gebhart/patrepeval huggingface dataset:
A Brief History of Statistical Models for Network Analysis and Open Challenges (2012)

Networks are ubiquitous in science. They have also become a focal point for discussion in everyday life. Formal statistical models for the analysis of network data have emerged as a major topic of interest in diverse areas of study, and most of these involve a form of graphical representation. Probability models on graphs date back to 1959. Along with empirical studies in social psychology and sociology from the 1960s, these early works generated an active “social science network community” and a substantial literature in the 1970s. This effort moved into the statistical literature in the late 1970s and 1980s, and the past decade has seen a burgeoning network literature coming out of statistical physics and computer science. In particular, the growth of the World Wide Web and the emergence of online “networking communities” such as Facebook, Google+, MySpace, LinkedIn, and Twitter, and a host of more specialized professional network communities have intensified interest in the study of networks and network data. This article reviews some of these developments, introduces some relevant statistical models for static network settings, and briefly points to open challenges.
Fluorescence Detection of MMP-9. I. MMP-9 Selectively Cleaves Lys-Gly-Pro-Arg-Ser-Leu-Ser-Gly-Lys Peptide (2011)

MMP-9 enzyme recognizes a peptide sequence Lys-Gly-Pro-Arg-Ser-Leu-Ser-Gly-Lys and cleaves the peptide into two parts. We synthesized a dual fluorophore beacon consisting of 5-FAM and Cy5 dyes. The fluorescence emission of the fluorescein moiety is dramatically quenched by Cy5 molecule due to Förster Resonance Energy Transfer (FRET) and the fluorescence of Cy5 is strongly enhanced. Upon addition of MMP-9 enzyme, the fluorescence of 5-FAM intensifies and Cy5 decreases. The control MMP-2 enzyme does not cause any changes in either 5-FAM or Cy5 fluorescence. We believe that our observation will help in early detection of elevated MMP-9 levels under disease conditions.
The solution structure of a monomeric insulin (1991)

The solution conformation of des-(B26-B30)-insulin (DPI) has been investigated by 1H-NMR spectroscopy. A set of 250 approximate interproton distance restraints, derived from two-dimensional nuclear Overhauser enhancement spectra, were used as the basis of a structure determination using distance geometry (DG) and distance-bound driven dynamics (DDD). Sixteen DG structures were optimized using energy minimization (EM) and submitted to short 5-ps restrained molecular dynamics (RMD) simulations. A further refinement of the DDD structure with the lowest distance errors was done by energy minimization, a prolonged RMD simulation in vacuo and a time-averaged RMD simulation. An average structure was obtained from a trajectory generated during 20-ps RMD. The final structure was compared with the des-(B26-B30)-insulin crystal structure refined by molecular dynamics and the 2-Zn crystal structure of porcine insulin. This comparison shows that the overall structure of des-(B26-B30)-insulin is retained in solution with respect to the crystal structures with a high flexibility at the N-terminal part of the A chain and at the N-terminal and C-terminal parts of the B chain. In the RMD run a high mobility of Gly A1, Asn A21 and of the side chain of Phe B25 is noticed. One of the conformations adopted by des-(B26-B30)-insulin in solution is similar to that of molecule 1 (Chinese nomenclature) in the crystal structure of porcine insulin.
Induction of transformation competence in <i>Azotobacter vinelandii</i> iron-limited cultures (1978)

Azotobacter vinelandii strains UW (Nif + ) or UW1 (Nif − ) were induced to form competent cells by growing cultures in Burk medium without added iron. Competent cells were generated in either liquid or solid medium. The competent culture was highly colored by the characteristic fluorescent green pigment of A. vinelandii but all pigmented cultures were not competent. In liquid culture, competent cells required a fixed nitrogen source (ammonia, nitrate, or urea) that was also a nitrogenase repressor. Glucose, sucrose, glycerol, and mannitol (1% w/v) were excellent C-sources for competence induction while acetate (1% w/v) and (β-hydroxybutyrate (0.2% w/v) were ineffective. Cells induced in liquid culture remained competent for a 12-h period before the end of the exponential growth phase, then competence decreased rapidly upon the initiation of the stationary phase of growth.
Early pregnancy factor: An extracellular chaperonin 10 homologue (1998)

