gebhart/patrepeval huggingface dataset:
ISG15 Inhibits Nedd4 Ubiquitin E3 Activity and Enhances the Innate Antiviral Response* (2008)

Interferons regulate diverse immune functions through the transcriptional activation of hundreds of genes involved in anti-viral responses. The interferon-inducible ubiquitin-like protein ISG15 is expressed in cells in response to a variety of stress conditions like viral or bacterial infection and is present in its free form or is conjugated to cellular proteins. In addition, protein ubiquitination plays a regulatory role in the immune system. Many viruses modulate the ubiquitin (Ub) pathway to alter cellular signaling and the antiviral response. Ubiquitination of retroviral group-specific antigen precursors and matrix proteins of the Ebola, vesicular stomatitis, and rabies viruses by Nedd4 family HECT domain E3 ligases is an important step in facilitating viral release. We found that Nedd4 is negatively regulated by ISG15. Free ISG15 specifically bound to Nedd4 and blocked its interaction with Ub-E2 molecules, thus preventing further Ub transfer from E2 to E3. Furthermore, overexpression of ISG15 diminished the ability of Nedd4 to ubiquitinate viral matrix proteins and led to a decrease in the release of Ebola VP40 virus-like particles from the cells. These results point to a mechanistically novel function of ISG15 in the enhancement of the innate anti-viral response through specific inhibition of Nedd4 Ub-E3 activity. To our knowledge, this is the first example of a Ub-like protein with the ability to interfere with Ub-E2 and E3 interaction to inhibit protein ubiquitination.
Role of carbon in hydrogenated amorphous silicon solar cell degradation (1984)

Experiments using a combination of capacitance and photovoltaic transient spectroscopy on hydrogenated amorphous silicon solar cells demonstrate that carbon produces a metastable defect with characteristic energy and emission time. This defect is involved in solar cell degradation.
Effect of age and sampling site on the chondro‐osteogenic potential of rabbit marrow‐derived mesenchymal progenitor cells (2000)

Four sequential bone-marrow aspirations from the ipsilateral tibia and iliac crest of New Zealand White rabbits, aged 4 months or 1, 2, or 3 years, were assayed in vitro and in vivo for their chondro-osteogenic potential. Nonhematopoietic cells from the samples of bone marrow were isolated and expanded in culture; their colony-forming efficiency was determined, and second-passage marrow-derived cells, referred to as mesenchymal progenitor cells, were loaded into porous calcium-phosphate ceramic cubes as carrier vehicles for an in vivo cartilage and bone-formation assay. The cubes were placed subcutaneously in nude BALB/C mice for 3 and 6 weeks. On histological examination, the cubes were scored for the presence of bone and cartilage in their pores, and average values for age groups and location were compared. At aspiration, the samples from the iliac crest exhibited an overall reduction in cell concentration with increasing age, and at the first harvest time, they showed a decrease in colony-forming efficiency and cube score with increasing age. This study demonstrated that repeated bone-marrow aspirations may be performed and may have an enhancing effect on the osteochondral progenitor cells of older animals.
Deep attractor network for single-microphone speaker separation (2017)

Despite the overwhelming success of deep learning in various speech processing tasks, the problem of separating simultaneous speakers in a mixture remains challenging. Two major difficulties in such systems are the arbitrary source permutation and unknown number of sources in the mixture. We propose a novel deep learning framework for single channel speech separation by creating attractor points in high dimensional embedding space of the acoustic signals which pull together the time-frequency bins corresponding to each source. Attractor points in this study are created by finding the centroids of the sources in the embedding space, which are subsequently used to determine the similarity of each bin in the mixture to each source. The network is then trained to minimize the reconstruction error of each source by optimizing the embeddings. The proposed model is different from prior works in that it implements an end-to-end training, and it does not depend on the number of sources in the mixture. Two strategies are explored in the test time, K-means and fixed attractor points, where the latter requires no post-processing and can be implemented in real-time. We evaluated our system on Wall Street Journal dataset and show 5.49% improvement over the previous state-of-the-art methods.
Rusya'da 1905–1920 yılları arasında tarihsel dönüşüm süreci ve siyasal tartışmalar (2004)

