gebhart/patrepeval huggingface dataset:
Low-floor decoders for LDPC codes (2009)

One of the most significant impediments to the use of LDPC codes in many communication and storage systems is the error-rate floor phenomenon associated with their iterative decoders. The error floor has been attributed to certain subgraphs of an LDPC code's Tanner graph induced by so-called trapping sets. We show in this paper that once we identify the trapping sets of an LDPC code of interest, a sum-product algorithm (SPA) decoder can be custom-designed to yield floors that are orders of magnitude lower than floors of the the conventional SPA decoder. We present three classes of such decoders: (1) a bi-mode decoder, (2) a bit-pinning decoder which utilizes one or more outer algebraic codes, and (3) three generalized-LDPC decoders. We demonstrate the effectiveness of these decoders for two codes, the rate-1/2 (2640,1320) Margulis code which is notorious for its floors and a rate-0.3 (640,192) quasi-cyclic code which has been devised for this study. Although the paper focuses on these two codes, the decoder design techniques presented are fully generalizable to any LDPC code.
Enzymatic synthesis of biotin-labeled polynucleotides: novel nucleic acid affinity probes. (1981)

Analogs of dUTP and UTP that contain a biotin molecule covalently bound to the C-5 position of the pyrimidine ring through an allylamine linker arm have been synthesized. These biotin-labeled nucleotides are efficient substrates for a variety of DNA and RNA polymerases in vitro. Polynucleotides containing low levels of biotin substitution (50 molecules or fewer per kilobase) have denaturation, reassociation, and hybridization characteristics similar to those of unsubstituted controls. Biotin-labeled polynucleotides, both single and double-stranded, are selectively and quantitatively retained on avidin-Sepharose, even after extensive washing with 8 M urea, 6 M guanidine hydrochloride, or 99% formamide. In addition, biotin-labeled polynucleotides can be selectively immunoprecipitated in the presence of antibiotin antibody and Staphylococcus aureus protein A. The unique features of biotin-labeled polynucleotides suggest that they will be useful affinity probes for the detection and isolation of specific DNA and RNA sequences.
Single magnetic microsphere placement and detection on-chip using current line designs with integrated spin valve sensors: Biotechnological applications (2002)

Superparamagnetic labels, 400 nm dextran iron oxide particles and 2 μm polymer encapsulated iron oxide microspheres, with biomolecules immobilized on the surface, e.g., the enzyme horseradish peroxidase (20–40 molecules per label) were controllably placed on chip sites (5×15 μm2) using tapered Al current lines (10–20 mA current) and moved to and from adjacent spin valve sensors [2×6 μm,2, magnetoresistance (MR) ∼5%]. Average MR signals of 1.2 and 0.6 mV were obtained for the detection of bulk numbers of 400 nm and 2 μm labels respectively using an on-chip field of 15 Oe and a sense current of 5 mA. The moment per label was calculated at 5×10−13 emu for the 400 nm labels and 5×10−12 emu for the 2 μm labels, illustrating the higher density of the 400 nm particles. MR signals of ∼100 μV were obtained for single 2 μm labels positioned over the spin valve sensor using an on-chip field of 15 Oe and 8 mA sense current. The corresponding sensor saturation occurred at ∼1 mV, with a noise level of ∼10 μV. The estimated maximum MR signal for one 2 μm label directly on top of the sensor was ∼400 μV. Biotechnological applications include high sensitivity biosensors and biochips for protein and DNA screening.
Phosphodiesterase 1 Upregulation in Pulmonary Arterial Hypertension (2007)

