gebhart/patrepeval huggingface dataset:
A Systems Biology Approach for the Investigation of the Heparin/Heparan Sulfate Interactome (2011)

A large body of evidence supports the involvement of heparan sulfate (HS) proteoglycans in physiological processes such as development and diseases including cancer and neurodegenerative disorders. The role of HS emerges from its ability to interact and regulate the activity of a vast number of extracellular proteins including growth factors and extracellular matrix components. A global view on how protein-HS interactions influence the extracellular proteome and, consequently, cell function is currently lacking. Here, we systematically investigate the functional and structural properties that characterize HS-interacting proteins and the network they form. We collected 435 human proteins interacting with HS or the structurally related heparin by integrating literature-derived and affinity proteomics data. We used this data set to identify the topological features that distinguish the heparin/HS-interacting network from the rest of the extracellular proteome and to analyze the enrichment of gene ontology terms, pathways, and domain families in heparin/HS-binding proteins. Our analysis revealed that heparin/HS-binding proteins form a highly interconnected network, which is functionally linked to physiological and pathological processes that are characteristic of higher organisms. Therefore, we then investigated the existence of a correlation between the expansion of domain families characteristic of the heparin/HS interactome and the increase in biological complexity in the metazoan lineage. A strong positive correlation between the expansion of the heparin/HS interactome and biosynthetic machinery and organism complexity emerged. The evolutionary role of HS was reinforced by the presence of a rudimentary HS biosynthetic machinery in a unicellular organism at the root of the metazoan lineage.
Biological properties of poliovirus encapsulated in lipid vesicles: antibody resistance and infectivity in virus-resistant cells. (1977)

We present evidence that poliovirus can be encapsulated in synthetic large phospholipid vesicles. The virus associated with the vesicles is found to be (i) resistant to antiserum against poliovirus and (ii) infectious for cells that are normally resistant to virus infection because of a membrane restriction. Our interpretation of these results is that the virus is entrapped in the interior aqueous space of the vesicles and that this vesicle-associated virus is introduced directly into the cytoplasm of the cells via fusion of the vesicles with the cellular plasma membrane, bypassing the surface receptor-mediated restriction.
Guidelines for noninvasive ventilation in acute respiratory failure (2006)

Background The term non-invasive ventilation (NIV) refers to the application of artificial ventilation without any conduit access to the airways i.e., without an endotracheal or tracheostomy tube. Recently, NIV has assumed a prominent role in the management of acute respiratory failure. By avoiding endotracheal intubation, NIV prevents complications associated with invasive ventilation like airway problems, nosocomial pneumonia (21%) and sinusitis (5-25%).
An automatic word spotting system for conversational speech (2005)

Sperry Univac is developing a linguistically oriented system for locating important words in conversational speech. The system uses acoustic, prosodic, and phonetic analyses to produce a phonetic description of the incoming speech. Next, phonetic dictionary representations of the keywords to be found are compared to all portions of the phonetic analysis. High scoring matches are then verified by aligning prestored spectral patterns with the spectral information found during analysis, and resulting good matches are announced as likely keyword occurrences. Current results are presented for this system, which is being developed and tested on bandlimited, conversational speech from a large, diverse speaker population.
Direct Pathway from Early/Recycling Endosomes to the Golgi Apparatus Revealed through the Study of Shiga Toxin B-fragment Transport (1998)

Shiga toxin and other toxins of this family can escape the endocytic pathway and reach the Golgi apparatus. To synchronize endosome to Golgi transport, Shiga toxin B-fragment was internalized into HeLa cells at low temperatures. Under these conditions, the protein partitioned away from markers destined for the late endocytic pathway and colocalized extensively with cointernalized transferrin. Upon subsequent incubation at 37 degreesC, ultrastructural studies on cryosections failed to detect B-fragment-specific label in multivesicular or multilamellar late endosomes, suggesting that the protein bypassed the late endocytic pathway on its way to the Golgi apparatus. This hypothesis was further supported by the rapid kinetics of B-fragment transport, as determined by quantitative confocal microscopy on living cells and by B-fragment sulfation analysis, and by the observation that actin- depolymerizing and pH-neutralizing drugs that modulate vesicular transport in the late endocytic pathway had no effect on B-fragment accumulation in the Golgi apparatus. B-fragment sorting at the level of early/recycling endosomes seemed to involve vesicular coats, since brefeldin A treatment led to B-fragment accumulation in transferrin receptor-containing membrane tubules, and since B-fragment colocalized with adaptor protein type 1 clathrin coat components on early/recycling endosomes. Thus, we hypothesize that Shiga toxin B-fragment is transported directly from early/recycling endosomes to the Golgi apparatus. This pathway may also be used by cellular proteins, as deduced from our finding that TGN38 colocalized with the B-fragment on its transport from the plasma membrane to the TGN.
Porous Metal−Organic Truncated Octahedron Constructed from Paddle-Wheel Squares and Terthiophene Links (2005)

