gebhart/patrepeval huggingface dataset:
Comparative Analysis of the Receptor-Like Kinase Family in Arabidopsis and Rice[W] (2004)

Receptor-like kinases (RLKs) belong to the large RLK/Pelle gene family, and it is known that the Arabidopsis thaliana genome contains >600 such members, which play important roles in plant growth, development, and defense responses. Surprisingly, we found that rice (Oryza sativa) has nearly twice as many RLK/Pelle members as Arabidopsis does, and it is not simply a consequence of a larger predicted gene number in rice. From the inferred phylogeny of all Arabidopsis and rice RLK/Pelle members, we estimated that the common ancestor of Arabidopsis and rice had >440 RLK/Pelles and that large-scale expansions of certain RLK/Pelle members and fusions of novel domains have occurred in both the Arabidopsis and rice lineages since their divergence. In addition, the extracellular domains have higher nonsynonymous substitution rates than the intracellular domains, consistent with the role of extracellular domains in sensing diverse signals. The lineage-specific expansions in Arabidopsis can be attributed to both tandem and large-scale duplications, whereas tandem duplication seems to be the major mechanism for recent expansions in rice. Interestingly, although the RLKs that are involved in development seem to have rarely been duplicated after the Arabidopsis-rice split, those that are involved in defense/disease resistance apparently have undergone many duplication events. These findings led us to hypothesize that most of the recent expansions of the RLK/Pelle family have involved defense/resistance-related genes.
Induction and nuclear translocation of thioredoxin by oxidative damage in the mouse kidney: independence of tubular necrosis and sulfhydryl depletion. (1997)

Adult T-cell leukemia-derived factor (ADF), originally defined as an interleukin-2 receptor inducer, is a human thioredoxin (TRX). ADF/TRX is a conserved multifunctional reductant presumably associated with redox regulation of the cellular environment; it works in vitro as a cytokine, free radical scavenger, activator of transcription factors, and substrate for several enzymes. In the present series of experiments, we studied the expression and intracellular localization of ADF/TRX in mouse kidney from two different renal tubular injury models: a free radical-associated model with ferric nitrilotriacetate (Fe-NTA) and a free radical-independent model with HgCl2. Markers of oxidative damage, such as 8-hydroxy-2'-deoxyguanosine, thiobarbituric acid-reactive substances, and 4-hydroxy-2-nonenal-modified proteins, were significantly increased in kidney from male C57B/6 mice 1 hour after a single intraperitoneal injection of Fe-NTA (5 mg iron/kg). However, in kidney from mice given a subcutaneous injection of HgCl2 (5 mg Hg/kg), none of these markers were increased, despite tubular necrosis with sulfhydryl depletion. In the Fe-NTA model only, Northern and Western blot analyses of the kidney revealed induction of ADF/TRX (> 2.5-fold) after 16 hours and translocation of ADF/TRX from the cytoplasmic to nuclear fraction (> 3.5-fold) after 24 hours. Immunohistochemistry showed a patchy distribution of ADF/TRX in the normal renal proximal tubules. In ex vivo experiments using serial normal kidney frozen sections, it was found that renal proximal tubules with low expression of ADF/TRX were more vulnerable to oxidative stress mediated by Fe-NTA. Collectively, these data suggest that: (a) ADF/TRX is induced and translocated to nuclei by oxidative damage mediated by Fe-NTA in the renal proximal tubules; (b) induction of ADF/TRX is independent of tubular necrosis or sulfhydryl depletion; and (c) ADF/TRX is involved in the cellular defense mechanisms in vivo against oxidative damage.
Deletion of the 7 Nicotinic Acetylcholine Receptor Gene Improves Cognitive Deficits and Synaptic Pathology in a Mouse Model of Alzheimer's Disease (2009)

