gebhart/patrepeval huggingface dataset:
Engineering an HIV Envelope Protein to Activate Germline B Cell Receptors of Broadly Neutralizing VRC01-Class Antibodies (2013)

The recent RV144 trial showed ~30% efficacy. Although\nthe protection was modest, the trial indicated for the first\ntime that a vaccine against HIV is possible. Immune correlate\nanalysis suggests that the observed protection was due to non-neutralizing\nantibody responses. This efficacy might be improved\nif a vaccine could elicit broadly neutralizing antibodies (bNAbs).\nOf particular interest for vaccine design are the potent VRC01-\nclass bNAbs targeting CD4 binding site on Env. Unfortunately, a\nnumber of studies have demonstrated that recombinant Env\nproteins do not bind germline-reverted VRC01 class Abs, indicating\nthat current vaccine strategies using recombinant Env are\nunable to activate progenitor B cells that ultimately give rise to\nVRC01 class Abs.
Esophageal Invasion by Lung Cancer (1984)

Esophageal wall invasion by primary lung carcinoma is an uncommon occurrence. When CT demonstrates a large primary parenchymal lung lesion that appears to cross the midline in the posterior mediastinum, dilute oral barium should be given during the CT examination to demonstrate the location of the esophagus. An esophagus involved by lung carcinoma may show contralateral displacement or partial obstruction. Furthermore, a malignant fistula between esophagus and trachea or lung may also be discovered.
The shape-shifting quasispecies of RNA: one sequence, many functional folds (2011)

E Unus pluribum, or "Of One, Many", may be at the root of decoding the RNA sequence-structure-function relationship. RNAs embody the large majority of genes in higher eukaryotes and fold in a sequence-directed fashion into three-dimensional structures that perform functions conserved across all cellular life forms, ranging from regulating to executing gene expression. While it is the most important determinant of the RNA structure, the nucleotide sequence is generally not sufficient to specify a unique set of secondary and tertiary interactions due to the highly frustrated nature of RNA folding. This frustration results in folding heterogeneity, a common phenomenon wherein a chemically homogeneous population of RNA molecules folds into multiple stable structures. Often, these alternative conformations constitute misfolds, lacking the biological activity of the natively folded RNA. Intriguingly, a number of RNAs have recently been described as capable of adopting multiple distinct conformations that all perform, or contribute to, the same function. Characteristically, these conformations interconvert slowly on the experimental timescale, suggesting that they should be regarded as distinct native states. We discuss how rugged folding free energy landscapes give rise to multiple native states in the Tetrahymena Group I intron ribozyme, hairpin ribozyme, sarcin-ricin loop, ribosome, and an in vitro selected aptamer. We further describe the varying degrees to which folding heterogeneity impacts function in these RNAs, and compare and contrast this impact with that of heterogeneities found in protein folding. Embracing that one sequence can give rise to multiple native folds, we hypothesize that this phenomenon imparts adaptive advantages on any functionally evolving RNA quasispecies.
Towards proximity pattern mining in large graphs (2010)

Mining graph patterns in large networks is critical to a variety of applications such as malware detection and biological module discovery. However, frequent subgraphs are often ineffective to capture association existing in these applications, due to the complexity of isomorphism testing and the inelastic pattern definition.
<title>A Single Chip Linear Array Picture Processor</title> (1983)

A CMOS programable picture processor*) with its own photodiod array is presented. The circuit is novel in that it includes an instruction set that permits most low-level picture processing operations. The chip is a parallel machine with a processing unit for each picture element. Images are binarized and are processed line by line. An experimental chip has been designed and is under fabrication.
A clinical trial for the safety and immunogenicity of a DNA-based immunotherapy in men with biochemically (PSA) relapsed prostate cancer. (2017)

