gebhart/patrepeval huggingface dataset:
Amelioration of human neutrophil elastase-induced emphysema in hamsters by pretreatment with an oligopeptide chloromethyl ketone (1989)

Human neutrophils are a likely source of elastase in the pathogenesis of human pulmonary emphysema. A study was undertaken to determine whether emphysema, induced in hamsters by intratracheal treatment with human neutrophil elastase (HNE), could be ameliorated by intratracheal instillation of succinyl-alanyl-alanyl-prolyl-valine-chloromethyl ketone (CMK). One mg of CMK was given to hamsters 1 h before 300 or 360 micrograms HNE or 1 h or 4 h after 360 micrograms HNE. The animals were studied eight weeks after treatment. The CMK given 4 h after HNE did not ameliorate the emphysema. The CMK given 1 h before HNE, ameliorated the development of emphysema but not bronchial secretory cell metaplasia. A molar ratio of instilled CMK to HNE of 128 was required for 50% in vivo effectiveness in ameliorating emphysema. Clearance studies indicated that 6.9% of the instilled CMK could be lavaged from the lungs 1 h after instillation. Therefore, an 8.9 to 1 molar ratio of lavageable CMK to HNE, at the time of HNE instillation, resulted in 50% protection. Using an in vitro assay with 3H-elastin as substrate, a 3 to 1 molar ratio of CMK to HNE was required to inhibit 50% of the elastolytic activity; 14% of the activity remained with an 18 to 1 molar ratio of CMK to HNE. Study of the in vivo effectiveness of anti-elastases, given as pretreatment in ameliorating HNE-induced emphysema and secretory cell metaplasia, is a reasonable bioassay, which may be used as a step in evaluating such agents for possible use in the prevention of human disease.
Rapid Removal of Organics and Oil Spills from Waters Using Silicone Rubber “Sponges” (2009)

We have developed a simple, robust, and efficient technology utilizing cheap and recoverable materials based on commercially available silicone elastomer networks for removing organic solvents and crude oil from waters. Hydrophobic and oleophilic properties of silicone elastomers endow poly(dimethyl siloxane) (PDMS) with the capacity to absorb a large variety of organics, including benzene (B), toluene (T), ethylbenzene (E), and xylene (X), commonly referred to as BTEX, and also crude oils, while at the same time enabling the organic “sponges” to float on waters, which facilitates straightforward handling. We developed a method for generating PDMS particles with variable sizes (ranging from hundreds nanometers to few millimeters) by drop-wise depositing siloxane/cross-linker mixtures into warm water, a process which leads to the cross-linking of the PDMS components. We have tested the capability of the PDMS particles to remove toluene and benzene from water. We also performed similar experiments by utilizing PDMS sheets. In both instances we observed a rapid sorption of the organic phase into PDMS; the amount of absorbed organic solvent depended on the concentration in water and the total mass (volume) of PDMS and did not depend on the geometry of the PDMS “sponge.” In addition, we have examined the uptake of toluene and benzene from toluene/benzene (T/B) mixtures dissolved in water. Our results indicate that the amount of benzene absorbed from the T/B mixtures into PDMS increases relative to the uptake from pure benzene/water solutions. This behavior is associated with toluene acting as a “surfactant” that effectively replaces the more unfavorable PDMS/B contacts with less costly T/B ones. Finally, a simple experiment demonstrates qualitatively that PDMS is also capable of removing crude oils from oil-contaminated waters.
Video-aware opportunistic network coding over wireless networks (2009)

In this paper, we study video streaming over wireless networks with network coding capabilities. We build upon recent work, which demonstrated that network coding can increase throughput over a broadcast medium, by mixing packets from different flows into a single packet, thus increasing the information content per transmission. Our key insight is that, when the transmitted flows are video streams, network codes should be selected so as to maximize not only the network throughput but also the video quality. We propose video-aware opportunistic network coding schemes that take into account both the decodability of network codes by several receivers and the importance and deadlines of video packets. Simulation results show that our schemes significantly improve both video quality and throughput. This work is a first step towards content-aware network coding.
Affinity Chromatography: A Review of Clinical Applications (1999)

