gebhart/patrepeval huggingface dataset:
Self-Assembly of Hydrophobin and Hydrophobin/Surfactant Mixtures in Aqueous Solution (2011)

The self-assembly of the protein hydrophobin, HFBII, and its self-assembly with cationic, anionic, and nonionic surfactants hexadecylterimethyl ammonium bromide, CTAB, sodium dodecyl sulfate, SDS, and hexaethylene monododecyl ether, C(12)E(6), in aqueous solution have been studied by small-angle neutron scattering, SANS. HFBII self-assembles in solution as small globular aggregates, consistent with the formation of trimers or tetramers. Its self-assembly is not substantially affected by the pH or electrolytes. In the presence of CTAB, SDS, or C(12)E(6), HFBII/surfactant complexes are formed. The structure of the HFBII/surfactant complexes has been identified using contrast variation and is in the form of HFBII molecules bound to the outer surface of globular surfactant micelles. The binding of HFBII decreases the surfactant micelle aggregation number for increasing HFBII concentration in solution, and the number of hydrophobin molecules bound/micelle increases.
Web-based configuration assistants (1998)

Configuration assistants are tools for guiding the final user in simple configuration tasks, such as product assembling and customization or study plans generation. For their wide availability, web-based configuration assistants are valuable in fields such as electronic commerce and information services. We describe a general approach for building web-based configuration assistants: from a high-level description of the configuration constraints and of the basic items, given in a declarative language, the hypertext files for user guidance and the Java code for constraint checking are generated. We claim that the general approach of process-oriented configuration, where the user is guided through the configuration process by an explanatory hypertext, as opposed to product-oriented configuration, where one starts from a high-level description of the product of the configuration, is better suited for many application domains.
Taverna: lessons in creating a workflow environment for the life sciences (2005)

Abstract Life sciences research is based on individuals, often with diverse skills, assembled into research groups. These groups use their specialist expertise to address scientific problems. The in silico experiments undertaken by these research groups can be represented as workflows involving the co‐ordinated use of analysis programs and information repositories that may be globally distributed. With regards to Grid computing, the requirements relate to the sharing of analysis and information resources rather than sharing computational power. The my Grid project has developed the Taverna Workbench for the composition and execution of workflows for the life sciences community. This experience paper describes lessons learnt during the development of Taverna. A common theme is the importance of understanding how workflows fit into the scientists' experimental context. The lessons reflect an evolving understanding of life scientists' requirements on a workflow environment, which is relevant to other areas of data intensive and exploratory science. Copyright © 2005 John Wiley &amp; Sons, Ltd.
The LuxS family of bacterial autoinducers: biosynthesis of a novel quorum‐sensing signal molecule (2001)

Many bacteria control gene expression in response to cell population density, and this phenomenon is called quorum sensing. In Gram-negative bacteria, quorum sensing typically involves the production, release and detection of acylated homoserine lactone signalling molecules called autoinducers. Vibrio harveyi, a Gram-negative bioluminescent marine bacterium, regulates light production in response to two distinct autoinducers (AI-1 and AI-2). AI-1 is a homoserine lactone. The structure of AI-2 is not known. We have suggested previously that V. harveyi uses AI-1 for intraspecies communication and AI-2 for interspecies communication. Consistent with this idea, we have shown that many species of Gram-negative and Gram-positive bacteria produce AI-2 and, in every case, production of AI-2 is dependent on the function encoded by the luxS gene. We show here that LuxS is the AI-2 synthase and that AI-2 is produced from S-adenosylmethionine in three enzymatic steps. The substrate for LuxS is S-ribosylhomocysteine, which is cleaved to form two products, one of which is homocysteine, and the other is AI-2. In this report, we also provide evidence that the biosynthetic pathway and biochemical intermediates in AI-2 biosynthesis are identical in Escherichia coli, Salmonella typhimurium, V. harveyi, Vibrio cholerae and Enterococcus faecalis. This result suggests that, unlike quorum sensing via the family of related homoserine lactone autoinducers, AI-2 is a unique, 'universal' signal that could be used by a variety of bacteria for communication among and between species.
[Value of transesophageal echocardiography in the cardiovascular assessment of an ischemic cerebral accident of suspected embolic origin]. (1994)

