gebhart/patrepeval huggingface dataset:
dMyc is required for larval growth and endoreplication in Drosophila (2004)

Members of the Myc family of proto-oncogenes have long been implicated in regulating proliferation, apoptosis and oncogenesis. Recently, transcriptional and biological studies have suggested a direct role for Myc in regulating growth. We have used dm(4), a new null allele of the Drosophila diminutive (dm) gene, which encodes dMyc on the X chromosome, to investigate a role for dMyc in larval endoreplicating tissues, where cellular growth and DNA replication occur in the absence of cell division. Hemizygous dm(4)/Y mutants arrest as second instar larvae, and fat body nuclei of dm(4)/Y mutants fail to attain normal size and normal levels of DNA, resulting from a reduced frequency of S-phase. Thus, dMyc is required for endoreplication and larval growth. In support of this, dMyc, as well as its antagonist dMnt, are expressed in larval tissues in a pattern consistent with their involvement in regulating endoreplication. Overexpression of dMyc in endoreplicating cells results in dramatic increases in nuclear DNA content and cell and nucleolar size, whereas dMnt overexpression has the opposite effect. BrdU incorporation and Cyclin E protein levels continue to oscillate in dMyc-overexpressing cells, indicating that the normal cell cycle control mechanisms are not disrupted. dMyc driven growth and endoreplication are strongly attenuated when the endocycle is blocked with Cyclin E or the cdk inhibitor p21. By contrast, the ability of dMyc to promote growth and endoreplication is only partly reduced when PI3K activity is blocked, suggesting that they influence distinct growth pathways. Our results indicate that larval growth and endoreplication are coupled processes that, although linked to cell cycle control mechanisms, are regulated by dMyc and dMnt.
A Subclass of Ras Proteins That Regulate the Degradation of IκB (2000)

Small guanosine triphosphatases, typified by the mammalian Ras proteins, play major roles in the regulation of numerous cellular pathways. A subclass of evolutionarily conserved Ras-like proteins was identified, members of which differ from other Ras proteins in containing amino acids at positions 12 and 61 that are similar to those present in the oncogenic forms of Ras. These proteins, κB-Ras1 and κB-Ras2, interact with the PEST domains of IκBα and IκBβ [inhibitors of the transcription factor nuclear factor kappa B (NF-κB)] and decrease their rate of degradation. In cells, κB-Ras proteins are associated only with NF-κB:IκBβ complexes and therefore may provide an explanation for the slower rate of degradation of IκBβ compared with IκBα.
Evaluation of <scp>D</scp>‐amino acid oxidase from <i>Rhodotorula gracilis</i> for the production of α‐keto acids: A reactor system (1994)

The study reports on the development of a bioreactor for the production of alpha-keto acids from D,L- or D-amino acids using Rhodotorula gracilis D-amino acid oxidase. D-amino acid oxidase was co-immobilized with catalase on Affi-Gel 10 matrix, and the reactor was operated as a continuous-stirred tank reactor (CSTR) or stirred tank with medium recycling conditions. The optimum substrate concentration and quantity of biocatalyst were determined (5 mM and 1.2 mg/L, respectively). Under optimum operating conditions, product formation was linearly related to both substrate and enzyme concentration, showing the system to be highly flexible. Under these conditions, in a stirred tank, over 90% conversion was achieved in 30 min with a maximum production of 0.23 g of pyruvic acid/day/enzyme units. Product was recovered by ion exchange chromatography. The operational stability of the reactor was high (up to 9.5 h of operation without loss of activity) and the inactivation half-life was not reached even after 18 h or 36 bioconversion cycles. This represents the first case of a reactor developed successfully with a D-amino acid oxidase.
Effect of cutting second-order chordae on in-vivo anterior mitral leaflet compound curvature. (2005)

