gebhart/patrepeval huggingface dataset:
Rescue of end fragments of yeast artificial chromosomes by homologous recombination in yeast (1991)

Yeast artificial chromosomes (YACs) provide a powerful tool for the isolation and mapping of large regions of mammalian chromosomes. We developed a rapid and efficient method for the isolation of DNA fragments representing the extreme ends of YAC clones by the insertion of a rescue plasmid into the YAC vector by homologous recombination. Two rescue vectors were constructed containing a yeast LYS2 selectable gene, a bacterial origin of replication, an antibiotic resistance gene, a polylinker containing multiple restriction sites, and a fragment homologous to one arm of the pYAC4 vector. The 'end-cloning' procedure involves transformation of the rescue vector into yeast cells carrying a YAC clone, followed by preparation of yeast DNA and transformation into bacterial cells. The resulting plasmids carry end-specific DNA fragments up to 20 kb in length, which are suitable for use as hybridization probes, as templates for direct DNA sequencing, and as probes for mapping by fluorescence in situ hybridization. These vectors are suitable for the rescue of end-clones from any YAC constructed using a pYAC-derived vector. We demonstrate the utility of these plasmids by rescuing YAC-end fragments from a human YAC library.
Functional annotation of the human retinal pigment epithelium transcriptome (2009)

Our study expands current knowledge of the RPE transcriptome by assigning new genes, and adding data about expression level and interindividual variation. Functional annotation suggests that the RPE has high levels of protein synthesis, strong energy demands, and is exposed to high levels of oxidative stress and a variable degree of inflammation. Our data sheds new light on the molecular composition of BM, adjacent to the RPE, and is useful for candidate retinal disease gene identification or gene dose-dependent therapeutic studies.
Impact of nonnutritive oral motor stimulation and infant massage therapy on oral feeding skills of preterm infants (2012)

We have shown that the provision of a nonnutritive oral motor therapy (NNOMT) or infant massage therapy (iMT) provided singly and in combination vs. no intervention shortens the number of days from start to independent oral feeding in very low birth weight infants. This study hypothesizes that infants who benefited from NNOMT and/or iMT will demonstrate enhanced maturation of their oral feeding skills (OFS) when compared to control counterparts. OFS levels were monitored using a recently developed scale that takes into account their nutritive sucking skills and endurance at time of assessment. It is a simple method that requires only the additional reading of the volume taken 5 minutes into the start of a feeding and information routinely recorded in patients' medical chart. Four OFS levels were identified, characterized by infant's proficiency (% volume taken during the first 5 min/volume prescribed) and rate of transfer monitored over the entire feeding session (ml/min); OFS level 1 being the most immature and 4 the most mature. In parallel with the benefits provided by NNOMT and/or iMT, we demonstrate the direct positive impact these interventions have on accelerating the maturation of infants' oral feeding skills.
Activation of telomerase in a human tumor. (1994)

Tumors owe their perverse growth potential to changes in the controls that normally restrain somatic cells. The nowfamiliar players in this drama include distorted genes for growth factors and their receptors, misdirected signaling molecules, and errant cell-cycle regulators. Through these alterations cells evade many of the growth constraints imposed by their environment. But are such uncontrolled cells licensed for infinite rounds of cell division? Recent advances suggest that telomere loss is yet another hurdle in the progression of human tumors and that this obstacle may be circumvented by the activation of telomerase. The speculation that telomerase may play a role in human cancer is not new and has been discussed in a variety of contexts (1-4). However, a study by Counter et al. (5) in this issue of the Proceedings demonstrates that telomerase is activated in ovarian carcinoma. Their data indicate that expression of telomerase and the resulting stabilization of telomeres may be important for the expansion of a human tumor. This commentary reviews the background to these findings and discusses possible contributions of telomere dynamics to the transformation of human cells. More general reviews on telomeres and telomerase can be found in refs. 6-9.
Conjunctive enhancement of enzymatic thrombolysis and prevention of thrombotic reocclusion with the selective factor Xa inhibitor, tick anticoagulant peptide. Comparison to hirudin and heparin in a canine model of acute coronary artery thrombosis. (1992)

