gebhart/patrepeval huggingface dataset:
A Theory of Generative ConvNet (2016)

We show that a generative random field model, which we call generative ConvNet, can be derived from the commonly used discriminative ConvNet, by assuming a ConvNet for multi-category classification and assuming one of the categories is a base category generated by a reference distribution. If we further assume that the non-linearity in the ConvNet is Rectified Linear Unit (ReLU) and the reference distribution is Gaussian white noise, then we obtain a generative ConvNet model that is unique among energy-based models: The model is piecewise Gaussian, and the means of the Gaussian pieces are defined by an auto-encoder, where the filters in the bottom-up encoding become the basis functions in the top-down decoding, and the binary activation variables detected by the filters in the bottom-up convolution process become the coefficients of the basis functions in the top-down deconvolution process. The Langevin dynamics for sampling the generative ConvNet is driven by the reconstruction error of this auto-encoder. The contrastive divergence learning of the generative ConvNet reconstructs the training images by the auto-encoder. The maximum likelihood learning algorithm can synthesize realistic natural image patterns.
Tandem Mass Spectrometry of Sulfated Heparin-Like Glycosaminoglycan Oligosaccharides (2003)

The structural characterization of heparin-like glycosaminoglycans (HLGAGs) is a major challenge in glycobiology. These linear, sulfated oligosaccharides are expressed on animal cell surfaces, in extracellular matrixes, basement membranes, and mast cell granules and bind with varying degrees of specificity to families of proteases, growth factors, chemokines, and blood coagulation proteins. Cell surface HLGAGs bind growth factors and growth factor receptors and serve as coreceptors in these interactions. Understanding of the mechanism and regulation of growth factor-receptor binding requires efficient determination of cell surface HLGAG structures and the variations in their expression in response to the cellular environment. The solution to this problem entails rapid, sensitive structural analysis of these molecules. To date, HLGAG sequencing requires multistep processes that combine chemical and enzymatic degradation with gel-based or mass spectrometry-based detection systems. Although tandem mass spectrometry has revolutionized proteomics, the fragility of sulfate groups has limited its usefulness in the analysis of HLGAGs. This work demonstrates that tandem mass spectrometry can be effectively used to determine HLGAG structures while minimizing losses of SO3. First, collision-induced dissociation (CID) is shown to produce abundant backbone cleavage ions for HLGAG oligosaccharides, provided that most sulfate groups are deprotonated. Fragmentation of different precursor ion charge states produces complementary data on the structure of the HLGAG. Second, calcium ion complexation of HLGAGs stabilizes the sulfate groups, increases the relative abundances of backbone cleavage ions, and decreases the abundances of ions produced from SO3 losses.
DNA Sensing on a DNA Probe-Modified Electrode Using Ferrocenylnaphthalene Diimide as the Electrochemically Active Ligand (2000)

Naphthalene diimide derivative 1 carrying ferrocenyl moieties at the termini of imide substituents binds intact calf thymus DNA 4 times more strongly than the denatured DNA, and its complex with the intact DNA dissociates 80 times more slowly than that with the denatured DNA. On the basis of these observations, ligand 1 was applied to a probe of electrochemical DNA sensing. A thiol-linked single-stranded DNA probe was immobilized through the S-Au bonding to 20-30 pmol/mm2 on a gold electrode. Following hybridization with the complementary DNA, the electrode was soaked in a solution containing 1 (intercalation step) and then washed with buffer for 5 s. The cyclic voltammogram and differential pulse voltammogram for this electrode gave an electrochemical signal due to the redox reaction of 1 that was bound to the double-stranded DNA on the electrode. Thus, dA20 and the yeast choline transport gene were quantitated at the subpicomole level. The sensitivity of DNA detection was improved to 10 zmol by reducing the amount of immobilized DNA probe and protecting the uncovered surface of the electrode with 2-mercaptoethanol.
Integration of COSMO‐based methodologies into commercial process simulators: Separation and purification of reuterin (2012)

