gebhart/patrepeval huggingface dataset:
Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes (1999)

Recognition of transcription regulation sites (operators) is a hard problem in computational molecular biology. In most cases, small sample size and low degree of sequence conservation preclude the construction of reliable recognition rules. We suggest an approach to this problem based on simultaneous analysis of several related genomes. It appears that as long as a gene coding for a transcription regulator is conserved in the compared bacterial genomes, the regulation of the respective group of genes (regulons) also tends to be maintained. Thus a gene can be confidently predicted to belong to a particular regulon in case not only itself, but also its orthologs in other genomes have candidate operators in the regulatory regions. This provides for a greater sensitivity of operator identification as even relatively weak signals are likely to be functionally relevant when conserved. We use this approach to analyze the purine (PurR), arginine (ArgR) and aromatic amino acid (TrpR and TyrR) regulons of Escherichia coli and Haemophilus influenzae. Candidate binding sites in regulatory regions of the respective H.influenzae genes are identified, a new family of purine transport proteins predicted to belong to the PurR regulon is described, and probable regulation of arginine transport by ArgR is demonstrated. Differences in the regulation of some orthologous genes in E.coli and H.influenzae, in particular the apparent lack of the autoregulation of the purine repressor gene in H.influenzae, are demonstrated.
Towards a Chaucerian Poetic (1984)

In the Prologue to The Legend of Good Women (F, 97–100; G, 81–8) Chaucer makes his most extended comments on literature, and emphasises three main points: the importance of traditional stories; the problem of belief in them; and his presentation of the 'naked text'. Another point is implicit, his own presence in the poem, even though he refuses responsibility. From here we may make a start towards establishing the nature of his poetic.KeywordsSpecific RealisationVerbal RealisationGood WomanCanterbury TaleBiblical NarrativeThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Phase II trial of ipilimumab monotherapy in melanoma patients with brain metastases. (2010)

8523 Background: Ipilimumab (Ipi), a human monoclonal antibody that blocks CTLA-4, has activity in advanced melanoma. We present results from a phase II trial (CA184-042) to assess Ipi safety and activity in advanced melanoma patients (pts) with brain metastases (mets). Methods: This 2-stage trial required > 2 objective responses (ORs) among the first 21 pts in order to proceed to stage 2 of Arm A and to open Arm B. Ptshad measurable brain mets with at least one lesion > 0.5 cm and/or 2 lesions > 0.3 cm, and none > 3 cm in diameter. Prior whole brain radiotherapy and stereotactic radiotherapy to non-index lesions were allowed. Pts were steroid-free (Arm A) or required steroids for symptoms of brain mets at study entry (Arm B). Ipi at 10 mg/kg was given by IV, every 3 weeks for 4 doses; responding or stable pts could receive maintenance ipilimumab at 10 mg/kg, every 12 weeks. Tumor assessments by modified WHO criteria were performed every 6 weeks, beginning at week 6; ORs and SD were confirmed 4 weeks after the criteria were first met. Results: The study accrued 51 pts in Arm A and 21 pts in Arm B. In Arm A, 4/51 pts had a partial response (PR) and 5/51 pts had stable disease (SD) in global lesions (brain + non-CNS) at week 12, with additional unconfirmed responses. When evaluating brain lesions only in Arm A, there were 5 PRs and 6 SDs at week 12, with additional unconfirmed responses. The duration of responses ranged from 3 to 12+ months, and duration of SD ranged from 1 to 7 months. Median global PFS was 1.9 months (95% CI, 1.2–3.0). The analysis of pts enrolled in Arm B is ongoing. There were no unexpected toxicities in either arm. CNS AEs of any grade occurred in 38 of 51 pts (74.5%) (grade 3–4 in 14 pts [27.5%]) in Arm A, and in 12 of 21 pts (57.1%) (grade 3–4 in 6 pts [28.6%]) in Arm B. The most common CNS events (> 10% of pts) of any grade were headache, dizziness, and seizures; all but one were attributable to disease. There was no association between brain edema or cerebral hemorrhage and OR. Conclusions: Ipi has a similar level of activity in brain and non-CNS lesions. This is the first study to prospectively evaluate Ipi in advanced melanoma pts with brain mets, and the data support its potential use as a treatment for these pts. The analyses are ongoing and final data will be presented. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Bristol-Myers Squibb Bristol-Myers Squibb Bristol-Myers Squibb Bristol-Myers Squibb
DVI parallel image compression (1989)