Background— Pulmonary arterial hypertension (PAH) is a life-threatening disease, characterized by vascular smooth muscle cell hyperproliferation. The calcium/calmodulin-dependent phosphodiesterase 1 (PDE1) may play a major role in vascular smooth muscle cell proliferation. Methods and Results— We investigated the expression of PDE1 in explanted lungs from idiopathic PAH patients and animal models of PAH and undertook therapeutic intervention studies in the animal models. Strong upregulation of PDE1C in pulmonary arterial vessels in the idiopathic PAH lungs compared with healthy donor lungs was noted on the mRNA level by laser-assisted vessel microdissection and on the protein level by immunohistochemistry. In chronically hypoxic mouse lungs and lungs from monocrotaline-injected rats, PDE1A upregulation was detected in the structurally remodeled arterial muscular layer. Long-term infusion of the PDE1 inhibitor 8-methoxymethyl 3-isobutyl-1-methylxanthine in hypoxic mice and monocrotaline-injected rats with fully established pulmonary hypertension reversed the pulmonary artery pressure elevation, structural remodeling of the lung vasculature (nonmuscularized versus partially muscularized versus fully muscularized small pulmonary arteries), and right heart hypertrophy. Conclusions— Strong upregulation of the PDE1 family in pulmonary artery smooth muscle cells is noted in human idiopathic PAH lungs and lungs from animal models of PAH. Inhibition of PDE1 reverses structural lung vascular remodeling and right heart hypertrophy in 2 animal models. The PDE1 family may thus offer a new target for therapeutic intervention in pulmonary hypertension.
Enhancement of autophagy is a potential modality for tumors refractory to radiotherapy (2011)

Radiotherapy is a well-established treatment for cancer. However, the existence of radioresistant cells is one of the major obstacles in radiotherapy. In order to understand the mechanism of cellular radioresistance and develop more effective radiotherapy, we have established clinically relevant radioresistant (CRR) cell lines, which continue to proliferate under daily exposure to 2 Gray (Gy) of X-rays for >30 days. X-ray irradiation significantly induced autophagic cells in parental cells, which was exiguous in CRR cells, suggesting that autophagic cell death is involved in cellular radiosensitivity. An autophagy inducer, rapamycin sensitized CRR cells to the level of parental cells and suppressed cell growth. An autophagy inhibitor, 3-methyladenine induced radioresistance of parental cells. Furthermore, inhibition of autophagy by knockdown of Beclin-1 made parental cells radioresistant to acute radiation. These suggest that the suppression of autophagic cell death but not apoptosis is mainly involved in cellular radioresistance. Therefore, the enhancement of autophagy may have a considerable impact on the treatment of radioresistant tumor.
Entropy of association of methane in water: a new molecular dynamics computer simulation (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEntropy of association of methane in water: a new molecular dynamics computer simulationDavid E. Smith, Ling Zhang, and A. D. J. HaymetCite this: J. Am. Chem. Soc. 1992, 114, 14, 5875–5876Publication Date (Print):July 1, 1992Publication History Published online1 May 2002Published inissue 1 July 1992https://pubs.acs.org/doi/10.1021/ja00040a068https://doi.org/10.1021/ja00040a068research-articleACS PublicationsRequest reuse permissionsArticle Views614Altmetric-Citations135LEARN 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
Optimizing Smith-Waterman for the Cell Broadband Engine (2008)

Motivation: As new processors become available, the SingleInstruction Multiple-Data Smith-Waterman implementations need to be adapted to the processors instruction set to get maximum performance. One recent processor, the Cell Broadband Engine has eight independent vector processors. To take advantage of the Cell’s vector engines, the implementation needs to take into account the limited resources of the vector engine and the limits of the instruction set. Results: The adapted Smith-Waterman implementation running on a single 3.2 GHz Cell Broadband Engine achieved speeds of >16 billion cell update per second with the ability to handle sequences of 32K residues. Availability: http://farrar.michael.googlepages.com/striped.tgz
Optical Systems with Resolving Powers Exceeding the Classical Limit* (1966)

