gebhart/patrepeval huggingface dataset:
Interaction of Vaccinia Virus Complement Control Protein with Human Complement Proteins: Factor I-Mediated Degradation of C3b to iC3b1 Inactivates the Alternative Complement Pathway (1998)

Vaccinia virus complement control protein (VCP) is a virulence determinant of vaccinia virus that helps protect the virus from the complement attack of the host. To characterize the interaction of VCP with C3 and C4 and understand the mechanism by which VCP inactivates complement, we have expressed VCP in a yeast expression system and compared the biologic activity of the purified protein to that of human factor H and complement receptor 1 (CR1). Recombinant VCP bound to C3 and the proteolytically cleaved form of C3 (C3b), but not to the 135,300-m.w. fragment of C3 generated using elastase (C3c) and the 35,000-m.w. fragment of C3 generated using elastase (C3d) and inhibited both the classical and alternative pathways of complement activation. Although rVCP was less effective at inhibiting the alternative pathway than factor H or CR1, it was more effective than factor H at inhibiting the classical pathway. Unlike factor H, rVCP was unable discriminate between alternative pathway-mediated lysis of rabbit and sheep E. A comparison of the cofactor activity in factor I-mediated cleavage of C3b suggested that in contrast to factor H and CR1, which displayed cofactor activity for the three sites, rVCP displayed cofactor activity primarily for the first site, leading to generation of C3b cleaved by factor I between Arg1281-Ser1282 (iC3b1). Its cofactor activity for C4b cleavages was similar to that of soluble complement receptor type 1. Purification and functional analysis of iC3b1 showed that it was unable to interact with factor B to form the alternative pathway C3 convertase, C3b,Bb. These results suggest that the interaction of VCP with C3 is different from that of factor H and CR1 and that VCP-supported first cleavage of C3b by factor I is sufficient to render C3b nonfunctional.
Using dynamic accounts to enable access to advanced resources through science gateways (2009)

Science Gateways have emerged as a valuable solution for providing large numbers of users with access to advanced computing resources. Additionally, they can hide many of the complexities often associated with using such resources effectively. Many gateways use a community account, which is shared by all gateway users on the backend compute resource. In some cases this can lead to problems when it comes to segregation of user data. To address this issue, we have investigated the use of dynamic accounts, where each gateway user is dynamically allocated their own account on the backend resource. We describe some of the features of the Dynamic Account service and explain how it has been integrated into the TeraGrid Visualization Gateway. We also discuss problems encountered, identify remaining open issues, and describe directions for future work.
Latency-rate servers: a general model for analysis of traffic scheduling algorithms (2002)

In this paper, we develop a general model, called latency-rate servers (LR-servers), for the analysis of traffic scheduling algorithms in broadband packet networks. The behavior of an LR scheduler is determined by two parameters-the latency and the allocated rate. We show that several well-known scheduling algorithms, such as weighted fair queueing, virtualclock, self-clocked fair queueing, weighted round robin, and deficit round robin, belong to the class of LR-servers. We derive tight upper bounds on the end-to-end delay, internal burstiness, and buffer requirements of individual sessions in an arbitrary network of LR-servers in terms of the latencies of the individual schedulers in the network, when the session traffic is shaped by a leaky bucket. Thus, the theory of LR-servers enables computation of tight upper-bounds on end-to-end delay and buffer requirements in a network of servers in which the servers on a path may not all use the same scheduling algorithm. We also define a self-contained approach to evaluate the fairness of LR-servers and use it to compare the fairness of many well-known scheduling algorithms.
Majorana Edge States in Interacting One-Dimensional Systems (2011)

We show that one-dimensional electron systems in the proximity of a superconductor that support Majorana edge states are extremely susceptible to electron-electron interactions. Strong interactions generically destroy the induced superconducting gap that stabilizes the Majorana edge states. For weak interactions, the renormalization of the gap is nonuniversal and allows for a regime in which the Majorana edge states persist. We present strategies of how this regime can be reached.
Varying the effective mass of geophones (2001)