Transoesophageal echocardiography (TOE) is a new modality of cardiac investigation allowing examination of cardiac structures and anomalies previously inaccessible to ultrasound. TOE is performed under local anaesthesia after fasting the subject for more than 4 hours and after premedication when the patient is admitted to hospital. In the assessment of an ischaemic cerebral vascular accident, TOE may reveal potential sources of emboli such as intracavitary thrombi and tumours (left atrium and left atrial appendage), atherosclerosis of the aortic arch, vegetations. Certain indirect causes may also be more clearly identified: aneurysm of the interatrial septum, patent foramen ovale for which the causal relationship is more difficult to establish. Intra-atrial blood stasis ("spontaneous echo contrast") is perfectly analysed in the form of intra-atrial "smoke" observed in the presence of atrial dilatation, particularly in the presence of atrial fibrillation and mitral valve obstruction (mitral stenosis, valve prosthesis). The indication for TOE in this context is currently under evaluation, particularly in young patients. It is routinely indicated in patients with known heart disease when peripheral embolism is suspected, looking for intracavitary thrombosis, generally not seen on transthoracic echocardiography.
Metabolic Biofouling of Glucose Sensors in Vivo: Role of Tissue Microhemorrhages (2011)

These results support our hypothesis that tissue hemorrhage and resulting blood clots near the sensor can result in lowered local blood glucose concentrations due to metabolism of glucose by the clot. The lowered local blood glucose concentration led to low glucose readings from the still functioning sensor that did not reflect the systemic glucose level.
Corporate Debt Value, Bond Covenants, and Optimal Capital Structure (1994)

ABSTRACT This article examines corporate debt values and capital structure in a unified analytical framework. It derives closed‐form results for the value of long‐term risky debt and yield spreads, and for optimal capital structure, when firm asset value follows a diffusion process with constant volatility. Debt values and optimal leverage are explicitly linked to firm risk, taxes, bankruptcy costs, risk‐free interest rates, payout rates, and bond covenants. The results elucidate the different behavior of junk bonds versus investment‐grade bonds, and aspects of asset substitution, debt repurchase, and debt renegotiation.
The t(X;1)(p11.2;q21.2) translocation in papillary renal cell carcinoma fuses a novel gene PRCC to the TFE3 transcription factor gene (1996)

The specific chromosomal translocation t(X;1)(p11.2;q21.2) has been observed in human papillary renal cell carcinomas. In this study we demonstrated that this translocation results in the fusion of a novel gene designated PRCC at 1q21.2 to the TFE3 gene at Xp11.2. TFE3 encodes a member of the basic helix-loop-helix (bHLH) family of transcription factors originally identified by its ability to bind to microE3 elements in the immunoglobin heavy chain intronic enhancer. The translocation is predicted to result in the fusion of the N-terminal region of the PRCC protein, which includes a proline-rich domain, to the entire TFE3 protein. Notably the generation of the chimaeric PRCC-TFE3 gene appears to be accompanied by complete loss of normal TFE3 transcripts. This work establishes that the disruption of transcriptional control by chromosomal translocation is important in the development of kidney carcinoma in addition to its previously established role in the aetiology of sarcomas and leukaemias.
Cancellation of non-conservative scattering forces in optical traps by counter-propagating beams (2015)

Non-conservative forces in optical tweezers generate undesirable behavior, such as particle loss due to radiation pressure and the preclusion of the thermodynamic equilibrium. Here, we rigorously derive criteria for the elimination of non-conservative forces, and describe how these criteria can be met by a large class of counter-propagating, focused optical beams.
Control of peripheral T‐cell tolerance and autoimmunity via the CTLA‐4 and PD‐1 pathways (2008)