The potent antithrombotic effects of rTAP in this model directly implicate de novo thrombin formation as a major source of thrombin activity within the highly thrombogenic residual thrombus. These findings suggest that direct inhibition of prothrombinase activity may be an effective strategy in the development of a new class of conjunctive agents.
A Synthetic Peptide Derived From Human Immunodeficiency Virus Type 1 gp120 Downregulates the Expression and Function of Chemokine Receptors CCR5 and CXCR4 in Monocytes by Activating the 7-Transmembrane G-Protein–Coupled Receptor FPRL1/LXA4R (1999)

Because envelope gp120 of various strains of human immunodeficiency virus type 1 (HIV-1) downregulates the expression and function of a variety of chemoattractant receptors through a process of heterologous desensitization, we investigated whether epitopes derived from gp120 could mimic the effect. A synthetic peptide domain, designated F peptide, corresponding to amino acid residues 414-434 in the V4-C4 region of gp120 of the HIV-1 Bru strain, potently reduced monocyte binding and chemotaxis response to macrophage inflammatory protein 1beta (MIP-1beta) and stromal cell-derived factor 1alpha (SDF-1alpha), chemokines that use the receptors CCR5 and CXCR4, respectively. Further study showed that F peptide by itself is an inducer of chemotaxis and calcium mobilization in human monocytes and neutrophils. In cross-desensitization experiments, among the numerous chemoattractants tested, only the bacterial chemotactic peptide fMLF, when used at high concentrations, partially attenuated calcium mobilization induced by F peptide in phagocytes, suggesting that this peptide domain might share a 7-transmembrane, G-protein-coupled receptor with fMLF. By using cells transfected with cDNAs encoding receptors that interact with fMLF, we found that F peptide uses an fMLF receptor variant, FPRL1, as a functional receptor. The activation of monocytes by F peptide resulted in downregulation of the cell surface expression of CCR5 and CXCR4 in a protein kinase C-dependent manner. These results demonstrate that activation of FPRL1 on human moncytes by a peptide domain derived from HIV-1 gp120 could lead to desensitization of cell response to other chemoattractants. This may explain, at least in part, the initial activation of innate immune responses in HIV-1-infected patients followed by immune suppression.
Outliers detection and correction for cooperative distributed online learning in Wireless sensor network (2017)

The recent distributed online convex optimization framework has developed in Wireless sensor networks (WSN) provide the promising approach for solving approximately stochastic optimization problem over network of sensors follows distributed manner. In practice, most of real environmental sensing activities are highly dynamic where noisy sensory information often appears and affects to the learning performance. However, the original distributed saddle point (DSPA) algorithm is lack of considering about the consequence of falsification in online learning. Based on the simulation observations conducted in this paper, we figure out the fluctuation and the slow convergence rate leads to overall prediction performance reduction of distributed online least square problem. Therefore, we propose an integrated outliers detection, correction mechanism in order to stabilize prediction and improve convergence rate.
A Guide to Simple and Informative Binding Assays (2010)

The aim of binding assays is to measure interactions between two molecules, such as a protein binding another protein, a small molecule, or a nucleic acid. Hard work is required to prepare reagents, but flaws in the design of many binding experiments limit the information obtained. In particular many experiments fail to measure the affinity of the reactants for each other. This essay describes simple methods to get the most out of valuable reagents in binding experiments.
Structure–Activity Relationships and Design of Viral Mutagens and Application to Lethal Mutagenesis (2013)

While mutation is the driving force behind evolution, most mutations are detrimental; therefore, elevating the mutation rate of a virus should diminish fitness. Because riboviruses and retroviruses have high mutation rates, a small increase in their mutation rates could exceed their threshold of viability. This approach, elevation of the viral mutation rate beyond the threshold of viability, extinction catastrophe or lethal mutagenesis, was proposed over a decade ago as a novel chemotherapeutic strategy. Extinction catastrophe induced by promutagenic nucleosides has been demonstrated in cell culture models, but most mutagens are carcinogenic and are poorly tolerated. Thus, clinical translation of viral mutagens has been difficult, casting doubt on the clinical viability of this strategy. This Perspective covers recent advances in the use of promutagenic nucleosides and the Vif-APOBEC interaction as chemotherapeutic strategies for targeting viral mutation rates.
Expression of sucrase-isomaltase mRNA along the villus-crypt axis in the rat small intestine. (1992)

