gebhart/patrepeval huggingface dataset:
(+)-Pinoresinol/(+)-Lariciresinol Reductase from Forsythia intermedia (1996)

Lignans are a widely distributed class of natural products, whose functions and distribution suggest that they are one of the earliest forms of defense to have evolved in vascular plants; some, such as podophyllotoxin and enterodiol, have important roles in cancer chemotherapy and prevention, respectively. Entry into lignan enzymology has been gained by the approximately 3000-fold purification of two isoforms of (+)-pinoresinol/(+)-lariciresinol reductase, a pivotal branchpoint enzyme in lignan biosynthesis. Both have comparable ( approximately 34.9 kDa) molecular mass and kinetic (Vmax/Km) properties and catalyze sequential, NADPH-dependent, stereospecific, hydride transfers where the incoming hydride takes up the pro-R position. The gene encoding (+)-pinoresinol/(+)-lariciresinol reductase has been cloned and the recombinant protein heterologously expressed as a functional beta-galactosidase fusion protein. Its amino acid sequence reveals a strong homology to isoflavone reductase, a key branchpoint enzyme in isoflavonoid metabolism and primarily found in the Fabaceae (angiosperms). This is of great evolutionary significance since both lignans and isoflavonoids have comparable plant defense properties, as well as similar roles as phytoestrogens. Given that lignans are widespread from primitive plants onwards, whereas the isoflavone reductase-derived isoflavonoids are mainly restricted to the Fabaceae, it is tempting to speculate that this branch of the isoflavonoid pathway arose via evolutionary divergence from that giving the lignans.
Three-dimensional optical storage inside transparent materials (1996)

We present a novel method for three-dimensional optical data storage that has submicrometer size resolution, provides a large contrast in index of refraction, and is applicable to a wide range of transparent materials. Bits are recorded by use of a 0.65-N.A. objective to focus 100-fs laser pulses inside the material. The laser pulse produces a submicrometer-diameter structurally altered region with high contrast in index of refraction. We record binary information by writing such bits in multiple planes and read it out with a microscope objective with a short depth of field. We demonstrate data storage and retrieval with 2-microm in-plane bit spacing and 15-microm interplane spacing (17 Gbits/cm(3)). Scanning electron microscopy and atomic force microscopy show structural changes confined to an area 200 nm in diameter.
MultiFab (2015)

We have developed a multi-material 3D printing platform that is high-resolution, low-cost, and extensible. The key part of our platform is an integrated machine vision system. This system allows for self-calibration of printheads, 3D scanning, and a closed-feedback loop to enable print corrections. The integration of machine vision with 3D printing simplifies the overall platform design and enables new applications such as 3D printing over auxiliary parts. Furthermore, our platform dramatically expands the range of parts that can be 3D printed by simultaneously supporting up to 10 different materials that can interact optically and mechanically. The platform achieves a resolution of at least 40 μm by utilizing piezoelectric inkjet printheads adapted for 3D printing. The hardware is low cost (less than $7,000) since it is built exclusively from off-the-shelf components. The architecture is extensible and modular -- adding, removing, and exchanging printing modules can be done quickly. We provide a detailed analysis of the system's performance. We also demonstrate a variety of fabricated multi-material objects.
Discriminative Reranking for Natural Language Parsing (2005)

This article considers approaches which rerank the output of an existing probabilistic parser. The base parser produces a set of candidate parses for each input sentence, with associated probabilities that define an initial ranking of these parses. A second model then attempts to improve upon this initial ranking, using additional features of the tree as evidence. The strength of our approach is that it allows a tree to be represented as an arbitrary set of features, without concerns about how these features interact or overlap and without the need to define a derivation or a generative model which takes these features into account. We introduce a new method for the reranking task, based on the boosting approach to ranking problems described in Freund et al. (1998). We apply the boosting method to parsing the Wall Street Journal treebank. The method combined the log-likelihood under a baseline model (that of Collins [1999]) with evidence from an additional 500,000 features over parse trees that were not included in the original model. The new model achieved 89.75% F-measure, a 13% relative decrease in F-measure error over the baseline model's score of 88.2%. The article also introduces a new algorithm for the boosting approach which takes advantage of the sparsity of the feature space in the parsing data. Experiments show significant efficiency gains for the new algorithm over the obvious implementation of the boosting approach. We argue that the method is an appealing alternative-in terms of both simplicity and efficiency-to work on feature selection methods within log-linear (maximum-entropy) models. Although the experiments in this article are on natural language parsing (NLP), the approach should be applicable to many other NLP problems which are naturally framed as ranking tasks, for example, speech recognition, machine translation, or natural language generation.
Interaction of diiodothyronines with isolated cytochromec oxidase (1994)