At the heart of DVI is an image compression and expansion technology that uses proprietary chips to expand an image in real time from a bit stream that has been compressed on a large computer at non-real time rates. This article describes how the compression algorithm is used and how it was ported.
Thermoregulatory Thresholds for Vasoconstriction in Patients Anesthetized with Various 1-Minimum Alveolar Concentration Combinations of Xenon, Nitrous Oxide, and Isoflurane (1999)

Xenon inhibits thermoregulatory control more than isoflurane, whereas nitrous oxide is the least effective in this respect.
The molecular biology of influenza viruses and paramyxoviruses (1993)

Abstract Orthomyxoviruses and paramyxoviruses are important aetiological agents of disease in man and animals. Each year disease outbreaks caused by these viruses result in extensive morbidity and mortality. In recent years major advances have been made in our knowledge and understanding of the structure and function of orthomyxovirus and paramyxovirus genes and the proteins that they encode. In particular, the complete genome sequences of many strains of influenza A, B, and C viruses and paramyxoviruses have been obtained. The expression of cDNA copies of individual genes has led to the elucidation of coding strategies used by these viruses and has also permitted study of the synthesis and maturation of many virally-encoded proteins in the absence of other virus gene products.
Infrared spectroscopy for clinical diagnosis of dental pulp vitality (2012)

Transmission spectra of wet human teeth and dentin slices, together with blood of different flow rates were investigated over a wide spectral range, from visible to terahertz (THz) light. The results make it possible to find the optimum light frequency for an all-optical determination of pulpal blood flow and, consequently, for clinically diagnosis of tooth vitality.
Discovery of 1-(4-(4-Propionylpiperazin-1-yl)-3-(trifluoromethyl)phenyl)-9-(quinolin-3-yl)benzo[h][1,6]naphthyridin-2(1H)-one as a Highly Potent, Selective Mammalian Target of Rapamycin (mTOR) Inhibitor for the Treatment of Cancer (2010)

The mTOR protein is a master regulator of cell growth and proliferation, and inhibitors of its kinase activity have the potential to become new class of anticancer drugs. Starting from quinoline 1, which was identified in a biochemical mTOR assay, we developed a tricyclic benzonaphthyridinone inhibitor 37 (Torin1), which inhibited phosphorylation of mTORC1 and mTORC2 substrates in cells at concentrations of 2 and 10 nM, respectively. Moreover, Torin1 exhibits 1000-fold selectivity for mTOR over PI3K (EC(50) = 1800 nM) and exhibits 100-fold binding selectivity relative to 450 other protein kinases. Torin1 was efficacious at a dose of 20 mg/kg in a U87MG xenograft model and demonstrated good pharmacodynamic inhibition of downstream effectors of mTOR in tumor and peripheral tissues. These results demonstrate that Torin1 is a useful probe of mTOR-dependent phenomena and that benzonaphthridinones represent a promising scaffold for the further development of mTOR-specific inhibitors with the potential for clinical utility.
Adenovirus-mediated gene transfer and expression of human β-glucuronidase gene in the liver, spleen, and central nervous system in mucopolysaccharidosis type VII mice (1997)