Bu calismanin amaci, Rus Devriminin hangi tarihsel ve dusunsel kosullar icinde olustugunu, bu kosullarda meydana gelen degisikliklerin Lenin’in teorik dunyasina nasil yansidigini ve devrim stratejisini belirlerken ne tur etkilerde bulundugunu anlamaya ve gostermeye yoneliktir.Rusya’da devrimci donusum sorunsalina Lenin acisindan bakildiginda sosyalizmin gerceklesmesi icin bir devrime ihtiyac vardir. Ancak, Rusya’nin kendine ozgu kosullari goz onunde bulunduruldugunda, isci sinifinin “bilinclendirilmesi” gerekliligi on plana cikar. Lenin, bu noktadan sonra kitlelerin bilinclendirilmesinin merkezi esaslara dayali orgutlenmis disiplinli bir parti araciligiyla asilabilecegini iddia eder.Klasik Bati kapitalizminin gelisimine bakildiginda burjuva devrimleri diye adlandirilan tarihsel donusum sureclerinin burjuvazinin onderliginde farkli sosyal katmanlarla kurulan ittifaklar onculugunde gerceklestirildigi gorulecektir. Rus burjuvazisinin guclu olmayisi burjuva devrimini guclestiren temel faktorlerden biridir. Bu noktadan sonra Lenin, kapitalizmin gorece gelistigi ve guclu burjuvazinin olmadigi ulkelerde isci-koylu ittifaki temelinde burjuva demokratik devriminin gerceklestirebilecegi iddiasinda bulunur.1917 Devrimi sonrasinda devletin, sinifsiz toplum idealinin gerceklestirilmesi yonunde bazi ekonomik duzenlemelerin yapilabilmesi icin, varligini proletarya diktatorlugu adi altinda bir sure daha devam etmesi gerekliligi anlayisini ortaya atar. Ayrica Lenin, kapitalizmin farkli bir asamasinda –emperyalist asamada- isci sinifinin sosyalist devrim stratejisinin degisebilecegi ongorusunde bulunur.
International working group for myelofibrosis research and treatment response assessment and long‐term follow‐up of 50 myelofibrosis patients treated with thalidomide‐prednisone based regimens (2010)

We have previously reported the benefits of combination therapy with thalidomide and prednisone for the improvement of cytopenias and splenomegaly for patients with myelofibrosis (MF); both primary and those arising from an antecedent polycythemia vera (PV) and essential thrombocythemia (ET). We report here the overall efficacy of three different thalidomide-prednisone based regimens (alone or in combination with either oral cyclophosphamide for three months or continuous weekly etanercept) when assessed by the IWG-MRT response criteria which were developed after completion of these studies. Additionally we report on the durability of response and long-term follow-up. We observed an overall response rate of 28% by IWG-MRT criteria (mostly clinical improvement - 22% anemia, 8% splenomegaly) with a median duration of response of 8.5 months. Toxicities primarily consisted of neuropathy (Grade 3 or higher neuropathy in 6%) and cytopenias (Grade 3 or higher in 20%). After a median follow-up of three years, fourteen patients (28%) had expired from MF at the time of this analysis with median survival of 36 months.
Cardiovascular Biology of Interleukin-6 (2009)

Interleukin-6 (IL-6) is a multifunctional pro-inflammatory cytokine that is tightly regulated and expressed at low levels in healthy individuals. Increased IL-6 expression has been associated with a variety of diseases, including inflammatory conditions such as atherosclerosis and cardiovascular disease (obesity, myocardial infarction and type II diabetes). Cytokines including IL-6 and tumour necrosis factor alpha as well as acute phase proteins such as C-reactive protein (CRP) and fibrinogen are key biochemical risk factors for the development of these disease conditions. IL-6 is the key cytokine responsible for the stimulus of synthesis and secretion of CRP. IL-6 activates cell surface signalling via the assembly of IL-6, the IL-6 receptor (IL-6R) and the signalling receptor gp130. Assembly of the (hexameric) signalling complex of IL-6, IL-6R and gp130 occurs in a sequential manner and therefore this signalling complex lends itself to several potential sites for drug targeting. This review discusses some of the mechanisms of IL-6 signalling on various aspects of cardiovascular biology as well as some recent developments in drug targeting of this complex.
Cartilage-inducing factor-A. Apparent identity to transforming growth factor-beta. (1986)