Diiodothyronines (3,3'-T2 and 3,5-T2) stimulate the activity of isolated cytochrome c oxidase (COX) from bovine heart mitochondria. Maximal stimulation of activity (about 50%) is obtained with 3,3'-T2 at pH 6.4 and with 3,5-T2 at pH 7.4. In contrast, 3,5,3'-triiodothyronine (T3) exhibited no or little stimulation of COX activity. Binding of the hormones to COX leads to conformational changes as shown by modified visible spectra of the oxidized enzyme. It is suggested that 'short-term' effects of thyroid hormones on mitochondrial respiration are at least partly due to the allosteric interaction of diiodothyronines with the COX complex.
Circulating endothelin in acute ischaemic syndromes. (1992)

Plasma endothelin is raised in chronic heart failure and in the aftermath of acute myocardial infarction but not in stable or unstable angina. After myocardial infarction endothelin concentrations are raised whereas concentrations of atrial natriuretic factor are relatively low. The role of endothelin in the pathogenesis of acute myocardial infarction and its interactions with other humoral factors require further investigation.
Compressive 4D spectro-volumetric imaging (2016)

In this Letter, we present a method for hyperspectral imaging of three-dimensional objects. A compressive sensing approach is utilized to remedy the acquisition effort required to capture the large amount of data. The spectral dimension is compressively sensed by means of a liquid crystal-based encoder, and the volumetric data are captured using a synthetic aperture integral imaging setup. We demonstrate reconstruction of spectro-volumetric tesseracts with hundreds of spectral bands at different depths without compromise of spatial resolution.
Glucagon‐like Peptide‐1 and Myocardial Protection: More than Glycemic Control (2009)

Pharmacologic intervention for the failing heart has traditionally targeted neurohormonal activation and ventricular remodeling associated with cardiac dysfunction. Despite the multitude of agents available for the treatment of heart failure, it remains a highly prevalent clinical syndrome with substantial morbidity and mortality, necessitating alternative strategies of targeted management. One such area of interest is the ability to modulate myocardial glucose uptake and its impact on cardioprotection. Glucose-insulin-potassium (GIK) infusions have been studied for decades, with conflicting results regarding benefit in acute myocardial infarction. Based on the same concepts, glucagon-like peptide-1-[7-36] amide (GLP-1) has recently been demonstrated to be a more effective alternative in left ventricular (LV) systolic dysfunction. This paper provides a review on the current evidence supporting the use of GLP-1 in both animal models and humans with ischemic and nonischemic cardiomyopathy.
Starvation-dependent differential stress resistance protects normal but not cancer cells against high-dose chemotherapy (2008)

Strategies to treat cancer have focused primarily on the killing of tumor cells. Here, we describe a differential stress resistance (DSR) method that focuses instead on protecting the organism but not cancer cells against chemotherapy. Short-term starved S. cerevisiae or cells lacking proto-oncogene homologs were up to 1,000 times better protected against oxidative stress or chemotherapy drugs than cells expressing the oncogene homolog Ras2(val19). Low-glucose or low-serum media also protected primary glial cells but not six different rat and human glioma and neuroblastoma cancer cell lines against hydrogen peroxide or the chemotherapy drug/pro-oxidant cyclophosphamide. Finally, short-term starvation provided complete protection to mice but not to injected neuroblastoma cells against a high dose of the chemotherapy drug/pro-oxidant etoposide. These studies describe a starvation-based DSR strategy to enhance the efficacy of chemotherapy and suggest that specific agents among those that promote oxidative stress and DNA damage have the potential to maximize the differential toxicity to normal and cancer cells.
Discovery of Novel Cyanamide-Based Inhibitors of Cathepsin C (2010)