Compound curvature along the AMVL central-meridian appears to be an intrinsic leaflet property that persists even without support from second-order chordae, whereas concave curvature in the commissure-commissure axis is more dependent on intact second-order chordae. Leaflet compound curvature must be incorporated into future finite element models to characterize leaflet stresses accurately. The importance of second-order chordae in maintaining leaflet shape must be considered during mitral repair. A larger ROC increases leaflet stresses, while reversal of ROC changes tensile stress to compressive stress; this might trigger deleterious leaflet remodeling after chordal cutting.
Localized surface plasmon induced enhancement of electron-hole generation with silver metal island at n-Al:ZnO/p-Cu2O heterojunction (2015)

Localized surface plasmon induced generation of electron-hole pairs with inclusion of metal islands of noble metal like Ag can enhance the photocurrent. A heterostructure of n-Al:ZnO/p-Cu2O with inclusion of Ag metalislands at the junction has been fabricated. I-V characteristic curve of these heterostructures shows a significant enhancement of photocurrent under the illumination (1.5 AMU). This enhancement of photocurrent is attributed to the supply of hot electrons generated in silver metal nanoislands. It has also been shown that inclusion of metal islands increases the absorption of solar spectrum in visible region at 500 nm. Enhancement of photocurrent may also be due to the direct resonance energy transfer from Localized Surface Plasmons of metal islands to Cu2O.
Encode, Tag, Realize: High-Precision Text Editing (2019)

Eric Malmi, Sebastian Krause, Sascha Rothe, Daniil Mirylenka, Aliaksei Severyn. Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing (EMNLP-IJCNLP). 2019.
Sum capacity optimization of the MIMO Gaussian MAC (2003)

In this work, we study the sum capacity of a Gaussian multiple-input multiple-output multiple-access channel with a sum power constraint. In order to develop an efficient algorithm for maximization of the sum capacity, we extend recent results regarding the duality between the vector multiple access channel and broadcast channel and the Sato bound. We enhance the iterative Water-filling algorithm from Wei Yu et al. (2002) to converge into the optimum power allocation.
Role of Reactive Oxygen Intermediates and Cognate Redox Signaling in Disease Resistance (2000)

Plants have evolved a plethora of sophisticated defense mechanisms to resist their potential colonization by microbial pathogens and parasites. Preformed physical and chemical barriers constitute the first line of defense. Superimposed upon these is a battery of inducible responses, their engagement
Parathyroid hormone–related protein (PTHrP) as a causative factor of cancer‐associated wasting: Possible involvement of PTHrP in the repression of locomotor activity in rats bearing human tumor xenografts (2005)

Nude rats bearing the LC-6-JCK human lung cancer xenograft displayed cancer-associated wasting syndrome in addition to humoral hypercalcemia of malignancy. In these rats, not only PTHrP but also several other human proinflammatory cytokines, such as IL-6, leukemia-inducing factor, IL-8, IL-5 and IL-11, were secreted to the bloodstream. Proinflammatory cytokines induce acute-phase reactions, as evidenced by a decrease of serum albumin and an increase in alpha1-acid glycoprotein. Tumor resection abolished the production of proinflammatory cytokines and improved acute-phase reactions, whereas anti-PTHrP antibody affected neither proinflammatory cytokine production nor acute-phase reactions. Nevertheless, tumor resection and administration of anti-PTHrP antibody similarly and markedly attenuated not only hypercalcemia but also loss of fat, muscle and body weight. Body weight gain by anti-PTHrP antibody was associated with increased food consumption; increased body weight from anti-PTHrP antibody was observed when animals were freely fed but not when they were given the same feeding as those that received only vehicle. Furthermore, nude rats bearing LC-6-JCK showed reduced locomotor activity, less eating and drinking and low blood phosphorus; and anti-PTHrP antibody restored them. Although alendronate, a bisphosphonate drug, decreased blood calcium, it affected neither locomotor activity nor serum phosphorus level. These results indicate that PTHrP represses physical activity and energy metabolism independently of hypercalcemia and proinflammatory cytokine actions and that deregulation of such physiologic activities and functions by PTHrP is at least in part involved in PTHrP-induced wasting syndrome.
Structure and Synthesis of Nectrisine, a New Immunomodulator Isolated from a Fungus. (1991)