A metal-organic truncated octahedron (termed MOP-28) has been constructed from six rigid square-shaped Cu2(CO2)4 paddle-wheel building units and twelve 2,2':5',2' '-terthiophene-5,5' '-dicarboxylate (TTDC) linkers. TTDC linker in the cis,cis conformation provides the critical 90 degrees linkage for this unique construction. The porous structure of MOP-28 is maintained even after the removal of guest species, as evidenced by this compound's nitrogen sorption isotherm of Type I characteristics and unprecedented surface area (Langmuir surface area 1100 m2/g, BET surface area 914 m2/g) among materials composed of discrete molecules.
The Power Presenter: Technique, Style, and Strategy from America's Top Speaking Coach (2009)

PREFACE: The Wrong Way and the Right Way to Coach Presentations. Case Study: Dizzy Gillespie. INTRODUCTION: How Speaking Style and Delivery Can Raise the Value of an IPO. Case Studies: Cisco Systems Isilon Systems Two Weeks of an IPO Road Show RetailRoadshow.com CHAPTER 1: Your Actions Speak Louder than Your Words. Case Studies: Ronald Reagan Dr. Sacks' Aphasic Patients Nikita Khrushchev Marcel Marceau. CHAPTER 2: The Crucial Task: Creating Audience Empathy. Case Studies: The Deer in the Headlights Revisited Shocking British Couples Italian Laboratory Monkeys Robert Krulwich Bob Dole Gray Davis versus Arnold Schwarzenegger Barack Obama. CHAPTER 3: The Butterflies in Your Stomach. Case Study: September Morn. CHAPTER 4: How to Prepare Your Content. Case Studies: Will Poole and Jeff Raikes, Microsoft Patrick McGovern, IDG. CHAPTER 5: You Can Be a Power Presenter-Charisma Not Required. Case Studies: The Transformations of George W. Bush and Bill Clinton. CHAPTER 6: The Mental Method of Presenting: Make the Butterflies Fly in Formation. Case Studies: The Actors Studio Barack Obama versus Hillary Rodham Clinton Libby Dole Carly Simon Marya McCabe, Microsoft Lawrence Steinman, MD The Squinting Woman. CHAPTER 7: Learn to Speak with Your Body Language. Case Studies: Joe Moglia, TD Ameritrade Marshall Klaus, MD Sir Isaac Newton Generals Richard Neal and H. Norman Schwarzkopf The Kennedy-Nixon Debate. CHAPTER 8: Control Your Cadence. Case Studies: The Frenchman Who Paused Jazz Artists Frank Sinatra, Ella Fitzgerald, Amanda Carr, and Dizzy Gillespie General Israel Putnam Ludwig van Beethoven Dr. Krzysztof Izdebski and Claude Steinberg, Pacific Voice and Speech Foundation Leonard Bernstein Lorin Maazel The Further Transformation of George W. Bush. CHAPTER 9: Masters of the Game. Case Studies: Sir Winston Churchill John F. Kennedy Reverend Martin Luther King, Jr. Reverend Billy Graham Ronald Reagan Barack Obama. CHAPTER 10: What Every Speaker Can Learn from Barack Obama. Case Studies: Abraham Lincoln John F. Kennedy Sir Winston Churchill Reverend Martin Luther King, Jr. Ronald Reagan John McCain. CHAPTER 11: Graphics Synchronization. Case Studies: Federico Fellini Olivier Fontana, Microsoft Bill Jasper, Dolby Laboratories Goldman Sachs. CHAPTER 12: Graphics and Narrative. Case Studies: Leslie Culbertson, Intel Katherine Crothall, PhD, Animas Eric Tardif, Piper Jaffray Abraham Lincoln. CHAPTER 13: The Power Presentations Pyramid. Case Study: The NAFTA Debate: Al Gore vs. Ross Perot. CHAPTER 14: Coda-Ending with the Beginning. Case Studies: Ronald Reagan and Joe Moglia Reprised Cindy Burgdorf, SanDisk. ACKNOWLEDGMENTS. NOTES. INDEX.
Development of pro-angiogenic engineered transcription factors for the treatment of cardiovascular disease (2004)