A new theorem on the ultimate limit of performance of optical systems is established: Not the bandwidth of the transferred spatial frequencies but only the number of degrees of freedom of the optical message transmitted by a given optical system is invariant. It is therefore possible (a) to extend the bandwidth by reducing the object area, (b) to extend the bandwidth in the x direction while proportionally reducing it in the y direction, so that the two-dimensional bandwidth is constant, and (c) to double the bandwidth when transmitting information about one state of polarization only.To achieve this, the optical systems are modified by inserting two suitable masks (generally gratings) into optically conjugate planes of object and image space. The transfer and spread function of the modified systems are calculated for the case of coherent illumination.
Recent developments in atrial fibrillation (2005)

Atrial fibrillation, the most commonly encountered arrhythmia in clinical practice, is associated with substantial morbidity and mortality. Its incidence and prevalence are increasing, and it represents a growing clinical and economic burden. Recent research has highlighted new approaches to both pharmacological and non-pharmacological management strategies. Clinicians need to have a sound working knowledge of atrial fibrillation and to be up to date with the emerging evidence to guide treatment and improve outcomes in these patients.

In this article, we highlight the recent advances in atrial fibrillation. We searched PubMed/Medline, Embase, and Cochrane databases by using the keywords “atrial fibrillation,” “rate,” “rhythm,” “anticoagulation,” and “non-pharmacological.” We also searched references of recent major articles and key reviews, and we obtained articles where necessary.

Atrial fibrillation affects an estimated 2.2 million adults in the United States.1 In the United Kingdom alone, more than 46 000 new cases of atrial fibrillation are diagnosed every year.2 The prevalence of atrial fibrillation doubles with each advancing decade from the age of 50.3 Independent risk factors include male sex, increasing age, hypertension, diabetes, smoking, valvular heart disease, and myocardial infarction.4 Left atrial dilatation, left ventricular hypertrophy, and impaired left ventricular systolic function are also associated with atrial fibrillation.5 Compared with people in sinus rhythm, those in atrial fibrillation have a sixfold increased risk of stroke and twofold increased risk of death. For those with rheumatic heart disease, the risk of stroke is increased up to 18-fold.6

The nomenclature used to classify atrial fibrillation has been diverse. Recent guidelines recommend a classification system based on the temporal pattern of the arrhythmia (fig 1).7



Fig 1 
Classification of atrial fibrillation.*When a patient has had two or more episodes of atrial fibrillation, this is termed recurrent. Both paroxysmal and persistent atrial fibrillation …
Delineation and synthesis of the membrane receptor-binding domain of sex hormone-binding globulin. (1990)

Sex hormone-binding globulin (SHBG) is a plasma glycoprotein which binds certain steroids. It, in turn, binds to a specific receptor on cell membranes. This work was undertaken to identify, isolate, sequence, and synthesize the region of SHBG that interacts with its membrane receptor. To accomplish this, highly purified human SHBG was digested with trypsin. The SHBG-derived tryptic peptides were separated by high performance liquid chromatography. They were evaluated for their ability to compete with 125I-SHBG for binding to the SHBG receptor solubilized from human prostatic membranes. Only a single peptide, corresponding to residues 48-57 of the known sequence of human SHBG, inhibited receptor binding. A synthetic decapeptide with this amino acid sequence also competitively inhibited SHBG binding.
Publisher’s Note: Demonstration of a Quantum Controlled-NOT Gate in the Telecommunications Band [Phys. Rev. Lett.100, 133603 (2008)] (2008)

Received 4 April 2008DOI:https://doi.org/10.1103/PhysRevLett.100.149903©2008 American Physical Society
Co-Tracking Using Semi-Supervised Support Vector Machines (2007)

