gebhart/patrepeval huggingface dataset:
Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals (2003)

We propose a framework for modeling sequence motifs based on the Maximum Entropy principle (MEP).We recommend approximating short sequence motif distributions with the Maximum Entropy Distribution (MED) consistent with low-order marginal constraints estimated from available data, which may include dependencies between non-adjacent as well as adjacent positions.Finally, we suggest mechanistically-motivated ways of comparing models.
High-Affinity CD25-Binding IL-2 Mutants Potently Stimulate Persistent T Cell Growth (2005)

We have used directed evolution to construct IL-2 mutants that bind the IL-2 alpha receptor subunit (IL-2Ralpha, CD25) with affinities comparable to that of the IL-15-IL-15 alpha receptor subunit (IL-15Ralpha) interaction. T cells proliferate for up to 6 days following a 30 minute incubation with these IL-2 mutants, which may lead to potential applications for cancer and viral immunotherapy. Several alternative mechanisms have been proposed to explain the contrasting effects of IL-2 and IL-15 on T cell proliferation and death. These IL-2 mutants exhibit T cell growth response-receptor occupancy curves indistinguishable from that for IL-15, suggesting that much of the difference between wild-type IL-2 and IL-15 effects arises simply from their 1000-fold differing affinities for their private alpha receptor subunits.
Dissociable Neural Systems Resolve Conflict from Emotional versus Nonemotional Distracters (2007)

The human brain protects the processing of task-relevant stimuli from interference ("conflict") by task-irrelevant stimuli via attentional biasing mechanisms. The lateral prefrontal cortex has been implicated in resolving conflict between competing stimuli by selectively enhancing task-relevant stimulus representations in sensory cortices. Conversely, recent data suggest that conflict from emotional distracters may be resolved by an alternative route, wherein the rostral anterior cingulate cortex inhibits amygdalar responsiveness to task-irrelevant emotional stimuli. Here we tested the proposal of 2 dissociable, distracter-specific conflict resolution mechanisms, by acquiring functional magnetic resonance imaging data during resolution of conflict from either nonemotional or emotional distracters. The results revealed 2 distinct circuits: a lateral prefrontal "cognitive control" system that resolved nonemotional conflict and was associated with enhanced processing of task-relevant stimuli in sensory cortices, and a rostral anterior cingulate "emotional control" system that resolved emotional conflict and was associated with decreased amygdalar responses to emotional distracters. By contrast, activations related to both emotional and nonemotional conflict monitoring were observed in a common region of the dorsal anterior cingulate. These data suggest that the neuroanatomical networks recruited to overcome conflict vary systematically with the nature of the conflict, but that they may share a common conflict-detection mechanism.
Structural, antigenetic and transcriptional characteristics in peripheral blood CD34+ progenitor cells from polycythemia vera patients: Evidence for delayed determination (2003)

Polycythemia vera (PV) is a clonal disorder characterized by trilinear hematopoietic proliferation. PV progenitors are hypersensitive to several growth factors although their receptor expression is reduced or absent. In this study selected CD34+ peripheral blood (PB) cells from PV patients, PB healthy donors and patients with secondary polycythemia (SP) were investigated and compared concerning frequency, morphology, antigen expression, transcription of differentiation markers and proliferation as well as apoptosis rate following short-term culture. The highest amount of CD34+ cells was found in the SP group while the frequency was slightly lower but more variable in PV. Native PV CD34+ cells varied in shape and form and developed intracytoplasmatic organelles like mitochondria and a more extended Golgi apparatus while in the other groups they constituted a uniform phenotype. However, no premature transcripts for glycophorin A (GypA) and CD41b, both markers for advanced erythropoiesis and megakaryopoiesis, could be detected in sorted PV progenitors. Also, coexpression for early acting hematopoietic cytokine receptors IL-3Ralpha and c-Kit and for initial erythropoiesis (GypC) or megakaryopoiesis (CD61) was similar in the different groups. Performing 96 h cocultures with bone marrow (BM) fibroblasts the frequency of CD34+ cells was elevated, downregulation of IL-3Ralpha delayed, coexpression of GypC reduced and proliferative activity higher in the PV group. Our results suggest that primitive hematopoiesis is altered in PV because PB CD34+ cells in this disease are characterized by a maturation dissociation with increased activation in untreated populations and a delayed differentiation in short-term cultures.
Using Advanced Encryption Standard (AES) Counter Mode With IPsec Encapsulating Security Payload (ESP) (2004)

community, and requests discussion and suggestions for improvements.
DNA Sequence of Two Closely Linked Human Leukocyte Interferon Genes (1981)

