gebhart/patrepeval huggingface dataset:
Identification of class II major histocompatibility complex and T cell receptor binding sites in the superantigen toxic shock syndrome toxin 1. (1995)

Superantigens, in association with class II major histocompatibility complex (MHC) molecules, activate T cells bearing particular beta chain variable domains of the T cell receptor (TCR). Unlike conventional peptide antigens, superantigens bind as intact proteins to TCR and MHC molecules outside their peptide binding sites. To characterize these interactions at the molecular level, random point mutations were generated in the gene encoding toxic shock syndrome toxin 1, a bacterial superantigen associated with toxic shock syndrome. Functionally impaired mutants were identified based on their lack of murine and human T cell stimulatory activities, and experiments analyzing binding to human histocompatibility leukocyte antigen-DR molecules differentiated residues involved in MHC from TCR binding. The results showed that the great majority of mutations are clustered in two distinct regions of the toxic shock syndrome toxin 1 molecule. The class II MHC binding site is located in the hydrophobic region of the NH2-terminal domain, and the TCR binding site is primarily in the major central groove of the COOH-terminal domain. These studies provide insight into the interactions necessary for superantigen-mediated disease in humans.
Design of midinfrared photodetectors enhanced by surface plasmons on grating structures (2006)

The authors propose to exploit the unique properties of surface plasmons to enhance the signal-to-noise ratio of midinfrared photodetectors. The proposed photodetector consists of a slit in a metallic slab filled with absorptive semiconductor material. Light absorption in the slit is enhanced due to Fabry-Perot resonances. Further absorption enhancement is achieved by surrounding the slit with a series of periodic grooves that enable the excitation of surface plasmons that carry electromagnetic energy towards the slit. Using this scheme, they design and optimize a photodetector operating at λ0=9.8μm with a roughly 250 times enhancement in the absorption per unit of volume of semiconductor material compared to conventional photodetectors operating at the same wavelength.
NXY-059 for the Treatment of Acute Ischemic Stroke (2007)

NXY-059 is ineffective for the treatment of acute ischemic stroke within 6 hours after the onset of symptoms. (ClinicalTrials.gov number, NCT00061022 [ClinicalTrials.gov].)
Temporal Cluster of Herpes Simplex Encephalitis: Investigation by Restriction Endonuclease Cleavage of Viral DNA (1980)

Eight patients with brain biopsy-proven herpes simplex encephalitis were seen at the Massachusetts General Hospital, Boston, within a three-month period in the summer of 1977. The unusual temporal clustering of these cases engendered a formal epidemiologic investigation. No significant link among these patients was uncovered, and analysis of the cleavage products of seven of the eight viral isolates produced by the restriction endonucleases HsuI and HpaI showed that they were different. This cluster thus appears to have been a random event. Its occurrence, however, emphasizes that herpes encephalitis is not a rare disease in this country. In addition, the utility of restriction enzyme cleavage of DNA in clarifying the epidemiology of viral disease is underscored.
Response and Remission Rates in Different Subpopulations With Major Depressive Disorder Administered Venlafaxine, Selective Serotonin Reuptake Inhibitors, or Placebo (2001)

These data suggest that men and women have comparable responses to SSRIs and venlafaxine across various age groups. Moreover, patients exhibited a more rapid onset and a greater likelihood of remission with venlafaxine therapy than with SSRI therapy regardless of age or gender.
Mechanism of selective inhibition of human immunodeficiency virus by ingenol triacetate (1996)

Ingenol 3,5,20-triacetate (ITA), one of the ingenol derivatives, is a selective inhibitor of human immunodeficiency virus (HIV) replication in vitro. ITA inhibited the replication of HIV strains in MT-4 cells at concentrations of 0.051 to 0.65 microM. This concentration was approximately 10(3)-fold lower than its cytotoxic threshold. The mechanism of action of ITA is primarily attributed to the inhibition of viral adsorption to the host cells, but it is distinct from the mechanism of inhibition by other adsorption inhibitors.
How super is supercontraction? Persistent versus cyclic responses to humidity in spider dragline silk (2009)