Affinity chromatography is a type of liquid chromatography that makes use of biological-like interactions for the separation and specific analysis of sample components. This review describes the basic principles of affinity chromatography and examines its use in the testing of clinical samples, with an emphasis on HPLC-based methods. Some traditional applications of this approach include the use of boronate, lectin, protein A or protein G, and immunoaffinity supports for the direct quantification of solutes. Newer techniques that use antibody-based columns for on- or off-line sample extraction are examined in detail, as are methods that use affinity chromatography in combination with other analytical methods, such as reversed-phase liquid chromatography, gas chromatography, and capillary electrophoresis. Indirect analyte detection methods are also described in which immunoaffinity chromatography is used to perform flow-based immunoassays. Other applications that are reviewed include affinity-based chiral separations and the use of affinity chromatography for the study of drug or hormone interactions with binding proteins. Some areas of possible future developments are then considered, such as tandem affinity methods and the use of synthetic dyes, immobilized metal ions, molecular imprints, or aptamers as affinity ligands for clinical analytes.
MRI Detection of Uterine Necrosis After Uterine Artery Embolization for Fibroids (2004)

MRI Detection of Uterine Necrosis After Uterine Artery Embolization for FibroidsHelena Gabriel1, Christina M. Pinto1, Manish Kumar1 2, Paul Nikolaidis1, Frank H. Miller1, David M. Weinrach3 and Robert L. Vogelzang1Audio Available | Share
Neurologic and motor dysfunctions in APP transgenic mice (2012)

The discovery of gene mutations underlying autosomal dominant Alzheimer's disease has enabled researchers to reproduce several hallmarks of this disorder in transgenic mice, notably the formation of Aβ plaques in brain and cognitive deficits. APP transgenic mutants have also been investigated with respect to survival rates, neurologic functions, and motor coordination, which are all susceptible to alteration in Alzheimer dementia. Several transgenic lines expressing human mutated or wild-type APP had higher mortality rates than non-transgenic controls with or without the presence of Aβ plaques. Mortality rates were also elevated in APP transgenic mice with vascular amyloid accumulation, thereby implicating cerebrovascular factors in the precocious death observed in all APP transgenic models. In addition, myoclonic jumping has been described in APP mutants, together with seizure activity, abnormal limb-flexion and paw-clasping reflexes, and motor coordination deficits. The neurologic signs resemble the myoclonic movements, epileptic seizures, pathological reflexes, and gait problems observed in late-stage Alzheimer's disease.
Activation of dimeric ABA receptors elicits guard cell closure, ABA-regulated gene expression, and drought tolerance (2013)

Abscisic acid (ABA) is an essential molecule in plant abiotic stress responses. It binds to soluble pyrabactin resistance1/PYR1-like/regulatory component of ABA receptor receptors and stabilizes them in a conformation that inhibits clade A type II C protein phosphatases; this leads to downstream SnRK2 kinase activation and numerous cellular outputs. We previously described the synthetic naphthalene sulfonamide ABA agonist pyrabactin, which activates seed ABA responses but fails to trigger substantial responses in vegetative tissues in Arabidopsis thaliana. Here we describe quinabactin, a sulfonamide ABA agonist that preferentially activates dimeric ABA receptors and possesses ABA-like potency in vivo. In Arabidopsis, the transcriptional responses induced by quinabactin are highly correlated with those induced by ABA treatments. Quinabactin treatments elicit guard cell closure, suppress water loss, and promote drought tolerance in adult Arabidopsis and soybean plants. The effects of quinabactin are sufficiently similar to those of ABA that it is able to rescue multiple phenotypes observed in the ABA-deficient mutant aba2. Genetic analyses show that quinabactin's effects in vegetative tissues are primarily mediated by dimeric ABA receptors. A PYL2-quinabactin-HAB1 X-ray crystal structure solved at 1.98-Å resolution shows that quinabactin forms a hydrogen bond with the receptor/PP2C "lock" hydrogen bond network, a structural feature absent in pyrabactin-receptor/PP2C complexes. Our results demonstrate that ABA receptors can be chemically controlled to enable plant protection against water stress and define the dimeric receptors as key targets for chemical modulation of vegetative ABA responses.
Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells (2013)