The discovery of potent and selective cyanamide-based inhibitors of the cysteine protease cathepsin C is detailed. Optimization of the template with regard to plasma stability led to the identification of compound 17, a potent cathepsin C inhibitor with excellent selectivity over other cathepsins and potent in vivo activity in a cigarette smoke mouse model.
NLRX1 Regulates Effector and Metabolic Functions of CD4+ T Cells (2017)

Nucleotide oligomerization domain-like receptor X1 (NLRX1) has been implicated in viral response, cancer progression, and inflammatory disorders; however, its role as a dual modulator of CD4<sup>+</sup> T cell function and metabolism has not been defined. The loss of NLRX1 results in increased disease severity, populations of Th1 and Th17 cells, and inflammatory markers (IFN-γ, TNF-α, and IL-17) in mice with dextran sodium sulfate-induced colitis. To further characterize this phenotype, we used in vitro CD4<sup>+</sup> T cell-differentiation assays and show that NLRX1-deficient T cells have a greater ability to differentiate into an inflammatory phenotype and possess greater proliferation rates. Further, NLRX1<sup>-/-</sup> cells have a decreased responsiveness to immune checkpoint pathways and greater rates of lactate dehydrogenase activity. When metabolic effects of the knockout are impaired, NLRX1-deficient cells do not display significant differences in differentiation or proliferation. To confirm the role of NLRX1 specifically in T cells, we used an adoptive-transfer model of colitis. Rag2<sup>-/-</sup> mice receiving NLRX1<sup>-/-</sup> naive or effector T cells experienced increased disease activity and effector T cell populations, whereas no differences were observed between groups receiving wild-type or NLRX1<sup>-/-</sup> regulatory T cells. Metabolic effects of NLRX1 deficiency are observed in a CD4-specific knockout of NLRX1 within a <i>Citrobacter rodentium</i> model of colitis. The aerobic glycolytic preference in NLRX1<sup>-/-</sup> effector T cells is combined with a decreased sensitivity to immunosuppressive checkpoint pathways to provide greater proliferative capabilities and an inflammatory phenotype bias leading to increased disease severity.
REAL-TIME POLYMERASE CHAIN REACTION ANALYSIS REVEALS AN EVOLUTION OF CYTOKINE MRNA PRODUCTION IN ALLOGRAFT ACCEPTOR MICE1 (2001)

A broad array of cytokine mRNAs may be stockpiled for future use in cardiac allografts, regardless of whether the grafts will be accepted or rejected. This stockpile is continuously replenished for as long as the graft survives, thereby obscuring any changes in immune disposition of the graft recipient toward graft alloantigens. However, such changes can be revealed by challenge with donor alloantigens at a distant site (DTH challenge). In allograft acceptor mice, this disposition evolves from pro-inflammatory to anti-inflammatory.
Topical 5-fluorouracil solution in the treatment of warts—clinical experience and percutaneous absorption (1988)

Disseminated warts in six patients were pre-treated with topical 5-fluorouracil solution three times daily for 5 consecutive days. Curettage was then carried out under local anaesthesia. During pre-treatment less than 0.1% of the dose applied was absorbed through the skin. The warts had not reappeared in 5 of the 6 patients at follow-up 1 year later.
cis Element Decoy Against Nuclear Factor-κB Attenuates Development of Experimental Autoimmune Myocarditis in Rats (2001)