Abstract The conceptual design of a new process is developed via computer‐aided simulation for separating and purifying reuterin, an antimicrobial substance obtained by bacterial fermentation of glycerol, from its mixture with the nonfermented substrate, the main subproduct of the process (1,3‐propanediol) and water. The nondatabank components included in the simulations are created by using the structures derived from quantum mechanical calculations and the properties (molecular weight, normal boiling point, and mass density) estimated by COSMO‐RS method. The unknown remainder properties are estimated by the methods and models used by default in Aspen Plus (v7.3). The COSMOSAC property model, also implemented in Aspen Plus, is specified with the molecular volumes and sigma profiles obtained by COSMO‐RS. The properties (boiling temperatures, densities, VL equilibria, etc.) predicted for glycerol, 1,3‐propanediol, water, and their mixtures by COSMO‐based methods agree reasonably well with experimental reported values, whereas those obtained for reuterin derivatives are consistent with the behavior of amphoteric compounds having strong capabilities to interact attractively with hydrogen donor and acceptor groups all together. The process consists of a two‐stage distillation operation, the first of which removes the water and the second one separates reuterin as a 99.5 wt %‐pure bottom product. The second column operates at low pressure (ca. 40 kPa) to avoid thermal decomposition of reuterin (over 280°C) and guaranties 99.9% recovery of the desired product. Water removing offers different heat integration and energy‐saving opportunities considering that condenser pressure of the first column can be increased to ∼15 bar preserving the thermal integrity of the reuterin. Dimensions of the equipments as well as capital and operating costs are evaluated. © 2012 American Institute of Chemical Engineers AIChE J, 2012
Eukaryotic mRNA Decapping (2004)

Eukaryotic mRNAs are primarily degraded by removal of the 3' poly(A) tail, followed either by cleavage of the 5' cap structure (decapping) and 5'->3' exonucleolytic digestion, or by 3' to 5' degradation. mRNA decapping represents a critical step in turnover because this permits the degradation of the mRNA and is a site of numerous control inputs. Recent analyses suggest decapping of an mRNA consists of four central and related events. These include removal, or inactivation, of the poly(A) tail as an inhibitor of decapping, exit from active translation, assembly of a decapping complex on the mRNA, and sequestration of the mRNA into discrete cytoplasmic foci where decapping can occur. Each of these steps is a demonstrated, or potential, site for the regulation of mRNA decay. We discuss the decapping process in the light of these central properties, which also suggest fundamental aspects of cytoplasmic mRNA physiology that connect decapping, translation, and storage of mRNA.
GnRH Agonists and Antagonists in Cancer Therapy (2003)

Gonadotropin releasing hormone (GnRH) is a hypothalamic decapeptide that binds to GnRH receptors on pituitary gonadotrope cells to modulate the synthesis and secretion of the gonadotropins, luteinizing hormone (LH) and follicle-stimulating hormone (FSH). These gonadotropins in turn regulate gonadal steroidogenesis and gametogenesis. Chemical characterization and structure-activity analysis of GnRH variants containing systematic amino acid substitutions led to the discovery of GnRH superagonists and antagonists. These peptides are widely used for the treatment of clinical conditions in which modulation of or interference with sex hormone production is beneficial to prevent development or progression of benign conditions (e.g. endometriosis, uterine fibroids) or malignant tumors (e.g. breast, ovarian, endometrial and prostate carcinoma). When compared to native GnRH, GnRH superagonists have increased potency for the short-term release of gonadotropins. However, they show paradoxical action in that chronic treatment with superagonists results in inhibition of gonadotropin production as a result of desensitization of the gonadotropes and down regulation of its receptor. In contrast, GnRH antagonists produce a rapid and dose-dependent suppression of gonadotropin release by competitive blockade of the GnRH receptors without any initial stimulatory effect as seen with superagonists. In recent years, a search for peptidomimetic compounds to replace peptides as therapeutic agents has been undertaken to find compounds with higher affinity for the GnRH receptor but do not have the disadvantages of peptides. Such efforts have resulted in the identification and development of small-molecule non-peptide compounds that are sufficiently stable in vivo and possess favorable pharmacological parameters comparable to peptide antagonists. Some of these compounds are being tested in human volunteers and the preliminary results are very encouraging.
The effect of chemical and nanotopographical modifications on the early stages of osseointegration. (2008)