Spider dragline silk has enormous potential for the development of biomimetic fibers that combine strength and elasticity in low density polymers. These applications necessitate understanding how silk reacts to different environmental conditions. For instance, spider dragline silk ;supercontracts' in high humidity. During supercontraction, unrestrained dragline silk contracts up to 50% of its original length and restrained fibers generate substantial stress. Here we characterize the response of dragline silk to changes in humidity before, during and after supercontraction. Our findings demonstrate that dragline silk exhibits two qualitatively different responses to humidity. First, silk undergoes a previously unknown cyclic relaxation-contraction response to wetting and drying. The direction and magnitude of this cyclic response is identical both before and after supercontraction. By contrast, supercontraction is a ;permanent' tensioning of restrained silk in response to high humidity. Here, water induces stress, rather than relaxation and the uptake of water molecules results in a permanent change in molecular composition of the silk, as demonstrated by thermogravimetric analysis (TGA). Even after drying, silk mass increased by approximately 1% after supercontraction. By contrast, the cyclic response to humidity involves a reversible uptake of water. Dried, post-supercontraction silk also differs mechanically from virgin silk. Post-supercontraction silk exhibits reduced stiffness and stress at yield, as well as changes in dynamic energy storage and dissipation. In addition to advancing understanding supercontraction, our findings open up new applications for synthetic silk analogs. For example, dragline silk emerges as a model for a biomimetic muscle, the contraction of which is precisely controlled by humidity alone.
A randomized trial of classical and medium‐chain triglyceride ketogenic diets in the treatment of childhood epilepsy (2008)

This study has shown classical and MCT ketogenic diet protocols to be comparable in efficacy and tolerability; both ways of implementing the diet have their place in the treatment of childhood epilepsy.
Dendronized Gold Nanoparticles for siRNA Delivery (2012)

Dendronized gold nanoparticles (AuNPs) are effective nanocarriers for small interfering RNA (siRNA) delivery. Electrostatic condension of these AuNPs with siRNA provides efficient silencing (∼50%) without cytotoxicity.
Identification of Barkor as a mammalian autophagy-specific factor for Beclin 1 and class III phosphatidylinositol 3-kinase (2008)

Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in human. Dysfunction of autophagy has been implicated in multiple human diseases including cancer. The identification of novel autophagy factors in mammalian cells will provide critical mechanistic insights into how this complicated cellular pathway responds to a broad range of challenges. Here, we report the cloning of an autophagy-specific protein that we called Barkor (Beclin 1-associated autophagy-related key regulator) through direct interaction with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex. Barkor shares 18% sequence identity and 32% sequence similarity with yeast Atg14. Elimination of Barkor expression by RNA interference compromises starvation- and rapamycin-induced LC3 lipidation and autophagosome formation. Overexpression of Barkor leads to autophagy activation and increased number and enlarged volume of autophagosomes. Tellingly, Barkor is also required for suppression of the autophagy-mediated intracellular survival of Salmonella typhimurium in mammalian cells. Mechanistically, Barkor competes with UV radiation resistance associated gene product (UVRAG) for interaction with Beclin 1, and the complex formation of Barkor and Beclin1 is required for their localizations to autophagosomes. Therefore, we define a regulatory signaling pathway mediated by Barkor that positively controls autophagy through Beclin 1 and represents a potential target for drug development in the treatment of human diseases implicated in autophagic dysfunction.
Nanoditches Fabricated Using a Carbon Nanotube as a Contact Mask (2002)