It has been recently shown that the Alzheimer's disease (AD) pathogenic peptide amyloid beta(1-42) (Abeta(1-42)) binds to the alpha7 nicotinic acetylcholine receptor (alpha7nAChR) with high affinity and the alpha7nAChR and Abeta(1-42) are both found colocalized in neuritic plaques of human brains with AD. Moreover, the intraneuronal accumulation of Abeta(1-42) was shown to be facilitated by its high-affinity binding to the alpha7nAChR, and alpha7nAChR activation mediates Abeta-induced tau protein phosphorylation. To test the hypothesis that alpha7nAChRs are involved in AD pathogenesis, we used a transgenic mouse model of AD overexpressing a mutated form of the human amyloid precursor protein (APP) and lacking the alpha7nAChR gene (APPalpha7KO). We have shown that, despite the presence of high amounts of APP and amyloid deposits, deleting the alpha7nAChR subunit in the mouse model of AD leads to a protection from the dysfunction in synaptic integrity (pathology and plasticity) and learning and memory behavior. Specifically, APPalpha7KO mice express APP and Abeta at levels similar to APP mice, and yet they were able to solve a cognitive challenge such as the Morris water maze test significantly better than APP, with performances comparable to control groups. Moreover, deleting the alpha7nAChR subunit protected the brain from loss of the synaptic markers synaptophysin and MAP2, reduced the gliosis, and preserved the capacity to elicit long-term potentiation otherwise deficient in APP mice. These results are consistent with the hypothesis that the alpha7nAChR plays a role in AD and suggest that interrupting alpha7nAChR function could be beneficial in the treatment of AD.
Expansion of Noncanonical V-Arm-Containing tRNAs in Eukaryotes (2015)

Transfer RNA (tRNA) is essential for the translation of genetic information into proteins, and understanding its molecular evolution is important if we are to understand the genetic code. In general, long variable-arm (V-arm) structures form in tRNA(Leu), tRNA(Ser), and bacterial and organellar tRNA(Tyr). However, as we have previously reported, noncanonical V-arms occur in nematode tRNA(Gly) and tRNA(Ile), and potentially affect translational fidelity. Here, we comprehensively analyzed 69 eukaryotic genome sequences and examined the evolutionary divergence of the V-arm-containing tRNAs. In total, 253 V-arm-containing tRNAs, with neither leucine nor serine anticodons, were identified in organisms ranging from nematodes to fungi, plants, and vertebrates. We defined them as "noncanonical V-arm-containing tRNAs" (nov-tRNAs). Moreover, 2,415 nov-tRNA-like sequences lacking some of the conserved features of tRNAs were also identified, largely in vertebrate genomes. These nov-tRNA/nov-tRNA-like sequences can be categorized into three types, based on differences in their possible evolutionary origins. The type A nov-tRNAs in nematodes probably evolved not only from tRNA(Leu) but also from tRNA(Ser) and other isotypes on several independent occasions. The type B nov-tRNAs are dispersed abundantly throughout vertebrate genomes, and seem to have originated from retrotransposable elements. The type C nov-tRNAs may have been acquired from plant chloroplasts or from bacteria through horizontal transfer. Our findings provide unexpected insight into the evolution of the tRNA molecule, which was diverse and occurred independently in nematodes, vertebrates, and plants.
Bicyclic Peptide Inhibitor Reveals Large Contact Interface with a Protease Target (2012)

From a large combinatorial library of chemically constrained bicyclic peptides we isolated a selective and potent (K(i) = 53 nM) inhibitor of human urokinase-type plasminogen activator (uPA) and crystallized the complex. This revealed an extended structure of the peptide with both peptide loops engaging the target to form a large interaction surface of 701 Å(2) with multiple hydrogen bonds and complementary charge interactions, explaining the high affinity and specificity of the inhibitor. The interface resembles that between two proteins and suggests that these constrained peptides have the potential to act as small protein mimics.
Investigations into the survival of Mycoplasma gallisepticum, Mycoplasma synoviae and Mycoplasma iowae on materials found in the poultry house environment (1994)

Following preliminary experiments to determine suitable methods for studying mycoplasma survival, suspensions of Mycoplasma gallisepticum (four strains), Mycoplasma synoviae (two strains) or Mycoplasma iowae (two strains) were seeded onto replicate samples of cotton, rubber, straw, shavings, timber, food, feathers and human hair. The organisms were also seeded onto human skin, ear and nasal mucosa. All samples were cultured for viability after 4, 8, 12 and 24 h, and then daily up to 6 days. The identity of recovered mycoplasmas was confirmed by indirect immunofluorescence. All three Mycoplasma species survived for the longest time on feathers with M. gallisepticum surviving between 2 and 4 days and M. synoviae 2 to 3 days. The type strain of M. iowae remained viable for 5 days on feathers, while the field strain was still viable at the end of the 6-day experiment. This strain also survived for at least 6 days on human hair and several other materials. M. gallisepticum survived on human hair up to 3 days and one recent field isolate also survived in the nose for 24 h. Survival times of the organisms were generally less on other materials although M. gallisepticum could be isolated from straw, cotton and rubber samples after 2 days.
Genetic evolution of radial basis function coverage using orthogonal niches (1996)

