gebhart/patrepeval huggingface dataset:
The BRCA‐1 binding protein BRAP2 is a novel, negative regulator of nuclear import of viral proteins, dependent on phosphorylation flanking the nuclear localization signal (2009)

This study describes for the first time the ability of the novel BRCA1-binding protein 2 (BRAP2) to inhibit the nuclear import of specific viral proteins dependent on phosphorylation. Ectopic expression of BRAP2 in transfected African green monkey kidney COS-7 cells was found to significantly reduce nuclear localization signal (NLS)-dependent nuclear accumulation of either simian virus SV40 large-tumor antigen (T-ag) or human cytomegalovirus DNA polymerase processivity factor ppUL44; this was also observed in HL-60 human promyelocytic leukemia cells on induction of BRAP2 expression by vitamin D3 treatment. BRAP2 inhibition of nuclear accumulation was dependent on phosphorylation sites flanking the respective NLSs, where substitution of the cyclin-dependent kinase site T124 of T-ag with Ala or Asp prevented or enhanced BRAP2 inhibition of nuclear import, respectively. Substitution of T427 within the NLS of ppUL44 gave similar results, whereas no effect of BRAP2 was observed on nuclear targeting of other viral proteins, such as herpes simplex virus-1 pUL30, which lacks a phosphorylation site near its NLS, and the human immunodeficiency virus-1 Tat protein. Pulldowns/AlphaScreen assays indicated direct, high-affinity binding of BRAP2(442-592) to T-ag(111-135), strictly dependent on negative charge at T124 and the NLS. All results are consistent with BRAP2 being a novel, phosphorylation-regulated negative regulator of nuclear import, with potential as an antiviral agent.
Defending against malicious peripherals with Cinch (2016)

Malicious peripherals designed to attack their host computers are a growing problem. Inexpensive and powerful peripherals that attach to plug-and-play buses have made such attacks easy to mount. Making matters worse, commodity operating systems lack coherent defenses, and users are often unaware of the scope of the problem. We present Cinch, a pragmatic response to this threat. Cinch uses virtualization to attach peripheral devices to a logically separate, untrusted machine, and includes an interposition layer between the untrusted machine and the protected one. This layer regulates interaction with devices according to user-configured policies. Cinch integrates with existing OSes, enforces policies that thwart real-world attacks, and has low overhead.
Rice UDP-Glucose Pyrophosphorylase1 Is Essential for Pollen Callose Deposition and Its Cosuppression Results in a New Type of Thermosensitive Genic Male Sterility (2007)

UDP-glucose pyrophosphorylase (UGPase) catalyzes the reversible production of glucose-1-phosphate and UTP to UDP-glucose and pyrophosphate. The rice (Oryza sativa) genome contains two homologous UGPase genes, Ugp1 and Ugp2. We report a functional characterization of rice Ugp1, which is expressed throughout the plant, with highest expression in florets, especially in pollen during anther development. Ugp1 silencing by RNA interference or cosuppression results in male sterility. Expressing a double-stranded RNA interference construct in Ugp1-RI plants resulted in complete suppression of both Ugp1 and Ugp2, together with various pleiotropic developmental abnormalities, suggesting that UGPase plays critical roles in plant growth and development. More importantly, Ugp1-cosuppressing plants contained unprocessed intron-containing primary transcripts derived from transcription of the overexpression construct. These aberrant transcripts undergo temperature-sensitive splicing in florets, leading to a novel thermosensitive genic male sterility. Pollen mother cells (PMCs) of Ugp1-silenced plants appeared normal before meiosis, but during meiosis, normal callose deposition was disrupted. Consequently, the PMCs began to degenerate at the early meiosis stage, eventually resulting in complete pollen collapse. In addition, the degeneration of the tapetum and middle layer was inhibited. These results demonstrate that rice Ugp1 is required for callose deposition during PMC meiosis and bridges the apoplastic unloading pathway and pollen development.
Insulin detemir is a fully efficacious, low affinity agonist at the insulin receptor (2010)

Insulin detemir is fully efficacious compared with human insulin on all metabolic endpoints measured in vitro and in vivo. The fact that the potency estimates are method-dependent emphasizes the importance of establishing full dose-response relationships when characterizing insulin detemir.
Cellular and molecular mechanics by atomic force microscopy: Capturing the exocytotic fusion pore  <i>in vivo</i> ? (1997)