The identification of the trans-acting factors and cis-regulatory modules that are involved in human pluripotent stem cell (hPSC) maintenance and differentiation is necessary to dissect the operating regulatory networks in these processes and thereby identify nodes where signal input will direct desired cell fate decisions in vitro or in vivo. To deconvolute these networks, we established a method to influence the differentiation state of hPSCs with a CRISPR-associated catalytically inactive dCas9 fused to an effector domain. In human embryonic stem cells, we find that the dCas9 effectors can exert positive or negative regulation on the expression of developmentally relevant genes, which can influence cell differentiation status when impinging on a key node in the regulatory network that governs the cell state. This system provides a platform for the interrogation of the underlying regulators governing specific differentiation decisions, which can then be employed to direct cellular differentiation down desired pathways.
Different T helper cell types and antibody isotypes generated by saline and gene gun DNA immunization (1997)

Several routes and methods of DNA immunization have been shown to generate Ab, Th cells, and CTL responses. However, few studies have directly compared the immune responses generated by different routes and methods of DNA immunization. Utilizing an influenza hemagglutinin (H1)-expressing plasmid, we compared the immune response produced by saline injection of DNA into skin or muscle, and gene gun immunization of skin or muscle. We found that saline-DNA immunization raised a predominantly Th1 response with mostly IgG2a anti-H1 Ab, while gene gun DNA immunization produced a predominantly Th2 response with mostly IgG1 anti-H1 Abs. These distinct types of immune responses were generated by the method, not the route, of DNA immunization. The initial immunization established the Th cell-type of the immune response. The Th cell-type did not change with further DNA immunizations by the same or the alternate method, or after a viral challenge. The ability to generate different Th types was not due to differences in the doses of DNA used in saline and gene gun DNA immunization. These findings have important implications for vaccine design and studies of the mechanism of Th cell differentiation.
The costs of surgery for limb-threatening ischemia. (1986)

The clinical courses of 106 patients with limb-threatening ischemia were traced for as long as 5 years to determine the cost of their care. Seventy-eight patients initially treated with vascular reconstruction accrued an average of $40,769 +/- $3726 in costs over a mean follow-up period of 805 +/- 57 days, during which they had an average of 2.4 +/- 0.2 hospitalizations or 67 +/- 6 inpatient days. Twenty-eight high-risk patients treated with primary amputation accrued $40,563 +/- $4729 in costs over a mean follow-up period of 663 +/- 97 days, during which they had an average of 2.2 +/- 0.3 hospitalizations or 85 +/- 10 inpatient days. Successful revascularization resulted in lower costs ($28,374) than did primary amputation ($40,563) or failed reconstruction ($56,809). Patients with ischemic tissue loss accrued costs more rapidly than did patients with rest pain only. The high cost of providing care for these patients and the advent of diagnosis related group reimbursement mandate that proposed treatment protocols be evaluated not only for their effectiveness but also for their cost-effectiveness.
Fabrication of ultrathin, highly uniform thin-film SOI MOSFETs with low series resistance using pattern-constrained epitaxy (1997)

We report a novel fabrication process for self-aligned, ultrathin, highly uniform thin-film SOI MOSFETs with low series resistance. Self-aligned, ultrathin SOI n-MOSFETs with 8 nm-50 nm undoped channel were fabricated. For n-MOSFETs with a 0.2 /spl mu/m effective channel length, a saturation transconductance of 242 mS/mm, and a low series resistance (R/sub s/d/=333 /spl Omega//spl middot//spl mu/m) were obtained.
Thrombolytic Therapy for Stroke (2001)

Thrombolytic therapy has recently been shown to be beneficial in the setting of acute myocardial infarction, and thrombolysis resulting in vascular recanalization has been achieved in several other human disease states, including stroke. Advances in the understanding of the fibrinolytic system have led to the development of several new and distinctive thrombolytic strategies. Animal studies of stroke have been encouraging with regard to arterial recanalization and safety. Clinically, the availability of brain computed tomography has allowed pilot studies to proceed by providing rapid identification of patients with nonhemorrhagic stroke. Arterial recanalization has been demonstrated in patients with ischemic stroke following the administration of any one of several thrombolytic drugs. Placebo-controlled trials have not been completed, and so clinical benefit has not been established. Even though the development of brain hemorrhage has been an infrequent complication, the very high morbidity and mortality have been worrisome. Ironically, thrombolytic therapy holds promise for treatment of subarachnoid hemorrhage and perhaps also for spontaneous intracerebral hemorrhage. Human studies have been limited, but complications have been modest, and clinical outcomes have been encouraging.
On the selection of median structure for image filtering (1995)