Comparison of the sequence of the N-terminal 30 amino acids of cartilage-inducing factor-A (CIF-A) from bovine demineralized bone with the corresponding sequence of human transforming growth factor-beta (TGF-beta) revealed 100% identity. Furthermore, CIF-A stimulated normal rat kidney fibroblasts to become anchorage-independent and form colonies in soft agar (in the presence of epidermal growth factor) in a manner similar to TGF-beta. Similarly, TGF-beta from human platelets induced rat muscle mesenchymal cells to differentiate and synthesize cartilage-specific macromolecules in a manner equivalent to CIF-A. These data show that CIF-A and TGF-beta are closely related or identical molecules and that these factors may be involved in cell differentiation including cartilage formation as the first step in endochondral bone formation.
An efficient vehicles navigation methodology using dynamic changes in local maps (2002)

An efficient, low cost car navigation methodology is presented, by taking into account the dynamic changes that occur in real traffic environments. The methodology proposed is based on the fusion of local maps and additional region information and the GPS coordinates. The CD-ROMs will not able to include in their databases information related with the current status of the traffic delays, construction, detours, accidents, traffic readjustments, etc. occurred in several geographic regions. The solution of this type of problems is the use continuous transmission of the local maps, which include all the current changes at a certain region, via a radio or TV station. A navigation system built in a vehicle will receive the local maps and will fuse in them the GPS coordinates in order to locate the vehicle, as light spot, on the map. This approach provides to the driver several choices and sufficient information for a safe, convenient travel. It will also save lives in case of accidents and traffic delays.
The synthesis of protected 5′-mercapto-2′,5′-dideoxyribonucleoside-3′-0-phosphorainidites; uses of 5′-mercapto-oligodeoxyribonucleotides (1987)

The syntheses of the four novel, base protected 5'-(S-triphenylmethyl)mercapto-2',5'-dideoxyribonucleoside-3 '-O-(2-cyanoethyl N,N-diisopropylphosphoramidites) are described. These compounds have been used to prepare 5'-(S-triphenylmethyl) mercapto-oligodeoxyribonucleotides, which are readily purified by reversed phase h.p.l.c., owing to the highly lipophilic trityl group. After cleavage of the S-trityl group by silver or mercuric ions, the free thiol moiety can be coupled to a wide variety of reagents, generating very useful probes. Fluorescent labelled 5'-mercapto-oligodeoxyribonucleotides are being used for automated DNA sequencing without radioactivity, and heavy metal labelled 5'-mercapto-oligonucleotides will be used in X-ray crystallography.
Chitinase cDNA Cloning and mRNA Induction by Fungal Elicitor, Wounding, and Infection (1988)

Chitinase, which catalyzes the hydrolysis of beta-1,4 N-acetylglucosamine linkages of the fungal cell wall polymer chitin, is a component of the inducible defenses of plants. We show that chitinase synthesis is stimulated in bean (Phaseolus vulgaris L.) cell suspension cultures treated with fungal cell wall elicitors and in hypocotyls in response to infection with the fungus Colletotrichum lindemuthianum. Chitinase cDNA clones were isolated by antibody screening of a lambdagt11 cDNA library containing sequences complementary to poly A(+) RNA from elicited cells. The identity of these clones was confirmed by nucleotide sequence analysis and comparison of the deduced amino acid sequence with that determined for the amino-terminal sequence of bean chitinase. Elicitor causes a very rapid activation of chitinase transcription with a 10-fold stimulation after 5 minutes and 30-fold increase within 20 minutes. This leads to a marked, transient accumulation of chitinase transcripts with maximum levels 2 hours after elicitor treatment, concomitant with the phase of rapid enzyme synthesis. Chitinase transcripts also markedly accumulate in wounded and infected hypocotyls. Chitinase cDNA sequences hybridize to several genomic fragments suggesting there are several chitinase genes in the bean genome.
Use of Antagonist Peptides to Inhibit In Vitro T Cell Responses to Par j1, the Major Allergen of Parietaria judaica Pollen (1999)