The atomic force microscope (AFM) is a remarkably simple instrument that can measure forces down to piconewtons and can resolve force changes caused by the displacement of its probe by a fraction of a nanometer. Furthermore, these measurementscanbedoneunderwater,allowingforthestudy of biological material under conditions that resemble thosein vivo.TheAFMfunctionslikeaminiaturephonograph.Asharp tip,mountedonacantilever,interactswiththesample,causing minutedeflectionsthatcanbecalibratedasaforce.TheAFM, in its force-measuring mode, has been applied to the study of molecular mechanics. For example, the laboratory of Hermann Gaub in Munich succeeded in the remarkable feat of measuring the adhesion force between single avidin‐biotin pairs (’160 pN; ref. 1). These measurements were independently confirmed by molecular dynamic simulations of the avidin‐biotininteractionthatrevealedtheatomictrajectoryof a rupture and predicted the associated forces (2). Hence, the techniquesofmolecularmechanicsnowrivalthecapabilitiesof patch-clamp techniques (3) in describing the activity of single proteins. The patch-clamp technique seals a lipid membrane, containingionchannelproteins,ontoaglasspipetteelectrode. Ioniccurrentsflowingthroughasingleionchannelproteinare then easily measured, reporting on the conformational states of the transmembrane protein. In contrast to the patch-clamp technique, useful mainly for the characterization of ion channels, molecular mechanics studies can be done on single proteins or more complex structures that do not carry an associated electrical activity. ThemostfamiliaruseoftheAFMisincreatingtopographic imagesofasample.ThisisdonebyscanningtheAFMtipover the sample and recording the z axis displacement required to maintain a constant contact force. The nanometer resolution of the AFM imaging technique has been used to examine the structural features of proteins, producing data that is comparable to that obtained by x-ray crystallography (4). However, the biggest promise of the AFM technique is in the measurement of the activity of single protein structuresin vivoduring signaling events or during other types of cellular activities. Indeed, we may be getting close. A recent example demonstratedthatitispossibletoobserveconformationalchangesin the structure of a single nuclear pore in Xenopus oocyte nuclear envelopes (5). However, these measurements were doneinfixedtissue.RecentworkfromthelaboratoryofBhanu
Reduction of Aliasing Effects of RF PWM Modulated Signals by Cross Point Estimation (2014)

The trend in transmitter systems is to move the digital domain closer toward the antenna using digital modulators and drivers to reduce circuit complexity and to save power. One promising approach is the use of RF pulse width modulation (RF PWM). Unfortunately purely digital discrete time RF PWM suffers from aliasing problems which limit the achievable resolution. For a 40 MHz bandwidth signal at 2.6 GHz carrier frequency for example the achievable signal quality is limited to ~ 43 dBc. This paper describes the root cause of this effect, an error in the determination of the cross points, due to the sampled nature of the signal and proposes a method to compensate for it. It is shown that by interpolating the signal and estimating the cross points the signal quality can be significantly improved. The interpolation is simplified by interpolating the decomposed outphasing signals instead of the full signal. This has the advantage that a constant instead of a phase modulated reference function can be used. It is shown that by simple cross point estimation the signal quality can already be improved to 65 dBc. When either considering a second modulator or when using a delta sigma like noise shaping architecture the signal quality can be further enhanced to 75 dBc.
B7h Triggering Inhibits Umbilical Vascular Endothelial Cell Adhesiveness to Tumor Cell Lines and Polymorphonuclear Cells (2010)

Vascular endothelial cells (ECs) are key players in leukocyte recruitment into tissues and metastatic dissemination of tumor cells. ECs express B7h, which is the ligand of the ICOS T cell costimulatory molecule. The aim of this work was to assess the effect of B7h triggering by a soluble form of ICOS (ICOS-Fc) on the adhesion of colon carcinoma cell lines to HUVECs. We found that B7h triggering inhibited HUVEC adhesiveness to HT29 and DLD1 cells (by 50 and 35%, respectively) but not to HCT116 cells. The effect was dependent on the ICOS-Fc dose and was detectable as early as 30 min after treatment and was still present after 24 h. It was inhibited by soluble anti-ICOS reagents (mAb and B7h-Fc) and silencing of B7h on HUVECs, and it was not displayed by an F119S mutated form of ICOS-Fc that does not bind B7h. HUVEC treatment with ICOS-Fc did not modulate expression of adhesion molecules and cytokines, but it substantially downmodulated ERK phosphorylation induced by E-selectin triggering or osteopontin, which may influence HUVEC adhesiveness. Moreover, HUVEC treatment with ICOS-Fc also inhibited adhesion of polymorphonuclear cells and several tumor cell lines from different origins. Therefore, the B7h-ICOS interaction may modulate spreading of cancer metastases and recruitment of polymorphonuclear cells in inflammatory sites, which opens a view on the use of ICOS-Fc as an immunomodulatory drug.
Spatial-Temporal Relation Networks for Multi-Object Tracking (2019)