Chemical modifications used in the present study were capable of producing a particular nanotopography, and together with the ions present at the implant surface, may explain the increased removal torque values after a healing period of 4 weeks.
The Realization of Computer Generated Integral Imaging Based on Two Step Pickup Method (2010)

A three-dimensional (3D) scene is built up, and a camera array is used to simulate a micro-lens array to pick up the 3D scene in 3DS MAX software. Based on the principle of two step pickup method in computer generated integral imaging, the mathematical model of the secondary pickup is proposed, and the secondary integral image is synthesized using the proposed mathematical model. A vivid 3D scene is reconstructed using computational and optical methods.
Glomerular expression of nephrin and synaptopodin, but not podocin, is decreased in kidney sections from women with preeclampsia (2007)

We conclude that down-regulation of nephrin and synaptopodin is associated with proteinuria in women with preeclampsia. Recent studies have demonstrated that soluble vascular endothelial growth factor receptor 1 (sFlt-1) levels are elevated in preeclampsia compared with normal pregnancy. Studies in mice have shown that sFlt-1 may play a role in inducing proteinuria by neutralizing vascular endothelial growth factor (VEGF) and suppressing nephrin. Proteinuria and elevations of sFlt-1 in preeclampsia are temporally related, further supporting a possible role of sFlt-1 in the dysregulation of podocyte foot-process proteins.
The Effects of Ingesting Polylactate or Glucose Polymer Drinks during Prolonged Exercise (1991)

Five trained, fasted male cyclists rode a cycle ergometer three times at 50% of VO2max for 180 min. Using a balanced order, double-blind procedure, subjects were given either a solution containing polylactate (PL: 80% polylactate, 20% sodium lactate, in 7% solution with water), glucose polymer (GP: multidextrin in 7% solution with water), or control (C: water sweetened with aspartame) 5 min before exercise and at 20-min intervals during exercise. Venous blood samples were taken at rest and at 20-min intervals during exercise. In general, PL and GP rendered similar results except that pH and bicarbonate (HCO3-) were higher in PL. There were no differences between treatments in perceived exertion, sodium, potassium, chloride, lactate, heart rate, oxygen consumption, rectal temperature, or selected skin temperatures. These data show that polylactate may help maintain blood glucose and enhance blood buffering capacity during prolonged exercise and could be a useful component in an athletic fluid replacement beverage.
Mining association rules between sets of items in large databases (1993)

We are given a large database of customer transactions. Each transaction consists of items purchased by a customer in a visit. We present an efficient algorithm that generates all significant association rules between items in the database. The algorithm incorporates buffer management and novel estimation and pruning techniques. We also present results of applying this algorithm to sales data obtained from a large retailing company, which shows the effectiveness of the algorithm.
Novel DNA Intercalators Based on the Pyridazino[1‘,6‘:1,2]pyrido[4,3-b]indol-5-inium System (1999)

A new class of DNA intercalators based on the 8H-pyridazino[1‘,6‘:1,2]pyrido[4,3-b]indol-5-inium system in which the cationic nature of the chromophore is provided by a brigdehead quaternary nitrogen has been obtained. These cations along with 10H-indolo[3,2-c]pyridazino[1,6-a]quinolin-5-inium, 13H-dibenz[f,h]indolo[3‘,2‘:3,4]pyrido[1,2-b]cinnolin-10-inium, and 5H-acenaphtho[1‘,2‘:3‘,4‘]pyridazino[1‘,6‘:1,2]pyrido[4,3-b]indol-8-inium were synthesized by the Westphal reaction of carbolinium derivatives with various 1,2-dicarbonyl compounds. When these tetra-, penta-, and heptacyclic heteroaromatic nuclei were evaluated as DNA intercalators using UV−vis spectroscopy, viscometric determinations, and unwinding angle determinations, we found that only the 8H-pyridazino[1‘,6‘:1,2]pyrido[4,3-b]indol-5-inium cations behaved as DNA intercalators. Molecular modeling studies allowed the preferred orientation of the intercalating chromophore within a CpG intercalation site to be explored and will provide help in the rational design of novel bis-intercalators based on these chromophores.
P2 purinergic receptors on osteoblasts and osteoclasts: Potential targets for drug development (2000)