Abstract Traditionally, acquiring seismic data has rested on the assumption that geophone mass should be as small as possible. When Steeples and coworkers in 1999 planted 72 geophones automatically and simultaneously with a farm tillage implement, the effective mass of each of the geophones was significantly increased. We examined how the mass of a geophone affects changes in traveltime, amplitude, frequency, and overall data quality by placing various external masses on top of 100-Hz vertical geophones. Circular barbell weights of 1.1-, 11.3-, and 22.7 kg; an 8.2-kg bag of lead shot; and a 136-kg stack of barbell weights were placed on top of geophones during data acquisition. In addition, a very large mass in the form of a truck was parked on top of two of the geophones. Four seismic sources supplying a broad range of energies were tested: a sledgehammer, a .22-caliber rifle, a 30.06 rifle, and an 8-gauge Betsy Seisgun. Spectral analysis revealed that the smaller weights had the greatest effects on the capacities of the geophones to replicate the earth's motion. Consequently, using geophones with a large effective mass as part of an automatic geophone-planting device would not necessarily be detrimental to the collection of high-quality near-surface seismic data.
Biosynthesis of the thiazole moiety of thiamin (vitamin B1) in higher plant chloroplasts. (1991)

The chloroplast stromal proteins from spinach condense the two heterocyclic moieties of vitamin B1--4-methyl-5-(beta-hydroxyethyl)thiazole and 2-methyl-4-amino-5-hydroxymethylpyrimidine--in the presence of MgATP. We have taken advantage of this observation to study thiazole synthesis. We present data indicating that pyruvate, glyceraldehyde 3-phosphate, tyrosine, cysteine, and MgATP are required for this synthesis and that pyruvate and glyceraldehyde 3-phosphate can be replaced by 1-deoxy-D-threo-2-pentulose. The thiazole synthesis occurs at a sustained, low rate of 140 pmol per mg of protein per hr.
Parathyroid hormone-related protein as a potential target of therapy for cancer-associated morbidity (2000)

PTHrP is a promising molecular target for the development of a novel mode of treatment for patients with cancer-associated morbidity.
Combinatorial Effects of Lapatinib and Rapamycin in Triple-Negative Breast Cancer Cells (2011)

Triple-negative breast cancers, which lack estrogen receptor, progesterone receptor, and HER2/neu overexpression, account for approximately 15% of breast cancers, but occur more commonly in African Americans. The poor survival outcomes seen with triple-negative breast cancers patients are, in part, due to a lack of therapeutic targets. Epidermal growth factor receptor (EGFR) is overexpressed in 50% of triple-negative breast cancers, but EGFR inhibitors have not been effective in patients with metastatic breast cancers. However, mTOR inhibition has been shown to reverse resistance to EGFR inhibitors. We examined the combination effects of mTOR inhibition with EGFR inhibition in triple-negative breast cancer in vitro and in vivo. The combination of EGFR inhibition by using lapatinib and mTOR inhibition with rapamycin resulted in significantly greater cytotoxicity than the single agents alone and these effects were synergistic in vitro. The combination of rapamycin and lapatinib significantly decreased growth of triple-negative breast cancers in vivo compared with either agent alone. EGFR inhibition abrogated the expression of rapamycin-induced activated Akt in triple-negative breast cancer cells in vitro. The combination of EGFR and mTOR inhibition resulted in increased apoptosis in some, but not all, triple-negative cell lines, and these apoptotic effects correlated with a decrease in activated eukaryotic translation initiation factor (eIF4E). These results suggest that mTOR inhibitors could sensitize a subset of triple-negative breast cancers to EGFR inhibitors. Given the paucity of effective targeted agents in triple-negative breast cancers, these results warrant further evaluation.
The N‐terminal half of the heavy chain of botulinum type A neurotoxin forms channels in planar phospholipid bilayers (1987)