e14634 Background: Introducing amino acid sequence changes in highly expressed self-antigens for prostate cancer (PCa) patients (pts) might lead to avoidance of immune tolerance. We evaluated a DNA vaccine (INO-5150) including SynCon PSA and PSMA. Administration of INO-5150 to PCa pts along with plasmid encoded adjuvant IL-12 (INO-9012) via electroporation (EP) is postulated to break tolerance, resulting in antigen-specific immune responses which could lead to stabilization of disease progression. Methods: Phase I, open-label, multicenter study of PCa pts post-definitive therapy with a rising PSA ≥ 1.0 ng/ml after surgery, or ≥ 2.0 ng/ml above nadir after RT and PSADT > 3 months, testosterone > 150 ng/dL, no concomitant androgen deprivation therapy and no evidence of metastases within 12 months. We evaluated safety, tolerability and for efficacy signals. INO-5150 low (2 mg, arms A and C) or high (8.5 mg, arms B and D) dose with or without INO-9012 (1 mg) was administered IM followed by EP in total 4 dosing arms on Day 0 and at Wks 3, 12, and 24 in 60 planned pts (15/arm). Pts were followed for 72 Wks. Results: 62 pts, 16 each in arms A and D and 15 in B and C were enrolled. Median age: 69.5 yrs (range 55.4-87.7), Gleason score: 7 (5-10), time from initial diagnosis: 8.2 yrs (0.5-23.8) and ECOG PS: 0 (0-1). As of data cutoff of 23Jan17, 52 pts had EOT visit, 7 withdrawn from treatment and 6 (10%) reported disease progression, 3 biochemical and 3 radiographic. Median serum PSA at enrollment was 4.6 ng/mL (range 1.2, 113.7) and at EOT was 6.5 ng/mL (0.1, 73.6). Median PSADT at enrollment was 8.7 months (3.1, 218.1) and at EOT it was 3.1 months (-23.1, 100.0). Safety: no reports of Grade 4-5 SAEs. 6 Grade 3 SAEs in 5 pts: presyncope, cardiac disorder, fall, neoplasm, ALT and AST elevation. Grade 1-3 AEs reported in 51 (82%) pts: 12 (75%) in Arm A, 13 (87%) B, 13 (87%) C, and 13 (81%) in D. Common AEs were injection site pain (24/39%), swelling (14/23%), erythema (14/23%), all Grade 1-2. Conclusions: INO-5150 (+) and (-) INO-9012 was generally safe and well-tolerated at all 4 dose levels in this patient population. Preliminary data suggest PSA stabilization in some patients. Immune analyses are ongoing. (NCT02514213) Clinical trial information: NCT02514213.
New Synthetic Approach to Polyaryl Strands Containing Pyridine and Pyrimidine Units (2000)

The synthesis of hexaaromatic strand 4 in which pyridyl and pyrimidyl units are linked both directly and by a one-atom spacer is reported. The C-linkage is introduced by double nucleophilic substitution reaction of a carbanion at the bromopyridyl moiety of building block 2a.
Primary Structure of the Glycans from Human Lactotransferrin (1982)

The polypeptide chain of human lactotransferrin possesses two glycoslyation sites to which glycans are linked through an N-(beta-aspartyl)-N-acetylglucosaminylamine bond and which are structurally heterogenous. After chymotryptic or pronase digestions, glycopeptides with five different glycan structures could be isolated. For three of them, the structure has been determined by the application of methanolysis, methylation analysis, hydrazinolysis/nitrous deamination, enzymatic cleavage and 1H-NMR spectroscopy at 360 MHz: Glycopeptides A and B: NeuAc(alpha 2-6)Gal(beta 1-4)GlcNAc(beta 1-2)Man(alpha 1-3)[NeuAc(alpha 2-6)Gal(beta 1-4)GlcNAc(beta 1-2)Man(alpha 1-6)]Man(beta 1-4)GlcNAc(beta-1-4)[Fuc(alpha 1-6)]GlcNAc(beta 1-)Asn; Glycopeptide C: NeuAc(alpha 2-6)(Gal(beta 1-4)GlcNAc(beta 1-2)Man(alpha 1-3)(Gal(beta 1-4)[Fuc(alpha 1-3)]GlcNAc(beta 1-2)Man(alpha 1-6))Man(beta 1-4)GlcNAc(beta 1-4)[Fuc(alpha 1-6)]GlcNAc(beta 1-)Asn. Glycopeptide D: NeuAc(alpha 2-6)Gal(beta 1-4)GlcNAc(beta 1-2)Man(alpha 1-3)[Gal(beta 1-4)GlcNAc(beta 1-2)Man(alpha 1-6)]Man(beta 1-4)Glc-NAc(beta 1-4)[Fuc(alpha 1-6)]GlcNAc(beta 1-)Asn. Two other glycopeptides were obtained in very low amount and possess more complex structures.
Early Chelation Therapy for Injected Pu-238 and Am-241 in the Rat: Comparison of 3,4,3-LIHOPO, DFO-HOPO, DTPA-DX, DTPA and DFOA (1993)