Gene therapies that use engineered transcription factors to regulate a patient's own endogenous genetic loci offer several advantages over cDNA-based approaches, including the capacity to upregulate all splice variants of a therapeutic gene. Currently, two engineered transcription factors are being developed for use in gene-mediated revascularisation therapies of cardiovascular disease. Both proteins target a powerful, constitutive transcriptional activation module to a defined sequence in the promoter region of vascular endothelial growth factor-A via linkage to an appropriately specific DNA-binding domain, either the basic helix-loop-helix motif of hypoxia-inducible factor-1alpha (HIF-1alpha) or a designed zinc finger protein. Both factors activate the expression of vascular endothelial growth factor-A in cellular studies and induce angiogenesis in animal models of cardiovascular disease. Phase I studies are underway for the HIF-1alpha-based factor and are expected to commence for the zinc finger protein-based factor by the second half of 2004.
Analysis of the Evolution of PIR Foams in the Context of the Phase Out of HCFCs (2003)

PIR foams are known for their outstanding fire properties and for their good insulation performances. The fire behavior can be attributed to the aromatic structure of the isocyanurate ring and to the nonflammability of the blowing agent that is used nowadays. For environmental reasons, HCFC-141b will have to be phased out as of 01.01.2003 for the production of PIR laminates boards, in Europe and in the United States. This evolution represents a challenge for the producers as they need to find a high performance alternative in a relatively short period of time. As a major requirement, this alternative will have to maintain the properties of the PIR foams, notably the fire behavior and the k-value at a high quality level. Several blowing agent alternatives have been presented, and some of them have already been implemented in production plants. Among them, pentane is seen as a candidate for economical reasons, but because of its high flammability, its use shows some limitations. The nonflammable alternative HFC-365mfc/HFC-227ea has proven to be an interesting alternative to obtain a good insulation value and good fire properties. Besides, the existence of azeotropic blends between HFC-365mfc and the pentane isomers increases the degree of freedom of the system and makes the optimization process easier. When using the right combination of blowing agent, it is possible to reach an interesting compromise between the insulation characteristics, the fire performance and the cost of the system. An analysis of properties of PIR foams produced with the several alternatives will be presented in this paper.
Influence of film stress and thermal oxidation on the generation of dislocations in silicon (1978)

The experimental data presented here show that the generation of dislocations in Si along Si3N4 edges is due to the cumulative effect of the Si3N4 stress field near the nitride edge and to the point defects produced during thermal oxidation. Within our experimental range, the stress along the Si3N4 edges alone is not sufficient to generate dislocations in silicon. We have determined a critical ratio of Si3N4 thickness to SiO2 thickness which does not lead to the generation of dislocations.
Getting More from Less (2002)

We describe two novel sequence similarity search algorithms, FASTS and FASTF, that use multiple short peptide sequences to identify homologous sequences in protein or DNA databases. FASTS searches with peptide sequences of unknown order, as obtained by mass spectrometry-based sequencing, evaluating all possible arrangements of the peptides. FASTF searches with mixed peptide sequences, as generated by Edman sequencing of unseparated mixtures of peptides. FASTF deconvolutes the mixture, using a greedy heuristic that allows rapid identification of high scoring alignments while reducing the total number of explored alternatives. Both algorithms use the heuristic FASTA comparison strategy to accelerate the search but use alignment probability, rather than similarity score, as the criterion for alignment optimality. Statistical estimates are calculated using an empirical correction to a theoretical probability. These calculated estimates were accurate within a factor of 10 for FASTS and 1000 for FASTF on our test dataset. FASTS requires only 15-20 total residues in three or four peptides to robustly identify homologues sharing 50% or greater protein sequence identity. FASTF requires about 25% more sequence data than FASTS for equivalent sensitivity, but additional sequence data are usually available from mixed Edman experiments. Thus, both algorithms can identify homologues that diverged 100 to 500 million years ago, allowing proteomic identification from organisms whose genomes have not been sequenced.
<i>Helicobacter pylori,</i> Peptic Ulcer Disease and Inhibition of Gastric Acid Secretion (1992)

