gebhart/patrepeval huggingface dataset:
A Scalable and Programmable Architecture for the Continuous Restricted Boltzmann Machine in VLSI (2007)

The continuous restricted Boltzmann machine (CRBM) has been attractive as a probabilistic model both useful in biomedical applications and hardware-amenable. To implement a large-scale CRBM system for real applications, the performance of the CRBM under hardware constraints must be investigated. This paper examines the effects of parameter precision on the performance of the CRBM, identifies the required precision for modelling real biomedical data, and finally proposes a scalable and programmable architecture based on which a CRBM-embedded intelligent system can be formed
Comparing machine learning classifiers for diagnosing glaucoma from standard automated perimetry. (2002)

MoG, using the entire visual field and age for input, interpreted SAP better than the global indices of STATPAC. Machine classifiers may augment the global indices of STATPAC.
Development in lipid analysis: Some new extraction techniques and in situ transesterification (2000)

The development of methods for analyzing fatty acids that provide rapid and reliable results is currently in great demand. Recently, different lipid extraction procedures such as microwave or supercritical fluid extraction have heen researched. Both procedures avoid the use of large volumes of solvents and provide rapid lipid isolations. Only a few papers have reported work on microwave extraction, hut many studies ahout supercritical fluid extraction have heen carried out and have heen gaining acceptance within the scientific community. Avoiding the lipid isolation step, hy synthesizing fatty acid esters hy simultaneous lipid extraction and derivatization through in situ reactions, has also heen proposed. The saving of time and reagents is significant. Owing to the differences among the procedures, some knowledge of their characteristics is essential in order to improve methods and achieve reliable and accurate results. Clearly, results depend on factors such as the type of catalysis selected, the use of nonpolar solvents, heating applied during the synthesis, and the degree of suitability of the procedure chosen for the particular features of each sample.
Parallel concatenated trellis coded modulation (2002)

In this paper, we propose a new solution to parallel concatenation of trellis codes with multilevel amplitude/phase modulations and a suitable bit by bit iterative decoding structure. Examples are given for throughput 2 and 4 bits/sec/Hz with 8 PSK, 16 QAM, and 64 QAM modulations. For parallel concatenated trellis codes in the examples, rate 2/3 and 4/5, 8, and 16-state binary convolutional codes with Ungerboeck mapping by set partitioning (natural mapping), a reordered mapping, and Gray code mapping are used. The performance of these codes is within 1 dB from the Shannon limit at a bit error probability of 10/sup -7/ for a given throughput, which outperforms the performance of all codes reported in the past for the same throughput.
Charagram: Embedding Words and Sentences via Character n-grams (2016)

We present CHARAGRAM embeddings, a simple approach for learning character-based compositional models to embed textual sequences. A word or sentence is represented using a character n-gram count vector, followed by a single nonlinear transformation to yield a low-dimensional embedding. We use three tasks for evaluation: word similarity, sentence similarity, and part-of-speech tagging. We demonstrate that CHARAGRAM embeddings outperform more complex architectures based on character-level recurrent and convolutional neural networks, achieving new state-of-the-art performance on several similarity tasks. 1
Light‐induced gene expression of fructose 1,6‐bisphosphate aldolase during heterotrophic growth in a cyanobacterium, Synechocystis sp. PCC 6803 (2008)

Synechocystis sp. PCC 6803 exhibits light-activated heterotrophic growth (LAHG) under dark conditions with glucose as a carbon source. The light activation is remarkable at a late period of photoautotrophic preculture, such as the late-linear and stationary growth phases. To understand the physiological effects of light irradiation and glucose under LAHG conditions, their effects on the expression of soluble proteins were analyzed by means of 2D-PAGE. Various soluble proteins, which were minimal under photoautotrophic preculture conditions, were observed clearly under LAHG conditions, suggesting that proteins were synthesized actively under these conditions. Fructose 1,6-bisphosphate aldolase, one of the glycolytic enzymes, was found to be induced under LAHG conditions on 2D-PAGE. The activity of fructose 1,6-bisphosphate aldolase, which had decreased during photoautotrophic preculture, also increased under LAHG conditions, similar to the mRNA level of the encoding gene, fbaA. In addition, we found that a deletion mutant of sll1330, a putative gene containing a helix-turn-helix DNA-binding motif, could not grow under LAHG conditions, whereas it could grow photoautotrophically. The increases in the protein level of FbaA and fbaA gene expression observed in wild-type cells under LAHG conditions were greatly inhibited in the deletion mutant. These results suggest that the regulation of fbaA gene expression by way of sll1330 is one of the important processes in Synechocystis sp. PCC 6803 under light pulse LAHG conditions.
Generative modeling of convolutional neural networks (2016)