Chelating agents were tested for removal of simultaneously injected Pu-238 and Am-241 from the rat. The effectiveness of early single chelate injections of Pu-238 retention in tissues decreased in the order 3,4,3-LIHOPO > DFO-HOPO > DTPA > DTPA-DX, and for Am-241 in the order 3,4,3-LIHOPO > DTPA-DX > DTPA >> DFO-HOPO. DTPA-DX showed a special ability to remove Am-241 from the liver. Injected 3,4,3-LIHOPO decreased the contents of Pu-238 in bone and liver to 9 and 3%, respectively, of those in untreated controls. Corresponding values for Am-241 in bone and liver were 30 and 6%, respectively, which indicates that 3,4,3-LIHOPO (unlike DFO-HOPO) is not a plutonium-specific chelator. The effectiveness of prompt single oral treatment with 3,4,3-LIHOPO and DFO-HOPO in reducing retention of actinides was comparable with that of those chelators injected with 1 h delay and at one-third of the oral dose. When 3,4,3-LIHOPO was administered by continuous infusion, a superior effect was achieved with total chelate amounts only slightly exceeding that given as single injection. The retention of PU-238 and Am-241 in bones was reduced to < 5 and 10% of controls, respectively; the contents in the liver were < 2% of controls.
Antihyperglycaemic effect of 'Ilogen-Excel', an ayurvedic herbal formulation in streptozotocin-induced diabetes mellitus. (2007)

'Ilogen-Excel', an Ayurvedic herbal formulation is composed of eight medicinal plants (Curcuma longa, Strychnos potatorum, Salacia oblonga, Tinospora cordifolia, Vetivelia zizanioides, Coscinium fenestratum, Andrographis paniculata and Mimosa pudica). The present study evaluates the antihyperglycemic effect of 'Ilogen-Excel' in streptozotocin induced diabetic rats. Rats were rendered diabetic by streptozotocin (STZ) (45 mg/kg body weight). Oral administration of 'Ilogen-Excel' (50 mg/kg and 100 mg/kg) for 60 days resulted in significantly lowered levels of blood glucose and significantly increased levels of plasma insulin, hepatic glycogen and total hemoglobin. 'Ilogen-Excel' administration also decreased the levels of glycosylated hemoglobin, plasma thiobarbituric acid reactive substances, hydroperoxides, ceruloplasmin and vitamin E in diabetic rats. Plasma reduced glutathione and vitamin C were significantly elevated by oral administration of 'Ilogen-Excel'. Administration of insulin normalized all the biochemical parameters studied in diabetic rats. The effect at a dose of 100 mg/kg was more pronounced than 50 mg/kg and brought back all the parameters to near normal levels. Thus, our study shows the antihyperglycemic effects of 'Ilogen-Excel' in STZ-induced diabetic rats. Our study also shows that combined therapy is better than individual therapy.
Bowman-Birk inhibitor concentrate prevents atrophy, weakness, and oxidative stress in soleus muscle of hindlimb-unloaded mice (2006)

Antigravity muscles atrophy and weaken during prolonged mechanical unloading caused by bed rest or spaceflight. Unloading also induces oxidative stress in muscle, a putative cause of weakness. We tested the hypothesis that dietary supplementation with Bowman-Birk inhibitor concentrate (BBIC), a soy protein extract, would oppose these changes. Adult mice were fed a diet supplemented with 1% BBIC during hindlimb unloading for up to 12 days. Soleus muscles of mice fed the BBIC-supplemented diet weighed less, developed less force per cross-sectional area, and developed less total force after unloading than controls. BBIC supplementation was protective, blunting decrements in soleus muscle weight and force. Cytosolic oxidant activity was assessed using 2',7'-dichlorofluorescin diacetate. Oxidant activity increased in unloaded muscle, peaking at 3 days and remaining elevated through 12 days of unloading. Increases in oxidant activity correlated directly with loss of muscle mass and were abolished by BBIC supplementation. In vitro assays established that BBIC directly buffers reactive oxygen species and also inhibits serine protease activity. We conclude that dietary supplementation with BBIC protects skeletal muscle during prolonged unloading, promoting redox homeostasis in muscle fibers and blunting atrophy-induced weakness.
Multi-AUV based cooperative observations (2004)

In this paper, we propose a wired multi-AUV system and applications. AUVs are interconnected by a smart cable that contains fiber optics 3D positioning sensors. This cable connection enable to localization and communication of AUVs. Using this cable, we propose a hand-in-hand system (HS) for AUV localization and development to accomplish the given task. Experiments were carried out to demonstrate and confirm the efficiency of the proposed system.
Recording of Electrically Evoked Neural Activity and Bladder Pressure Responses in Awake Rats Chronically Implanted With a Pelvic Nerve Array (2020)