Early pregnancy factor (EPF) has been identified as a homologue of chaperonin 10 (cpn10) with immunosuppressive and growth factor properties. As a homologue of cpn10, it belongs to the heat shock family of proteins (hsp) but, unlike other members of this family, EPF is detected extracellularly. Early pregnancy factor was first discovered in pregnancy serum by the rosette inhibition test, and the novelty of its discovery was that its presence could diagnose pregnancy within 6-24 h of a fertile mating. As well as being a monitor of the presence of a viable embryo, it is necessary for embryonic survival. In this capacity it acts as both an immunosuppressant and growth factor. Early pregnancy factor is also a product of proliferating primary and neoplastic cells and functions as an autocrine growth factor both in vivo and in vitro. It has a modifying effect on the outcome of experimental autoimmune encephalomyelitis, an animal model of multiple sclerosis. Early pregnancy factor is considered to be one of the major factors involved in the modification of multiple sclerosis observed during pregnancy.
Anti-pinhole Imaging (1982)

By complementing a pinhole to produce an isolated opaque spot, the light ordinarily blocked from the pinhole image is transmitted, and the light ordinarily transmitted is blocked. A negative geometrical image is formed, distinct from the familiar 'bright-spot' diffraction image. Anti-pinhole, or 'pinspeck' images are visible during a solar eclipse, when the shadows of objects appear crescent-shaped. Pinspecks demonstrate unlimited depth of field, freedom from distortion and large angular field. Images of different magnification may be formed simultaneously. Contrast is poor, but is improvable by averaging to remove noise and subtraction of a d.c. bias. Pinspecks may have application in X-ray space optics, and might be employed in the eyes of simple organisms.
SmedGD: the Schmidtea mediterranea genome database (2007)

The planarian Schmidtea mediterranea is rapidly emerging as a model organism for the study of regeneration, tissue homeostasis and stem cell biology. The recent sequencing, assembly and annotation of its genome are expected to further buoy the biomedical importance of this organism. In order to make the extensive data associated with the genome sequence accessible to the biomedical and planarian communities, we have created the Schmidtea mediterranea Genome Database (SmedGD). SmedGD integrates in a single web-accessible portal all available data associated with the planarian genome, including predicted and annotated genes, ESTs, protein homologies, gene expression patterns and RNAi phenotypes. Moreover, SmedGD was designed using tools provided by the Generic Model Organism Database (GMOD) project, thus making its data structure compatible with other model organism databases. Because of the unique phylogenetic position of planarians, SmedGD (http://smedgd.neuro.utah.edu) will prove useful not only to the planarian research community, but also to those engaged in developmental and evolutionary biology, comparative genomics, stem cell research and regeneration.
On the Application of Factor Graphs and the Sum–Product Algorithm to ISI Channels (2005)

In this paper, based on the application of the sum-product (SP) algorithm to factor graphs (FGs) representing the joint a posteriori probability (APP) of the transmitted symbols, we propose new iterative soft-input soft-output (SISO) detection schemes for intersymbol interference (ISI) channels. We have verified by computer simulations that the SP algorithm converges to a good approximation of the exact marginal APPs of the transmitted symbols if the FG has girth at least 6. For ISI channels whose corresponding FG has girth 4, the application of a stretching technique allows us to obtain an equivalent girth-6 graph. For sparse ISI channels, the proposed algorithms have advantages in terms of complexity over optimal detection schemes based on the Bahl-Cocke-Jelinek-Raviv (BCJR) algorithm. They also allow a parallel implementation of the receiver and the possibility of a more efficient complexity reduction. The application to joint detection and decoding of low-density parity-check (LDPC) codes is also considered and results are shown for some partial-response magnetic channels. Also in these cases, we show that the proposed algorithms have a limited performance loss with respect to that can be obtained when the optimal "serial" BCJR algorithm is used for detection. Therefore, for their parallel implementation, they represent a favorable alternative to the modified "parallel" BCJR algorithm proposed in the literature for the application to magnetic channels.
Cleavage of cellulose by a CBM33 protein (2011)