Single-walled carbon nanotubes (SWCNTs) and multiple-walled nanotubes (MWCNTs) were used as contact masks to create nanoditches within a thin layer of oxide-covered Ti. The nanotubes buried in the Ti film can be removed by ultrasonication, leaving the Ti layer with well-formed uniform ditches up to several μm in length and as narrow as 10 nm in width. The width of the nanoditches is determined by the diameter of the departing nanotube. The technique presented may help to build electrode-to-span molecules or may furnish a template to fabricate nanowires of various materials.
Effect of vitamin A supplementation on rhodopsin mutants threonine-17 → methionine and proline-347 → serine in transgenic mice and in cell cultures (1998)

A therapeutic effect of vitamin A supplementation on the course of photoreceptor degeneration, previously reported for patients with retinitis pigmentosa, was tested in two transgenic mouse models of this disease, each carrying a dominant rhodopsin mutation. The threonine-17 --> methionine (T17M) mutation is a class II rhodopsin mutation, characterized by a thermal instability/folding defect and minimal regeneration with the chromophore. The proline-347 --> serine (P347S) mutation belongs to class I, comprised of a smaller number of mutations that exhibit no recognized biochemical abnormality in vitro. In the present study, each of the two mouse models was fed a diet containing 2.5 mg of vitamin A palmitate (control) or 102.5 mg of vitamin A palmitate (high vitamin A) per kilogram of diet. Dark-adapted, full-field electroretinograms showed that the high vitamin A diet significantly reduced the rate of decline of a-wave and b-wave amplitudes in the T17M mice but had no significant effect on the decline of electroretinogram amplitude in the P347S mice. Correspondingly, histologic evaluation revealed that the treatment was associated with significantly longer photoreceptor inner and outer segments and a thicker outer nuclear layer in the T17M mice but had no effect on photoreceptor morphology in the P347S mice. In a separate series of experiments, the instability defect of the T17M mutant opsin expressed in vitro was partially alleviated by inclusion of 11-cis-retinal in the culture media. These results show that vitamin A supplementation slows the rate of photoreceptor degeneration caused by a class II rhodopsin mutation. Vitamin A supplementation may confer therapeutic benefit by stabilizing mutant opsins through increased availability of the chromophore.
Urokinase Plasminogen Activator/Urokinase-specific Surface Receptor Expression and Matrix Invasion by Breast Cancer Cells Requires Constitutive p38α Mitogen-activated Protein Kinase Activity (2000)

Overexpression of urokinase plasminogen activator (uPA) and its receptor (uPAR) has been well documented in a wide variety of tumor cells. In breast cancer, expression of uPA/uPAR is essential for tumor cell invasion and metastasis. However, the mechanism responsible for uPA/uPAR expression in cancer cells remains unclear. In the studies reported here, we show that endogenous p38 MAPK activity correlates well with breast carcinoma cell invasiveness. Treatment of highly invasive BT549 cells with a specific p38 MAPK inhibitor SB203580 diminished both uPA/uPAR mRNA and protein expression and abrogated the ability of these cells to invade matrigel, suggesting that p38 MAPK signaling pathway is involved in the regulation of uPA/uPAR expression and breast cancer cell invasion. We also demonstrated that SB203580-induced reduction in uPA/uPAR mRNA expression resulted from the de- stabilization of uPA and uPAR mRNA. Finally, by selectively inhibiting p38alpha or p38beta MAPK isoforms, we demonstrate that p38alpha, rather than p38beta, MAPK activity is essential for uPA/uPAR expression. These studies suggest that p38alpha MAPK signaling pathway is important for the maintenance of breast cancer invasive phenotype by promoting the stabilities of uPA and uPAR mRNA.
Treatment of complex regional pain syndrome: a review of the evidence Traitement du syndrome de douleur regionale complexe: une revue des donnees probantes (2010)