A single recombinant lambda bacteriophage isolated from a human genome library contains two closely related human interferon genes of the leukocyte or alpha type. The two genes are separated by 12 kilobase pairs and are oriented in the same direction with respect to transcription. Comparisons of the DNA sequences of these two genes and interferon complementary DNA clones indicate that the two interferon genes lack intervening sequences.
Meeting technology challenges of pervasive augmented reality games (2006)

Pervasive games provide a new type of game combining new technologies with the real environment of the players. While this already poses new challenges to the game developer, requirements are even higher for pervasive Augmented Reality games, where the real environment is additionally enhanced by virtual game items.
Detection of Multiple Allergen-specific IgEs on Microarrays by Immunoassay with Rolling Circle Amplification (2000)

limit (15 and 22 below the limits for the Stratus and Immulite assays, respectively) and 42 (12%) had both results below the respective detection limits. Regression analysis was performed on the 268 remaining samples: Immulite cTnI 1.84 (Stratus cTnI) 1.1 g/L; r 0.977; S yx 4.7 g/L. The high slope might result from a lack of standardization between cTnI assays (2 ) and/or a difference in the reactivities of the antibodies used to the various circulating forms of the protein (3-6 ). We routinely used an upper reference limit (URL) of 0.6 g/L for the Stratus cTnI assay. To estimate the corresponding value for the Immulite cTnI assay, we established the relationship between the two assays in 137 samples with Stratus cTnI values 5 g/L: Immulite cTnI 1.51 (Stratus cTnI) 0.27; r 0.924. The estimated Immulite URL (based on the regression) corresponding to a Stratus value of 0.6 g/L was 1.18 g/L (Fig. Using these cutoffs, we studied 80 patients admitted to the intensive care unit (37 with acute myocardial infarction, 22 with unstable angina, and 21 with chest pain). Heparinized samples were collected on admission. The Stratus (0.6 g/L) and estimated Immulite (1.18 g/L) URLs gave specificities of 93% [95% confidence interval (CI), 69.6 -98.8%] and 95% (95% CI, 76.2-99.9%), respectively, for acute coronary syndrome (vs 21 chest pain patients) and sensitivities of 95% (95% CI, 85.9 -98.9%) and 92% (95% CI, 81.3-97.2%), respectively.
Pigment epithelium-derived factor (PEDF) differentially protects immature but not mature cerebellar granule cells against apoptotic cell death (1998)

We have shown previously that pigment epithelium-derived factor (PEDF) acts as a survival factor for cerebellar granule cell neurons in culture, as well as protecting them against glutamate toxicity. In this study we have examined effects of PEDF on apoptotic cell death. We find that the granule cells die of apoptosis throughout the culture period, what we have termed "natural" apoptosis. PEDF prevents this natural apoptosis if added to immature cells, within the first 2 days in vitro (DIV), and the effect is maintained for up to DIV12. However, PEDF has no effect if added to mature cells at DIV5. Similar results are obtained when apoptosis is induced by shifting the cells from a serum- and 25 mM KCl-containing medium to serum-free medium with 5 mM KCl. PEDF most effectively blocks induced apoptosis in immature cells (DIV2) when added 24 hr prior to the change of medium, but still provides some protection when added simultaneously. However, 24 hr pretreatment with PEDF has a minimal effect when apoptosis is induced in mature DIV6 cells; addition at the same time is completely ineffective. Two polypeptide fragments of PEDF, only one of which contains the serine-protease inhibitory site, are equally active, supporting previous results which suggest that the neurotrophic effects of PEDF are not mediated by protease inhibition. We conclude that PEDF protects immature but not mature granule cells against both natural and induced apoptosis.
Correlation Between the Behavior of Magnetic Iron Oxide Particles in the Lungs of Rabbits and Phagocytosis (1984)