The structure of a novel immunomodulator, nectrisine (1), has been elucidated on the basis of chemical and spectroscopic evidence. Its absolute stereochemistry was predicted on the basis of the dibenzoate chirality rule and finally confirmed by a synthesis from D-glucose.
Expression and Contribution of B7-1 (CD80) and B7-2 (CD86) in the Early Immune Response to <i>Leishmania major</i> Infection (1999)

CD28 interactions promote T cell responses, and whether B7-1 or B7-2 is utilized may influence Th cell subset development. CD28 blockade by CTLA-4Ig treatment or by targeted gene disruption has yielded different conclusions regarding the role of CD28 in the development of Th1 and Th2 cells following Leishmania major infection. In this study, we demonstrate that B7-mediated costimulation is required for the development of the early immune response following infection of resistant or susceptible mice. In contrast, CD28-/- BALB/c mice infected with L. major produce cytokines comparable to those of infected wild-type mice. Treatment of CD28-/- mice with CTLA-4Ig did not diminish this response, suggesting that a B7-independent pathway(s) contributes to the early immune response in these mice. In conventional BALB/c or C3H mice, B7-2 functions as the dominant costimulatory molecule in the initiation of early T cell activation following L. major infection, leading to IL-4 or IFN-gamma production, respectively. The preferential interaction of B7-2 with its ligand(s) in the induction of these responses correlates with its constitutive expression relative to that of B7-1. However, B7-1 can equally mediate costimulation for the production of either IL-4 or IFN-gamma when expressed at high levels. Thus, in leishmaniasis, costimulation involving B7-1 or B7-2 can result in the production of either Th1 or Th2 cytokines, rather than a preferential induction of one type of response.
A per-survivor phase acquisition and tracking algorithm for detection of TCM signals with phase jitter and frequency error (1997)

In this letter we investigate the performance of a per-survivor phase estimation algorithm for detection of trellis-coded modulation (TCM) signals in the presence of phase jitter and frequency error. Phase and frequency estimates are derived based on a second-order phase-locked loop (PLL)-like algorithm. A simplified transient and steady-state analysis of the algorithm recursive equations is derived. A heuristic blind phase acquisition scheme is proposed and shown to achieve good results. Computer simulations are used to compare the algorithm's performance to other methods described in the literature.
A Simple Yet Effective Technique for Global Wiring (1987)

A simple algorithm to perform global wiring is described. Repeated iterations of the algorithm tend to improve the quality of wiring by rerouting around congested areas. Various parameters can be set to give preference to short routes or to reduce the time taken by the algorithm. The algorithm has been tried out for several master-slice chips containing up to 3500 cells with good results. The technique is easily extended to standard cell chip design. An implementation for global wiring of a structured custom chip design style is described along with results. The technique is adaptable to higher level packaging such as chips on modules or modules on a board.
New and Improved Procedures for Gas Sampling and Analysis in the National Air Sampling Network (1967)

The NASN sampler for the collection of gaseous pollutants has been modified to increase its versatility and efficiency. Oxides of nitrogen are collected in bubblers employing a 70-100 μ frit with a collection efficiency of approximately 50% depending upon the frit porosity. Included in the sampler is a bubbler for the collection of aldehydes in which the aldehyde-MBTH complex is stable at least two weeks. This inert bubbler, which is constructed of polypropylene and Teflon, makes it possible for samples to be collected over the network and analyzed at a central laboratory. In addition, gaseous ammonia is collected in 0.1N H2SO4. This collecting system has an efficiency of greater than 85%. Low-level samples are analyzed automatically employing Nesslerization, whereas high-level samples from source emissions may be collected in indicating boric acid and titrated with 0.02N H2SO4. The sampler will accommodate either 50 or 100 ml polypropylene collecting tubes.
Clustering Software Artifacts Based on Frequent Common Changes (2005)