Classically, the CD28/cytotoxic T-lymphocyte antigen-4 (CTLA-4) and B7 families of cell surface molecules regulate complex signaling pathways that profoundly affect T-cell responses. The recent identification and characterization of additional CD28 and B7 family members including programmed death-1 (PD-1), programmed death ligand-1 (PD-L1) (B7-H1), and PD-L2 (B7-DC) has added to the complexity and greater appreciation of how surface molecules control T-cell activation and peripheral tolerance. CD28/B7 interactions mediate co-stimulation and significantly enhance peripheral T-cell responses. CTLA-4, in contrast, interacting with the same B7 molecules, results in decreased T-lymphocyte activity and regulates the immune response. Similarly, PD-1 interactions with PD-L1 and PD-L2 downmodulate T-cell immune responses. Despite these similarities, the regulatory roles of the CTLA-4 and PD-1 pathways are distinct. This may be due, at least in part, to the differential expression patterns of the CTLA-4 and PD-1 ligands both temporally and spatially. This article examines the role of CTLA-4 and PD-1 in limiting autoreactivity and establishing peripheral self-tolerance with the hypothesis that CTLA-4 signals are required early in the lymph node during initiation of an immune response and PD-1 pathways act late at the tissue sites to limit T-cell activity.
Iron availability is transiently improved by intravenous iron medication in patients on chronic hemodialysis. (1995)

Iron deficiency is common in hemodialysis patients, particularly if they are on recombinant human erythropoietin (rHuEPO) therapy. Ten anemic patients (hemoglobin concentration 89 +/- 2.2 g/l, mean +/- SEM) on hemodialysis with either storage (serum-ferritin < 60 mg/l) and/or functional (S-transferrin saturation < or = 17%) iron deficiency were followed for 5 weeks. During the first 3 weeks they were given 100 mg of iron dextran on 10 consecutive dialysis sessions. Half of the patients were concomitantly treated with rHuEPO. Iron therapy resulted in a rapid elevation in serum transferrin iron saturation from 11 +/- 1.5% to 80 +/- 7.2% (p < 0.0001), but it decreased to pre-treatment levels within 2 weeks after discontinuation of iron therapy. Serum ferritin concentration increased from 157 +/- 73 mg/l to 434 +/- 105 mg/l during iron therapy (p < 0.0001). In spite of this only 4 patients (2 rHuEPO treated) responded and had a hemoglobin increment > 10 g/l. In the whole group serum transferrin receptor (TfR) levels remained stable, but increased after the cessation of iron dextran only in the rHuEPO treated patients (p < 0.01). In the responders the TfR levels were higher during iron therapy than in the nonresponders (p < 0.02). In an attempt to explain the resistance to iron therapy, serum concentrations of C-reactive protein (CRP), tumor necrosis factor-alpha (TNF-alpha) and interleukin-1b (IL-1b) were also analyzed.(ABSTRACT TRUNCATED AT 250 WORDS)
Ferric carboxymaltose-induced hypophosphataemia after kidney transplantation. (2017)

Administration of a single dose of FCM may induce transient and mostly asymptomatic renal phosphate wasting and hypophosphataemia in kidney transplant recipients. This appears to be explained by an increase in FGF-23 concentration.
Interactive pen-and-ink illustration (1994)

We present an interactive system for creating pen-and-ink illustrations. The system uses stroke textures—collections of strokes arranged in different patterns—to generate texture and tone. The user “paints” with a desired stroke texture to achieve a desired tone, and the computer draws all of the individual strokes.
Single-channel mixed speech recognition using deep neural networks (2014)

In this work, we study the problem of single-channel mixed speech recognition using deep neural networks (DNNs). Using a multi-style training strategy on artificially mixed speech data, we investigate several different training setups that enable the DNN to generalize to corresponding similar patterns in the test data. We also introduce a WFST-based two-talker decoder to work with the trained DNNs. Experiments on the 2006 speech separation and recognition challenge task demonstrate that the proposed DNN-based system has remarkable noise robustness to the interference of a competing speaker. The best setup of our proposed systems achieves an overall WER of 19.7% which improves upon the results obtained by the state-of-the-art IBM superhuman system by 1.9% absolute, with fewer assumptions and lower computational complexity.
Targeted Intracellular Delivery of Antisense Oligonucleotides via Conjugation with Small-Molecule Ligands (2010)