The convolutional neural networks (ConvNets) have proven to be a powerful tool for discriminative learning. Recently researchers have also started to show interest in the generative aspects of ConvNets in order to gain a deeper understanding of what ConvNets have learned and how to further improve them. This paper investigates generative modeling of ConvNets. The main contributions include: (1) We construct a generative model for the ConvNet in the form of exponential tilting of a reference distribution. (2) We propose a generative gradient for pre-training ConvNets by a non-parametric importance sampling scheme. It is fundamentally different from the commonly used discriminative gradient, and yet shares the same computational architecture and cost as the latter. (3) We propose a generative visualization method for the ConvNets by sampling from an explicit parametric image distribution. The proposed visualization method can directly draw synthetic samples for any given node in a trained ConvNet by the Hamiltonian Monte Carlo algorithm, without resorting to any extra hold-out images. Experiments on the challenging ImageNet benchmark show that the proposed generative gradient pre-training helps improve the performances of ConvNets in both supervised and semi-supervised settings, and the proposed generative visualization method generates meaningful and varied samples of synthetic images from a large and deep ConvNet.
TolC is Required for Pathogenicity ofXylella fastidiosainVitis viniferaGrapevines (2007)

Xylella fastidiosa infects a wide range of hosts and causes serious diseases on some of them. The complete genomic sequences of both a citrus variegated chlorosis (CVC) and a Pierce's disease (PD) strain revealed two type I protein secretion plus two multidrug resistance efflux systems, and all evidently were dependent on a single tolC homolog. Marker exchange mutagenesis of the single tolC gene in PD strain Temecula resulted in a total loss of pathogenicity on grape. Importantly, the tolC- mutant strains were not recovered after inoculation into grape xylem, strongly indicating that multidrug efflux is critical to survival of this fastidious pathogen. Both survival and pathogenicity were restored by complementation using tolC cloned in shuttle vector pBBR1MCS-5, which was shown to replicate autonomously, without selection, for 60 days in Temecula growing in planta. These results also demonstrate the ability to complement mutations in X. fastidiosa.
Inhalation rate of sodium cromoglycate determines plasma pharmacokinetics and protection against AMP-induced bronchoconstriction in asthma (1988)

We have investigated whether the inspiratory flow at which sodium cromoglycate (SCG) is inhaled influences the efficacy of SCG. Seven atopic asthmatic subjects (age 25 +/- 2 yrs) inhaled dry powder SCG from a Spinhaler on separate occasions at three flow rates, maximum (V1), 100 l.min-1 (V2), and 50 l.min-1 (V3), or placebo, according to a double-blind structured study. Thirty minutes after administration a bronchial provocation test was performed with adenosine 5'-monophosphate (AMP). Blood samples for measurement of plasma SCG concentration were taken and the area under the plasma concentration-time curve (AUC) calculated for each flow rate. Both inspiratory flow rate and AUC correlated significantly with the degree of protection afforded against AMP-induced bronchoconstriction (r = 0.73, p less than 0.001; r = 0.66, p less than 0.001). These findings indicate that the flow rate used to inhale powdered SCG is a major factor in determining the protective efficacy of this drug against bronchial challenge and therefore has important clinical implications.
Botulinum toxin potentiates cancer radiotherapy and chemotherapy. (2006)

The opening of the vascular bed induced by BoNT-A offers a way to significantly increase the response of tumors to radiotherapy and chemotherapy.
The human MUC2 intestinal mucin has cysteine-rich subdomains located both upstream and downstream of its central repetitive region. (1992)