Extracellular nucleotides like ATP bind to cell surface receptors (P2 purinergic receptors) in many tissues. P2X receptor subtypes are intrinsic ion channels that mediate depolarization and influx of Ca2+, whereas the P2Y receptor subtypes couple through G proteins to activation of phospholipase Cβ and mobilization of intracellular Ca2+. In nonskeletal tissues, extracellular ATP functions in neurotransmission, stimulation of secretion, regulation of cell proliferation, and induction of apoptosis. Multiple subtypes of P2 purinergic receptors are expressed in bone. P2Y purinergic receptors have been identified in osteoblasts and osteoclasts, and P2X purinergic receptors in osteoclasts. Bone cells exhibit a number of functional responses when exposed to extracellular nucleotides. These include enhancement of osteoblast responses to parathyroid hormone and stimulation of osteoclast formation and resorptive activity. Nucleotides accumulate at sites of inflammation and tissue injury, and therefore may serve as paracrine regulators of bone cell function in diseases such as rheumatoid arthritis and periodontitis. In addition, autocrine/paracrine signaling via release of nucleotides may underlie the physiological responses of skeletal tissues to mechanical stimuli. This article reviews work from our laboratories and others on the identity of purinergic receptor subtypes in osteoblasts and osteoclasts, their associated signal transduction mechanisms, and their roles in regulating bone cell function. We discuss the potential of P2 purinergic receptors as targets for the development of anabolic and antiresorptive drugs aimed at the treatment of osteoporosis and other bone disorders. Drug Dev. Res. 49:187–200, 2000. © 2000 Wiley-Liss, Inc.
Simultaneous analysis of steady‐state intracellular pH and cell morphology by automated laser scanning cytometry (2007)

We report here that LSC is an excellent and highly reproducible platform for pHi determination, and provides the added advantage of simultaneous imaging of cells before, during, and after pH measurements.
Incorporation of 5′-N-BOC-2′, 5′-Dideoxynucleoside-3′-O-Phosphoramidites Into Oligonucleotides by Automated Synthesis (1997)

Abstract An efficient method for synthesizing 5′-Boc-5′-amino-2′, 5′- dideoxynucleoside phosphoramidites and conditions for their incorporation in solid-phase oligonucleotide synthesis are presented.
Cloning of the β Cell High-Affinity Sulfonylurea Receptor: a Regulator of Insulin Secretion (1995)

Sulfonylureas are a class of drugs widely used to promote insulin secretion in the treatment of non-insulin-dependent diabetes mellitus. These drugs interact with the sulfonylurea receptor of pancreatic beta cells and inhibit the conductance of adenosine triphosphate (ATP)-dependent potassium (KATP) channels. Cloning of complementary DNAs for the high-affinity sulfonylurea receptor indicates that it is a member of the ATP-binding cassette or traffic ATPase superfamily with multiple membrane-spanning domains and two nucleotide binding folds. The results suggest that the sulfonylurea receptor may sense changes in ATP and ADP concentration, affect KATP channel activity, and thereby modulate insulin release.
An approach to treatment resistance in schizophrenia (1999)

Currently, patients with schizophrenia are usually considered refractory to treatment if they continue to be floridly symptomatic despite receiving treatment with conventional antipsychotic agents. Attempts to improve their response by increasing the dosage, adding supplementary drugs, or switching to agents of another class have not been very successful, and may increase side-effects. Clozapine can be effective, but it is a difficult drug to administer and has therefore been reserved for patients who are doing poorly. With the recent introduction of newer, safer antipsychotic agents, however, even patients who have milder refractory symptoms that persist after treatment with conventional antipsychotics can now be treated.
Phenomenological magnetic modeling of Au:Fe:Au nano-onions (2000)