Mucopolysaccharidosis type VII (Sly syndrome) is a lysosomal storage disease caused by inherited deficiency of the lysosomal enzyme beta-glucuronidase. A murine model of this disorder has been well characterized and used to study a number of forms of experimental therapies, including gene therapy. We produced recombinant adenovirus that expresses human beta-glucuronidase and administered this recombinant adenovirus to beta-glucuronidase-deficient mice intravenously. The beta-glucuronidase activities in liver and spleen were elevated to 40% and 20%, respectively, of the heterozygote enzymatic level at day 16. Expression persisted for at least 35 days. Pathological abnormalities of these tissues were also improved, and the elevated levels of urinary glycosaminoglycans were reduced in treated mice. However, the beta-glucuronidase activity in kidney and brain was not significantly increased. After administration of the recombinant adenovirus directly into the lateral ventricles of mutant mice, the beta-glucuronidase activity in crude brain homogenates increased to 30% of heterozygote activity. Histochemical demonstration of beta-glucuronidase activity in brain revealed that the enzymatic activity was mainly in ependymal cells and choroid. However, in some regions, the adenovirus-mediated gene expression was also evident in brain parenchyma associated with vessels and in the meninges. These results suggest that adenovirus-mediated gene delivery might improve the central nervous system pathology of mucopolysaccharidosis in addition to correcting visceral pathology.
Frequent Nonrandom Activation of Germ-Line Genes in Human Cancer (2004)

The growing class of cancer/germ-line genes is characterized by a unique expression pattern with transcription restricted to germ cells and cancer cells. It is not known which fraction of germ-line genes is ectopically activated in tumor cells and whether this fraction displays common features as compared with strictly germ-line genes remaining silent in cancer. Using an unbiased genome-wide scanning approach, representative samples of both cancer/germ-line genes as well as strictly germ-line-specific genes were determined. Comparative analysis disclosed highly significant diametric characteristics for these two categories of genes with regard to sex specificity, developmental stage of physiological expression during gametogenesis, chromosomal localization, and epigenetic regulation of expression. Our findings provide class predictors for germ cell-specific gene activation in cancer. The identification of highly congruent expression patterns in cancer and in DNA methyltransferase-deficient cells suggests an underlying common epigenetic mechanism for activation of germ-line genes in cancer.
Basic fibroblast growth factor in neuronal cultures of human fetal brain (1990)

The presence of basic fibroblast growth factor (bFGF) was investigated in neuronal cells derived from 12 and 18 week-old human fetal brain cultures. To this purpose, the ability of bFGF to stimulate plasminogen activator (PA) production in fetal bovine aortic endothelial GM 7373 cells was used as an assay for this molecule in neuronal cell extracts. The identity of the PA-stimulating activity of neuronal cell extract with bFGF was confirmed by its high affinity for heparin and by its cross-reactivity with polyclonal antibodies to human placental bFGF. These antibodies recognized a Mr 18,000 cell-associated protein both in Western blot and in immuno-precipitation experiments. All the neurons showed bFGF immunoreactivity, as demonstrated by immunocytochemical staining, while nonneuronal cells were unstained. The data demonstrate for the first time that cultured human fetal brain neurons contain and synthesize bFGF.
Detection and representation of scenes in videos (2005)

This paper presents a method to perform a high-level segmentation of videos into scenes. A scene can be defined as a subdivision of a play in which either the setting is fixed, or when it presents continuous action in one place. We exploit this fact and propose a novel approach for clustering shots into scenes by transforming this task into a graph partitioning problem. This is achieved by constructing a weighted undirected graph called a shot similarity graph (SSG), where each node represents a shot and the edges between the shots are weighted by their similarity based on color and motion information. The SSG is then split into subgraphs by applying the normalized cuts for graph partitioning. The partitions so obtained represent individual scenes in the video. When clustering the shots, we consider the global similarities of shots rather than the individual shot pairs. We also propose a method to describe the content of each scene by selecting one representative image from the video as a scene key-frame. Recently, DVDs have become available with a chapter selection option where each chapter is represented by one image. Our algorithm automates this objective which is useful for applications such as video-on-demand, digital libraries, and the Internet. Experiments are presented with promising results on several Hollywood movies and one sitcom.
Joint impulse response shortening (2002)