Changes of software systems are less expensive and less error-prone if they affect only one subsystem. Thus, clusters of artifacts that are frequently changed together are subsystem candidates. We introduce a two-step method for identifying such clusters. First, a model of common changes of software artifacts, called co-change graph, is extracted from the version control repository of the software system. Second, a layout of the co-change graph is computed that reveals clusters of frequently co-changed artifacts. We derive requirements for such layouts, and introduce an energy model for producing layouts that fulfill these requirements. We evaluate the method by applying it to three example systems, and comparing the resulting layouts to authoritative decompositions.
Neurokinin‐1 receptor (NK‐1R) expression is induced in human colonic epithelial cells by proinflammatory cytokines and mediates proliferation in response to substance P (2003)

We have previously shown that the receptor for substance P (SP), neurokinin-1 receptor (NK-1R), is a marker of human mucosal but not peripheral mononuclear cells. In the present study, we investigate NK-1R expression in the human colonic mucosa in vivo, particularly in the epithelial cells. We investigate the influence of proinflammatory Th1 cytokines and SP on expression and function of NK-1R in colonic epithelial cells in vitro. Using in situ hybridization to detect NK-1R mRNA, and immunohistochemistry to detect NK-1R protein, colonic epithelial cells were found to express NK-1R in vivo. In contrast, colon epithelial cell lines (Caco-2, HT29, SW620, T84) were negative for NK-1R mRNA and protein. However, stimulation with a proinflammatory cytokine cocktail containing IFN-gamma, TNF-alpha, and IL-1beta, caused induction of NK-1R expression. Expression of NK-1R in human colonic epithelial cells in vivo may therefore reflect cytokine conditioning by the mucosal microenvironment. SP did not alter ion transport in monolayers of cytokine-treated T84 cells. While SP stimulated epithelial ion transport in colonic mucosae ex vivo, this was not a direct effect of SP on the epithelial cells, and appeared to be neurally mediated. However, SP (10(-10)-10(-8) M) elicited a dose-dependent proliferative effect on cytokine-stimulated, but not unstimulated, SW620 cells. Proliferation of the epithelial cells in response to SP was mediated specifically via cytokine-induced NK-1R, since an NK-1R-specific antagonist (Spantide 1) completely blocked SP-mediated proliferation in the cytokine-treated cells. Our results therefore demonstrate that proinflammatory cytokines induce expression of NK-1R in human colonic epithelial cell lines, and that SP induces proliferation of the epithelial cells via cytokine-induced NK-1R.
Subitizing: An analysis of its component processes. (1982)

SUMMARY The term subitizing was coined by Kaufman, Lord, Reese, and Volkmann in 1949 to describe the rapid, confident, and accurate report of the numerosity of arrays of elements presented for short durations. They noted that this process, different from counting and estimating, was restricted to arrays with 6 or fewer elements. Ever since the general awareness of some such process in the nineteenth century, the phenomenon has been a benchmark for the limited capacity of human consciousness, Previous research, as well as the data in these experiments, shows that the reaction time function for different arrays (ranging in size from 1 to 15) has a shallow slope for arrays with 1 to 3 elements followed by a straight line slope for arrays of 4 to 6 or 7, at which point the reaction time discontinuity typically occurs; reaction times then stay fairly constant as the array size increases, and the numerosity response becomes much less accurate. When the array is exposed for unlimited presentation time, the reaction time slope is a straight line from size 4 to as large as 30 or 40. In the latter case, subjects are clearly counting the array. Apart from replicating the previous findings under a variety of conditions, we have shown that subjects can make a very fast countability judgment indicating whether or not they could, if requested, give an accurate numerosity response. These judgments are fast and produce a yes response within the subitizing range, and a no response thereafter. Developmental data had indicated that children count arrays as small as 2 and 3; adults seem to give a more automatic response, shown ajso in the fast reaction times to those array sizes. The suggestion that this response is an acquired one to certain frequently appearing canonical patterns of two and three events (pairs/lines and triples/ triangles) was explored in another experiment in which subjects were given canonical patterns for arrays of up to 10. These data showed that within very few trials the response to these canonical patterns was just as fast and accurate as the response to the smaller (1 to 3) array sizes. Finally, the data demonstrated that the slope for array sizes from 4 to 6 with short exposure time was indistinguishable from the slope for array sizes from 4 to 15 under an unlimited exposure condition. We concluded that the reaction time function found in subitizing consists of three processes: a response to arrays of 1 to 3 that is fast and accurate and is based on acquired canonical patterns; a,response to arrays of 4 to 6 or 7 that is based on mental counting, that is, the counting of arrays that can be kept in consciousness (attention); and an estimating response for arrays larger than 6 that cannot be held in consciousness for mental counting.
Adaptive buffer sizing for TCP flows in 802.11e WLANs (2008)