Nuclear factor-kappaB (NFkappaB) plays a significant role in the coordinated transactivation of cytokine, inducible NO synthase (iNOS), and adhesion molecule genes. Although inflammation is an essential pathological feature of myocarditis, the role of NFkappaB in this process remains obscure. We examined the role of NFkappaB in the progression of rat experimental autoimmune myocarditis (EAM) and tested the hypothesis that NFkappaB blockade with a decoy against the cis element of NFkappaB can prevent the progression of EAM. Lewis rats were immunized with purified porcine cardiac myosin to establish EAM on day 0. NFkappaB decoy was infused into the rat coronary artery on day 0 (group NF0), 7 (group NF7), or 14 (group NF14) and harvested on day 21. Scrambled decoy was infused on day 0 (group SD0), 7 (group SD7), or 14 (group SD14) and served for control groups. The ratios of myocarditis-affected areas to the ventricular cross-sectional area of all treatment groups were significantly lower than those of the control groups (group NF0, 33+/-18% versus SD0, 53+/-14%; group NF7, 19+/-15% versus SD7, 50+/-16%; and group NF14, 34+/-10% versus SD14, 52+/-14%). Immunohistochemical and immunoblot analyses showed expression of ICAM-1, iNOS, IL-2, and TNFalpha in myocardium of scrambled decoy groups, and this expression was effectively suppressed by NFkappaB decoy treatment. Thus, we found that NFkappaB is a key regulator in the progression of EAM and that in vivo transfection of NFkappaB decoy reduces the severity of EAM.
Development and Characterization of a Potent Immunoconjugate Targeting the Fn14 Receptor on Solid Tumor Cells (2011)

TNF-like weak inducer of apoptosis (TWEAK) and fibroblast growth factor (FGF)-inducible 14 (Fn14) are a TNF superfamily ligand-receptor pair involved in many cellular processes including proliferation, migration, differentiation, inflammation, and angiogenesis. The Fn14 receptor is expressed at relatively low levels in normal tissues, but it is known to be dramatically elevated in a number of tumor types, including brain and breast tumors. Thus, it seems to be an excellent candidate for therapeutic intervention. We first analyzed Fn14 expression in human tumor cell lines. Fn14 was expressed in a variety of lines including breast, brain, bladder, skin, lung, ovarian, pancreatic, colon, prostate, and cervical cancer cell lines. We then developed an immunoconjugate containing a high-affinity anti-Fn14 monoclonal antibody (ITEM-4) conjugated to recombinant gelonin (rGel), a highly cytotoxic ribosome-inactivating N-glycosidase. Both ITEM-4 and the conjugate were found to bind to cells to an equivalent extent. Confocal microscopic analysis showed that ITEM4-rGel specifically and rapidly (within 2 hours) internalized into Fn14-positive T-24 bladder cancer cells but not into Fn14-deficient mouse embryonic fibroblasts. Cytotoxicity studies against 22 different tumor cell lines showed that ITEM4-rGel was highly cytotoxic to Fn14-expressing cells and was 8- to 8 × 10(4)-fold more potent than free rGel. ITEM4-rGel was found to kill cells by inducing apoptosis with high-mobility group box 1 protein release. Finally, ITEM4-rGel immunoconjugate administration promoted long-term tumor growth suppression in nude mice bearing T-24 human bladder cancer cell xenografts. Our data support the use of an antibody-drug conjugate approach to selectively target and inhibit the growth of Fn14-expressing tumors.
Integrated circuit yield statistics (1983)

The random failure statistics for the yield of mass-produced semiconductor integrated circuits are derived by considering defect and fault formation during the manufacturing process. This approach allows the development of a yield theory that includes many models that have been used previously and also results in a practical control model for integrated circuit manufacturing. Some simpler formulations of yield theory that have been described in the literature are compared to the model. Application of the model to yield management are discussed and examples given.
Inhibition of the alternative pathway of human complement by structural analogues of sialic acid. (1988)

Liposomes were used to determine whether gangliosides containing certain structurally defined analogues of sialic acid could inhibit activation of the alternative pathway of human C. Gangliosides containing sialic acid residues with modifications in the N-acetyl group, carboxyl group, or polyhydroxylated tail were either isolated from natural sources or prepared by chemical modification of the native sialic acid structure. Sialic acid lost more than 90% of its inhibitory activity after removal of just the C9 carbon from the polyhydroxylated tail. Sialic acid was also unable to inhibit activation after converting the carboxyl group to a hydroxymethyl group. Galactose oxidase/NaB3H4 treatment of liposomes containing gangliosides with native or modified sialic acid residues confirmed that neither modification altered the amount of gangliosides exposed at the liposome surface. Changing the N-linked acetyl group to a glycolyl group had no effect on the inhibitory activity of sialic acid. These data further define the structural features of sialic acid that are important in regulation of alternative pathway activation. Both the C9 carbon of the polyhydroxylated tail and the carboxyl group are essential for this function; whereas, the N-linked acetyl group may be modified without loss of activity.
Novel alternating phase-shift mask with improved phase accuracy (1997)