This paper treats tracking as a foreground/background classification problem and proposes an online semi- supervised learning framework. Initialized with a small number of labeled samples, semi-supervised learning treats each new sample as unlabeled data. Classification of new data and updating of the classifier are achieved simultaneously in a co-training framework. The object is represented using independent features and an online support vector machine (SVM) is built for each feature. The predictions from different features are fused by combining the confidence map from each classifier using a classifier weighting method which creates a final classifier that performs better than any classifier based on a single feature. The semi-supervised learning approach then uses the output of the combined confidence map to generate new samples and update the SVMs online. With this approach, the tracker gains increasing knowledge of the object and background and continually improves itself over time. Compared to other discriminative trackers, the online semi-supervised learning approach improves each individual classifier using the information from other features, thus leading to a more robust tracker. Experiments show that this framework performs better than state-of-the-art tracking algorithms on challenging sequences.
<title>Development of a penicillin biosensor using a single optical imaging fiber</title> (1995)

A penicillin biosensor has been fabricated by photodepositing penicillin-sensitive polymer matrices and pH-sensitive polymer matrices on different regions of an optical imaging fiber. Penicillin is detected by coupling the enzymatic activity of penicillinase with the pH sensitivity of fluorescein. Penicillin concentration is correlated to the pH change in the microenvironment of the penicillin-sensitive matrix relative to the pH of the sample solution. This dual sensor removes the need to maintain a constant solution pH when measuring penicillin and should enhance greatly the application of biosensors.
An oleate 12-hydroxylase from Ricinus communis L. is a fatty acyl desaturase homolog. (1995)

Recent spectroscopic evidence implicating a binuclear iron site at the reaction center of fatty acyl desaturases suggested to us that certain fatty acyl hydroxylases may share significant amino acid sequence similarity with desaturases. To test this theory, we prepared a cDNA library from developing endosperm of the castor-oil plant (Ricinus communis L.) and obtained partial nucleotide sequences for 468 anonymous clones that were not expressed at high levels in leaves, a tissue deficient in 12-hydroxyoleic acid. This resulted in the identification of several cDNA clones encoding a polypeptide of 387 amino acids with a predicted molecular weight of 44,407 and with approximately 67% sequence homology to microsomal oleate desaturase from Arabidopsis. Expression of a full-length clone under control of the cauliflower mosaic virus 35S promoter in transgenic tobacco resulted in the accumulation of low levels of 12-hydroxyoleic acid in seeds, indicating that the clone encodes the castor oleate hydroxylase. These results suggest that fatty acyl desaturases and hydroxylases share similar reaction mechanisms and provide an example of enzyme evolution.
Lipid-derived nanoparticles for immunostimulatory RNA adjuvant delivery (2012)

The specific activation of Toll-like receptors (TLRs) has potential utility for a variety of therapeutic indications including antiviral immunotherapy and as vaccine adjuvants. TLR7 and TLR 8 may be activated by their native ligands, single-stranded RNA, or by small molecules of the imidazoquinoline family. However the use of TLR7/8 agonists for in vivo therapy is limited by instability, in the case of RNA, or systemic biodistribution and toxicity in the case of small molecule agonists. We hypothesized that unique lipid-like materials, termed “lipidoids,” could be designed to efficiently deliver immunostimulatory RNA (isRNA) to TLR-expressing cells to drive innate and adaptive immune responses. A library of lipidoids was synthesized and screened for the ability to induce type I IFN activation in human peripheral blood mononuclear cells when combined with isRNA oligonucleotides. Effective lipidoid-isRNA nanoparticles, when tested in mice, stimulated strong IFN-α responses following subcutaneous injection, had robust antiviral activity that suppressed influenza virus replication, and enhanced antiovalbumin humoral and cell-mediated responses when used as a vaccine adjuvant. Further, we demonstrate that whereas all immunological activity was MyD88-dependent, certain materials were found to engage both TLR7-dependent and TLR7-independent activity in the mouse suggestive of cell-specific delivery. These lipidoid formulations, which are materials designed specifically for delivery of isRNA to Toll-like receptors, were superior to the commonly used N -[1-(2,3-dioleoyloxy)propyl]- N,N,N -trimethylammonium methylsulfate–RNA delivery system and may provide new tools for the manipulation of TLR responses in vitro and in vivo.
Neuroprotection in Cerebral Ischaemia: Facts and Fancies – The Need for New Approaches (2003)