Antigenic peptides with substituted side chains inhibit immune responses to a number of recall Ags from infectious agents in vitro. Here we show that the same strategy can be applied to peptides derived from a pollen protein, the major allergen of Parietaria judaica(Par j1), a plant responsible for most allergenic sensitization in the southern Mediterranean area. Three T cell lines responding to Par j1 protein were used to identify a stimulatory peptide. Two different monosubstituted altered peptide ligands (APL) were identified that bound to the HLA-DR of the responders, did not stimulate the T cell lines on their own, and decreased the response to subsaturating amounts of the unmodified stimulatory peptide. Most important, these APL were able to inhibit the response of these cell lines to intact Par j1 protein. A third monosubstituted peptide bound to the HLA-DR but did not show inhibitory activity. The two APL had a lower affinity than the unsubstituted peptide for the HLA-DR. The last two observations make MHC blockade an unlikely explanation for the observed effect. These results indicate the action of a specific peptide-mediated antagonism that may be useful in controlling the T cell component of an allergic response.
Both Amino- and Carboxyl-Terminal Sequences within IκBα Regulate Its Inducible Degradation (1996)

Nuclear expression and consequent biological action of the eukaryotic NF-kappa B transcription factor complex are tightly regulated through its cytoplasmic retention by an ankyrin-rich inhibitory protein termed I kappa B alpha. I kappa B alpha specifically binds to and masks the nuclear localization signal of the RelA subunit of NF-kappa B, thereby effectively sequestering this transcription factor complex in the cytoplasm. Specific cellular activation signals lead to the rapid proteolytic degradation of I kappa B alpha and the concomitant nuclear translocation of NF-kappa B. However, the precise biochemical mechanisms underlying the inhibitory effects of I kappa B alpha on RelA and its inducible pattern of degradation remain unclear. By using HeLa cells transfected with various cDNAs end-coding epitope-tagged mutants of I kappa B alpha, our studies demonstrate the following: (i) sequences within the 72-amino-acid N-terminal region of I kappa B alpha are required for tumor necrosis factor alpha (TNF-alpha)-induced degradation but are fully dispensable for I kappa B alpha binding to and inhibition of RelA; (ii) serine residues located at positions 32 and 36 within the N-terminal region of I kappa B alpha represent major sites of induced phosphorylation (substitution of these serine residues with alanine abrogates TNF-alpha-induced degradation of I kappa B alpha); (iii) the C-terminal 40 residues of I kappa B alpha (amino acids 277 to 317), which include a PEST-like domain, are entirely dispensable for TNF-alpha-induced degradation and inhibition of RelA; (iv) a glutamine- and leucine-rich (QL) region of I kappa B alpha located between residues 263 and 277 and overlapping with the sixth ankyrin repeat is required for both inducible degradation and inhibition of RelA function; (v) regulation of I kappa B alpha degradation by this QL-rich region appears to occur independently of phosphorylation at serines 32 and 36. These findings thus indicate that I kappa B alpha is generally organized within distinct modular domains displaying different functional and regulatory properties. These studies have also led to the identification of a novel class of dominant-negative I kappa B alpha molecules that retain full inhibitory function on NF-kappa B yet fail to undergo stimulus-induced degradation. These molecules, which lack N-terminal sequences, potently inhibit TNF-alpha-induced activation of the human immune deficiency virus type 1 kappa B enhancer, thus indicating their possible use as general inhibitors of NF-kappa B.
Biochemical and immunological properties of urinary angiotensinase A and dipeptidylaminopeptidase IV. Their use as markers in patients with renal cell injury. (1992)

Dipeptidyl peptidase IV (EC 3.4.14.5) and angiotensinase A (EC 4.4.11.7) were purified to homogeneity from pooled urine concentrate of patients with renal damage, using ultrafiltration, ammonium sulphate precipitation, lectin affinity chromatography, FPLC-ion-exchange(Mono-Q-)chromatography, and FPLC-gel filtration (Superdex). Based on the specific enzyme activity of the starting material, dipeptidyl peptidase IV was enriched 1629 fold, angiotensinase A 1183 fold. The relative molecular masses, Michaelis constants and isoelectric points were determined. Negative staining of the purified enzymes revealed globular proteins (5-7 nm). Antisera raised against dipeptidyl peptidase IV and angiotensinase A reacted specifically with tubular and, in the case of anti-angiotensinase A sera, with tubular and glomerular structures. In addition, urinary membrane vesicles of proximal tubule origin were eluted with the void volume (Superdex-gel filtration), indicating heavy epithelial cell disintegration. Both soluble tissue enzymes (dipeptidyl peptidase IV, angiotensinase A) and vacuolar blebs shed from epithelia contribute to proteinuria, as was shown in patients with glomerulonephritis, interstitial nephritis, diabetic nephropathy and, for angiotensinase A, in patients with essential arterial hypertension.
A polymer tandem solar cell with 10.6% power conversion efficiency (2013)