We developed an alternating phase shift mask that offers a sufficient phase accuracy for manufacturing sub-0.18 micrometer devices with 248 nm deep-UV lithography. This mask has a Cr/spin-on-glass/quartz structure. Our mask fabrication process utilizes some new techniques which include the use of a SOG shifter with extra thickness, a two step SOG etching, and an additional wet etchign process for phase adjustment. Our process showed a good performance, and a phase controllability of 180 plus or minus 0.7 degrees was achieved. Phase uniformity was less than 3 degrees over a 100 mm square area. It was nearly equal to the uniformity of the SOG thickness. These results prove that the additional etching process is very effective at improving phase accuracy.
Transforming growth factor-beta stimulates wound healing and modulates extracellular matrix gene expression in pig skin: incisional wound model. (1991)

Enhanced wound healing is elicited by exogenous administration of transforming growth factor- beta 1 (TGF- beta 1) in split-thickness, excisional wounds in the pig (Quaglino, Lab Invest 63:307-319, 1990). A study was designed to investigate if the selective and localized effects of TGF-beta 1 found in the previous model were dependent upon the type of wound or could be considered a more general effect of the cytokine. Transdermal, sutured incisions in the pig were evaluated by conventional histology and by in situ hybridization to reveal locally affected gene expression of collagen, elastin, fibronectin, stromelysin, TGF- beta 1, and basic fibroblast growth factor. Granulation tissue formation was markedly enhanced at 6 d by a single injection of recombinant human TGF beta 1 at the time of wound closure. Although granulation tissue was confined within the margins of the incisional wound, prominent differences in hybridization signals were observed between control and treated wounds. The stimulatory effect of TGF- beta 1 on granulation tissue formation was accompanied by a distinct enhancement in cells expressing mRNA for several different extracellular matrix proteins including collagens type I and III and elastin, whereas a single injection of human recombinant TGF beta 1 (4 micrograms) at the wound site diminished the expression of the neutral metalloprotease, stromelysin, and enhanced the frequency and intensity of cells expressing TGF- beta 1. The data reinforce the concept that TGF- beta 1 can act as a potent, auto-inductive modulator of connective tissue remodeling during the repair process.
Altering Cognitive and Brain States Through Cortical Entrainment (2014)

Introduction: Presentation of binaural auditory beats (BAB) can entrain brain rhythms, such as beta (~12-20 Hz) or theta (~4-7 Hz).For example, in a pilot study, we found that BAB stimulation in the beta range effected task-related changes in beta waves, whereas stimulation in the theta range affected theta-wave activity.The present study replicates and extends this work to examine the effect of BAB stimulation on working memory performance, as well as oscillatory brain activity. Methods:We recorded event-related potential (ERP) responses from 256 locations on the head surface as participants complete a working memory (N-back) task.In this task, participants view a series of letters.The task is to indicate when a letter is the same as a letter that appeared N trials back (e.g., 2 trials back).BAB stimulation is delivered stereophonically through ear buds.Results: Behavioral outcomes include accuracy of target detection and reaction time.These data indicate effects of BAB stimulation on working memory.Wavelet decomposition is used to quantify changes in amplitude of EEG activity within different frequency bands and across time.Averaged EEG, time-locked to the target, captures changes in visual attention to targets.We have three predictions: (i) the BAB procedure will induce greater levels or beta or theta (depending on condition), and (ii) entrainment of beta will affect performance on the one-back task, whereas (iii) entrainment of theta will have little or no effect. Conclusion:Given that different brain rhythms appear to be associated with different cognitive functions, such as improved attentional focus, there is growing interest in the use of BAB stimulation to alter brain and cognitive function.In the present experiment, we test the hypothesis that beta stimulation will lead to increased beta-wave activity and improved performance in a working memory task.This study is part of a larger project that investigates the use of BAB to affect working memory and the learning and retention of new words.