Recent studies have been reviewed to establish the possible importance of the interaction between Helicobacter pylori infection and gastric acid secretion. H. pylori infection results in increased gastrin release, but this does not lead to gastric acid hypersecretion and gastrin normalizes after eradication of the infection. An optimal, well-tolerated treatment strategy against H. pylori infection has not yet been clearly defined. One potentially useful approach may be to improve the antibacterial efficacy of antibiotics by effectively regulating gastric acidity. H2-receptor antagonists have no effect against H. pylori infection, while omeprazole (an acid pump inhibitor) appears to have a bacteriostatic action. Combination therapy with omeprazole and amoxycillin has been found to eradicate H. pylori in 50-80% of patients with duodenal ulcer, leading to a significant reduction in ulcer recurrence.
Applications of 3D spherical transforms to personalization of head-related transfer functions (2016)

Head-related transfer functions (HRTFs) depend on the shape of the human head and ears, motivating HRTF personalization methods that detect and exploit morphological similarities between subjects in an HRTF database and a new user. Prior work determined similarity from sets of morphological parameters. Here we propose a non-parametric morphological similarity based on a harmonic expansion of head scans. Two 3D spherical transforms are explored for this task, and an appropriate shape similarity metric is defined. A case study focusing on personalisation of interaural time differences (ITDs) is conducted by applying this similarity metric on a database of 3D head scans.
Treatment of Advanced Pancreatic Carcinoma with 90Y-Clivatuzumab Tetraxetan: A Phase I Single-Dose Escalation Trial (2011)

(90)Y-Clivatuzumab tetraxetan was well tolerated with manageable hematologic toxicity at the maximal tolerated (90)Y dose, and is a potential new therapeutic for advanced pancreatic cancer.
Avidity and Bactericidal Activity of Antibody Elicited by Different Haemophilus influenzae Type b Conjugate Vaccines (1992)

Oligo-CRM and PRP-T conjugate vaccines elicit higher avidity antibody than PRP-OMPC, and high-avidity antibody is more potent than low-avidity antibody in serum bactericidal assays. Consideration should be given to including measurement of antibody avidity in assessment of new vaccines since avidity may affect the ability of serum antibody to confer protection against disease.
Sulfur volatiles from Allium spp. affect Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae), response to citrus volatiles (2010)

The Asian citrus psyllid, Diaphorina citri Kuwayama, vectors Candidatus Liberibacter asiaticus (Las) and Candidatus Liberibacter americanus (Lam), the presumed causal agents of huanglongbing. D. citri generally rely on olfaction and vision for detection of host cues. Plant volatiles from Allium spp. (Alliaceae) are known to repel several arthropod species. We examined the effect of garlic chive (A. tuberosum Rottl.) and wild onion (A. canadense L.) volatiles on D. citri behaviour in a two-port divided T-olfactometer. Citrus leaf volatiles attracted significantly more D. citri adults than clean air. Volatiles from crushed garlic chive leaves, garlic chive essential oil, garlic chive plants, wild onion plants and crushed wild onion leaves all repelled D. citri adults when compared with clean air, with the first two being significantly more repellent than the others. However, when tested with citrus volatiles, only crushed garlic chive leaves and garlic chive essential oil were repellent, and crushed wild onions leaves were not. Analysis of the headspace components of crushed garlic chive leaves and garlic chive essential oil by gas chromatography-mass spectrometry revealed that monosulfides, disulfides and trisulfides were the primary sulfur volatiles present. In general, trisulfides (dimethyl trisulfide) inhibited the response of D. citri to citrus volatiles more than disulfides (dimethyl disulfide, allyl methyl disulfide, allyl disulfide). Monosulfides did not affect the behaviour of D. citri adults. A blend of dimethyl trisulfide and dimethyl disulfide in 1:1 ratio showed an additive effect on inhibition of D. citri response to citrus volatiles. The plant volatiles from Allium spp. did not affect the behaviour of the D. citri ecto-parasitoid Tamarixia radiata (Waterston). Thus, Allium spp. or the tri- and di-sulphides could be integrated into management programmes for D. citri without affecting natural enemies.
Mechanical Strain Suppresses Inducible Nitric-oxide Synthase in Cardiac Myocytes (1998)

