gebhart/patrepeval huggingface dataset:
Strategies targeting cellular senescence (2018)

Cellular senescence is a physiological phenomenon that has both beneficial and detrimental consequences. Senescence limits tumorigenesis and tissue damage throughout the lifetime. However, at the late stages of life, senescent cells increasingly accumulate in tissues and might also contribute to the development of various age-related pathologies. Recent studies have revealed the molecular pathways that preserve the viability of senescent cells and the ones regulating their immune surveillance. These studies provide essential initial insights for the development of novel therapeutic strategies for targeting senescent cells. At the same time they stress the need to understand the limitations of the existing strategies, their efficacy and safety, and the possible deleterious consequences of senescent cell elimination. Here we discuss the existing strategies for targeting senescent cells and upcoming challenges in translating these strategies into safe and efficient therapies. Successful translation of these strategies could have implications for treating a variety of diseases at old age and could potentially reshape our view of health management during aging.
Selective predisposition to bacterial infections in IRAK-4–deficient children: IRAK-4–dependent TLRs are otherwise redundant in protective immunity (2007)

Human interleukin (IL) 1 receptor-associated kinase 4 (IRAK-4) deficiency is a recently discovered primary immunodeficiency that impairs Toll/IL-1R immunity, except for the Toll-like receptor (TLR) 3- and TLR4-interferon (IFN)-alpha/beta pathways. The clinical and immunological phenotype remains largely unknown. We diagnosed up to 28 patients with IRAK-4 deficiency, tested blood TLR responses for individual leukocyte subsets, and TLR responses for multiple cytokines. The patients' peripheral blood mononuclear cells (PBMCs) did not induce the 11 non-IFN cytokines tested upon activation with TLR agonists other than the nonspecific TLR3 agonist poly(I:C). The patients' individual cell subsets from both myeloid (granulocytes, monocytes, monocyte-derived dendritic cells [MDDCs], myeloid DCs [MDCs], and plasmacytoid DCs) and lymphoid (B, T, and NK cells) lineages did not respond to the TLR agonists that stimulated control cells, with the exception of residual responses to poly(I:C) and lipopolysaccharide in MDCs and MDDCs. Most patients (22 out of 28; 79%) suffered from invasive pneumococcal disease, which was often recurrent (13 out of 22; 59%). Other infections were rare, with the exception of severe staphylococcal disease (9 out of 28; 32%). Almost half of the patients died (12 out of 28; 43%). No death and no invasive infection occurred in patients older than 8 and 14 yr, respectively. The IRAK-4-dependent TLRs and IL-1Rs are therefore vital for childhood immunity to pyogenic bacteria, particularly Streptococcus pneumoniae. Conversely, IRAK-4-dependent human TLRs appear to play a redundant role in protective immunity to most infections, at most limited to childhood immunity to some pyogenic bacteria.
Mitochondrial N-formylmethionyl proteins as chemoattractants for neutrophils. (1982)

Mitochondria synthesize several hydrophobic proteins. Like bacteria, mitochondria initiate protein synthesis with an N-formylmethionine residue. Because N-formylmethionyl peptides have been found to be chemotactic for polymorphonuclear leukocytes (PMN), mitochondria isolated from cultured human cells and purified bovine mitochondrial proteins were tested for PMN chemotactic activity in vitro. Nondisrupted mitochondria were not chemotactic. However, intact mitochondria that had been incubated with a lysosomal lysate did stimulate PMN migration. Antibodies directed against two mitochondrial enzymes, cytochrome oxidase and ATPase, (both of which contain mitochondrially synthesized subunits) but not anti-C3 or anti-C5 decreased mitochondrially derived chemotactic activity. In addition, purified bovine mitochondrial N-formylmethionyl proteins stimulated PMN migration in vitro, whereas nonformylated mitochondrial proteins did not. Furthermore, the chemotactic activity of purified mitochondrial proteins and disrupted mitochondria was decreased by the formyl peptide antagonist butyloxycarbonyl-phenylalanine-leucine-phenylalanine-leucine-phenylalanine. Finally, disrupted mitochondria and purified mitochondrial proteins stimulated PMN-directed migration (chemotaxis), according to accepted criteria. In addition to other chemotactic factors, release of N-formylmethionyl proteins from mitochondria at sites of tissue damage, may play a role in the accumulation of inflammatory cells at these sites.
G1 delay in cells overexpressing prostaglandin endoperoxide synthase-2. (1996)