Five New Zealand white male rabbits were exposed (30 min; 300 mg/m3) to a submicrometric magnetic iron oxide aerosol (gamma-Fe2O3) produced by burning iron pentacarbonyl in a reducing atmosphere. After aerosol inhalation, an external magnetic field was applied to the rabbits to magnetize and align the ferrimagnetic particles within their lungs. After removal of the external field, a remanent magnetic field was detectable at the body surface. Using a flux-gate magnetometer probe in an enclosure shielded against external magnetic noise, the peak remanent field after magnetization was measured periodically during the next 6 weeks. After each magnetization, the strength of the remanent field decayed rapidly with time (relaxation). The mechanism responsible is particle rotation caused by tissue, cell, organelle, or Brownian movement. The rate of relaxation changed with time after particle inhalation, especially during the first day; changes in the relaxation rate correlated with an estimate of in situ particle phagocytosis during that time. Analysis of pulmonary lavage fluid from 15 rabbits into which radioactive gold-198 had been intratracheally instilled showed that, at 1 hr after instillation, 27% of the gold had been phagocytized, whereas at 16 hr 91% had been ingested. The strength of the magnetic field immediately after each magnetization (that is, before relaxation) was used to estimate the amount of iron oxide in the lungs. At 1 day after exposure, 96.8 +/- 8.8% (mean +/- standard error) of the initial dust was still present; at 10 days, 67.9 +/- 16.2%; and at 40 days, 16.0 +/- 4.6%. It is concluded that ferrimagnetic particles can serve as an easily measured, long-lasting marker that can be used for noninvasive studies of clearance and of particle phagocytosis and as a probe for intracellular processes such as organelle motion.
Activity of FEN1 Endonuclease on Nucleosome Substrates Is Dependent upon DNA Sequence but Not Flap Orientation (2011)

We demonstrated previously that human FEN1 endonuclease, an enzyme involved in excising single-stranded DNA flaps that arise during Okazaki fragment processing and base excision repair, cleaves model flap substrates assembled into nucleosomes. Here we explore the effect of flap orientation with respect to the surface of the histone octamer on nucleosome structure and FEN1 activity in vitro. We find that orienting the flap substrate toward the histone octamer does not significantly alter the rotational orientation of two different nucleosome positioning sequences on the surface of the histone octamer but does cause minor perturbation of nucleosome structure. Surprisingly, flaps oriented toward the nucleosome surface are accessible to FEN1 cleavage in nucleosomes containing the Xenopus 5S positioning sequence. In contrast, neither flaps oriented toward nor away from the nucleosome surface are cleaved by the enzyme in nucleosomes containing the high-affinity 601 nucleosome positioning sequence. The data are consistent with a model in which sequence-dependent motility of DNA on the nucleosome is a major determinant of FEN1 activity. The implications of these findings for the activity of FEN1 in vivo are discussed.
Automatic Machine Knitting of 3D Meshes (2018)

We present the first computational approach that can transform three-dimensional (3D) meshes, created by traditional modeling programs, directly into instructions for a computer-controlled knitting machine. Knitting machines are able to robustly and repeatably form knitted 3D surfaces from yarn but have many constraints on what they can fabricate. Given user-defined starting and ending points on an input mesh, our system incrementally builds a helix-free, quad-dominant mesh with uniform edge lengths, runs a tracing procedure over this mesh to generate a knitting path, and schedules the knitting instructions for this path in a way that is compatible with machine constraints. We demonstrate our approach on a wide range of 3D meshes.
Protein Recognition by Short Peptide Reversible Inhibitors of the Chromatin-Modifying LSD1/CoREST Lysine Demethylase (2013)

The combinatorial assembly of protein complexes is at the heart of chromatin biology. Lysine demethylase LSD1(KDM1A)/CoREST beautifully exemplifies this concept. The active site of the enzyme tightly associates to the N-terminal domain of transcription factors of the SNAIL1 family, which therefore can competitively inhibit the binding of the N-terminal tail of the histone substrate. Our enzymatic, crystallographic, spectroscopic, and computational studies reveal that LSD1/CoREST can bind to a hexapeptide derived from the SNAIL sequence through recognition of a positively charged α-helical turn that forms upon binding to the enzyme. Variations in sequence and length of this six amino acid ligand modulate affinities enabling the same binding site to differentially interact with proteins that exert distinct biological functions. The discovered short peptide inhibitors exhibit antiproliferative activities and lay the foundation for the development of peptidomimetic small molecule inhibitors of LSD1.
Progress toward Ignition with Noncryogenic Double-Shell Capsules (2000)