Recent progress in multiple object tracking (MOT) has shown that a robust similarity score is key to the success of trackers. A good similarity score is expected to reflect multiple cues, e.g. appearance, location, and topology, over a long period of time. However, these cues are heterogeneous, making them hard to be combined in a unified network. As a result, existing methods usually encode them in separate networks or require a complex training approach. In this paper, we present a unified framework for similarity measurement which could simultaneously encode various cues and perform reasoning across both spatial and temporal domains. We also study the feature representation of a tracklet-object pair in depth, showing a proper design of the pair features can well empower the trackers. The resulting approach is named spatial-temporal relation networks (STRN). It runs in a feed-forward way and can be trained in an end-to-end manner. The state-of-the-art accuracy was achieved on all of the MOT15-17 benchmarks using public detection and online settings.
Adversarial Training Versus Weight Decay (2018)

Performance-critical machine learning models should be robust to input perturbations not seen during training. Adversarial training is a method for improving a model's robustness to some perturbations by including them in the training process, but this tends to exacerbate other vulnerabilities of the model. The adversarial training framework has the effect of translating the data with respect to the cost function, while weight decay has a scaling effect. Although weight decay could be considered a crude regularization technique, it appears superior to adversarial training as it remains stable over a broader range of regimes and reduces all generalization errors. Equipped with these abstractions, we provide key baseline results and methodology for characterizing robustness. The two approaches can be combined to yield one small model that demonstrates good robustness to several white-box attacks associated with different metrics.
Inhibition of <i>Fusarium moniliforme</i> var. <i>subglutinans</i>, the causal agent of pine pitch canker, by the soil bacterium <i>Arthrobacter</i> sp. (1981)

A species of Arthrobacter was recovered during culture of the causal organism of pitch canker of southern pines. Fusarium moniliforme var. subglutinans (FMS). Arthrobacter is a relatively common soil bacterium and is lytic to several fungal pathogens in the soil. Soil samples from two seed orchards with pitch canker and one from a healthy pine plantation all yielded Arthrobacter. These isolates were evaluated for their ability to inhibit the growth of FMS isolates from pitch canker tissue and from soil in areas with high pitch canker disease incidence, and to several other species of Fusarium isolated from the same soil samples where Arthrobacter was recovered. Generally the pitch canker isolates were more sensitive to Arthrobacter than the soil fusaria. There was variation in the ability of the Arthrobacter isolates to inhibit the growth of the fusaria recovered from the soil at the three different test sites. Light and scanning electron microscope observations revealed that hyphae of FMS growing near an isolate of Arthrobacter were enlarged, producing many vesicularlike structures. The surface of these hyphae was warped and wrinkled in comparison with normal hyphae.
A low loss/highly rugged IGBT-generation based on a self aligned process with double implanted n/n/sup +/-emitter (2002)

A new 1200 V-IGBT chip is presented which has an optimized planar cell structure for lowest on-state voltage, but that nevertheless guarantees a very high degree of ruggedness. The key point for these features is a new self aligned process concept with a double implanted submicron emitter structure, which will be the basis also for a lower voltage IGBT (600 V) as well as for high voltage IGBTs (1600 V and higher).
Randomized Clinical Trial of Long-Acting Somatostatin for Autosomal Dominant Polycystic Kidney and Liver Disease (2010)

There are no proven, effective therapies for polycystic kidney disease (PKD) or polycystic liver disease (PLD). We enrolled 42 patients with severe PLD resulting from autosomal dominant PKD (ADPKD) or autosomal dominant PLD (ADPLD) in a randomized, double-blind, placebo-controlled trial of octreotide, a long-acting somatostatin analogue. We randomly assigned 42 patients in a 2:1 ratio to octreotide LAR depot (up to 40 mg every 28+/-5 days) or placebo for 1 year. The primary end point was percent change in liver volume from baseline to 1 year, measured by MRI. Secondary end points were changes in total kidney volume, GFR, quality of life, safety, vital signs, and clinical laboratory tests. Thirty-four patients had ADPKD, and eight had ADPLD. Liver volume decreased by 4.95%+/-6.77% in the octreotide group but remained practically unchanged (+0.92%+/-8.33%) in the placebo group (P=0.048). Among patients with ADPKD, total kidney volume remained practically unchanged (+0.25%+/-7.53%) in the octreotide group but increased by 8.61%+/-10.07% in the placebo group (P=0.045). Changes in GFR were similar in both groups. Octreotide was well tolerated; treated individuals reported an improved perception of bodily pain and physical activity. In summary, octreotide slowed the progressive increase in liver volume and total kidney volume, improved health perception among patients with PLD, and had an acceptable side effect profile.
The roasting and leaching of Witwatersrand pyrite concentrates (1979)