The heavy chain of botulinum type A neurotoxin forms channels in planar phospholipid bilayer membranes. Channel activity is confined to the N-terminal half of this chain; the C-terminal half is inactive. Channel activity is stimulated by low pH (4.5-5.5) on the cis side (the side to which protein is added), neutral pH on the opposite (trans) side, and cis positive voltages. These findings are strikingly similar to those previously reported for analogous fragments of diphtheria and tetanus toxins.
Transforming growth factor-β1 acts cooperatively with sodium n-butyrate to induce differentiation of normal human keratinocytes (1992)

Growth factors with established biological activity toward cultured normal human epidermal keratinocytes (NHEKs) (e.g., transforming growth factor-beta, TGF-beta; retinoic acid, RA) initiate programmed changes in cellular maturation which differ with regard to the specific differentiation pathway (normal or abnormal) analyzed. Sodium butyrate (NaB) initiates one form of epidermal differentiation leading to enhanced cornified envelope (CE) formation which involves abrogation of the normally inhibitory effect of RA on NHEK maturation. NaB also induces TGF-beta mRNA in the maturing suprabasal compartment, suggesting that TGF-beta may play a role in NaB-initiated NHEK differentiation. Treatment with TGF-beta 1 alone, however, only marginally increased (by twofold) the number of detergent-resistant CEs compared to control NHEKs and did not alter the prevalence of fully mature enucleated CEs. TGF-beta 1 was quite effective in inducing significant levels of CE expression when used simultaneously with suboptimal concentrations of NaB. The cooperative action of suboptimal NaB and TGF-beta 1 generated numbers of CEs which, in fact, exceeded the incidence of mature CEs formed in response to optimal levels of NaB alone. Neutralizing antibodies to TGF-beta, moreover, effectively reduced the incidence of CE formation in cultures treated with optimal NaB concentrations, further implicating endogenous TGF-beta activity in the NaB-initiated NHEK differentiation model. It is suggested, therefore, that within the NaB-induced pathway of NHEK differentiation, TGF-beta can positively modulate expression of the differentiated phenotype but alone is insufficient for generation of mature CEs.
A putative viral defence mechanism in archaeal cells (2006)

Clusters of regularly spaced direct repeats, separated by unconserved spacer sequences, are ubiquitous in archaeal chromosomes and occur in some plasmids. Some clusters constitute around 1% of chromosomal DNA. Similarly structured clusters, generally smaller, also occur in some bacterial chromosomes. Although early studies implicated these clusters in segregation/partition functions, recent evidence suggests that the spacer sequences derive from extrachromosomal elements, and, primarily, viruses. This has led to the proposal that the clusters provide a defence against viral propagation in cells, and that both the mode of inhibition of viral propagation and the mechanism of adding spacer-repeat units to clusters, are dependent on RNAs transcribed from the clusters. Moreover, the putative inhibitory apparatus (piRNA-based) may be evolutionarily related to the interference RNA systems (siRNA and miRNA), which are common in eukarya. Here, we analyze all the current data on archaeal repeat clusters and provide some new insights into their diverse structures, transcriptional properties and mode of structural development. The results are consistent with larger cluster transcripts being processed at the centers of the repeat sequences and being further trimmed by exonucleases to yield a dominant, intracellular RNA species, which corresponds approximately to the size of a spacer. Furthermore, analysis of the extensive clusters of Sulfolobus solfataricus strains P1 and P2B provides support for the presence of a flanking sequence adjoining a cluster being a prerequisite for the incorporation of new spacer-repeat units, which occurs between the flanking sequence and the cluster. An archaeal database summarizing the data will be maintained at http://dac.molbio.ku.dk/dbs/SRSR/.
Molecular Dynamics Simulation of a GM3 Ganglioside Bilayer (2004)