The human MUC2 mucin is a large secretory glycoconjugate that coats the epithelia of the intestines, airways, and other mucus membrane-containing organs. Previous work has shown that this mucin contains an extended tandem repeat-containing domain rich in Thr and Pro. In the present work we describe two additional regions of this mucin located both upstream and downstream of the tandem repeat array. The carboxyl-terminal domain contains 984 residues and can be divided into mucin-like (139 residues) and cysteine-rich (845 residues) subdomains. This latter subdomain exhibits varying degrees of sequence similarity to a wide range of mucins and mucin-like proteins including those isolated from rats, pigs, cows, and frogs. We also report here the sequence of 1270 residues lying immediately upstream of the tandem repeats. This region contains a repetitive, mucin-like subdomain and a second cysteine-rich stretch of more than 700 residues. Both cysteine-rich subdomains of this mucin have sequence similarity with von Willebrand factor, a serum protein that exists as a disulfide-linked polymer. This suggests that these cysteine-rich subdomains are important in the catenation of mucin monomers into oligomers, the structures that confer viscoelasticity upon mucus.
Effect of the μ-Opioid Agonist DAMGO on Medial Basal Hypothalamic Neurons in Beta-Endorphin Knockout Mice (2000)

The endogenous opioid neurotransmitter beta-endorphin (beta-END), a product of the proopiomelanocortin (POMC) gene, is strongly implicated in the control of the female reproductive cycle, stress responses, and antinociception. Using selective gene targeting, we have generated a strain of mice that do not express any beta-END. These mice exhibit both normal reproduction and normal basal and stress-induced hypothalamic-pituitary-axis activity, but exhibit a significantly attenuated opioid-mediated stress-induced analgesia. To further understand the cellular bases of these responses, we have studied mediobasal hypothalamic (MBH) neurons, including POMC neurons, using whole-cell patch recording in an in vitro slice preparation. Twenty-seven MBH cells were recorded in wild-type and 25 MBH cells were recorded in beta-END knockout mice. Neurons from both genotypes showed a significant positive correlation between DAMGO concentration (from 30 nM to 10 microM) and the induced outward K(+) current. The genotypes did not differ, however, in either the DAMGO-induced maximum outward current response or EC(50), or for the maximal response to the GABA(B) agonist baclofen. Furthermore, quantitative receptor autoradiography utilizing (3)H-DAMGO did not reveal any differences in total mu-opioid receptor binding between genotypes. Therefore, we conclude that the complete absence of beta-END throughout development did not alter either the expression of mu-opioid receptors or their coupling to K(+) channels in MBH neurons.
Synthesis of 1,3-dioxin-4-one derivatives. (1983)

A facile and general synthesis of 2, 2-dimethyl-1, 3-dioxin-4-one derivatives (1) is reported. Treatment of β-keto acids with a mixture of acetone, acetic anhydride, and conc. sulfuric acid or with a mixture of isopropenyl acetate and conc. sulfuric acid gave 2, 2-dimethyl-1, 3-dioxin-4-ones (1). Similar treatment of tert-butyl esters of β-keto acids also gave 1.
Mutational studies of human immunodeficiency virus type 1 reverse transcriptase : the involvement of residues 183 and 184 in the fidelity of DNA synthesis (1996)

The high error rates characteristic of human immunodeficiency virus type-1 reverse transcriptase (HIV-1 RT) are a presumptive source of the viral hypermutability that impedes prevention and therapy of acquired immunodeficiency syndrome (AIDS). We have analyzed two mutants of HIV-1 RT by conducting a comparative study of the accuracy of DNA synthesis. Each mutant bears a single amino acid substitution adjacent to the two aspartic acid residues at positions 185 and 186 in the highly conserved DNA polymerase active site. The first mutant, Met 184-->Leu (M184L), displays a marked reduction in both misinsertion and mispair extension, suggesting a fidelity of DNA synthesis significantly higher than that of the wild-type HIV-1 RT. The second mutant, Tyr 183-->Phe (Y183F), shows a decrease in mispair extension with no significant change in misincorporation. Thus, the overall pattern of error-proneness of DNA synthesis is: wild-type HIV-1 RT > Y183F > M184L. Taken together, it is possible that residues 183 and 184 contribute to the low fidelity of DNA synthesis characteristic of the reverse transcriptases of HIV-1, HIV-2 and possibly, of other lentiviruses. Our observations may bear on the nature of potential mutations responsible for resistance to the nucleoside analogs used in chemotherapy of AIDS.
Ligand Docking and Structure-based Virtual Screening in Drug Discovery (2007)