Bioelectronic medical devices are well established and widely used in the treatment of urological dysfunction. Approved targets include the sacral S3 spinal root and posterior tibial nerve, but an alternate target is the group of pelvic splanchnic nerves, as these contain sacral visceral sensory and autonomic motor pathways that coordinate storage and voiding functions of the bladder. Here, we developed a device suitable for long-term use in an awake rat model to study electrical neuromodulation of the pelvic nerve (homolog of the human pelvic splanchnic nerves). In male Sprague-Dawley rats, custom planar four-electrode arrays were implanted over the distal end of the pelvic nerve, close to the major pelvic ganglion. Electrically evoked compound action potentials (ECAPs) were reliably detected under anesthesia and in chronically implanted, awake rats up to 8 weeks post-surgery. ECAP waveforms showed three peaks, with latencies that suggested electrical stimulation activated several subpopulations of myelinated A-fiber and unmyelinated C-fiber axons. Chronic implantation of the array did not impact on voiding evoked in awake rats by continuous cystometry, where void parameters were comparable to those published in naïve rats. Electrical stimulation with chronically implanted arrays also induced two classes of bladder pressure responses detected by continuous flow cystometry in awake rats: voiding contractions and non-voiding contractions. No evidence of tissue pathology produced by chronically implanted arrays was detected by immunohistochemical visualization of markers for neuronal injury or noxious spinal cord activation. These results demonstrate a rat pelvic nerve electrode array that can be used for preclinical development of closed loop neuromodulation devices targeting the pelvic nerve as a therapy for neuro-urological dysfunction.
Aberrant over-expression of a forkhead family member, FOXO1A, in a brain tumor cell line (2007)

The CNS-PNET cell line, PER-453, expresses FOXO1A at very high levels relative to most normal and cancer cells from a broad range of tissues. The FOXO1A open reading frame is wild type in the PER-453 cell line and the abnormally high FOXO1A mRNA expression is not due to mutations affecting the 5'-UTR or proximal promoter. Over expression of FOXO1A may be the result of PER-453 specific epimutations or imbalances in regulatory factors acting at the promoter and/or 3'-UTR.
Behavior Insights for an Incentive-Based Active Demand Management Platform (2015)

Most current Travel Demand Management (TDM) programs such as vanpooling, ridesharing, or transit focus on managing travel demand of specific groups of commuters but are limited in effectively managing demand for automobile drivers, who are unable or unwilling to participate in such programs. This paper highlights results from a pilot field study conducted in a large west coast city experiencing major traffic congestion, and documents results of the use of an incentive-based active demand management (ADM) system focusing on automobile commuters. The system, called “Metropia,” predicts future traffic conditions, applies a proprietary routing algorithm to find time-dependent shortest paths for different departure times, and, based on user request, provides automobile travelers with multiple departure times and route choices. Each of these travel choices are assigned points values, with higher points (and thus more valuable rewards) available for travelling during off-peak times and less congested routes, and lower points available for peak traffic travel times. The goal of this ADM system is to improve traffic flow and commuter travel times citywide, alleviating heavily congested areas without the use of new roadway construction by incentivizing travelers to change their travel behavior and avoid traffic congestion. The level of rewards points available to users (commuters) by the system depends on the travelers’ behavioral change degree and their contributions to traffic congestion alleviation. This system was implemented in Los Angeles, Calif., USA, as a small scale pilot field study carried out beginning April 2013 and lasting for 10 weeks. Results from this field study show the system is able to accurately predict travel time with Relative Mean Absolute Error (RMAE) as low as 15.20%. Significant travel behavior changes were observed which validate the concept of using incentives to influence people's travel behavior. Furthermore, field study results show 20% travel time can be saved for people who changed their travel behavior.
Rapid and Sensitive Detection of Shigella spp. and Salmonella spp. by Multiple Endonuclease Restriction Real-Time Loop-Mediated Isothermal Amplification Technique (2015)