Median filtering is a powerful tool for reducing noise in images, particular for long-tailed noise distributions. However, the choice of filter mask is critical. The proper choice depends on the image and noise statistics, which are often unknown. We propose cross-validation as a method for selecting a median filter structure directly from the corrupted image data. This method requires no knowledge of the statistics of the noise or image. We demonstrate the value of this method with several examples.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Analog Binding Properties of Insulin Receptor Mutants (1997)

Recent studies utilizing alanine scanning mutagenesis have identified a major ligand binding domain of the secreted recombinant insulin receptor composed of two subdomains, one between amino acids 1 and 120 and the other between amino acids 704 and 716. In order to obtain a more detailed characterization of these subdomains, we examined the binding of an insulin superanalog, des-(B25-30)-[His-A8, Asp-B10, Tyr-B25 alpha-carboxamide]insulin, to alanine mutants of the ligand binding determinants of these subdomains. cDNAs encoding mutant secreted recombinant receptors were transiently expressed in 293 EBNA cells, and the binding properties for this analog of the expressed receptors were evaluated. In general des-(B25-30)-[His-A8, Asp-B10, Tyr-B25 alpha-carboxamide]insulin binding correlated with insulin binding, suggesting that both peptides bound to the receptor in a similar manner. Alanine mutations of eight amino acids (Asn15, Phe64, Phe705, Glu706, Tyr708, Leu709, Asn711, and Phe714) of the receptor produced the most profound decreases in affinity for des-(B25-30)-[His-A8, Asp-B10, Tyr-B25 alpha-carboxamide]insulin, suggesting that interactions with these amino acids contributed the major part of the free energy of the ligand-receptor interaction. Mutation of Arg14 and His710 to Ala produced receptors with undetectable insulin binding but an affinity for des-(B25-30)-[His-A8, Asp-B10, Tyr-B25 alpha-carboxamide]insulin only 8-23-fold less than for native receptor. Further analog studies were performed to elucidate this paradox. The receptor binding potencies of His-A8 and Asp-B10 insulins for these receptor mutants appeared to parallel their relative potencies for native receptor. In contrast the receptor binding potency of des-(B25-30)-[Tyr-B25 alpha-carboxamide]insulin was disproportionately increased for these mutants when compared with its potency for native receptor.
Normal human endometrial cells in culture: Characterization and immortalization of epithelial and stromal cells by SV 40 large T antigen (1995)

Thirty endometrial biopsies were cultured in order to separate stromal and epithelial cells. Using epidermal growth factor (EGF), cortisol, cholera toxin, insulin with 5% horse serum for epithelial cells or a medium with 20% fetal calf serum for stromal cells, we could specifically enrich endometrial culture in epithelial or stromal cells and culture them for 1 or 2 months. These cultures retained the phenotypic characteristics of epithelial (cytokeratins, mucin HMFG 1) and stromal (vimentin, smooth muscle actin, desmin) lineage by immunostaining analysis. Epithelial and stromal cultures from one individual were respectively immortalized by the SV 40 large T antigen. The immortalized cell lines kept the phenotype of the normal cells from which they derived.
Stepwise prediction of conformational discontinuous B‐cell epitopes using the Mapitope algorithm (2007)

Mapping the epitope of an antibody is of great interest, since it contributes much to our understanding of the mechanisms of molecular recognition and provides the basis for rational vaccine design. Here we present Mapitope, a computer algorithm for epitope mapping. The algorithm input is a set of affinity isolated peptides obtained by screening phage display peptide-libraries with the antibody of interest. The output is usually 1-3 epitope candidates on the surface of the atomic structure of the antigen. We have systematically tested the performance of Mapitope by assessing the effect of the algorithm parameters on the final prediction. Thus, we have examined the effect of the statistical threshold (ST) parameter, relating to the frequency distribution and enrichment of amino acid pairs from the isolated peptides and the D (distance) and E (exposure) parameters which relate to the physical parameters of the antigen. Two model systems were analyzed in which the antibody of interest had previously been co-crystallized with the antigen and thus the epitope is a given. The Mapitope algorithm successfully predicted the epitopes in both models. Accordingly, we formulated a stepwise paradigm for the prediction of discontinuous conformational epitopes using peptides obtained from screening phage display libraries. We applied this paradigm to successfully predict the epitope of the Trastuzumab antibody on the surface of the Her-2/neu receptor in a third model system.
The AP1-dependent secretion of galectin-1 by Reed–Sternberg cells fosters immune privilege in classical Hodgkin lymphoma (2007)