We consider the provision of access point buffers in WLANs. We first demonstrate that the default use of static buffers in WLANs leads to either undesirable channel under-utilisation or unnecessary high delays, which motivates the use of dynamic buffer sizing. Although adaptive algorithms have been proposed for wired Internet, a number of fundamental new issues arise in WLANs which necessitates new algorithms to be designed. These new issues include the fact that channel bandwidth is time-varying, the mean service rate is dependent on the level of channel contention, and packet inter-service times vary stochastically due to the random nature of CSMA/CA operation. We propose an adaptive sizing algorithms which is demonstrated to be able to maintain high throughput efficiency whilst achieving low delay.
Pathologic gene expression in Gaucher disease: up-regulation of cysteine proteinases including osteoclastic cathepsin K (2000)

Deficiency of lysosomal acid β-glucosidase induces glycolipid storage in the macrophages of Gaucher disease but the pathways of multisystem tissue injury and destruction are unknown. To investigate the cognate molecular pathology of this inflammatory disorder, genes that were differentially expressed in spleen samples from a patient with Gaucher disease (Gaucher spleen) were isolated. Of 64 complementary DNA (cDNA) fragments sequenced from an enriched Gaucher cDNA library, 5 encode lysosomal proteins (cathepsins B, K, and S, α-fucosidase, and acid lipase), 10 encode other known proteins, and 2 represent novel sequences from human macrophage cell lines. Transcript abundance of the cathepsins, novel genes, pulmonary and activation-regulated chemokine (PARC), and NMB, a putative tumor suppressor gene, was greatly increased. Immunoblotting showed increased mature forms of all 3 cathepsins found in samples of Gaucher spleens. Immunofluorescence microscopy showed strong cathepsin B and K reactions in sinusoidal endothelium and Gaucher cells. The respective means, plus or minus SD, of cathepsin B, K, and S activities were 183 ± 35, 97 ± 39, and 91 ± 45 nmol/min/mg protein in 4 Gaucher spleens, and 26 ± 4, 10.5 ± 2, and 4.0 ± 2.1 nmol/min/mg protein in 3 control spleens. Plasma cathepsin B, K, and S activities were also elevated in Gaucher disease plasma (P < .001), but compared with control plasma samples, neither cathepsin B nor K activities were significantly elevated in 8 patients with nonglycosphingolipid lysosomal storage diseases or in 9 patients with other glycosphingolipidoses, which suggests disease specificity. All 3 cathepsin activities were increased 2-fold to 3-fold in Gaucher sera compared with control sera. In all 6 patients treated by enzyme replacement for 16-22 months, serum cathepsin activities decreased significantly (P < .01). Longitudinal studies confirmed the progressive reduction of proteinase activities during imiglucerase therapy but in 3 Gaucher patients with mild disease not so treated, serum cathepsin activities remained constant or increased during follow-up. Enhanced expression of cysteine proteinases may promote tissue destruction. Moreover, the first identification of aberrant cathepsin K expression in hematopoietic tissue other than osteoclasts implicates this protease in the breakdown of the matrix that characterizes lytic bone lesions in Gaucher disease.