Inertial confinement fusion implosions using capsules with two concentric shells separated by a low density region (double shells) are reported which closely follow one dimensional (1D) radiatively driven hydrodynamics simulations. Capsule designs which mitigate Au M-band radiation asymmetries appear to correspond more closely to 1D simulations than targets lacking mitigation of hohlraum drive M-band nonuniformities. One capsule design achieves over 50% of the unperturbed 1D calculated yield at a convergence ratio of 25.5, comparable to that of a double-shell design for an ignition capsule at the National Ignition Facility.
Poly(β-L-malate) hydrolase from Plasmodia ofPhysarum polycephalum (1995)

A 68-kDa extracellular glycoprotein from Physarum polycephalum that hydrolyses specifically poly(β-L-malic acid) by removing monomers of L-malic acid in an exolytic manner has been purified and characterized. The enzyme was purified 1740-fold from the culture medium by ammonium sulfate precipitation, hydrophobic interaction chromatography on butyl-Toyopearl, and gel permeation chromatography on Superdex 200 to a specific activity of 9.0 μmol∙min −1 ∙mg −1 . The hydrolase was also purified from the cytosol, which contained 1 mg in 43 g cells in contrast to 1 mg extracellular enzyme in 28 L of culture medium. The pH optimum was pH 3.5 as a result of the effect of an acidic side chain on V max and the preferred binding of poly(β-L-malate) in the ionized form. Intracellular hydrolase was only marginally active on [ 14 C]poly(β-L-malate) that had been injected into plasmodia. Poly(L-aspartate), poly(L-glutamate), poly(vinyl sulfate), and poly(acrylate) were neither bound nor degraded by the hydrolase. Poly(β-hydroxybutyric acid), which was considered the reduced form of poly(β-L-malate), was not a substrate. The enzyme is neither a metallo- nor a serine-esterase, and is distinct from poly(3-hydroxybutyric acid) depolymerases. It is related to a glucosidase with respect to hydrophobic interaction chromatography, the pH-activity dependence, and its inhibition with mercuribenzoate, N-bromosuccinimide, and D-gluconolactone, but not the use of the substrates.Key words: poly(β-L-malate), polymalatase, Physarum polycephalum, biodegradative polymer.
Long Live the Mature B Cell--a BAFFling Mystery Resolved (2001)

What determines whether transitional B cells newly emerged from the bone marrow will differentiate further to become mature, long-lived, circulating B lymphocytes? In a Perspective, Waldschmidt and Noelle discuss new findings showing that the TNF family ligand BAFF and its receptor BAFF-R are crucial for selecting transitional B cells into the mature B cell pool (Thompson et al., Schiemann et al.).
Learning actions from the Web (2009)

This paper proposes a generic method for action recognition in uncontrolled videos. The idea is to use images collected from the Web to learn representations of actions and use this knowledge to automatically annotate actions in videos. Our approach is unsupervised in the sense that it requires no human intervention other than the text querying. Its benefits are two-fold: 1) we can improve retrieval of action images, and 2) we can collect a large generic database of action poses, which can then be used in tagging videos. We present experimental evidence that using action images collected from the Web, annotating actions is possible.
Traditional and Nonlinear Heart Rate Variability Are Each Independently Associated with Mortality after Myocardial Infarction (2005)

Nonlinear HRV is associated with mortality post-MI. However, as with traditional HRV, this is diluted by CABG surgery post-MI and by diabetes. Results suggest that decreased long-term HRV and increased randomness of heart rate are each independent risk factors for mortality post-MI.
Immunologic Escape After Prolonged Progression-Free Survival With Epidermal Growth Factor Receptor Variant III Peptide Vaccination in Patients With Newly Diagnosed Glioblastoma (2010)

EGFRvIII-targeted vaccination in patients with GBM warrants investigation in a phase III, randomized trial.
Boundary Hash for Memory-Efficient Deep Packet Inspection (2008)

Network intrusion detection and prevention systems (NIDPSs) are critical for network security. The deep packet inspection (DPI) operation consumes a significant amount of resources in NIDPS. This is because to detect malicious activity DPI searches a database of signatures for each byte of every packet. In this paper, we develop a highly space-efficient data structure for hardware realization of minimal perfect hash functions (MPHFs). This data structure is simple to construct, requires 7 n bits to represent the MPHF for a set of n keys and allows high-speed DPI.
A Vital Stain for the Golgi Apparatus (1985)