We investigated the effects of precisely controlled mechanical strain on nitric-oxide synthase activity in cultured neonatal rat cardiac myocytes. Incubation of cardiac myocytes for 24 h with 4 ng/ml interleukin-1beta and 100 units/ml interferon-gamma stimulated an increase in nitric oxide production, inducible nitric-oxide synthase (iNOS) mRNA, and iNOS protein. Mechanical strain suppressed nitric oxide production, iNOS mRNA, and iNOS protein stimulated by cytokines in an amplitude-dependent manner. Losartan (1 microM), an angiotensin II type 1 receptor antagonist, weakly inhibited the effect of strain, suggesting that paracrine angiotensin II is not the mediator of the strain effect. In addition, cycloheximide (10 microM), a protein synthesis inhibitor, inhibited the effect of strain by 46%. Transforming growth factor-beta (1 ng/ml) suppressed iNOS mRNA expression, but anti-transforming growth factor-beta antibody (30 microg/ml) did not block the effect of strain. In contrast, staurosporine (100 nM; a nonselective protein kinase inhibitor), calphostin C (1 microM; a selective protein kinase C inhibitor), and pretreatment with phorbol 12-myristate 13-acetate abolished the effect of strain. Genistein (100 microM), a tyrosine kinase inhibitor, partially inhibited the effect of strain. Thus, cyclic mechanical deformation suppresses cytokine-induced iNOS expression in cardiac myocytes, and this effect is mediated at least partially via activation of protein kinase C.
TESLA Coil Research (1992)

High repetition rate Tesla type high average power resonance transformers are considered in detail. Issues of RF power processing and apparatus scalability are addressed both analytically and experimentally. It has been found that, by employing appropriate switching durations and trapping energy in transmission line resonators, it is possible to increase the output of Tesla type resonance transformers by more than an order of magnitude over the conventional k = 0.6 optimum design . The voltage step-up phenomenon is attributed to standing waves, and has been demonstrated over a frequency range that varies by more than a factor of 1,000, from VLF through VHF. While some propose using resonance transformers, because of their high average power capability, to repetitively pulse relativistic electron beams (REBs) in open air, it appears that REBs are too unstable and REB diodes are presently too fragile for practical small arms weaponry. Our investigation and experiments have led to a focused plasma discharge alternative to beam composed of fundamental particles. The technique employs a particulated macroscopic beam. This appears to be a robust directable discharge mechanism which may overcome the fragility issue for REB's. Photographic documentation and a physical explanation for the directed discharge phenomena are presented.
Randomized Phase II Trial of Erlotinib Versus Temozolomide or Carmustine in Recurrent Glioblastoma: EORTC Brain Tumor Group Study 26034 (2009)

Erlotinib has insufficient single-agent activity in unselected GBM. No clear biomarker associated with improved outcome to erlotinib was identified.
Use of Wallstents for hemodialysis access-related venous stenoses and occlusions untreatable with balloon angioplasty. (1995)

Wallstents are safe to deploy for dialysis access. Wallstents are useful for treating lesions that fail angioplasty and catheter-related central venous occlusions.
Integration of interventional MRI with computer-assisted surgery (2001)

Interventional MRI (IMRI) has entered into a new stage in which computer-based techniques play an increasing role in planning, monitoring, and controlling the procedures. The use of interactive imaging, navigational image guidance techniques, and image processing methods is demonstrated in various applications. The integration of intraoperative MRI guidance and computer-assisted surgery will greatly accelerate the clinical utility of image-guided therapy in general and interventional MRI in particular. J. Magn. Reson. Imaging 2001;13:69-77.