Selective delivery of antisense or siRNA oligonucleotides to cells and tissues via receptor-mediated endocytosis is becoming an important approach for oligonucleotide-based pharmacology. In most cases receptor targeting has been attained using antibodies or peptide-type ligands. Thus, there are few examples of delivering oligonucleotides using the plethora of small-molecule receptor-specific ligands that currently exist. In this report we describe a facile approach to the generation of mono- and multivalent conjugates of oligonucleotides with small-molecule ligands. Using the sigma-receptor ligand anisamide as an example, we describe conversion of the ligand to a phosphoramidite and direct incorporation of this moiety into the oligonucleotide by solid-phase DNA synthesis. We generated mono- and trivalent conjugates of anisamide with a splice switching antisense oligonucleotide (SSO) and tested their ability to modify splicing of a reporter gene (luciferase) in tumor cells in culture. The trivalent anisamide-SSO conjugate displayed enhanced cellular uptake and was markedly more effective than an unconjugated SSO or the monovalent conjugate in modifying splicing of the reporter. Significant biological effects were attained in the sub-100 nM concentration range.
Transfer of the octopine T-DNA segment to plant cells mediated by different types of Agrobacterium tumor- or root-inducing plasmids: generality of virulence systems (1984)

Genetic complementation studies demonstrated that the transfer to plant cells of the octopine T-DNA, entirely present as the only part of the tumor-inducing (Ti) plasmid on the plasmid pAL1050, was effected by the virulence systems from related plasmids, viz. the nopaline Ti plasmid pTiC58, the limited host range plasmid pTiAg57, and the root-inducing (Ri) plasmid pRi1855. Rhizobium symbiosis plasmids were not capable of effecting the introduction of pAL1050 into plant cells.
Effect of Genome Size on AAV Vector Packaging (2009)

Adeno-associated virus (AAV) vector genomes have been limited to 5 kilobases (kb) in length because their packaging limit was thought to be similar to the size of the parent AAV genome. Recent reports claim that significantly larger vector genomes can be packaged intact. We examined the packaged vector genomes from plasmid-encoded AAV vectors that ranged from 4.7 to 8.7 kb in length, using AAV types 2, 5, and 8 capsids. Southern blot analysis indicated that packaged AAV vector genomes never exceeded 5.2 kb in length irrespective of the size of the plasmid-encoded vector or the capsid type. This result was confirmed by vector genome probing with strand-specific oligonucleotides. The packaged vector genomes derived from plasmid-encoded vectors exceeding 5 kb were heterogeneous in length and truncated on the 5' end. Despite their truncated genomes, vector preparations produced from plasmid-encoded vectors exceeding 5.2 kb mediated reporter gene expression in vitro at high multiplicity of infection (MOI). The efficiency of expression was substantially lower than that of reporter vectors with genomes <5 kb in length. We propose that transcriptionally functional, intact vector genomes are generated in cells transduced at high MOI from the fragmentary genomes of these larger vectors, probably by recombination.
Lactadherin (Formerly BA46), a Membrane-Associated Glycoprotein Expressed in Human Milk and Breast Carcinomas, Promotes Arg-Gly-Asp (RGD)-Dependent Cell Adhesion (1997)

Lactadherin, a major glycoprotein of the human milk fat globule membrane, is abundant in human breast milk and expressed in human breast carcinomas. Previously, we have shown that the mature protein, formerly known as BA46, has three domains: an epidermal growth factor (EGF)-like domain containing an Arg-Gly-Asp (RGD) cell adhesion sequence and C1 and C2 domains similar to those found in coagulation factors V and VIII. An alignment of lactadherin with its bovine (MGP57/53) and murine (MFG-E8) homologs shows that the RGD sequence has been conserved during evolution, suggesting that the RGD sequence is not fortuitous. We demonstrate that lactadherin purified using Triton X-114 phase partitioning promotes RGD-dependent cell attachment of green monkey kidney cells (MA104), mouse fibroblast cells (3T3-L1), and breast carcinoma cells (ELL-G). A lactadherin-specific monoclonal antibody, Mc3, inhibits attachment to purified lactadherin, suggesting that contaminants in the purification are not responsible for binding. In addition, the anti-integrin alpha(v)beta3 monoclonal antibody LM609 inhibits cell attachment of MA104 cells to lactadherin. These results demonstrate that lactadherin promotes RGD-dependent cell adhesion via integrins. Denaturation of lactadherin with heat and reducing conditions diminished cell attachment, suggesting that optimal cell attachment to RGD is dependent on the structural presentation of the sequence.
A randomized, parallel-arm, phase II trial to assess the efficacy of preoperative ixabepilone with or without cetuximab in patients with triple-negative breast cancer (TNBC). (2014)