Colorectal cancer is the second leading cause of death from cancer in the United States. Continuous use of aspirin and other nonsteroidal anti-inflammatory drugs (NSAIDs) has been shown to reduce the risk of colorectal cancer in humans by 40-50%. Patients with familial adenomatous polyposis who take NSAIDs, such as sulindac, undergo a regression of intestinal adenomas. Rodents exposed to carcinogens that cause colon cancer have a 50-60% reduction in the size and number of colonic tumors when treated continuously with NSAIDs. One common target for these drugs is prostaglandin endoperoxide synthase, also referred to as cyclooxygenase (COX). We and others have shown recently that COX-2 levels are increased dramatically in 85-90% of human colorectal adenocarcinomas and in 40-50% of colonic adenomas. We prepared intestinal epithelial cells that express the COX-2 gene permanently and found that they have altered adhesion properties and resist undergoing apoptosis. We report here that these cells also have a 3-fold increase in the duration of G1, lower levels of cyclin D1 protein, and a marked decrease in retinoblastoma kinase activity associated with cyclin-dependent kinase 4. The delay in G1 transit may relate to the resistance of these cells to undergo programmed cell death, which could affect their tumorigenic potential.
Albumin-bound formulation of paclitaxel (Abraxane&reg; ABI-007) in the treatment of breast cancer (2009)

Breast cancer is the most common type of malignancy diagnosed in women. In the metastatic setting this disease is still uncurable. Taxanes represent an important class of antitumor agents which have proven to be fundamental in the treatment of advanced and early-stage breast cancer, but the clinical advances of taxanes have been limited by their highly hydrophobic molecular status. To overcome this poor water solubility, lipid-based solvents have been used as a vehicle, and new systemic formulations have been developed, mostly for paclitaxel, which are Cremophor-free and increase the circulation time of the drug. ABI-007 is a novel, albumin-bound, 130-nm particle formulation of paclitaxel, free from any kind of solvent. It has been demonstrated to be superior to an equitoxic dose of standard paclitaxel with a significantly lower incidence of toxicities in a large, international, randomized phase III trial. The availability of new drugs, such as Abraxane, in association with other traditional and non-traditional drugs (new antineoplastic agents and targeted molecules), will give the oncologist many different effective treatment options for patients in this setting.
The Xen-Blanket (2012)

Current Infrastructure as a Service (IaaS) clouds operate in isolation from each other. Slight variations in the virtual machine (VM) abstractions or underlying hypervisor services prevent unified access and control across clouds. While standardization efforts aim to address these issues, they will take years to be agreed upon and adopted, if ever. Instead of standardization, which is by definition provider-centric, we advocate a user-centric approach that gives users an unprecedented level of control over the virtualization layer. We introduce the Xen-Blanket, a thin, immediately deployable virtualization layer that can homogenize today's diverse cloud infrastructures. We have deployed the Xen-Blanket across Amazon's EC2, an enterprise cloud, and a private setup at Cornell University. We show that a user-centric approach to homogenize clouds can achieve similar performance to a paravirtualized environment while enabling previously impossible tasks like cross-provider live migration. The Xen-Blanket also allows users to exploit resource management opportunities like oversubscription, and ultimately can reduce costs for users.
Molecular Dynamics Simulations to Investigate the Aggregation Behaviors of the Aß(17–42) Oligomers (2009)