In discrete multitone (DMT) transceivers an intelligent guard time sequence, called a cyclic prefix, is inserted between symbols to ensure that samples from one symbol do not interfere with the samples of another symbol. The length of the cyclic prefix is determined by the length of the impulse response of the effective physical channel. Using a long cyclic prefix reduces the throughput of the transceiver. To avoid using a long cyclic prefix, a short time-domain FIR filter is used to shorten the effective channel's impulse response. In full duplex transceivers echo cancellation may be required. The complexity of the echo canceller is directly related to the length of the echo path. This paper explores a joint shortening approach for determining the coefficients for this time-domain filter to jointly shorten both the channel and echo path impulse responses.
Turnstile device for heralded single photons: Coulomb blockade of electron and hole tunneling in quantum confinedp-i-nheterojunctions (1994)

We show that if a double-barrier mesoscopic p-i-n heterojunction is driven by an alternating voltage source, then Coulomb blockade and quantum confinement effects together can suppress the quantum fluctuations usually associated with electron and hole injection processes in semiconductors. It is therefore possible to generate heralded single-photon states without the need for a high-impedance current source. Since the frequency of the alternating voltage source determines the repetition rate of the single-photon states and the magnitude of the junction current, the present scheme promises high precision photon-flux and current standards.
A VLSI design for a trace-back Viterbi decoder (1992)

A systolic Viterbi decoder for convolutional codes is developed which uses the trace-back method to reduce the amount of data needed to be stored in registers. It is shown that this new algorithm requires a smaller chip size and achieves a faster decoding time than other existing methods.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Supramolecular photochemistry in zeolites: From catalysts to sunscreens (2007)

Zeolites are nanoporous, crystalline aluminosilicate materials comprised of a series of strictly uniform channels and cavities repeating along the tri-directional structure of the lattice. Over the last 30 years, researchers have increasingly recognized the desirable properties of these materials as hosts for photochemical reactions. This review will endeavor to draw attention to the properties of zeolite materials that make them appealing substrates for hosting guest molecules during photochemical reactions. An overview of some classical examples in zeolite host-guest photochemistry will be presented along with a brief description of a new use for zeolite materials as protective encapsulators.
Counting Low-Copy Number Proteins in a Single Cell (2007)

We have designed a microfluidic device in which we can manipulate, lyse, label, separate, and quantify the protein contents of a single cell using single-molecule fluorescence counting. Generic labeling of proteins is achieved through fluorescent-antibody binding. The use of cylindrical optics enables high-efficiency (approximately 60%) counting of molecules in micrometer-sized channels. We used this microfluidic device to quantify beta2 adrenergic receptors expressed in insect cells (SF9). We also analyzed phycobiliprotein contents in individual cyanobacterial cells (Synechococcus sp. PCC 7942) and observed marked differences in the levels of specific complexes in cell populations that were grown under nitrogen-depleted conditions.
Borna disease in rhesus monkeys as a model for uveo‐cerebral symptoms (1980)

Borna disease, a naturally occurring encephalomyelitis of horses and sheep, was induced in rhesus monkeys after intracerebral infection with virus containing rabbit brain suspension. The animals developed neurological disorders followed by a severe encephalomyelitis which was accompanied by a retinopathy. In all the analyzed brain and retina tissue pieces, virus-specific antigen could be demonstrated by immunoelectrophoretic techniques. Antibodies could be demonstrated by the intermediate gel technique as well as by the immunofluorescence test in the serum and the cerebrospinal fluid of all the monkeys. The histopathological findings in the brain and the eye might be comparable to certain types of encephalitis in man and to pathological changes in the eye of human patients, the etiologies of which are still obscure. An attempt was also made to study cell-mediated immunity by a chromium release assay in infected animals, the results of which might provide, together with the histopathological observations, strong evidence for the role of lymphocytes in the pathogenesis of BD infection in rhesus monkeys.
Parenting, personality and the family court (1999)

H is a universal finding in family research conducted about children who reach the attention of mental health or counselling services that such children are more likely than the general population to come either from broken families or from families in which the parental relationship is poor. Studies of the individual parents reveal that the likelihood that they will have a mental illness or a personality disorder is significantly increased over the rate in the general population. While figures vary, it is safe to say that the rate of relationship dysfunction and the rate of parental mental health problems in these families is at least twice that in the general population.
Microchip Module for Blood Sample Preparation and Nucleic Acid Amplification Reactions (2001)