A first molecular dynamics simulation of a fully hydrated GM3 ganglioside bilayer is presented. Several properties characterizing the membrane structure and surrounding water are evaluated and compared to known data related to phospholipids. Our results are in good agreement with experimental small-angle X-ray scattering data. Overall, the simulated bilayer shows very long relaxation times such that a full equilibration is attained in about 30 ns. The long equilibration time is due to the slow relaxation of the torsional angle at the level of the galactose−sialic acid linkage. Once equilibrated, GM3 exhibits a good packing of the hydrophilic moieties, due to preferential alignment of its longitudinal axis along the bilayer normal, and a high degree of disorder in the tail region. The ionic nature of the hydrophilic heads manifests itself in a slow decay of the water orientational order parameter.
Studies in the indole series. Part IV. Tetrahydro-1H-pyrido[4,3-b]-indoles as serotonin antagonists (1968)

A series of tetrahydro-1H-pyrido[4,3-b]indoles has been made by Fischer cyclisation of arylhydrazones of 1-substituted-4-piperidones. Some of these compounds have been shown to have high anti-serotonin activity when submitted to pharmocological tests in vitro.
Femtosecond written fiber Bragg Grating in non-photosensitive rare-earth-doped fiber (2006)

We report on the realization of FBGs in a standard Er-doped fiber written into the non-photosensitive core by femtosecond laser pulses. Efficient laser operation is demonstrated using this technique.
Microbiome and Allergic Diseases (2018)

Allergic diseases, such as respiratory, cutaneous, and food allergy, have dramatically increased in prevalence over the last few decades. Recent research points to a central role of the microbiome, which is highly influenced by multiple environmental and dietary factors. It is well established that the microbiome can modulate the immune response, from cellular development to organ and tissue formation exerting its effects through multiple interactions with both the innate and acquired branches of the immune system. It has been described at some extent changes in environment and nutrition produce dysbiosis in the gut but also in the skin, and lung microbiome, inducing qualitative and quantitative changes in composition and metabolic activity. Here, we review the potential role of the skin, respiratory, and gastrointestinal tract (GIT) microbiomes in allergic diseases. In the GIT, the microbiome has been proven to be important in developing either effector or tolerant responses to different antigens by balancing the activities of Th1 and Th2 cells. In the lung, the microbiome may play a role in driving asthma endotype polarization, by adjusting the balance between Th2 and Th17 patterns. Bacterial dysbiosis is associated with chronic inflammatory disorders of the skin, such as atopic dermatitis and psoriasis. Thus, the microbiome can be considered a therapeutical target for treating inflammatory diseases, such as allergy. Despite some limitations, interventions with probiotics, prebiotics, and/or synbiotics seem promising for the development of a preventive therapy by restoring altered microbiome functionality, or as an adjuvant in specific immunotherapy.
Cancer of the uterine cervix: clinical value of squamous cell carcinoma antigen (SCC) measurements. (1997)

The clinical value of SCC levels has been evaluated in four groups of women affected by cervical carcinoma. Among the 116 newly diagnosed patients, the SCC pretreatment level was elevated in 57% of cases and was strictly correlated with clinical stage (Ib to IV: p = < 0.01) and histotype (squamous cell carcinoma versus others: p = 0.0005). No significant difference was found in relation to nodal status. For the 28 patients submitted to neoadjuvant chemotherapy clinical response was correlated with the change in serum SCC level: stable or rising serum level indicated that the disease was unchanged or progressive, respectively. In the group of 48 patients affected by recurrent carcinoma, a raised SCC level was found in 71% of cases, with a lead time ranging from 0 to 12 months. No identification of the site of recurrence could be extrapolated from the value of SCC. As to the 108 regularly monitored patients, no significant difference in the risk to develop recurrence was shown for patients with a raised SCC level at the time of primary diagnosis (NED) versus relapsed: p = > 0.05).
Human acute leukemia cells injected in NOD/LtSz‐scid/IL‐2Rγ null mice generate a faster and more efficient disease compared to other NOD/scid‐related strains (2008)