Ligand-docking-based methods are starting to play a critical role in lead discovery and optimization, thus resulting in new 'drug-candidates'. They offer the possibility to go beyond the pool of existing active compounds, and thus find novel chemotypes. A brief tutorial on ligand docking and structure-based virtual screening is presented highlighting current problems and limitations, together with the most recent methodological and algorithmic developments in the field. Recent successful applications of docking-based tools for hit discovery, lead optimization and target-biased library design are also presented. Special consideration is devoted to ongoing efforts to account for protein flexibility in structure-based virtual screening.
Aortic disease in Marfan syndrome: surgery, results, and special aspects (1995)

Marfan syndrome is a hereditary disorder of the connective tissue. Due to genetic determination by a mutation localized on chromosome 15, pathological fibrillin, an essential structural protein of elastic fibers, is synthesized. This leads to a disarray of fibers with resultant hyperelasticity and weakness. The expression of the disease is pleiomorphic, but in general it affects the ocular, skeletal and/or cardiovascular systems. The complications of cardiovascular manifestations, in particular aortic aneurysmatic dilatation and dissection without arterial hypertension and at an early age, have for a long time been limiting the life expectancy of these patients to about 40 years (8, 12, 19, 20). With the introduction of Bentall’s technique for composite aortic root replacement, significant improvements for Marfan patients could be achieved. This was especially the case if they were operated upon electively, usually before the diameter of the ascending aorta reached 6 cm (9).
Metabotropic Glutamate Receptors: Novel Targets for Drug Development (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMetabotropic Glutamate Receptors: Novel Targets for Drug DevelopmentThomas Knoepfel, Rainer Kuhn, and Hans AllgeierCite this: J. Med. Chem. 1995, 38, 9, 1417–1426Publication Date (Print):April 1, 1995Publication History Published online1 May 2002Published inissue 1 April 1995https://pubs.acs.org/doi/10.1021/jm00009a001https://doi.org/10.1021/jm00009a001research-articleACS PublicationsRequest reuse permissionsArticle Views470Altmetric-Citations218LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Acute subjective effects in LSD- and MDMA-assisted psychotherapy (2020)

LSD and MDMA are currently used medically in Switzerland mainly in patients with posttraumatic stress disorder and depression in group settings, producing similar acute responses as in research subjects. The data may serve as a basis for further controlled studies of substance-assisted psychotherapy.
A simplified and efficient germline-specific CRISPR/Cas9 system forDrosophilagenomic engineering (2013)

The type II CRISPR/Cas9 system (clustered regularly interspaced short palindromic repeats/CRISPR-associated) has recently emerged as an efficient and simple tool for site-specific engineering of eukaryotic genomes. To improve its applications in Drosophila genome engineering, we simplified the standard two-component CRISPR/Cas9 system by generating a stable transgenic fly line expressing the Cas9 endonuclease in the germline (Vasa-Cas9 line). By injecting vectors expressing engineered target-specific guide RNAs into Vasa-Cas9 fly embryos, mutations were generated from site-specific DNA cleavages and efficiently transmitted into progenies. Because Cas9 endonuclease is the universal component of the type II CRISPR/Cas9 system, site-specific genomic engineering based on this improved platform can be achieved with lower complexity and toxicity, greater consistency, and excellent versatility.
Short Communication: Net Uptake of Nonesterified Long Chain Fatty Acids by the Perfused Caudate Lobe of the Caprine Liver (2003)