An effective way to improve polymer solar cell efficiency is to use a tandem structure, as a broader part of the spectrum of solar radiation is used and the thermalization loss of photon energy is minimized. In the past, the lack of high-performance low-bandgap polymers was the major limiting factor for achieving high-performance tandem solar cell. Here we report the development of a high-performance low bandgap polymer (bandgap <1.4 eV), poly[2,7-(5,5-bis-(3,7-dimethyloctyl)-5H-dithieno[3,2-b:2',3'-d]pyran)-alt-4,7-(5,6-difluoro-2,1,3-benzothia diazole)] with a bandgap of 1.38 eV, high mobility, deep highest occupied molecular orbital. As a result, a single-junction device shows high external quantum efficiency of >60% and spectral response that extends to 900 nm, with a power conversion efficiency of 7.9%. The polymer enables a solution processed tandem solar cell with certified 10.6% power conversion efficiency under standard reporting conditions (25 °C, 1,000 Wm(-2), IEC 60904-3 global), which is the first certified polymer solar cell efficiency over 10%.
Global spatial normalization of human brain using convex hulls. (1999)

The global features of CH-spatially normalized brain images (position, orientation and size) were consistently transformed to match the Talairach Atlas in both MR and PET images. The CH method supports intermodality and intersubject global spatial normalization of tomographic brain images.
Advances in specific therapy for multiple sclerosis (1994)

During the past year, two new agents have been demonstrated to be of value in multiple sclerosis. The first agent, a form of recombinant interferon beta (Betaseron; Berlex Labs, Cedar Knolls, NJ), is effective in reducing relapses and also prevent accumulation of brain lesions over time, but has no demonstrated effect on the accumulation of disability over time. The second agent, methylprednisolone (Solumedrol; The Upjohn Co., Kalamozoo, MI), administered in megadose pulses over several days and followed by an oral prednisone taper, reduces the conversion rate of patients with optic neuritis to multiple sclerosis by approximately 50% over 2 years compared with placebo or oral prednisone alone. The mechanisms by which these agents exert their benefits are incompletely understood, but both have complex, relatively widespread effects on the immune systems. The demonstration of efficacy for both of these agents represent landmarks in the search for an effective treatment for multiple sclerosis; both agents seem to provide prophylaxis against future relapses, and methylprednisolone seems to delay the development of the disease. Their introduction into the clinical environment will undoubtedly have a profound effect on the day-to-day care of multiple sclerosis patients as well as the designs of future basic and clinical research. Other new therapies that have substantial potential for benefit in multiple sclerosis but require further definitive study include intramuscular copolymer 1 for relapsing disease and low-dose oral methotrexate and booster doses of intravenous cyclophosphamide for chronic progressive disease.
A Solution-Phase, Precursor Route to Polycrystalline SnO2 Nanowires That Can Be Used for Gas Sensing under Ambient Conditions (2003)

This paper describes a solution-based, precursor method for the facile synthesis of uniform nanowires containing rutile SnO2 nanocrystallites. In a typical procedure, nanowires of approximately 50 nm in diameters and up to 30 mum in length were obtained as a white precipitate by refluxing SnC2O4.2H2O and poly(vinylpyrrolidone) in ethylene glycol. Structural analyses by XRD, FT-IR, and TGA indicate that these highly anisotropic nanostructures were formed in an isotropic medium through the aggregation of chainlike precursors that were, in turn, formed via polyol-mediated oligomerization. These nanowires could be further converted to polycrystalline SnO2 by calcination in air at 500 degrees C. The resultant nanowires of SnO2 were highly porous and could be used for gas sensing with improved sensitivity and reversibility under ambient conditions. We have also demonstrated that this new approach could be extended to generate polycrystalline nanowires of other metal oxides such as In2O3 and anatase TiO2.
Discovering dynamic regulatory pathway by applying an auto regressive model to time series DNA microarray data (2005)

In this paper we propose a novel method to extract dynamic regulatory pathways from time-series DNA microarray data. To this aim, first a specialized clustering technique is applied that utilizes the available heuristic information about the biological system to form the clusters. Then, an auto regressive (AR) model is applied to model the interactions among all genes and to predict the gene expressions for the next time steps. We tested the proposed method on the eukaryotic cell cycle data. The results indicate that the proposed method can successfully predict the dynamic pathway involved in this biological process.