcome. Neither peak nor mean glutamate levels significantly improved a simple logistic regression model which used only age and presence of bilaterally unreactive pupils to predict survival. Using this methodology CSF glutamate concentrations did not display a dose-response relationship to severity of injury, electrophysiological deterioration, or predict clinical outcomes following TBI in a group of 55 patients. An early effect of glutamate, an effect dependent on time of exposure to glutamate or other modulating effects cannot be ruled out.
Lightweight linear types in system f° (2010)

We present System F°, an extension of System F that uses kinds to distinguish between linear and unrestricted types, simplifying the use of linearity for general-purpose programming. We demonstrate through examples how System F° can elegantly express many useful protocols, and we prove that any protocol representable as a DFA can be encoded as an F° type. We supply mechanized proofs of System F°'s soundness and parametricity properties, along with a nonstandard operational semantics that formalizes common intuitions about linearity and aids in reasoning about protocols.
A New Microfluidics-Based Droplet Dispenser for ICPMS (2014)

In this work, a novel droplet microfluidic sample introduction system for inductively coupled plasma mass spectrometry (ICPMS) is proposed and characterized. The cheap and disposable microfluidic chip generates droplets of an aqueous sample in a stream of perfluorohexane (PFH), which is also used to eject them as a liquid jet. The aqueous droplets remain intact during the ejection and can be transported into the ICP with >50% efficiency. The transport is realized via a custom-built system, which includes a membrane desolvator necessary for the PFH vapor removal. The introduction system presented here can generate highly monodisperse droplets in the size range of 40-60 μm at frequencies from 90 to 300 Hz. These droplets produced very stable signals with a relative standard deviation (RSD) comparable to the one achieved with a commercial droplet dispenser. Using the current system, samples with a total volume of <1 μL can be analyzed. Moreover, the capabilities of the setup for introduction and quantitative elemental analysis of single cells were described using a test system of bovine red blood cells. In the future, other modules of the modern microfludics can be integrated in the chip, such as on-chip sample pretreatment or parallel introduction of different samples.