The Golgi complex, a membranous organelle with important functions in membrane traffic and macromolecular synthesis, has been stained in living cells with a fluorescent sphingolipid. Cells were first incubated with liposomes containing N-[7-(4-nitrobenzo-2-oxa-1,3-diazole)]-6-aminocaproyl sphingosine (C6-NBD-ceramide), or with a bovine serum albumin complex of the fluorescent lipid, and then examined by fluorescence microscopy. An intensely fluorescent perinuclear structure was identified as the Golgi apparatus by its colocalization with known Golgi markers in fixed cells. C6-NBD-ceramide was used to observe the morphology of the Golgi apparatus in living cells in the presence or absence of monensin or Colcemid, and during mitosis. In all cases, C6-NBD-ceramide revealed a Golgi apparatus in the living cell that was identical to that obtained with conventional procedures that require fixation.
Development of a Hypusine Reagent for Peptide Synthesis (1997)

The synthesis of a reagent that enables the incorporation of the unusual amino acid (2S,9R)-hypusine (Hpu) into peptide sequences is described. The reagent, (2S,9R)-11-[(benzyloxycarbonyl)amino]-7-(carbobenzyloxy)-2-[(9-fluorenylmethoxycarbonyl)amino]-9-(tetrahydropyran-2-yloxy)-7-azaundecanoic acid, is utilized in the synthesis of a hexapeptide containing the primary pentapeptide sequence of the eukaryotic initiation factor eIF-5A, L-Cys-L-Thr-Gly-Hpu-L-His-Gly. The reagent is shown to be effective for both solution phase and Merrifield resin synthesis.
Studies on Asphaltenes through Analysis of Polar Fractions (1999)

Asphaltenes from Mobil crude oil were characterized by fractionation into components of different polarities. The fractions, varying from dense, shiny black particles that displayed a relative amount of order and crystallinity in their structure (the most polar fraction) to light, dull brown powder of a completely amorphous nature (the least polar fraction), revealed no significant differences in structure or content when analyzed by gel permeation chromatography and FTIR spectroscopy, yet displayed significantly different rates of dissolution in a differential reactor using an amphiphile/alkane solution of 10 wt % dodecylbenzenesulfonic acid in heptane. Further analysis suggested that the metal element content, especially iron, nickel, and vanadium, differentiates the most polar and the least polar fractions from each other. The effect of the presence of ferric (Fe3+) iron in an acidic medium during asphaltene precipitation from another crude oil (Chaguaramal) was then systematically studied. The results from these studies corroborate the earlier inference that the presence of metal ions such as Fe3+ plays a primary role in determining asphaltene polarity.
Multiple Charged and Aromatic Residues in CCR5 Amino-terminal Domain Are Involved in High Affinity Binding of Both Chemokines and HIV-1 Env Protein (1999)

CCR5 is a functional receptor for MIP-1alpha, MIP-1beta, RANTES (regulated on activation normal T cell expressed), MCP-2, and MCP-4 and constitutes the main coreceptor for macrophage tropic human and simian immunodeficiency viruses. By using CCR5-CCR2b chimeras, we have shown previously that the second extracellular loop of CCR5 is the major determinant for chemokine binding specificity, whereas the amino-terminal domain plays a major role for human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus coreceptor function. In the present work, by using a panel of truncation and alanine-scanning mutants, we investigated the role of specific residues in the CCR5 amino-terminal domain for chemokine binding, functional response to chemokines, HIV-1 gp120 binding, and coreceptor function. Truncation of the amino-terminal domain resulted in a progressive decrease of the binding affinity for chemokines, which correlated with a similar drop in functional responsiveness. Mutants lacking residues 2-13 exhibited fairly weak responses to high concentrations (500 nM) of RANTES or MIP-1beta. Truncated mutants also exhibited a reduction in the binding affinity for R5 Env proteins and coreceptor activity. Deletion of 4 or 12 residues resulted in a 50 or 80% decrease in coreceptor function, respectively. Alanine-scanning mutagenesis identified several charged and aromatic residues (Asp-2, Tyr-3, Tyr-10, Asp-11, and Glu-18) that played an important role in both chemokine and Env high affinity binding. The overlapping binding site of chemokines and gp120 on the CCR5 amino terminus, as well as the involvement of these residues in the epitopes of monoclonal antibodies, suggests that these regions are particularly exposed at the receptor surface.