gebhart/patrepeval huggingface dataset:
Grape-Derived Polyphenolics Prevent A Oligomerization and Attenuate Cognitive Deterioration in a Mouse Model of Alzheimer's Disease (2008)

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive impairments in memory and cognition. Extracellular accumulation of soluble high-molecular-weight (HMW) Abeta oligomers has been proposed to be largely responsible for AD dementia and memory deficits in the Tg2576 mice, a model of AD. In this study, we found that a naturally derived grape seed polyphenolic extract can significantly inhibit amyloid beta-protein aggregation into high-molecular-weight oligomers in vitro. When orally administered to Tg2576 mice, this polyphenolic preparation significantly attenuates AD-type cognitive deterioration coincidentally with reduced HMW soluble oligomeric Abeta in the brain. Our study suggests that grape seed-derived polyphenolics may be useful agents to prevent or treat AD.
Tunable Coupling in Circuit Quantum Electrodynamics Using a Superconducting Charge Qubit with aV-Shaped Energy Level Diagram (2011)

We introduce a new type of superconducting charge qubit that has a V-shaped energy spectrum and uses quantum interference to provide independently tunable qubit energy and coherent coupling to a superconducting cavity. Dynamic access to the strong coupling regime is demonstrated by tuning the coupling strength from less than 200 kHz to greater than 40 MHz. This tunable coupling can be used to protect the qubit from cavity-induced relaxation and avoid unwanted qubit-qubit interactions in a multiqubit system.
BH3 mimetic therapy: an emerging and promising approach to treating chronic lymphocytic leukemia (2013)

Chronic lymphocytic leukemia (CLL) is a disease characterized by inappropriate survival, and consequent accumulation in vivo , of genetically aberrant mature B lymphocytes. Central to maintaining the normal balance between life and death in most mammalian cells, including B lymphocytes, are intracellular proteins belonging to the Bcl-2 family. It is now 25 years since the discovery that Bcl-2 functions to protect cells from undergoing apoptosis [1]. Overexpression of Bcl-2 is associated with the development of various malignancies including follicular lymphoma and CLL. Moreover, high Bcl-2 expression confers resistance to traditional chemotherapeutics [2] and is associated with poor prognosis in selected diseases. Th ese features have made Bcl-2 an attractive therapeutic target especially in patients for whom cytotoxic treatment is either ineff ective or poorly tolerated. Homology with Bcl-2 defi nes a broad family of proteins that are key regulators of apoptosis. While some members of this family function similarly to Bcl-2 in blocking apoptosis (Bcl-x L , Bcl-W, Mcl-1, A1), others (Bax, Bak) mediate apoptosis by disrupting the integrity of the mitochondrial membrane, leading to caspase activation, which commits the cell to apoptotic death [3]. Still other Bcl-2-family members, the BH3-only proteins (including Bim, Bid, Bad, Noxa, Puma), are natural antagonists of Bcl-2 and its pro-survival relatives. Th e BH3-only proteins function as the physiological triggers for the induction of apoptosis [3]. As is the case for most critical cellular processes, whether a cell undergoes apoptosis is tightly regulated by the balance between Bcl-2-like prosurvival proteins and the activity of BH3-only proteins. In CLL, overexpression of Bcl-2 is universal, sequestering and neutralizing the activity of the BH3-only proteins, such as Bim. Bcl-2 thereby prevents the malignant cells from undergoing apoptosis despite endogenous and exogenous stresses, which would normally trigger cell death. Th is creates a scenario whereby the CLL cells remain alive inappropriately, but are paradoxically “ primed for death ” if the delicate balance between pro-survival and BH3-only proteins is perturbed [4].
Signal Processing for Improving Field Cross-correlation Function in Optical Coherence Tomography (1998)

Signal processing is used to enhance the field cross-correlation function in optical coherence tomography (OCT). This paper shows how the spurious signal resulting from an imperfect spectrum of broadband emitters can be cleaned up. It also demonstrates that, using a fairly simple deconvolution procedure, a factor of two enhancement in depth resolution can be achieved. An example of the enhanced resolution is shown using the signal from two microscope cover slides.
Probabilistic 3-D motion estimation for rolling shutter video rectification from visual and inertial measurements (2012)