Bacterial proteins categorized as family 33 carbohydrate-binding modules (CBM33) were recently shown to cleave crystalline chitin, using a mechanism that involves hydrolysis and oxidation. We show here that some members of the CBM33 family cleave crystalline cellulose as demonstrated by chromatographic and mass spectrometric analyses of soluble products released from Avicel or filter paper on incubation with CelS2, a CBM33-containing protein from Streptomyces coelicolor A3(2). These enzymes act synergistically with cellulases and may thus become important tools for efficient conversion of lignocellulosic biomass. Fungal proteins classified as glycoside hydrolase family 61 that are known to act synergistically with cellulases are likely to use a similar mechanism.
Multidrug Resistance: Molecular Biology Clinical Relevance (1989)

Journal Article Multidrug Resistance: Molecular Biology Clinical Relevance Get access Mace Rothenberg, Mace Rothenberg Division of Cancer Treatment, National Cancer InstituteBethesda, MD Search for other works by this author on: Oxford Academic PubMed Google Scholar Victor Ling Victor Ling * Division of Biological Research, The Ontario Cancer InstituteToronto, ON, Canada *Correspondence to: Dr. Victor Ling, Division of Biological Research, The Ontario Cancer Institute, 500 Sherbourne St., Toronto, ON, Canada M4X 1K9. Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 81, Issue 12, 21 June 1989, Pages 907–910, https://doi.org/10.1093/jnci/81.12.907 Published: 21 June 1989 Article history Received: 08 May 1989 Accepted: 08 May 1989 Published: 21 June 1989
Down-regulation of OPA1 alters mouse mitochondrial morphology, PTP function, and cardiac adaptation to pressure overload (2012)

These results suggest that, in adult cardiomyocytes, OPA1 plays an important role in mitochondrial morphology and PTP functioning. These properties may be critical for cardiac function under conditions of chronic pressure overload.
Underground storage tanks; Management's latest challenge (1987)

The author discusses how underground storage tanks (UST) issues have lately emerged as a most serious management concern for tank owners. Regulations at federal, state or local levels mandating upgrading and remedial action are either in place or under development across the country. Amendments to the Resource Conservation and Recovery Act (RCRA) passed in November 1984 required tanks to be registered by May 8, 1986, and by May 1987 a series of additional operating and management requirements will be specified by federal rules now under consideration.
A pervasive EEG-based biometric system (2011)

Identification of individuals is ubiquitous with increasing reliance by financial and governmental organizations on reliable and robust personal recognition systems to determine and confirm the identity and policy constraints for specific individuals in 'real-time' when reacting to service requests. The traditional identification approaches to user validation are not robust and deficiencies in such approaches are becoming increasingly apparent in the current information-oriented society. With developments in research into the human brain, biometric methods based on brain wave signals have received increased attention as an effective approach to user validation as an individuals' brain wave signals cannot be duplicated, discarded or stolen. Targeted at pervasive systems and the identified deficiencies in traditional approaches to user identification and validation, an electroencephalogram (EEG)-based biometric system for use in pervasive environments is proposed in this paper. A significant problem of EEG-based biometrics in pervasive environment is the requirement of real-time and convenience. In our study, only one active electrode with a portable EEG collection device was used and no other instructions to users for convenience; in addition, the signal analysis methods we used were efficient to achieve less time consumption. In our prototype system, 11 subjects were identified with recognition accuracy in the range 66.02% to 100%; the recognition accuracy increased with increases in the EEG sample time; and the computational time of signal analysis was about 0.5s. The low computational time of EEG data analysis validates this model when implemented in pervasive environments. For differing applications we can define a suitable balance point to optimize the conflicting demands of data collection time length and recognition accuracy.
Motor Score of the Unified Parkinson Disease Rating Scale as a Good Predictor of Lewy Body–Associated Neuronal Loss in the Substantia Nigra (2006)