Purpose This narrative review summarizes the evidence derived from randomized controlled trials pertaining to the treatment of complex regional pain syndrome (CRPS). Source Using the MEDLINE (January 1950 to April 2009) and EMBASE (January 1980 to April 2009) databases, the following medical subject headings (MeSH) were searched: ‘‘Complex Regional Pain Syndrome’’, ‘‘Reflex Sympathetic Dystrophy’’, and ‘‘causalgia’’ as well as the key words ‘‘algodystrophy’’, ‘‘Sudeck’s atrophy’’, ‘‘shoulder hand syndrome’’, ‘‘neurodystrophy’’, ‘‘neuroalgodystrophy’’, ‘‘reflex neuromuscular dystrophy’’, and ‘‘posttraumatic dystrophy’’. Results were limited to randomized controlled trials (RCTs) conducted on human subjects, written in English, published in peer-reviewed journals, and pertinent to treatment. Principal findings The search criteria yielded 41 RCTs with a mean of 31.7 subjects per study. Blinded assessment and sample size justification were provided in 70.7% and 19.5% of RCTs, respectively. Only biphosphonates appear to offer clear benefits for patients with CRPS. Improvement has been reported with dimethyl sulfoxide, steroids, epidural clonidine, intrathecal baclofen, spinal cord stimulation, and motor imagery programs, but further trials are required. The available evidence does not support the use of calcitonin, vasodilators, or sympatholytic and neuromodulative intravenous regional blockade. Clear benefits have not been reported with stellate/lumbar sympathetic blocks, mannitol, gabapentin, and physical/ occupational therapy. Conclusions Published RCTs can only provide limited evidence to formulate recommendations for treatment of CRPS. In this review, no study was excluded based on factors such as sample size justification, statistical power, blinding, definition of intervention allocation, or clinical outcomes. Thus, evidence derived from ‘‘weaker’’ trials may be overemphasized. Further well-designed RCTs are warranted.
Ventricular Dilation and Electrical Dyssynchrony Synergistically Increase Regional Mechanical Nonuniformity But Not Mechanical Dyssynchrony (2010)

Dilation and left bundle branch block combined synergistically decreased regional cardiac function. CURE and ISF were sensitive to this combination, but WTpeak was not. CURE and ISF also reflected the relative nonuniform distribution of regional work better than WTpeak. These findings might explain why CURE and ISF are better predictors of reverse remodeling in cardiac resynchronization therapy.
ChemInform Abstract: Cross‐Coupling Reactions of Organocopper Derivatives of Methylphosphonic Acid Esters and Amides with Aryl and Hetaryl Iodides Catalyzed by Palladium. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Adenoviral Vector-Delivered Pigment Epithelium-Derived Factor for Neovascular Age-Related Macular Degeneration: Results of a Phase I Clinical Trial (2006)

Twenty-eight patients with advanced neovascular age-related macular degeneration (AMD) were given a single intravitreous injection of an E1-, partial E3-, E4-deleted adenoviral vector expressing human pigment epithelium- derived factor (AdPEDF.11). Doses ranging from 10(6) to 10(9.5) particle units (PU) were investigated. There were no serious adverse events related to AdPEDF.11 and no dose-limiting toxicities. Signs of mild, transient intraocular inflammation occurred in 25% of patients, but there was no severe inflammation. Six patients experienced increased intraocular pressure that was easily controlled by topical medication. All adenoviral cultures were negative. At 3 and 6 months after injection, 55 and 50%, respectively, of patients treated with 10(6)-10(7.5) PU and 94 and 71% of patients treated with 10(8)-10(9.5) PU had no change or improvement in lesion size from baseline. The median increase in lesion size at 6 and 12 months was 0.5 and 1.0 disk areas in the low-dose group compared with 0 and 0 disk areas in the high-dose group. These data suggest the possibility of antiangiogenic activity that may last for several months after a single intravitreous injection of doses greater than 10(8) PU of AdPEDF.11. This study provides evidence that adenoviral vector-mediated ocular gene transfer is a viable approach for the treatment of ocular disorders and that further studies investigating the efficacy of AdPEDF.11 in patients with neovascular AMD should be performed.
Towards sustainable engineering practice: engineering frameworks for sustainability (1997)