Video acquired by handheld CMOS cameras may suffer from rolling shutter artifacts. Rolling shutter artifacts, which are due to the rows in the image sensor array being exposed sequentially from top to bottom, increase with the speed of the relative motion between the scene and camera. To rectify these artifacts, one needs to recover the projection parameters for each row. In this paper, we propose a probabilistic method to estimate 3-D camera rotation by using video and inertial measurements on the handheld platform, such as a smart phone. Our contributions are (1) an efficient sensor fusion algorithm using an extended Kalman filter, and (2) a quality assessment method using vanishing point detection. Experiments indicate that the proposed sensor fusion algorithm produces a more accurate orientation estimate and better rectifies rolling shutter artifacts.
Why are growth factors important in oligodendrocyte physiology? (2000)

Recent studies in chicken, rodents and transgenic mice have provided new insight on the nature of factors essential to oligodendrocyte development. Here we first review how sonic hedgehog (shh) graded signalling induces emergence of oligodendrocytes in the embryonic spinal cord from birds to man. We then discuss the way in which thyroid hormone successively signals different thyroid receptors to control fate determination, growth and differentiation in the oligodendrocyte lineage. Platelet-derived growth factor (PDGF) is a potent regulator of oligodendrocyte progenitor (OP) migration and proliferation, while insulin-like growth factor 1 (IGF-1) acts both on neurons and myelin-forming cells to promote myelination. The balance between OP proliferation and differentiation appears to be controlled by different sets of growth factors locally synthesized in the central nervous system (CNS) as well as glutamate. In experimental models of multiple sclerosis (MS), the neuregulin isoform glial growth factor 2, IGF-1 and some neurotrophins can promote remyelination after an episode of inflammatory demyelination. A future challenge is to determine how to induce multipotential neural precursors to generate migratory OP and enhance the remyelination process in the adult CNS.
Prevalence of and Risk Factors for Hepatic Steatosis in Northern Italy (2000)

Steatosis is frequently encountered in healthy persons and is almost always present in obese persons who drink more than 60 g of alcohol per day. Steatosis is more strongly associated with obesity than with heavy drinking, suggesting a greater role of overweight than alcohol consumption in accumulation of fat in the liver.
Identification of Host Proteins Required for HIV Infection Through a Functional Genomic Screen (2008)

HIV-1 exploits multiple host proteins during infection. We performed a large-scale small interfering RNA screen to identify host factors required by HIV-1 and identified more than 250 HIV-dependency factors (HDFs). These proteins participate in a broad array of cellular functions and implicate new pathways in the viral life cycle. Further analysis revealed previously unknown roles for retrograde Golgi transport proteins (Rab6 and Vps53) in viral entry, a karyopherin (TNPO3) in viral integration, and the Mediator complex (Med28) in viral transcription. Transcriptional analysis revealed that HDF genes were enriched for high expression in immune cells, suggesting that viruses evolve in host cells that optimally perform the functions required for their life cycle. This effort illustrates the power with which RNA interference and forward genetics can be used to expose the dependencies of human pathogens such as HIV, and in so doing identify potential targets for therapy.
Transcription-based amplification system and detection of amplified human immunodeficiency virus type 1 with a bead-based sandwich hybridization format. (1989)

The in vitro amplification of biologically important nucleic acids has proceeded principally by a strategy of DNA replication. Polymerase chain reaction was the first such protocol to achieve this goal. In this report, a transcription-based amplification system (TAS) is described. Each cycle of the TAS is composed of two steps. The first is a cDNA synthesis step that produces one copy of a double-stranded DNA template for each copy of RNA or DNA target nucleic acid. During the course of this cDNA synthesis step, a sequence recognized by a DNA-dependent RNA polymerase is inserted into the cDNA copy of the target sequence to be amplified. The second step is the amplification of the target sequence by the transcription of the cDNA template into multiple copies of RNA. This procedure has been applied to the detection of human immunodeficiency virus type 1 (HIV-1)-infected cells. After four cycles of TAS, the amplification of the vif region of the HIV-1 RNA genome was measured to be, on the average, 38- to 47-fold per cycle, resulting in a 2-5 x 10(6)-fold increase in the copy number of the original target sequence. This amplification by the TAS protocol allows the detection of fewer than one HIV-1-infected CEM cell in a population of 10(6) uninfected CEM cells. Detection of the TAS-generated RNA from HIV-1-infected cells can easily be accomplished by means of a bead-based sandwich hybridization protocol, which provides additional specificity for the identification of the amplified HIV-1-specific sequence.
Max-min Fair Rate Allocation in Multi-hop Wireless Ad Hoc Networks (2006)