A well-performing set of radial basis functions (RBFs) can emerge from genetic competition among individual RBFs. Genetic selection of the individual RBFs is based on credit sharing which localizes competition within orthogonal niches. These orthogonal niches are derived using singular value decomposition and are used to apportion credit for the overall performance of the RBF network among individual nonorthogonal RBFs. Niche-based credit apportionment facilitates competition to fill each niche and hence to cover the training data. The resulting genetic algorithm yields RBF networks with better prediction performance on the Mackey-Glass chaotic time series than RBF networks produced by the orthogonal least squares method and by k-means clustering.
Oligodeoxynucleotides containing 4-thiothymidine and 6-thiodeoxyguanosine as affinity labels for the Eco RV restriction endonuclease and modification methylase (1992)

4-Thiothymidine and 6-thiodeoxyguanosine were incorporated into synthetic dodecamers containing the recognition site d(GATATC) of the enzymes Eco RV endonuclease and Eco RV methyltransferase. Upon irradiation with long wavelength UV light (340-360 nm), these oligodeoxynucleotides were photochemically crosslinked to both enzymes. The yields were up to 35% with the methyltransferase, but lower (up to 6%) with the endonuclease. Oligodeoxynucleotides containing 4-thiothymidine generally gave higher yields of crosslinking than those containing 6-thiodeoxyguanosine. Although both specific (i.e. those containing the d(GATATC) sequence) and non-specific (lacking this sequence) photoreactive oligodeoxynucleotides gave rise to crosslinked products, the use of a non-reactive, competitive substrate oligodeoxynucleotide suppressed the crosslinking, indicating that the reaction takes place at the enzymes' active sites. Oligodeoxynucleotides containing 4-thiocyanatothymidine or 6-thiocyanatodeoxyguanosine were also prepared by treatment of the title oligomers with CNBr and KCN. The dodecamers containing 4-thiocyanatothymidine were found to covalently modify both enzymes under study, with levels of crosslinking reaching up to 42% with the endonuclease and up to 12% with the methyltransferase. No crosslinking was observed with oligodeoxynucleotides containing 6-thiocyanatodeoxyguanosine.
The B Subunit ofEscherichia coliHeat-Labile Enterotoxin Induces Both Caspase-Dependent and -Independent Cell Death Pathways in CD8+T Cells (2004)

The nontoxic B subunit of Escherichia coli heat-labile enterotoxin (EtxB) is a potent immunomodulatory molecule that acts both as an adjuvant and to stimulate immune deviation processes, resulting in the suppression of Th1-associated inflammatory responses. The ability of EtxB to alter immune reactivity is dependent on its ability to modulate immune cell function through binding to cell surface molecules, the principal receptor of which is the ubiquitous GM1-ganglioside. EtxB activates B cells and antigen-presenting cells and induces the selective apoptosis of murine CD8+ T cells. We postulated that these effects are mediated by the induction of intracellular signaling pathways following EtxB-receptor interaction. We have previously shown that CD8+ T-cell apoptosis induced by EtxB results from the activation of the transcription factor NF-kappaB and caspases. Here we report that while caspase activity is required for apoptosis, additional features of cell death are caspase independent. EtxB induces a rapid loss of mitochondrial membrane potential and cell viability that are unaffected by caspase inhibitors. In addition, our data suggest that these processes are independent of the activity of Bax and Bcl-2 but are mediated by nitric oxide synthase.
Trajectory triangulation: 3D reconstruction of moving points from a monocular image sequence (2000)

We consider the problem of reconstructing the 3D coordinates of a moving point seen from a monocular moving camera, i.e., to reconstruct moving objects from line-of-sight measurements only. The task is feasible only when some constraints are placed on the shape of the trajectory of the moving point. We coin the family of such tasks as "trajectory triangulation." We investigate the solutions for points moving along a straight-line and along conic-section trajectories, We show that if the point is moving along a straight line, then the parameters of the line (and, hence, the 3D position of the point at each time instant) can be uniquely recovered, and by linear methods, from at least five views. For the case of conic-shaped trajectory, we show that generally nine views are sufficient for a unique reconstruction of the moving point and fewer views when the conic is of a known type (like a circle in 3D Euclidean space for which seven views are sufficient). The paradigm of trajectory triangulation, in general, pushes the envelope of processing dynamic scenes forward. Thus static scenes become a particular case of a more general task of reconstructing scenes rich with moving objects (where an object could be a single point).
Lysyl Oxidase–Like 2 as a New Poor Prognosis Marker of Squamous Cell Carcinomas (2008)