Shigella and Salmonella are frequently isolated from various food samples and can cause human gastroenteritis. Here, a novel multiple endonuclease restriction real-time loop-mediated isothermal amplification technology (MERT-LAMP) were successfully established and validated for simultaneous detection of Shigella strains and Salmonella strains in only a single reaction. Two sets of MERT-LAMP primers for 2 kinds of pathogens were designed from ipaH gene of Shigella spp. and invA gene of Salmonella spp., respectively. Under the constant condition at 63°C, the positive results were yielded in as short as 12 min with the genomic DNA extracted from the 19 Shigella strains and 14 Salmonella strains, and the target pathogens present in a sample could be simultaneously identified based on distinct fluorescence curves in real-time format. Accordingly, the multiplex detection assay significantly reduced effort, materials and reagents used, and amplification and differentiation were conducted at the same time, obviating the use of postdetection procedures. The analytical sensitivity of MERT-LAMP was found to be 62.5 and 125 fg DNA/reaction with genomic templates of Shigella strains and Salmonella strains, which was consist with normal LAMP assay, and at least 10- and 100-fold more sensitive than that of qPCR and conventional PCR approaches. The limit of detection of MERT-LAMP for Shigella strains and Salmonella strains detection in artificially contaminated milk samples was 5.8 and 6.4 CFU per vessel. In conclusion, the MERT-LAMP methodology described here demonstrated a potential and valuable means for simultaneous screening of Shigella and Salmonella in a wide variety of samples.
Cloning of an Apobec-1-binding Protein That Also Interacts with Apolipoprotein B mRNA and Evidence for Its Involvement in RNA Editing (1997)

Apolipoprotein (apo)B mRNA editing is mediated by a multiprotein editosome complex. Apobec-1 is the catalytic component of this complex, but other proteins involved in editing have not been identified. We used the yeast two-hybrid system to identify an apobec-1-interacting protein, ABBP-1. ABBP-1 contains 331 amino acid residues and is identical to a previously reported human type A/B hnRNP except for a 47-residue insertion at its C-terminal region. It contains typical RNP motifs at its N-terminal half and glycine-rich motifs in the C-terminal region. Northern blot analysis indicates that ABBP-1 mRNA is distributed in multiple human tissues. By deletion analysis, we mapped the apobec-1-binding region to the glycine-rich domain. ABBP-1 also binds to apoB mRNA transcripts around the editing site and can be UV-cross-linked to them in vitro. Immnodepletion of ABBP-1 from an active apoB mRNA editing tissue extract inhibits its editing activity. Down-regulation of ABBP-1 in an apobec-1-expressing HepG2 cell line by transfection with an antisense ABBP-1 cDNA construct leads to inhibition of endogenous apoB mRNA editing. We conclude that ABBP-1 is an apobec-1-interacting protein that may play an important role in apoB mRNA editing.
Resolving ambiguity for cross-language retrieval (1998)

One of the main hurdles to improved CLIR effectiveness is resolving ambiguity associated with translation. Availability of resources is also a problem. First we present a technique based on co-occurrence statistics from unlinked corpora which can be used to reduce the ambiguity associated with phrasal and term translation.
Reduced deoxyribonuclease enzyme activity in response to high postinjury mitochondrial DNA concentration provides a therapeutic target for Systemic Inflammatory Response Syndrome (2018)

Prognostic/Epidemiological, level II.
Social marketing: two views, two opportunities. (1984)

Social marketing can refer to the promotion of either a product or an idea. The 1st approach includes the sale of a socially beneficial product such as condoms or oral rehydration salts. Although the product is generally subsidized to keep costs within the reach of consumers, the actual sale is considered critical because of its role in ensuring consumer motivation, increasing internal efficiency, and facilitating longterm self-sufficiency of the program. The 2nd approach stresses the promotion of socially beneficial ideas and practices rather than products, e.g. breastfeeding. Social products differ from commercial products in several important ways: they are more complex, often more controversial, less immediately satisfying to the consumer, require more spectacular results, and are aimed at an audience with fewer resources than most consumers of commercial products. In addition, there are many factors that make social marketing more difficult difficult than marketing in the commercial sector. Social programs have less control over the delivery system and consumer research is more complicated. Despite these differences, both social and commerical marketing are organized aroung the same 4 qualities: product, price, place, and promotion. The product must be configured to maximized consumer acceptance and use. Hidden costs must be considered. There must be an adequate distribution and supply system to ensure easy availability of the product. Finally, the product must be promoted through different communication channels by a wide array of techniques. Attention to these 4 factors can significantly enhance social service delivery of both products and ideas.
Using handheld devices to sup port augmented reality-based maintenance and assembly tasks (2015)

This paper studies the opportunities coming from the use of consumer devices like smartphones and tablets to perform maintenance and assembly procedures with Augmented Reality (AR). Pros and cons are evaluated by comparing completion times and errors made while executing a maintenance procedure with an AR-based tool and paper-based instructions.
CPAP Pressure Requirements for Obstructive Sleep Apnea Patients at Varying Altitudes (2010)

For obstructive sleep apnea patients living at altitude, changes in elevation between 10,100 ft (3075 m) and sea level do not significantly alter absolute CPAP pressure requirements.