A new type of materials, the nano-onions, has been shown to exhibit GMR. These nanostructured composites consist of a nonmagnetic core coated with a thin layer of a bulk ferromagnet with a passivating nonmagnetic surface layer. The nano-onion investigated had a 3 nm Au core, a 1 nm Fe layer, and a 2 nm Au coating; all values correspond to the radius. The materials were manufactured using a sequential reverse micelle technique, detailed elsewhere. The sample preparation method produces a powder sample was cold pressed into a pellet. Magnetic investigation of the sample indicated that the material was superparamagnetic with a blocking temperature of 52 K for particles approximately 8 nm in diameter. At 10 K, the coercivity was 420 Oe, indicating a large degree of order. The GMR was measured over the entire temperature range available. At 10 K, in 5 T, a 1% MR was observed. The GMR was modeled using a simple phenomenological magnetic model initially used to study GMR granular thin films. To more accurately match the physical parameters of reverse micelles, the conventional log-normal particle size distribution was replaced with a normal distribution. The model suggested that the system consisted of an ensemble of 1.3 nm particles with a standard deviation of 0.07. The model does not detect the entire 8 nm diam, rather it detects the individual walls of the shell. In this context, it has shown that a simple phenomenological model can accurately predict the magnetic and electronic behavior of nano-onions.
In vivo regulation of lipolysis in humans. (1994)

Fatty acids are important oxidative fuel for liver, kidney, skeletal muscle, and myocardium. There has been much interest in the role of fatty acids in the pathogenesis of non-insulin-dependent diabetes because they compete with glucose for oxygen and inhibit whole body glucose disposal via the 'Randle cycle,' Control of lipolysis in adipose tissue determines systemic fatty acid supply. A wide range of hormones and other substances have been recognized as regulators of lipolysis, but insulin and catecholamines appear to be the most important. The regulation of lipolysis, in most circumstances, provides a supply of lipid fuel exceeding the rate of lipid oxidation, requiring reesterification to triglyceride of surplus circulating free fatty acids. Thus, free fatty acid supply is usually not matched to the demand for lipid oxidation, and there is no known mechanism for accurately sensing such demand. This lax regulation may be disadvantageous in conditions such as aging, stress, obesity, and diabetes, where the antilipolytic effect of insulin is impaired and lipolysis is therefore increased. In these conditions, the surfeit of fatty acid may impair glucoregulation. In addition, the excess lipolysis may induce hypertriglyceridemia (via increased very low density lipoprotein production) and thus contribute to atherogenesis. Considerable additional research is needed in order to fully understand both normal lipolytic regulation and the abnormalities of lipolysis which accompany pathological conditions.
Sound and precise analysis of web applications for injection vulnerabilities (2007)

Web applications are popular targets of security attacks. One common type of such attacks is SQL injection, where an attacker exploits faulty application code to execute maliciously crafted database queries. Bothstatic and dynamic approaches have been proposed to detect or prevent SQL injections; while dynamic approaches provide protection for deployed software, static approaches can detect potential vulnerabilities before software deployment. Previous static approaches are mostly based on tainted information flow tracking and have at least some of the following limitations: (1) they do not model the precise semantics of input sanitization routines; (2) they require manually written specifications, either for each query or for bug patterns; or (3) they are not fully automated and may require user intervention at various points in the analysis. In this paper, we address these limitations by proposing a precise, sound, and fully automated analysis technique for SQL injection. Our technique avoids the need for specifications by consideringas attacks those queries for which user input changes the intended syntactic structure of the generated query. It checks conformance to this policy byconservatively characterizing the values a string variable may assume with a context free grammar, tracking the nonterminals that represent user-modifiable data, and modeling string operations precisely as language transducers. We have implemented the proposed technique for PHP, the most widely-used web scripting language. Our tool successfully discovered previously unknown and sometimes subtle vulnerabilities in real-world programs, has a low false positive rate, and scales to large programs (with approx. 100K loc).