Lysyl oxidase-like 2 (Loxl2) interacts with and stabilizes Snai1 transcription factor, promoting epithelial-mesenchymal transition. Either Loxl2 or Snai1 knock-down blocks tumor growth and induces differentiation, but the specific role of each factor in tumor progression is still unknown. Comparison of the gene expression profiles of the squamous cell carcinoma cell line HaCa4 after knocking-down Loxl2 or Snai1 revealed that a subset of epidermal differentiation genes was specifically up-regulated in Loxl2-silenced cells. In agreement, although both Loxl2- and Snai1-knockdown cells showed reduced in vivo invasion, only Loxl2-silenced cells exhibited a skin-like epidermal differentiation program. In addition, we show that expression of Loxl2 and Snai1 correlates with malignant progression in a two-stage mouse skin carcinogenesis model. Furthermore, we found that increased expression of both LOXL2 and SNAI1 correlates with local recurrence in a cohort of 256 human laryngeal squamous cell carcinomas. We describe for the first time that high levels of LOXL2 are associated with decreased overall and disease-free survival in laryngeal squamous cell carcinomas, lung squamous cell carcinoma, and lymph node-negative (N(0)) breast adenocarcinomas. Altogether, our results show that LOXL2 can be used as a new poor prognosis indicator in human squamous cell carcinomas promoting malignant transformation by both SNAI1-dependent and SNAI1-independent pathways.
The regulation of growth and differentiation of a murine B cell lymphoma. II. The inhibition of WEHI 231 by anti-immunoglobulin antibodies. (1981)

WEHI 231 is a murine B cell lymphoma, which from our previous studies is highly susceptible to a lipopolysaccharide (LPS) induced differentiation signal. In this paper we show that anti-immunoglobulin (Ig) antibody at low concentrations (0.1 micrograms/ml) inhibits cell proliferation and results in cell death. Heterologous sera specific for mu- and kappa-chains, and a monoclonal antibody (E4) developed in our laboratory and specific for mu-chain, profoundly suppressed the growth of WEHI 231 in both soft agar culture and liquid culture. The F(ab')2 fragments were as potent as intact Ig, indicating that neither Fc receptor binding nor complement activation were required for this inhibition of growth. Neither heterologous antibodies that bound to WEHI 231 but not to the Ig receptor, nor a monoclonal antibody that bound to non-Ig cell surface structures (a brain-associated antigen) inhibited the growth of WEHI 231. LPS did not prevent inhibition of growth by anti-Ig antibody, and even when addition of LPS preceded the addition of anti-Ig, profound inhibition occurred. WEHI 231 thus promises to be a convenient tool for investigating the mechanism of signal transmission by the Ig receptor.
Non-linear bone loss in oophorectomized women (1977)

Sequential bone loss in 37 women with bilateral oophorectomy was monitored by radiographic morphometry. The changes in mean width of the cortices of the 2nd, 3rd and 4th metacarpals of both hands were determined using a semiautomated computer-controlled morphometer. It was found that a significantly greater rate of decrease of mean cortical width occurred in those women first observed within three years of the artificial menopause than in the other members of the group.
Unsupervised Profiling Methods for Fraud Detection (2002)

Credit card fraud falls broadly into two categories: behavioural fraud and application fraud. Application fraud occurs when individuals obtain new credit cards from issuing companies using false personal information and then spend as much as possible in a short space of time. However, most credit card fraud is behavioural and occurs when details of legitimate cards have been obtained fraudulently and sales are made on a &amp;apos;Cardholder Not Present&amp;apos; basis. These sales include telephone sales and e-commerce transactions where only the card details are required. In this paper, we are concerned with detecting behavioural fraud through the analysis of longitudinal data. These data usually consist of credit card transactions over time, but can include other variables, both static and longitudinal. Statistical methods for fraud detection are often classification (supervised) methods that discriminate between known fraudulent and non-fraudulent transactions; however, these methods rely on accurate identification of fraudulent transactions in historical databases -- information that is often in short supply or non-existent. We are particularly interested in unsupervised methods that do not use this information but instead detect changes in behaviour or unusual transactions. We discuss two methods for unsupervised fraud detection in credit data in this paper and apply them to some real data sets. Peer group analysis is a new tool for monitoring behaviour over time in data mining situations. In particular, the tool detects individual accounts that begin to behave in a way distinct from accounts to which they had previously been similar. Each account is selected as a target account and is compared with all other accounts in the database, using either external comparison criteria or i...
A Novel Anti-inflammatory Role for Spleen-Derived Interleukin-10 in Obesity-Induced Inflammation in White Adipose Tissue and Liver (2012)