In this paper, a price-based rate allocation scheme for multi-hop wireless ad hoc networks is proposed. To accurately reflect the clique constraint of wireless ad hoc networks, the clique-based price is proposed to act as the congestion signal, which controls the end-to-end rates of multi-hop flows. Through simulation, the proposed scheme is shown to be able to effectively distribute the bandwidth, according to max-min fair criterion, to multi-hop flows from the end-to-end perspective
Engineering of 2,3-Butanediol Dehydrogenase To Reduce Acetoin Formation by Glycerol-Overproducing, Low-AlcoholSaccharomyces cerevisiae (2009)

Engineered Saccharomyces cerevisiae strains overexpressing GPD1, which codes for glycerol-3-phosphate dehydrogenase, and lacking the acetaldehyde dehydrogenase Ald6 display large-scale diversion of the carbon flux from ethanol toward glycerol without accumulating acetate. Although GPD1 ald6 strains have great potential for reducing the ethanol contents in wines, one major side effect is the accumulation of acetoin, having a negative sensory impact on wine. Acetoin is reduced to 2,3-butanediol by the NADH-dependent 2,3-butanediol dehydrogenase Bdh1. In order to investigate the influence of potential factors limiting this reaction, we overexpressed BDH1, coding for native NADH-dependent Bdh1, and the engineered gene BDH1(221,222,223), coding for an NADPH-dependent Bdh1 enzyme with the amino acid changes 221 EIA 223 to 221 SRS 223, in a glycerol-overproducing wine yeast. We have shown that both the amount of Bdh1 and the NADH availability limit the 2,3-butanediol dehydrogenase reaction. During wine fermentation, however, the major limiting factor was the level of synthesis of Bdh1. Consistent with this finding, the overproduction of native or engineered Bdh1 made it possible to redirect 85 to 90% of the accumulated acetoin into 2,3-butanediol, a compound with neutral sensory characteristics. In addition, the production of diacetyl, a compound causing off-flavor in alcoholic beverages, whose production is increased in glycerol-overproducing yeast cells, was decreased by half. The production of higher alcohols and esters, which was slightly decreased or unchanged in GPD1 ald6 cells compared to that in the control cells, was not further modified in BDH1 cells. Overall, rerouting carbons toward glycerol and 2,3-butanediol represents a new milestone in the engineering of a low-alcohol yeast with desirable organoleptic features, permitting the decrease of the ethanol contents in wines by up to 3 degrees.
Accurate Georegistration of Point Clouds Using Geographic Data (2013)

The Internet contains a wealth of rich geographic information about our world, including 3D models, street maps, and many other data sources. This information is potentially useful for computer vision applications, such as scene understanding for outdoor Internet photos. However, leveraging this data for vision applications requires precisely aligning input photographs, taken from the wild, within a geographic coordinate frame, by estimating the position, orientation, and focal length. To address this problem, we propose a system for aligning 3D structure-from-motion point clouds, produced from Internet imagery, to existing geographic information sources, including Google Street View photos and Google Earth 3D models. We show that our method can produce accurate alignments between these data sources, resulting in the ability to accurately project geographic data into images gathered from the Internet, by ``Googling'' a depth map for an image using sources such as Google Earth.
Essential Fatty Acids and the Brain (2003)

The ratio of membrane omega-3 to omega-6 PUFAs can be modulated by dietary intake. This ratio influences neurotransmission and prostaglandin formation, processes that are vital in the maintenance of normal brain function.
Effects of the immunomodulating agent R837 on acute and latent herpes simplex virus type 2 infections (1989)