Transplantation of human acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) primary cells and cell lines in different strains of immunodeficient mice has led to preclinical models extensively used to investigate acute leukemia stem cells, biology and drug sensitivity. We studied the engraftment kinetics of AML and ALL cell lines and primary cells in 3 strains of NOD.CB17-Prkdc(scid) (NOD/scid, NS)-related mice (NOD.Cg-Prkdc(scid)B2m(tm1Unc)/J, abbreviated NOD/scid/beta2 null, NSB; and NOD.Cg-Prkdc(scid)Il2rg(tm1Wjll)/SzJ, abbreviated NOD/scid/IL-2Rgamma null, NSG). The engraftment of human malignant cells was investigated by means of clinicopathological criteria, flow cytometry, PCR and immunohistochemistry. In NSG mice, we observed a significantly faster development of leukemia-related symptoms and a higher percentage of leukemia cells in the blood, in the marrow and in the spleen. The leukemia-related angiogenic switch (measured as the number of circulating endothelial cells and progenitors) was faster in NSG compared to NS and NSB mice. These models will be instrumental to studies on leukemia-initiating stem cells, leukemia biology, preclinical treatment studies, and to obtain patient-specific preclinical models to design and investigate patient-tailored therapies.
HyperPower: Power- and memory-constrained hyper-parameter optimization for neural networks (2018)

While selecting the hyper-parameters of Neural Networks (NNs) has been so far treated as an art, the emergence of more complex, deeper architectures poses increasingly more challenges to designers and Machine Learning (ML) practitioners, especially when power and memory constraints need to be considered. In this work, we propose HyperPower, a framework that enables efficient Bayesian optimization and random search in the context of power- and memory-constrained hyperparameter optimization for NNs running on a given hardware platform. HyperPower is the first work (i) to show that power consumption can be used as a low-cost, a priori known constraint, and (ii) to propose predictive models for the power and memory of NNs executing on GPUs. Thanks to HyperPower, the number of function evaluations and the best test error achieved by a constraint-unaware method are reached up to 112.99× and 30.12× faster, respectively, while never considering invalid configurations. HyperPower significantly speeds up the hyper-parameter optimization, achieving up to 57.20× more function evaluations compared to constraint-unaware methods for a given time interval, effectively yielding significant accuracy improvements by up to 67.6%.
Heterochromatin and Epigenetic Control of Gene Expression (2003)

Eukaryotic DNA is organized into structurally distinct domains that regulate gene expression and chromosome behavior. Epigenetically heritable domains of heterochromatin control the structure and expression of large chromosome domains and are required for proper chromosome segregation. Recent studies have identified many of the enzymes and structural proteins that work together to assemble heterochromatin. The assembly process appears to occur in a stepwise manner involving sequential rounds of histone modification by silencing complexes that spread along the chromatin fiber by self-oligomerization, as well as by association with specifically modified histone amino-terminal tails. Finally, an unexpected role for noncoding RNAs and RNA interference in the formation of epigenetic chromatin domains has been uncovered.
Generalized Sampling and Variance in Counterfactual Regret Minimization (2012)

In large extensive form games with imperfect information, Counterfactual Regret Minimization (CFR) is a popular, iterative algorithm for computing approximate Nash equilibria. While the base algorithm performs a full tree traversal on each iteration, Monte Carlo CFR (MCCFR) reduces the per iteration time cost by traversing just a sampled portion of the tree. On the other hand, MCCFR's sampled values introduce variance, and the effects of this variance were previously unknown. In this paper, we generalize MCCFR by considering any generic estimator of the sought values. We show that any choice of an estimator can be used to probabilistically minimize regret, provided the estimator is bounded and unbiased. In addition, we relate the variance of the estimator to the convergence rate of an algorithm that calculates regret directly from the estimator. We demonstrate the application of our analysis by defining a new bounded, unbiased estimator with empirically lower variance than MCCFR estimates. Finally, we use this estimator in a new sampling algorithm to compute approximate equilibria in Goofspiel, Bluff, and Texas hold'em poker. Under each of our selected sampling schemes, our new algorithm converges faster than MCCFR.