A computer numerical control-machined plexiglas-based microchip module was designed and constructed for the integration of blood sample preparation and nucleic acid amplification reactions. The microchip module is comprised of a custom-made heater-cooler for thermal cycling, a series of 254 microm x 254 microm microchannels for transporting human whole blood and reagents in and out of an 8--9 microL dual-purpose (cell isolation and PCR) glass-silicon microchip. White blood cells were first isolated from a small volume of human whole blood (<3 microL) in an integrated cell isolation--PCR microchip containing a series of 3.5-microm feature-sized "weir-type" filters, formed by an etched silicon dam spanning the flow chamber. A genomic target, a region in the human coagulation Factor V gene (226-bp), was subsequently directly amplified by microchip-based PCR on DNA released from white blood cells isolated on the filter section of the microchip mounted onto the microchip module. The microchip module provides a convenient means to simplify nucleic acid analyses by integrating two key steps in genetic testing procedures, cell isolation and PCR and promises to be adaptable for additional types of integrated assays.
SHP-1: the next checkpoint target for cancer immunotherapy? (2016)

The immense power of the immune system is harnessed in healthy individuals by a range of negative regulatory signals and checkpoints. Manipulating these checkpoints through inhibition has resulted in striking immune-mediated clearance of otherwise untreatable tumours and metastases; unfortunately, not all patients respond to treatment with the currently available inhibitors of cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) and programmed cell death protein 1 (PD-1). Combinatorial studies using both anti-CTLA-4 and anti-PD-1 demonstrate synergistic effects of targeting multiple checkpoints, paving the way for other immune checkpoints to be targeted. Src homology 2 domain-containing protein tyrosine phosphatase 1 (SHP-1) is a widely expressed inhibitory protein tyrosine phosphatase (PTP). In T-cells, it is a negative regulator of antigen-dependent activation and proliferation. It is a cytosolic protein, and therefore not amenable to antibody-mediated therapies, but its role in activation and proliferation makes it an attractive target for genetic manipulation in adoptive transfer strategies, such as chimeric antigen receptor (CAR) T-cells. This review will discuss the potential value of SHP-1 inhibition in future tumour immunotherapy.
Memory enhancement induced by hypothalamic/fornix deep brain stimulation (2008)

Bilateral hypothalamic deep brain stimulation was performed to treat a patient with morbid obesity. We observed, quite unexpectedly, that stimulation evoked detailed autobiographical memories. Associative memory tasks conducted in a double-blinded "on" versus "off" manner demonstrated that stimulation increased recollection but not familiarity-based recognition, indicating a functional engagement of the hippocampus. Electroencephalographic source localization showed that hypothalamic deep brain stimulation drove activity in mesial temporal lobe structures. This shows that hypothalamic stimulation in this patient modulates limbic activity and improves certain memory functions.
Dielectric enhancement and electrophoresis due to an electrochemical double layer: A uniform approximation (1984)

We present here a method to calculate the response of a charged, insulating sphere immersed in an electrolytic solution in the presence of an externally applied electric field. Due to the charge on the sphere, it acquires a layer of counterions on the outside known as the electrochemical double layer. Since this double layer is complex, the response of the sphere to an externally applied electric field is complicated. In the past, ad hoc models have been proposed to circumvent the difficulty in the analysis of this problem. Recently, we presented a rigorous analysis of this problem using the technique of matched asymptotic expansions commonly used in boundary layer theory. Our previous solution was not valid for high zeta potential that corresponded to a highly charged sphere. In this paper, we present an analysis where this restriction is removed, and incorporate the effect of induced solvent osmotic flow. Our solutions is valid for larger value of the zeta potential compared to previous works. When the zeta potential is zero, corresponding to an uncharged sphere, we reproduce the classical result of an insulating sphere in a conducting medium. When the zeta potential is high, we reproduce a correction to the result of Fixman and O’Brien. With the response of one sphere known, we can use it to calculate the dielectric response of an ensemble of spheres, for example, in a colloidal suspension.