In the acute stage of occlusive stroke, moderate reduction of blood flow results in a 'penumbra' of brain cells, often surrounding a core infarct, in which brain cells survive for a few hours but gradually die if reperfusion is not established. Increased knowledge of the complex pathophysiology in acute ischaemic stroke has led to the development of a great number of candidates for neuroprotective interventions. Many neuroprotective agents have proven efficacious in animal models, but so far no human study has shown a statistically significant benefit in patients with acute ischaemic stroke on primary endpoint measures. Some neuroprotective agents show beneficial effects on post hoc analyses, and some studies are still ongoing. FANCIES: In the early years of neuroprotective studies in stroke, it was thought that a drug with almost no adverse effects could be given by ambulance staff on the way to hospital and induce a clinically significant effect on outcome. Since there were only benefits and no risks, diagnostic skills by neurologists and neuroradiological evaluations would no longer be required. WHY HAVE NEUROPROTECTIVE AGENTS FAILED IN HUMAN STROKE TRIALS? There are several possible explanations why neuroprotective trials have been unable to prove an effect in addition to the eventuality that the basic concept is wrong. The effects of neuroprotective agents on infarct size are time dependent, and treatment has often been initiated much later than in successful experimental stroke models. Insufficient doses of the drugs and slow availability of the drug at the target area may be other explanations. Too small sample sizes in trials and imbalance of prognostically important baseline variables are examples of shortcomings in trial methodology. WHAT CAN BE DONE? FUTURE NEW APPROACHES: IN ANIMAL MODELS, preclinical testing of neuroprotective candidates should be standardized. Conventional stroke models with young and healthy animals may be replaced by older animals with common co-morbidity such as atherosclerosis. Highly effective new neuroprotective agents need to be discovered, and combination therapies should be tried. IN CLINICAL TRIALS, the greatest chances of success may be with neuroprotective concepts involving mechanisms in both ischaemic and reperfusion pathophysiology, in combination with a thrombolytic therapy protocol. Neuroprotective agents, possibly combinations of agents, should preferably approach several of these mechanisms. Treatments should be initiated early, at least within 3 h after stroke onset, by an intravenous route. The selected compound(s) should easily pass the blood-brain barrier. Neuroprotective agents shown to be highly effective in stroke models should be preferred, and doses used experimentally should be used also in the clinical setting. Trials should use randomization techniques, which reduce imbalances of prognostically important baseline variables, and the estimated sample size of a trial should be based on expectations of a modest clinical effect.
Redispersible Hybrid Nanopowders: Cerium Oxide Nanoparticle Complexes with Phosphonated-PEG Oligomers (2008)

Rare earth cerium oxide (ceria) nanoparticles are stabilized using end-functional phosphonated-PEG oligomers. The complexation process and structure of the resulting hybrid core-shell singlet nanocolloids are described, characterized, and modeled using light and neutron scattering data. The adsorption mechanism is nonstoichiometric, yielding the number of adsorbed chains per particle N(ads) = 270 at saturation. Adsorption isotherms show a high affinity of the phosphonate head for the ceria surface (adsorption energy DeltaG(ads) approximately -16kT) suggesting an electrostatic driving force for the complexation. The ease, efficiency, and integrity of the complexation is highlighted by the formation of nanometric sized cerium oxide particles covered with a well anchored PEG layer, maintaining the characteristics of the original sol. This solvating brushlike layer is sufficient to solubilize the particles and greatly expand the stability range of the original sol (<pH 3) up to pH = 9. We underscore two key attributes of the tailored sol: (i) strong UV absorption capability after functionalization and (ii) ability to redisperse after freeze-drying as powder in aqueous or organic solvents in varying concentrations as singlet nanocolloids. This robust platform enables translation of intrinsic properties of mineral oxide nanoparticles to critical end use.