The amyloid beta-peptides (Abetas) are the main protein components of amyloid deposits in Alzheimer's disease (AD). Detailed knowledge of the structure and assembly dynamics of Abeta is important for the development of properly targeted AD therapeutics. So far, the process of the monomeric Abeta assembling into oligomeric fibrils and the mechanism underlying the aggregation process remain unclear. In this study, several molecular dynamics simulations were conducted to investigate the aggregation behaviors of the Abeta(17-42) oligomers associated with various numbers of monomers (dimer, trimer, tetramer, and pentamer). Our results showed that the structural stability of the Abeta(17-42) oligomers increases with increasing the number of monomer. We further demonstrated that the native hydrophobic contacts are positive correlated with the beta-sheet contents, indicating that hydrophobic interaction plays an important role in maintaining the structural stability of the Abeta(17-42) oligomers, particularly for those associated with more monomers. Our results also showed that the stability of the C-terminal hydrophobic segment 2 (residues 30-42) is higher than that of the N-terminal hydrophobic segment 1 (residues 17-21), suggesting that hydrophobic segment 2 may act as the nucleation site for aggregation. We further identified that Met35 residue initiates the hydrophobic interactions and that the intermolecular contact pairs, Gly33-Gly33 and Gly37-Gly37, form a stable "molecular notch", which may mediate the packing of the beta-sheet involving many other hydrophobic residues during the early stage of amyloid-like fibril formation.
Histopathologic-Based Prognostic Factors of Colorectal Cancers Are Associated With the State of the Local Immune Reaction (2011)

Assessment of CD8(+) cytotoxic T lymphocytes in combined tumor regions provides an indicator of tumor recurrence beyond that predicted by AJCC/UICC-TNM staging.
Efficacy of Perioperative Thromboprophylactic Agents in the Maintenance of Anastamotic Patency and Survival of Rat Microvascular Free Groin Flaps (2003)

In this animal model, LMWH and pentoxifylline have significant thrombroprophylactic effects when used individually but not in combination.
Laser diode burn-in and reliability testing (2006)

More than 99 percent of all lasers manufactured in the world today are semiconductor laser diodes. Reliability is a concern in every laser diode application, whether it is a simple $10 laser pointer or a space-qualified optical transmitter link. The commercial success of a laser supplier rests largely on his ability to develop a robust manufacturing process that consistently produces reliable devices combined with the quantitative assurances he can provide to his customers proving the reliability of his devices. Over the past two decades, laser diode reliability testing techniques and equipment have evolved to support the diverse development of laser diodes.
An overview of MDCT for Time Domain Aliasing Cancellation (2014)

Modified Discrete Cosine Transform (MDCT) is a upcoming special transform implemented in areas of audio signal processing and compression. As, the name implies it is the modified form of DCT (Discrete Cosine Transform) that allows overlapping of segments (say 50%) and thereby it helps in avoiding artifacts. MDCT in general is a lapped transform that rectifies the problem of TDAC (Time Domain Aliasing Cancellation) and hence widely used in audio codec (.mp3, .wav) applications. The scope of this paper is to use MDCT in a system that overcomes the problem of TDAC and implementation of different windows those are capable with this transform. Finally, we calculate the MSE (Mean Squared Error) for the system with different inputs stating that perfect audio reconstruction is possible.
High-frequency ultrasound array element using thermoelastic expansion in an elastomeric film (2001)

The thermoelastic effect was used to produce high-frequency, broadband ultrasound in water. A pulsed diode laser, followed by an erbium-doped fiber amplifier, was focused onto a light-absorbing film deposited on a glass substrate. Conversion efficiency was improved by over 20 dB using an elastomeric film instead of a more commonly used metallic one. Radiation pattern measurements show that considerable energy is radiated at +/−45° for frequencies beyond 50 MHz. These results show that the thermoelastic effect can be used to produce phased arrays for high-frequency ultrasound imaging.
Simian immunodeficiency virus from African green monkeys (1988)