Obesity is associated with systemic low-grade inflammation and obesity-related metabolic disorders. Considering that obesity decreases the expression of proinflammatory cytokines in the spleen, we assessed the role of interleukin (IL)-10, an anti-inflammatory cytokine produced by the spleen, in the pathogenesis of obesity. Changes in obesity-related pathogenesis, including inflammatory responses in multiple organs, were assessed after systemic administration of exogenous IL-10 to splenectomy (SPX)-treated obese wild-type and IL-10 knockout (IL-10KO) mice. Obesity resulted in the inability of the spleen to synthesize cytokines, including IL-10, and proinflammatory cytokines in obesity are then likely to emerge from tissues other than the spleen because serum levels of IL-10, but not proinflammatory cytokines, decreased despite the expression of these cytokines in the spleen being reduced in high fat-induced obese mice. SPX aggravated the inflammatory response in white adipose tissue (WAT) and the liver and suppressed adiposity in WAT. However, it accentuated adiposity in the liver. These SPX-induced changes were inhibited by systemic administration of IL-10. Moreover, SPX had little effect on the inflammatory responses in WAT and the liver of IL-10KO mice. These data show the role of spleen-derived IL-10 in diet-induced changes as a result of inflammatory responses in WAT and the liver.
Quantum computing on long-lived donor states of Li in Si (2005)

We predict a gigantically long lifetime of the first excited state of an interstitial lithium donor in silicon. The nature of this effect roots in the anomalous level structure of the $1s$ Li manifold under external stress. Namely, the coupling between the lowest two states of the opposite parity is very weak and occurs via intervalley phonon transitions only. We propose to use these states under the controlled ac and dc stress to process quantum information. We find an unusual form of the elastic-dipole interaction between different donors. This interaction scales with the interdonor distance $R$ as ${R}^{\ensuremath{-}3}$ or ${R}^{\ensuremath{-}5}$ for the transitions between the states of the same or opposite parity, respectively. The long-range ${R}^{\ensuremath{-}3}$ interaction provides a high fidelity mechanism for two-qubit operations.
Highly Enantioselective Organocatalytic Conjugate Addition of Nitromethane to α,β‐Unsaturated Aldehydes: Three‐Step Synthesis of Optically Active Baclofen (2007)

Abstract An efficient, organocatalytic, highly enantioselective, conjugate addition reaction of nitromethane with α,β‐unsaturated aldehydes has been developed. The process serves as the key step for a practical 3‐step synthesis of chiral baclofen, an antispastic drug.
A Fast Liquid-Metal Droplet Microswitch Using EWOD-Driven Contact-Line Sliding (2008)

Liquid-metal (LM) droplet-based MEMS switches have mostly been restricted to slow applications until now due to the following reasons: (1) a relatively large switching gap (distance) needed to accommodate imprecise volumes and locations of droplets on the device and (2) lack of high-speed actuation to move the droplets quickly across the switching gap. To combat these problems, we explore switching by sliding the solid-LM-gas triple contact line rather than the entire droplet. This new approach allows us to use a microframe, which not only consistently positions the LM droplet but also makes the switching gap less sensitive to the errors in the deposited-droplet volume, allowing us to design microswitches with very small switching gaps (e.g., 10 mum for 600 mum-diameter droplets). Furthermore, a study of electrowetting-on-dielectric identifies a regime of fast contact-line sliding at the onset of droplet spreading. By moving the contact line fast across a small switching distance, we demonstrate a low-latency LM switch with 60 mus switch-on latency ( ~ 20 times better than other LM-switch technologies) and better than 5 mus signal rise/fall time, while boasting no contact bounce, as expected from an LM switch. High power-handling capability and long-term reliability are also discussed.