The UPDRS3 score is linearly linked to neuronal density, which, in Lewy body diseases, decreases exponentially with time at a similar pace in this series of elderly patients and in the younger patients described in the literature.
Wound-Induced Expression and Activation of WIG, a Novel Glycogen Synthase Kinase 3 (2000)

Glycogen synthase kinase 3 (GSK-3) is involved in the regulation of several physiological processes, including glycogen metabolism, protein synthesis, transcription factor activity, and developmental control. Although GSK-3-like genes have been isolated from plants, no function for any of these kinases has been defined. We report here that the alfalfa wound-induced gene (WIG, for wound-induced GSK-3), lencoding a functional plant GSK-3-like kinase, is activated when the alfalfa leaves are wounded. Although WIG transcripts are hardly detectable in mature leaves, WIG mRNA accumulates rapidly after wounding. Using a peptide antibody that specifically recognizes p53(WIG), we show that p53(WIG) kinase is activated immediately after wounding. Wound-induced activation of p53(WIG) kinase is a post-translational process, because the concentrations of p53(WIG) protein do not change in intact and wounded leaves, and inhibition of transcription or translation does not block activation by wounding. However, inactivation of p53(WIG) kinase, which usually occurs within 60 min after wounding, is dependent on transcription and translation of one or more protein factors. These data suggest that the WIG kinase is involved in wound signaling in plants.
A new low consumption 3D compass using integrated magnets and piezoresistive nano-gauges (2011)

We present for the first time a new concept for low-cost fabrication of a monolithic 3-axis MEMS compass using integrated permanent magnets and based on a technology compatible with inertial MEMS sensors. Piezoresistive gauges of nanometric scale enable to reduce the sensor size without sensitivity loss. Magnetometers were designed for sensitivities of 9V/T and resolutions less than 10nT/√Hz at a bridge current of 100μA and with an active surface of typically 200μm × 300μm. Ultra-low power consumption below 10μW can be achieved. First demonstrators have shown the good reliability of the concept and are in good agreement with design.
Propagation of Canine Distemper Virus in Suckling Hamsters (1955)

The Lederle strain of chick embryo adapted distemper virus was propagated in suckling hamsters through 16 serial transfers. The virus elicited a lethal infection in this host in 4-7 days following inoculation. Proof of the identity of the hamster-propagated agent was derived from serum neutralization tests in hamsters and from the successful immunization of ferrets.
Glucose metabolism in photoreceptor outer segments. Its role in phototransduction and in NADPH-requiring reactions. (1994)

Glucose metabolism in the photoreceptor rod outer segment produces both ATP (GTP) and NADPH to support phototransduction and NADPH-requiring processes in this organelle. Glycolysis in isolated bovine rod outer segments produces 44.0 +/- 6.4 nmol of ATP/min/mg of protein or 5.7 mM ATP/min. This rate of ATP production is more than sufficient to maintain the basal rate of cGMP synthesis (0.86 mM cGMP/min) in the dark requiring 1.7 mM ATP/min. Following photoexcitation, the 4.5-fold increase in the turnover of cGMP requires an ATP synthesis rate of up to 7.7 mM ATP/min (Ames, A., Walseth, T. F., Heyman, R. A., Barad, M., Graeff, R. M., and Goldberg, N. D. (1986) J. Biol. Chem. 261, 13034-13042). Under these conditions the rate of ATP production by glycolysis as measured in isolated rod outer segments is not sufficient for the regeneration of cGMP. Additional energy is most likely provided by the phosphocreatine shuttle which transports high energy phosphate groups in the form of creatine phosphate from the rod inner segment to the rod outer segment for conversion to ATP. The hexose monophosphate pathway in bovine rod outer segments can produce up to 39.8 +/- 2.2 nmol of NADPH/min/mg of protein. This rate of NADPH production is sufficient to support both the reduction of retinal to retinol (1.2 +/- 0.2 nmol of NADPH/min/mg of protein) following the photobleaching of rhodopsin and glutathione reduction (1.1 +/- 0.1 nmol of NADPH/min/mg of protein) for the protection of rod outer segments from oxidative damage. These studies provide insight into the contribution of anaerobic glycolysis and the hexose monophosphate pathway in providing energy and nucleotides for phototransduction and other outer segment processes.
Wildcard Search in Structured Peer-to-Peer Networks (2007)