Simian immunodeficiency virus (SIV) was isolated from the total peripheral blood mononuclear cell population and the monocyte-macrophage adherent cell population of three seropositive green monkeys originating from Kenya. SIV from these African green monkeys (SIVagm) was isolated and continuously produced with the MOLT-4 clone 8 (M4C18) cell line but not with a variety of other cells including HUT-78, H9, CEM, MT-4, U937, and uncloned MOLT-4 cells. Once isolated, these SIVagm isolates were found to replicate efficiently in M4C18, SupT1, MT-4, U937, and Jurkat-T cells but much less efficiently if at all in HUT-78, H9, CEM, and MOLT-4 cells. The range of CD4+ cells fully permissive for replication of these SIVagm isolates thus differs markedly from that of previous SIV isolates from macaques (SIVmac). These SIVagm isolates had a morphogenesis and morphology like that of human immunodeficiency virus (HIV) and other SIV isolates. Antigens of SIVagm and SIVmac cross-reacted by comparative enzyme-linked immunosorbent assay only with reduced efficiency, and optimal results were obtained when homologous antibody and antigen were used. Western blotting (immunoblotting) of purified preparations of SIVagm isolate 385 (SIVagm385) revealed major viral proteins of 120, 27, and 16 kilodaltons (kDa). The presumed major core protein of 27 kDa cross-reacted antigenically with the corresponding proteins of SIVmac (28 kDa) and HIV-1 (24 kDa) by Western blotting. Hirt supernatant replicative-intermediate DNA prepared from cells freshly infected with SIVagm hybridized to SIVmac and HIV-2 DNA probes. Detection of cross-hybridizing DNA sequences, however, required very low stringency, and the restriction endonuclease fragmentation patterns of SIVagm were not similar to those of SIVmac and HIV-2. The nucleotide sequence of a portion of the pol gene of SIVagm385 revealed amino acid identities of 65% with SIVmac142, 64% with HIV-2ROD, and 56% with HIV-1BRU; SIVagm385 is thus related to but distinct from previously described primate lentiviruses SIVmac, HIV-1, and HIV-2. Precise information on the genetic makeup of these and other SIV isolates will possibly lead to better understanding of the history and evolution of these viruses and may provide insight into the origin of viruses that cause acquired immunodeficiency syndrome in humans.
Vehicle detection and tracking for freeway traffic monitoring (2002)

An image processing and object tracking approach is proposed for the design of a video-based freeway traffic monitoring system. Proper estimation of the traffic speed in different lanes of a freeway allows for timely detection of possible congestions. The proposed method consists of a road modeling stage and a vehicle tracking stage. In the first stage, a three-dimensional model of the background road image is generated. In the tracking stage, each car in the scene is isolated and tracked over many frames. Experimental results on frame sequences taken from Santa Ana area freeways are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Construction of fowlpox virus vectors with intergenic insertions: expression of the beta-galactosidase gene and the measles virus fusion gene (1990)

A DNA fragment from fowlpox virus cloned on a plasmid vector was modified to contain foreign DNA inserts within an intergenic region. In a first step, a 32-base-pair intergenic region from the fowlpox virus genome corresponding to the position of the thymidine kinase locus in the vaccinia virus genome was enlarged to 55 base pairs by site-directed mutagenesis. A unique restriction endonuclease site introduced upstream of the intergenic region was then used to insert various foreign DNA fragments. The lacZ gene encoding beta-galactosidase and the measles virus gene encoding the fusion protein were positioned downstream of two vaccinia virus p7.5 promoter elements in either a direct repeat or inverted repeat orientation. Foreign DNA inserts contained within the fowlpox virus sequence were transferred to the viral genome by homologous recombination occurring in cells infected with a fowlpox virus temperature-sensitive mutant and transfected with both wild-type viral DNA and plasmid DNA. Recombinant viruses were selected for the expression of beta-galactosidase activity by screening for blue plaques in the presence of a chromogenic substrate. Stable recombinants expressing both the lacZ gene and the unselected measles gene were obtained when the p7.5 promoter was present as an inverted repeat. However, when the p7.5 promoter was in the direct repeat orientation, viral recombinants which initially expressed both gene inserts readily deleted the lacZ gene flanked by the promoter repeat. The methods described enable precise insertion and deletion of foreign genes in the fowlpox virus genome and could be applied to other intergenic regions of the same virus as well as other poxviruses.
The effect of tranexamic acid on measured menstrual loss and endometrial fibrinolytic enzymes in dysfunctional uterine bleeding (1994)