This document is intended to translate the confusing and often misunderstood principles of sustainability into useful hands-on information about sustainable approaches for many areas of engineering practice. It should be seen as an aid to understanding of the relevant sustainability issues in a number of sectors important to engineering practice.
Detection, typing, and subtyping of enteric adenoviruses 40 and 41 from fecal samples and observation of changing incidences of infections with these types and subtypes (1993)

Monoclonal antibody (MAb) preparations specific for the enteric adenoviruses of subgenus F (AdF) were generated and evaluated as typing reagents in virus neutralization tests and enzyme-linked immunosorbent assays (ELISAs). A panel of 11 genome types of adenovirus 40 (Ad40), 24 genome types of Ad41, and 47 adenovirus prototype strains was used to determine the specificities of the MAbs in the two assays. In this way two MAbs, MAb 40-1 (anti-Ad40) and MAb 41-1 (anti-Ad41) were selected. These two MAbs showed strict type specificity in both assays. A third MAb reacted in an ELISA with all 47 human adenovirus types. With two other MAbs, three antigenic subtypes of Ad41 could be distinguished by their reactivities in virus neutralization tests and ELISAs. On the basis of the five selected MAbs, a sensitive ELISA system was developed for the direct detection and simultaneous typing and subtyping of Ad40 and Ad41 present in stool specimens. The five MAbs were also used to study the epidemiology of infections with Ad40 and Ad41 in The Netherlands in the period 1981 through 1989. It was shown that there were no significant fluctuations in the annual incidence of the cluster of enteric adenoviruses as a whole. This cluster should therefore be considered to belong to the "endemic" rather than the "epidemic" adenoviruses. The relative incidence of Ad40 infections compared with that of Ad41 infections changed considerably during the period studied; the proportion of Ad41 infections rose from about 30% in 1981 to about 95% in 1986, after which it stabilized at 90 to 95%. The proportion of one of the subtypes of Ad41 (Ad41 subtype M3) increased from about 40 to 80% in the same period.
Developmental and growth factor-induced regulation of nestin in oligodendrocyte lineage cells (1995)

The expression and regulation of nestin, an intermediate filament protein associated with neuroepithelium-derived progenitor cells, was studied in developing oligodendrocytes. We analyzed glial cells cultured from late embryonic rat cerebral cortex, tissue prints from neonatal rat brains, and the oligodendrocyte cell line CG-4. Using cortical- or CG-4-derived oligodendrocyte lineage cells, Northern blot analysis demonstrated that nestin mRNA was highly expressed in proliferating O-2A progenitors, but downregulated in differentiated oligodendrocytes. Immunocytochemistry of cultured cells and tissue prints demonstrated that pre-O-2A cells and O-2A progenitors expressed high levels of the nestin protein. In contrast, nestin expression decreased during the pro-oligodendroblast stage, and the majority of oligodendrocytes were not labeled with anti-nestin antibodies. Culture conditions (PDGF+bFGF or B104-conditioned medium) that maintained O-2A progenitor proliferation and prevented differentiation enhanced expression of nestin mRNA transcripts and protein. In comparison, analysis of cortical astrocyte cultures demonstrated that type 1 astrocytes, but not type 2, expressed nestin mRNA and protein. Our findings demonstrate that nestin is expressed in developing glial cells, which is suggestive that this intermediate filament protein may play an important role during gliogenesis.
Queueing analysis of delay constrained voice traffic in a packet switching system (1989)

Unlike data traffic, the voice packet stream from a node has very high correlation between consecutive packets. In addition, in order for the speech to be properly reconstructed, a delay constraint must be satisfied. A queueing model that accurately predicts packet loss probabilities for such a system is presented. Analytical results are obtained from an embedded bivariate Markov chain and are validated by a simulation program. Based on this model, the impact of the delay constraint, talkspurt detection thresholds, and packet size on packet loss are studied. Two schemes, named 'instant' and 'random', for discarding late packets are considered. Simulation results show that better performance can be obtained by using the latter scheme.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Gatekeepers of organ growth (1997)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.