Sucrase-isomaltase has been used as a marker enzyme to study cell differentiation along the intestinal villus-crypt axis. Previous studies are in agreement that sucrase activity is confined to villus epithelial cells. However, immunoreactivity data are at conflict, with some studies reporting sucrase antigen in crypts as well as villi. To resolve this discrepancy, our goal was to determine the distribution of sucrase-isomaltase mRNA. A cDNA clone representing 3.0 kb of rat sucrase-isomaltase, including the sucrase active site, was characterized. Northern analysis of 12 tissues demonstrated a 6 kb transcript only in the small intestine. Jejunal cell fractions prepared by a washing technique showed declining levels of both sucrase activity and sucrase-isomaltase mRNA as well as increasing levels of thymidine kinase activity from early to later fractions. Since later fractions did not yield pure crypt cells, in situ hybridization using an 35S-labeled sucrase-isomaltase riboprobe was performed. The transition from zero to intense signal at the crypt-villus junction leads us to conclude that in the adult rat, sucrase-isomaltase gene expression is initiated only after cells leave the proliferative cycle and migrate onto the villi.
The CIRRUS banking network (1985)

The CIRRUS banking network makes coast-to-coast automatic banking transactions possible. The system will soon be able to handle international currency transactions and point-of-sale transactions in stores.
Diagnosis and management of paroxysmal nocturnal hemoglobinuria (2005)

The primary clinical manifestations of paroxysmal nocturnal hemoglobinuria (PNH) are hemolytic anemia, marrow failure, and thrombophilia. However, PNH is not a simple binary diagnosis and both flow cytometric characterization of glycosyl phosphatidylinositol–anchored protein expression on peripheral blood cells and marrow analysis are required for comprehensive disease classification. For optimum management, the contribution of both hemolysis and marrow failure to the complex anemia of PNH should be determined. Complement inhibition by eculizumab is a promising new approach to treating the hemolytic anemia. Stem cell transplantation is potentially curative, but the decision on use is best made on a case-by-case basis because of the heterogeneous natural history of the disease. PNH clone size and ethnic/geographic factors appear to influence thrombophilic propensity, but a consensus on prophylactic anticoagulation has not been reached. Involvement of unusual sites (hepatic, mesenteric, cerebral, dermal veins) is characteristic of the thrombophilia of PNH. Indefinite anticoagulation is recommended following a thromboembolic event and thrombolytic therapy should be considered for acute hepatic vein thrombosis (Budd-Chiari syndrome). Pregnancy in a patient with PNH is complicated and requires careful management including prophylactic anticoagulation. To obtain a broad overview of the natural history, approaches to management, and outcome, the International PNH Registry was recently established.
Appropriate prescribing of oral beta-lactam antibiotics. (2000)

Beta-lactam antibiotics include penicillins, cephalosporins and related compounds. As a group, these drugs are active against many gram-positive, gram-negative and anaerobic organisms. Information based on "expert opinion" and antimicrobial susceptibility testing supports certain antibiotic choices for the treatment of common infections, but less evidence-based literature is available to guide treatment decisions. Evidence in the literature supports the selection of amoxicillin as first-line antibiotic therapy for acute otitis media. Alternative drugs, such as amoxicillin-clavulanate, trimethoprim-sulfamethoxazole and cefuroxime axetil, can be used to treat resistant infections. Penicillin V remains the drug of choice for the treatment of pharyngitis caused by group A streptococci. Inexpensive narrow-spectrum drugs such as amoxicillin or trimethoprim-sulfamethoxazole are first-line therapy for sinusitis. Animal and human bites can be treated most effectively with amoxicillin-clavulanate. For most outpatient procedures, amoxicillin is the preferred agent for bacterial endocarditis prophylaxis. Beta-lactam antibiotics are usually not the first choice for empiric outpatient treatment of community-acquired pneumonia. Based on the literature, the role of beta-lactam antibiotics in the treatment of bronchitis, skin infections and urinary tract infections remains unclear.
Science Review: Vasopressin and the cardiovascular system part 2 - clinical physiology. (2003)