Fibrinolytic activity of the menstrual fluid is increased in dysfunctional uterine bleeding (DUB). We measured the effect of tranexamic acid on the menstrual blood loss and endometrial fibrinolytic enzymes in women with DUB (> 80 ml menstrual loss/cycle). Endometrial biopsies were taken between 24 and 36 hours after the onset of menstruation. Enzyme activity was assayed by measuring the rate of conversion of Glu-plasminogen to plasmin, using a chromogenic plasmin substrate. Antigen levels were measured using an enzyme linked immunoassay (ELISA) technique. Tranexamic acid reduced menstrual blood loss by 58% (p < 0.05). Endometrial tissue plasminogen activator activity and antigen and plasminogen activator inhibitor--type 1 antigen levels were significantly decreased by tranexamic acid. The effect of tranexamic acid on the fibrinolytic enzymes at local endometrial level may be responsible for its success in the treatment of menorrhagia.
A dataset for Movie Description (2015)

Audio Description (AD) provides linguistic descriptions of movies and allows visually impaired people to follow a movie along with their peers. Such descriptions are by design mainly visual and thus naturally form an interesting data source for computer vision and computational linguistics. In this work we propose a novel dataset which contains transcribed ADs, which are temporally aligned to full length HD movies. In addition we also collected the aligned movie scripts which have been used in prior work and compare the two different sources of descriptions. In total the MPII Movie Description dataset (MPII-MD) contains a parallel corpus of over 68K sentences and video snippets from 94 HD movies. We characterize the dataset by benchmarking different approaches for generating video descriptions. Comparing ADs to scripts, we find that ADs are far more visual and describe precisely what is shown rather than what should happen according to the scripts created prior to movie production.
Effects of Cromakalim and Nicorandil on Intraocular Pressure After Topical Administration in Rabbit Eyes (1995)

In the study two potassium channel activators, cromakalim and nicorandil, were investigated in rabbits using three different levels of intraocular pressures (IOPs), including alpha-chymotrypsin-induced ocular hypertension, hypotension (IOP recovery method) and normal tension. Cromakalim significantly increased IOP during the initial period in normotensive and hypotensive rabbits, but in the later time, reduced IOP in the alpha-chymotrypsin-induced model. Nicorandil had a similar but less potent effect. In addition, cromakalim also affected ocular blood flows, which had a trend to reduce blood flow about 2-3 hr later, after topical administration of the eyedrop. Two possible mechanisms for increasing IOP effect of potassium channel activators were: (a) enhancing the formation of aqueous humor; (b) relaxing the trabecular meshwork to reduce the outflow of aqueous humor.
Organosilane deposition for microfluidic applications (2011)

Treatment of surfaces to change the interaction of fluids with them is a critical step in constructing useful microfluidics devices, especially those used in biological applications. Silanization, the generic term applied to the formation of organosilane monolayers on substrates, is both widely reported in the literature and troublesome in actual application for the uninitiated. These monolayers can be subsequently modified to produce a surface of a specific functionality. Here various organosilane deposition protocols and some application notes are provided as a basis for the novice reader to construct their own silanization procedures, and as a practical resource to a broader range of techniques even for the experienced user.
Designs of terahertz waveguides for efficient parametric terahertz generation (2003)

We show that for a slab waveguide, while pump and idler waves are weakly affected by the waveguide, their parametrically generated terahertz (THz) wave propagates in the form of multimodes. These waves may destructively interfere with one another in terms of their phases, resulting in inefficient THz parametric conversion. To avoid this problem, we designed a THz slab or rib waveguide that supports a quasi-single or single mode. Using these waveguides, the threshold powers for achieving oscillations can be significantly reduced due to the waveguide confinement of the THz waves. In addition, modal indices of refraction can be tailored for achieving phase matching without complicated periodic poling.