The objective was to determine whether net uptake of various nonesterified long chain fatty acids differs in the caprine liver. Caudate lobes were isolated from four mature goats and perfused (1 ml/min x g wet tissue) with buffer containing 0.3 mM of each palmitic, stearic, oleic, linoleic, linolenic, eicosapentaenoic, and docosahexaenoic acids. The amount of fatty acid in the perfusate decreased over time for all fatty acids with the exception of stearic acid. There was no net uptake of stearic acid, which was significantly different from all other fatty acids examined, with the exception of oleic acid. Net hepatic uptake of oleic acid was numerically, but not significantly lower than palmitic, linoleic, linolenic, eicosapentaenoic, and docosahexaenoic acids. It was concluded that net uptake of fatty acids was similar for all fatty acids tested with the exception of stearic acid.
A Simple Technique for Mass Rearing Lutzomyia Longipalpis and Phlebotomus Papatasi (Diptera: Psychodidae) in the Laboratory1 (1983)

A simple technique for mass rearing phlebotomine sand flies (Phlebotomus papatasi and Lutzomyia longipalpis) in the laboratory is described. Using this method, 4000–5000 adults can be produced weekly with minimal labor (2–3 h of care per day). This is the first report of mass production of sand flies, a group of insects that heretofore has been difficult to colonize and maintain under laboratory conditions.
Incidence and Clinical Complications of Myelodysplastic Syndromes Among United States Medicare Beneficiaries (2010)

MDS is a common hematologic malignancy of the elderly, which places patients at risk for comorbid conditions. Transfusion dependency identifies patients with MDS at additional increased risk of organ impairment and shortened survival.
Molecular basis of glutamate toxicity in retinal ganglion cells (1997)

Loss of retinal ganglion cells (RGCs) is a hallmark of many ophthalmic diseases including glaucoma, retinal ischemia due to central artery occlusion, anterior ischemic optic neuropathy and may be significant in optic neuritis, optic nerve trauma, and AIDS. Recent research indicates that neurotoxicity is caused by excessive stimulation of receptors for excitatory amino acids (EAAs). In particular, the amino acid glutamate has been shown to act as a neurotoxin which exerts its toxic effect on RGCs predominantly through the N-methyl-D-aspartate (NMDA) subtype of glutamate receptor. NMDA-receptor-mediated toxicity in RGCs is dependent on the influx of extracellular Ca2+. The increase in [Ca2+]i acts as a second messenger that sets in motion the cascade leading to eventual cell death. Glutamate stimulates its own release in a positive feedback loop by its interaction with the non-NMDA receptor subtypes. Ca(2+)-induced Ca2+ release and further influx of Ca2+ through voltage-gated Ca2+ channels after glutamate-induced depolarization contribute to glutamate toxicity. In vitro and in vivo studies suggest that the use of selective NMDA receptor antagonists or Ca2+ channel blockers should be useful in preventing or at least abating neuronal loss in the retina. Of particular importance for future clinical use of NMDA receptor antagonists in the treatment of acute vascular insults is the finding that some drugs can prevent glutamate-induced neurotoxicity, even when administered a few hours after the onset of retinal ischemia.
Palladium Catalyst in DMSO for the Oxidation of Tolans to Benzils (1994)

Abstract Tolans(1) are effectively oxidized to benzils(2) by PdCl2/DMSO.
Alteration and abnormal expression of the c-myc oncogene in human multiple myeloma (1988)

Structural alterations of the c-myc oncogene in human Burkitt's lymphoma and mouse plasmacytoma suggest that this oncogene is involved in several B cell neoplasms. The possibility of c-myc alterations in human myeloma has not been explored, probably because the low proliferative activity characteristic of this tumor impairs the propagation of representative cell lines for the performance of adequate cytogenetic studies. This report describes alterations in the c-myc locus with concomitant elevated expression of mRNA in the tumor cells of two of 37 patients with multiple myeloma. In one case, somatic cell hybrid studies revealed that the cloned rearranged DNA was entirely derived from chromosome 8, thus indicating a novel mechanism of c-myc activation different from that in Burkitt's lymphoma. Seven other patients exhibited five- to 12-fold overexpression of c-myc RNA when compared with normal marrow cells. Elevated mRNA expression in about one fourth of our patients suggests that the c-myc oncogene has a pathogenetic role in the evolution of multiple myeloma.