Vasopressin is emerging as a rational therapy for vasodilatory shock states. In part 1 of the review we discussed the structure and function of the various vasopressin receptors. In part 2 we discuss vascular smooth muscle contraction pathways with an emphasis on the effects of vasopressin on ATP-sensitive K+ channels, nitric oxide pathways, and interaction with adrenergic agents. We explore the complex and contradictory studies of vasopressin on cardiac inotropy and coronary vascular tone. Finally, we summarize the clinical studies of vasopressin in shock states, which to date have been relatively small and have focused on physiologic outcomes. Because of potential adverse effects of vasopressin, clinical use of vasopressin in vasodilatory shock should await a randomized controlled trial of the effect of vasopressin's effect on outcomes such as organ failure and mortality.
Infections with Herpes Simplex Viruses (1986)

The Clinical Spectrum of HSV InfectionsHerpes simplex virus (HSV) has been isolated from nearly all visceral and mucocutaneous sites. The clinical manifestations and course of HSV infections depend on the anatomic site of the infection, the age and immune status of the host, and the antigenic type of the virus. First episodes of HSV disease, especially primary infections — that is, first infections with either HSV-1 or HSV-2 in which the host lacks HSV antibodies in acute-phase serum — are frequently accompanied by systemic signs and symptoms, involve both mucosal and extramucosal sites, are characterized by a longer duration . . .
Proximity extension of circular DNA aptamers with real-time protein detection (2005)

Multivalent circular aptamers or 'captamers' have recently been introduced through the merger of aptameric recognition functions with the basic principles of DNA nanotechnology. Aptamers have strong utility as protein-binding motifs for diagnostic applications, where their ease of discovery, thermal stability and low cost make them ideal components for incorporation into targeted protein assays. Here we report upon a property specific to circular DNA aptamers: their intrinsic compatibility with a highly sensitive protein detection method termed the 'proximity extension' assay. The circular DNA architecture facilitates the integration of multiple functional elements into a single molecule: aptameric target recognition, nucleic acid hybridization specificity and rolling circle amplification. Successful exploitation of these properties is demonstrated for the molecular analysis of thrombin, with the assay delivering a detection limit nearly three orders of magnitude below the dissociation constants of the two contributing aptamer-thrombin interactions. Real-time signal amplification and detection under isothermal conditions points towards potential clinical applications, with both fluorescent and bioelectronic methods of detection achieved. This application elaborates the pleiotropic properties of circular DNA aptamers beyond the stability, potency and multitargeting characteristics described earlier.
Associations among Erythroferrone and Biomarkers of Erythropoiesis and Iron Metabolism, and Treatment with Long-Term Erythropoiesis-Stimulating Agents in Patients on Hemodialysis (2016)

We identified a novel association between ESA and ERFE in patients on HD. Both DA and CERA increased levels of ERFE that regulated hepcidin 25 and led to iron mobilization from body stores during erythropoiesis.
A KINETIC STUDY OF THE THERMAL DECOMPOSITION OF SELECTED CYCLOHEXYL AND PHENYLSILANES. (1969)

Abstract : The thermal-decompositon kinetics of the following arylsilanes have been investigated using both static and flow techniques: monophenylsilane, diphenylsilane, triphenylsilane, tetraphenylsilane, diphenyldimethylsilane, and triphenylmethylsilane. The phenylhydrosilanes decompose via a bimolecular second-order redistribution reaction, with no evidence for free-radical formation. On the other hand, the main mode of decomposition of tetraphenylsilane involves elimination of phenyl radicals followed by attack of these radicals on the parent silane. The decomposition of the phenylmethylsilanes also proceeds via free-radical mechanism, but the main reaction path results in intramolecular cyclization, yielding compounds containing the dibenzosilole nucleus. Reasons for these three basically different modes of reaction are discussed in terms of substituent size and degree of (p-d)pi bonding between the phenyl rings and silicon. (Author)
Reach Extension and Capacity Enhancement of VCSEL-Based Transmission Over Single-Lane MMF Links (2016)