1133 Background: Epithelial growth factor receptor pathway (EGFR) is expressed in TNBC and may be important in a subset of this heterogeneous disease. We evaluated the efficacy and toxicity of an anti-EGFR antibody (cetuximab) combined with ixabepilone given to the TNBC patients (pts) in the neoadjuvant setting. This study was designed to detect an increase in pathological complete response (pCR) rate, defined as no residual disease in the breast, from 20% to 40% in each arm, using a Simon optimal two stage design, with one-sided alpha=10% and power=80%. At least three responses out of 12 patients were needed to proceed with second stage for each arm. Methods: All pts received 4 cycles of preoperative ixabepilone 40 mg/m2 every 3 weeks. In addition, patients were randomized to receive either 12 infusions of weekly cetuximab (400mg/m2 on week 1, then 250 mg/m2) or not. Race, proliferation rate, and TILs was correlated with pCR. Results: To date, a total of36 pts with stage II-IIIA TNBC were enrolled. Median age was 54 years (range 35-79 years) with median tumor size of 6.1 cm (range 2-18 cm). The median proliferation rate (Ki-67) was 67.2% (range 8%-95%). Pts were Hispanic (36%), White (39%), African-American (19%) and others (6%). In ixabepilone alone arm, pCR was observed in only 14.3%, and this monotherapy arm did not progress to second stage. To date, pCR was observed in 31.3% in ixabepilone/cetuximab arm, with 6 patients still on treatment. Adverse events for the combination arm were modest, mainly grade 1-2 (neutropenia: 4%, skin: 83 %, GI: 50 %, fatigue: 100 %). Grade 3 febrile neutropenia in 3 % were observed. No statistically significant correlation with race, Ki67, and TILs with pCR rate was observed. Conclusions: The addition of cetuximab to ixabepilone may improve the rate of pathological complete response in TNBC pts. There was no association between race or proliferation and response to ixabepilone and cetuximab. Evaluation of EGFR, p-EGFR and EGFR pathway -associated genes, PTEN, mutational analysis of PI3K/mTOR pathway and next generation genomic analysis is underway to evaluate for potential predictive biomarkers of response to EGFR inhibition. Clinical trial information: NCT01097642.
DOLLARSPOT DISEASE OF TURF AND ITS CAUSAL ORGANISM, SCLEROTINIA HOMOEOCARPA N.SP. (1937)

SUMMARY The disease of fine turf known in America as “dollarspot” occurs in all parts of Great Britain but is less prevalent than some other turf diseases. The causal organism exists as several strains which maintain their respective characteristics under natural and cultural conditions. The strains differ in capacity for spore production; one yields ascospores and conidia, another ascospores only, and others reduced sporiferous structures only. The U.S.A. strain and an Australian strain, as also some British isolants, belong to the last‐mentioned group. The organism is characterized by well‐developed aerial mycelium, parts of which become reddish brown or cinnamon in colour; by sclerotial structures of parchment‐like thickness, in size from small flakes to expansive areas, olivaceous to black in colour; and by sporiferous structures arising from sclerotial sources. The ascigerous fructification is an apothecium which reaches full development with ascospores in spring; the conidiophore becomes cupulate and bears conidia toward autumn. The rate of growth of the strains and germination of spores is recorded for the range pH. 4–8. The optimum temperature for growth of British strains is 20–25° C, the minimum 0–1° C, and the maximum 35–37° C. The possible influence of temperature on the establishment of non‐sporing strains abroad is discussed. The organism is named Sclerotinia homoeocarpa , and a Latin diagnosis is given.