We address wildcard search in structured peer-to-peer (P2P) networks, which, to our knowledge, has not yet been explored in the literature. We begin by presenting an approach based on some well-known techniques in information retrieval (IR) and discuss why it is not appropriate in a distributed environment. We then present a simple and novel technique to index objects for wildcard search in a fully decentralized manner, along with some search strategies to retrieve objects. Our index scheme, as opposed to a traditional IR approach, can achieve quite balanced loads, avoid hop spots and single point of failure, reduce storage and maintenance costs, and offer some ranking mechanisms for matching objects. We use the compact disc (CD) records collected in FreeDB (http://freedb.org) as the experimental data set to evaluate our scheme. The results confirm that our index scheme is very effective in balancing the load. Moreover, search efficiency depends on the information given in a query: the more the information, the higher the performance.
Controlled undercut microwave devices (1968)

The paper illustrates a new technique to define narrow windows in SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> layers by means of a carefully controlled undercut in SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> /Si <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> N <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</inf> flims, The method described takes advantage of the etching propertie of the silicon nitride and of its action as a mask against oxygen diffusion. Stripe Widths less than 1µ were obtained with good definition and uniformity on the whole wafer and without the difficulties normally encountered in micron-line photoengraving. The technique gives reproducible results, requires one masking operation only and seems to be suitable as a production process.
Regulation of the large ( 1000 kb) imprinted murine Ube3a antisense transcript by alternative exons upstream of Snurf/Snrpn (2004)

Most cases of Angelman syndrome (AS) result from loss or inactivation of ubiquitin protein ligase 3A (UBE3A), a gene displaying maternal-specific expression in brain. Epigenetic silencing of the paternal UBE3A allele in brain appears to be mediated by a non-coding UBE3A antisense (UBE3A-ATS). In human, UBE3A-ATS extends approximately 450 kb to UBE3A from the small nuclear ribonucleoprotein N (SNURF/SNRPN) promoter region that contains a cis-acting imprinting center (IC). The concept of a single large antisense transcript is difficult to reconcile with the observation that SNURF/SNRPN shows a ubiquitous pattern of expression while the more distal part of UBE3A-ATS, which overlaps UBE3A, is brain specific. To address this problem, we examined murine transcripts initiating from several alternative exons dispersed within a 500 kb region upstream of Snurf/Snrpn. Similar to Ube3a-ATS, these upstream (U) exon-containing transcripts are expressed at neuronal stages of differentiation in a cell culture model of neurogenesis. These findings suggest the novel hypothesis that brain-specific transcription of Ube3a-ATS is regulated by the U exons rather than Snurf/Snrpn exon 1 as previously suggested from human studies. In support of this hypothesis, we describe U-Ube3a-ATS transcripts where U exons are spliced to Ube3a-ATS with the exclusion of Snurf-Snrpn. We also show that the murine U exons have arisen by genomic duplication of segments that include elements of the IC, suggesting that the brain specific silencing of Ube3a is due to multiple alternatively spliced IC-Ube3a-ATS transcripts.
Cold active lipases – an update (2016)

Cold active lipases (CLPs) are gaining importance nowadays as they are increasingly used in fine chemical synthesis, bioremediation, food processing and as detergent additive. These enzymes exhibit high catalytic activity at low temperatures and flexibility to act at low water medium. Since they are active at low temperatures consume less energy and also stabilize fragile compounds in the reaction medium. CLPs are commonly obtained from psychrophilic microorganisms which thrive in cold habitats. Compared to mesophilic and thermophilic lipases, only a few CLPs were studied and industrially exploited so far. CLPs (C. antarctica lipase-A and C. antarctica lipase-B) from Candida antarctica isolated from Antarctic region are the well studied and industrially employed, and many are being followed up. This review updates the CLPs reported recently and the industrial applications of CLPs.