This paper reviews and examines several techniques for expanding the carrying capacity of multimode fiber (MMF) using vertical cavity surface emitting lasers (VCSELs). The first approach utilizes short wavelength division multiplexing in combination with MMF optimized for operation between 850 and 950 nm. Both nonreturn to zero (NRZ) and four-level pulse amplitude modulation (PAM4) signaling are measured and demonstrate up to 170-Gb/s postforward error correction transmission over 300 m. For single wavelength transmission, the use of selective modal launch to increase the optical bandwidth of a standard OM3 MMF to more than 2.1 GHz·km for standard MMF is presented. A statistical model is used to predict the bandwidth enhancement of installed MMF and indicates that significant link extension can be achieved using selective modal launch techniques. These results demonstrate the continued effectiveness of VCSEL-based MMF links in current and future data center environments.
Yeast cytosine deaminase improves radiosensitization and bystander effect by 5-fluorocytosine of human colorectal cancer xenografts. (2000)

The efficacy of cancer gene therapy using bacterial cytosine deaminase (bCD)/5-fluorocytosine (5-FC) enzyme/prodrug strategy is limited by the inefficiency of cytosine deaminase (CD)-catalyzed conversion of 5-FC into 5-fluorouracil (5-FU). We have shown previously that yeast CD (yCD) is more efficient at the conversion of 5-FC than bCD. In the current study, we hypothesized that the increased production of 5-FU by yCD would enhance the efficacy of the CD/5-FC treatment strategy by increasing the bystander effect as well as the efficacy of radiotherapy because of the radiosensitizing capacity of 5-FU. To test this hypothesis, we generated stable HT29 human colon cancer cell lines expressing either bCD (HT29/bCD) or yCD (HT29/yCD). The amount of 5-FU produced in HT29/yCD tumors after a single injection of 5-FC (1000 mg/kg, i.p.) was 15-fold higher than that produced in HT29/bCD tumors. In tumor-bearing nude mice, the average minimum relative tumor size (compared with pretreatment values) of HT29/bCD tumors treated with 5-FC and radiation (500 mg/kg i.p. and 3 Gy, 5 days a week for 2 weeks) was 0.55+/-0.1, compared with 0.01+/-0.01 in HT29/yCD tumors (P = 0.002). Moreover, an increased cytotoxic and radiosensitizing effect of 5-FC on bystander cells was observed in vitro and in vivo when yCD was expressed in HT29 cells instead of bCD. In mice bearing HT29 tumors containing 10% HT29/yCD cells, the combined treatment resulted in a minimum tumor size of 0.20+/-0.07 compared with 0.60+/-0.1 in 10% HT29/bCD cells (P < 0.001). These results demonstrate that the use of yCD in the CD/5-FC strategy has a high potential to improve the therapeutic outcome of combined gene therapy and radiotherapy in cancer patients.
Automatic Classification of Heartbeats Using ECG Morphology and Heartbeat Interval Features (2004)

A method for the automatic processing of the electrocardiogram (ECG) for the classification of heartbeats is presented. The method allocates manually detected heartbeats to one of the five beat classes recommended by ANSI/AAMI EC57:1998 standard, i.e., normal beat, ventricular ectopic beat (VEB), supraventricular ectopic beat (SVEB), fusion of a normal and a VEB, or unknown beat type. Data was obtained from the 44 nonpacemaker recordings of the MIT-BIH arrhythmia database. The data was split into two datasets with each dataset containing approximately 50,000 beats from 22 recordings. The first dataset was used to select a classifier configuration from candidate configurations. Twelve configurations processing feature sets derived from two ECG leads were compared. Feature sets were based on ECG morphology, heartbeat intervals, and RR-intervals. All configurations adopted a statistical classifier model utilizing supervised learning. The second dataset was used to provide an independent performance assessment of the selected configuration. This assessment resulted in a sensitivity of 75.9%, a positive predictivity of 38.5%, and a false positive rate of 4.7% for the SVEB class. For the VEB class, the sensitivity was 77.7%, the positive predictivity was 81.9%, and the false positive rate was 1.2%. These results are an improvement on previously reported results for automated heartbeat classification systems.