R837 is an immune modulator with no in vitro activity against herpes simplex virus (HSV). We evaluated topical R837 as therapy for genital HSV type 2 infection using the guinea pig model of this disease. Furthermore, we investigated the effect of R837 therapy on acute and latent neural HSV infections. Therapy initiated 12 h after viral inoculation and given twice a day significantly reduced the acute neural infection so that HSV was recovered from only 1 of 64 neural tissue specimens obtained from R837 recipients compared with 43 of 56 specimens obtained from placebo recipients (P less than 0.0001). R837 initiated 36 h after HSV inoculation and given once a day also significantly reduced the total mean lesion score of the acute disease from 14.1 +/- 4.3 to 2.6 +/- 5.3 (P less than 0.0001) and shortened the period of vaginal HSV shedding from 6.9 +/- 1.7 to 3.2 +/- 1.4 days (P less than 0.001). R837-treated animals also developed fewer HSV recurrences than did controls (2.0 +/- 1.7 versus 5.1 +/- 1.7; P less than 0.0002). Latent HSV was detected in 23 of 24 dorsal root ganglia explant cultures from placebo recipients but in only 2 of 30 cultures from R837-treated animals, and HSV in these 2 cultures was detectable only with the addition of a demethylating agent. Topical R837 exhibited in vivo anti-HSV activity, reducing both acute and latent neural infections as well as acute and recurrent genital disease.
Copper and iron are mobilized following myocardial ischemia: possible predictive criteria for tissue injury. (1993)

Direct evidence for substantial mobilization of copper in the coronary flow immediately following prolonged, but not short, cardiac ischemia is presented. In the first coronary flow fraction (CFF) of reperfusion (0.15 ml), after 35 min of ischemia, the level of copper (as well as of iron) was 8- to 9-fold higher than the preischemic value. The levels in subsequent CFFs decreased and reached the preischemic value, indicating that both metals appear in a burst at the resumption of coronary flow. When the first CFF was used in a reaction mixture containing ascorbate and salicylate, the latter underwent chemical hydroxylation and was converted to its dihydroxybenzoate derivatives. Likewise, this CFF promoted the ascorbate-driven DNA degradation. Subsequent 150 CFFs were serially collected and demonstrated low activities. Following 18 min of ischemia, the copper level in the first CFF of reperfusion was only 15% over the preischemic value. In contrast, the mobilization of iron into coronary flow was significant but markedly lower than after 35 min. The levels of copper and the redox activity of the first CFF correlated well with the degree of loss of cardiac function, after 18 and 35 min of ischemia, respectively. After 18 min of ischemia, cardiac function was about 50% and the damage is considered reversible, whereas after 35 min the functional loss exceeded 80% and is considered irreversible. These results are in accord with the causative role that copper and iron can play in heart injury following ischemia, by virtue of their capacity to catalyze the production of hydroxyl radicals, and could lead to the development of new modalities for intervention in tissue injury.
Immunohistochemical Expression of p16INK4a and bcl-2 According to HPV Type and to the Progression of Cervical Squamous Intraepithelial Lesions (2005)

Inactivation of the cell cycle inhibitor gene p16MTS1 seems to be involved in human papillomavirus (HPV)-related carcinogenesis because E6 and E7 oncoproteins may impair p16INK4a and, indirectly, bcl-2 functions. In this study, we analyzed the role of immunohistochemical expression of p16INK4a and bcl-2 in HPV-infected cervical biopsies as prognostic markers of the progression of squamous intraepithelial lesion (SIL). Sixty-five cervical biopsies were stratified into two subgroups according to the second biopsy: 27 of them maintained a low-grade (LG)-SIL diagnosis, and 38 progressed from LG-SIL to high-grade (HG)-SIL. p16INK4a and bcl-2 quantitative expression levels were measured by the immunoperoxidase method. PCR-DNA techniques were used to detect and type HPV. The Wilcoxon and Fisher exact tests were employed for the statistical analysis. In the group with an LG-SIL diagnosis at the second biopsy, no significant associations were found between p16INK4a and bcl-2 expression and presence of HPV16/18. In the group that progressed to HG-SIL, a significant association was observed between p16INK4a overexpression and HPV16/18 presence (p=0.021), but none with bcl-2 levels. It is concluded that immunohistochemical bcl-2 expression may not be useful for predicting the progression of HPV-related SIL. In contrast, p16INK4a overexpression seemed to be associated with HPV 16 and 18, suggesting that it may be a good marker for predicting SIL progression.
Subhalf-micron gate GaAs MESFET process using phase-shifting-mask technology (2002)