Classical Hodgkin lymphomas (cHLs) contain small numbers of neoplastic Reed-Sternberg (RS) cells within an extensive inflammatory infiltrate that includes abundant T helper (Th)-2 and T regulatory (Treg) cells. The skewed nature of the T cell infiltrate and the lack of an effective host antitumor immune response suggest that RS cells use potent mechanisms to evade immune attack. In a screen for T cell-inhibitory molecules in cHL, we found that RS cells selectively overexpressed the immunoregulatory glycan-binding protein, galectin-1 (Gal1), through an AP1-dependent enhancer. In cocultures of activated T cells and Hodgkin cell lines, RNAi-mediated blockade of RS cell Gal1 increased T cell viability and restored the Th1/Th2 balance. In contrast, Gal1 treatment of activated T cells favored the secretion of Th2 cytokines and the expansion of CD4+CD25high FOXP3+ Treg cells. These data directly implicate RS cell Gal1 in the development and maintenance of an immunosuppressive Th2/Treg-skewed microenvironment in cHL and provide the molecular basis for selective Gal1 expression in RS cells. Thus, Gal1 represents a potential therapeutic target for restoring immune surveillance in cHL.
Controls of Cell Proliferation in Yeast and Animals (2007)

Genetic studies using fission yeast (Schizosaccharomyces pombe) have identified a gene, cdc2, whose product (p34cdc2) is a protein kinase required for traversal of both the G1 and G2 cell cycle control points. Genetic complementation has been used to demonstrate that p34cdc2 homologues are functionally and structurally conserved in distantly related eukaryotes, and p34cdc2-related proteins are components of both maturation-promoting factor (MPF) and the M phase (growth-associated) histone H1 kinase. The p34cdc2 homologues of multicellular eukaryotes undergo potentially regulatory phosphorylation changes through the cell cycle. Phosphorylation on serine during late G1 is accompanied by a significant increase in p34cdc2 kinase activity which, by analogy with fission yeast, may betray a function related to control over entry into S phase. Phosphorylation on threonine and tyrosine in G2 precedes dephosphorylation of these residues during kinase hyperactivation and entry into mitosis. In addition, long-term control of expression of mammalian p34cdc2 homologues is likely to be exerted at the transcriptional level. These observations provide the framework of a universal model for the control of eukaryotic cell proliferation, in which the p34cdc2 protein kinase integrates multiple cues to signal the initiation of S phase and, subsequently, mitosis.
Phosphonate utilization by bacterial cultures and enrichments from environmental samples (1990)

A selection of axenic microbial strains and a variety of environmental samples were investigated with respect to the utilization of a series of natural and xenobiotic phosphonates as the sole phosphorus source for growth. Phosphonate degradation was observed only with bacteria and not with eucaryotic microorganisms. All representatives of the phosphonates examined supported bacterial growth, with the exception of methylphosphonate diethylester. Yet, distinctly different phosphonate utilization patterns were noted between phosphonate-positive strains. C-P bond cleavage by a photosynthetic bacterium is reported for the first time; growing photoheterotrophically, Rhodobacter capsulatus ATCC 23782 was able to utilize 2-aminoethylphosphonate and alkylphosphonates. Bacteria with the potential to utilize at least one of the phosphonate moieties from the xenobiotic phosphonates Dequest 2010, Dequest 2041, and Dequest 2060 were detected in all environments, with only two exceptions for Dequest 2010. Phosphonate P utilization to an extent of 94 and 97%, for Dequest 2010 and Dequest 2041, respectively, provided evidence that a complete breakdown of these compounds with respect to the C-P bond cleavage can be achieved by some bacteria. The results suggest that phosphonate-utilizing bacteria are ubiquitous, and that selected strains can degrade phosphonates that are more complex than those described previously.