For the purpose of an ultra-high-speed GaAs LSI, the phase-shifting-mask technology has been applied to the fabrication process of subhalf-micron gate GaAs MESFETs. The lithography of gate pattern was performed by the PEL (phase-shifter edge-line) mask technique with the double exposure process using the i-line stepper, where the resist spacing was precisely controlled by the exposure dose. The gate metal of W-Al was then etched by ECR plasma with no under-cut, which resulted in fine gate patterning. GaAs MESFETs fabricated in a 3-inch wafer have shown a good uniformity of Vth as small as 40 mV, and a high gm property of 424 mS/mm with a good uniformity of gm (3.5%) at the gate length of 0.22 mu m.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Emerging Roles of HTRA1 in Musculoskeletal Disease (2013)

High-temperature requirement serine protease A1 (HTRA1) is one of four known proteases belonging to the broadly conserved family of HTRA proteins. Although it was originally considered as representing an important modulator of tumorigenesis, an increasing number of reports have suggested that its influence on human disease may extend beyond cancer. HTRA1 has the capacity to degrade numerous extracellular matrix proteins, and as such, its potential involvement in diseases of the musculoskeletal system has been gaining increased attention. Musculoskeletal disease constitutes a wide variety of degenerative conditions that can manifest themselves in different ways such as joint and back pain, as well as deficiencies in skeletal bone quality, and ultimately result in significant suffering and reduced quality of life. Convincing data now exist to support a detrimental role for HTRA1 in the pathogenesis of joint and intervertebral disk degeneration. However, the function of HTRA1 in other closely related musculoskeletal diseases affecting bone and muscle remains unclear and largely unexplored. To help set the stage for future research, we discuss here some of the recent advances in our understanding of the role played by HTRA1 in musculoskeletal pathology.
Minimum crosstalk switchbox routing (1994)

As technology advances, interconnection wires are placed in closer proximity. Consequently, reduction of crosstalks between interconnection wires becomes an important consideration in VLSI design. In this paper, we study the gridded switchbox routing problems with the objectives of satisfying crosstalk constraints and minimizing the total crosstalk in the nets. We propose a new approach to the problems which utilizes existing switchbox routing algorithms and improves upon the routing results by re-assigning the horizontal and vertical wire segments to rows and columns, respectively, in an interative fashion. This approach can also be applied to the channel routing problem with crosstalk constraints. A novel mixed ILP formulation and effective procedures for reducing the number of variables and constraints in the mixed ILP formulation are then presented. The experimental results are encouraging.
Structured reasoning about actor systems (2013)

The actor model of distributed computing imposes important restrictions on concurrent computations in order to be valid. In particular, an actor language implementation must provide fairness, the property that if a system transition is infinitely often enabled, the transition must eventually happen. Fairness is fundamental to proving progress properties. We show that many properties of actor computation can be expressed and proved at an abstract level, independently of the details of a particular system of actors. As in abstract algebra, we formulate and prove theorems at the most abstract level possible, so that they can be applied at all more refined levels of the theory hierarchy. Our most useful abstract-level theorems concern persistence of actors, conditional persistence of messages, preservation of unique actor identifiers, monotonicity properties of actor local states, guaranteed message delivery, and general consequences of fairness. We apply the general actor theory to a concrete ticker and clock actor system, proving several system-specific properties, including conditional invariants and a progress theorem. We develop our framework within the Athena proof system, in which proofs are both human-readable and machine-checkable, taking advantage of it library of algebraic and relational theories.