Many of the pyrite concentrates produced at South African gold and uranium mines contain economically significant amounts of nickel, copper, and cobalt, apart from gold and uranium. In some cases these concentrates are leached for uranium, followed by roasting and cyanidation of the calcine for the extraction of the gold. Even if their intrinsic value is excluded, the presence of appreciable amounts of base metals can lead to excessive consumption of cyanide and zinc in the conventional process for the recovery of gold from calcines. The extent to which base metals, particularly cyanocides in the calcine, can be made soluble in water or in dilute acid by variation of the pyrite roasting conditions was investigated. An important finding of the investigation was that the conditions producing favourable base-metal sulphation (and hence solubility in water) also produced good sulphation of the uranium values that had not been extracted in a conventional leach of the original pyrite. Thus, if the pyrite is subjected to a sulphating roast followed by quenching in water (or dilute acid), it should be possible for the uranium to be extracted in improved yield. The need for leaching of the pyrite would therefore fall away. It was noted that sulphation roasting also resulted in improved gold extractions when the calcine was subsequently subjected to conventional cyanide-extraction procedures. From well-sulphated calcine, the dissolution of base metals and uranium appeared to be fairly independent of leaching pH, time, and temperature. On an inadequately sulphated calcine, Iow pH values during leaching gave increased extraction of copper and uranium but did not have a significant effect on the dissolution of nickel and cobalt. The extraction of uranium increased with increasing leaching time and temperature, while only longer times at a Iow pH value markedly improved the extraction of copper. The extraction of cobalt was fairly independent of leaching time and temperature, but the results were insufficient for a conclusive evaluation to be made of their effects on the dissolution of nickel. A cursory economic assessment 'indicated that sulphation roasting applied to the pyrites investigated is likely to be very profitable.
Sensor/data fusion based on value of information (2003)

Spatially distributed network of inexpensive, small and smart nodes with multiple onboard sensors is an important class of emerging networked systems for various applications. Since this network of sensors has to operate efflciently in adverse environments, it is important that these sensors process information efficiently and share information such that the decision accuracy is improved. One way to address this problem is to measure the value of information obtained from multiple sensors on the same sensor node as well as from the neighboring nodes and fuse that information if value is added in terms of improvement in decision accuracy. In this paper, the measures that are developed for assessing the value of information are described. These measures are then used in making a decision of fusing either features or data from multiple sensors and neighboring nodes. While making this decision whether the value is added by fusing the information, is verified by conditioning it on improving the decision accuracy. The measures and value added are verified by using real data collected at Twentynine Plams, CA, USA and in the context of target detection and classification. From the results of improvement in classification accuracy and probability of detection reported in this paper, it can be seen that the utilization of measure of value of information while fusing helps in improving the decision accuracy signijicantly.
Field Assessment and Specification Review for Roller-Integrated Compaction Monitoring Technologies (2011)

Roller-integrated compaction monitoring (RICM) technologies provide virtually 100-percent coverage of compacted areas with real-time display of the compaction measurement values. Although a few countries have developed quality control (QC) and quality assurance (QA) specifications, broader implementation of these technologies into earthwork construction operations still requires a thorough understanding of relationships between RICM values and traditional in situ point test measurements. The purpose of this paper is to provide: (a) an overview of two technologies, namely, compaction meter value (CMV) and machine drive power (MDP); (b) a comprehensive review of field assessment studies, (c) an overview of factors influencing statistical correlations, (d) modeling for visualization and characterization of spatial nonuniformity; and (e) a brief review of the current specifications.
MAC Protocol Adaptation in Cognitive Radio Networks: An Experimental Study (2009)

This paper presents an adaptive MAC (AMAC) protocol for supporting MAC layer adaptation in cognitive radio networks. MAC protocol adaptation is motivated by the flexibility of emerging software-defined radios which make it feasible to dynamically adjust radio protocols and parameters. Dynamic changes to the MAC layer may be useful in wireless networking scenarios such as tactical or vehicular communications where the radio node density and service requirements can vary widely over time. A specific control framework for the proposed AMAC is described based on the "CogNet" protocol stack which uses a "global control plane (GCP)" to distribute control information between nearby radios. A proof-of-concept AMAC prototype which switches between CSMA and TDMA is implemented using GNU radio platforms on the ORBIT radio grid testbed. Experimental results are given for both UDP and TCP with dynamic traffic variations. The results show that adaptive MAC can be implemented with reasonable control protocol overhead and latency, and that the adaptive network achieves improved performance relative to a conventional static system.
Beyond clicks (2013)

To understand whether a user is satisfied with the current search results, implicit behavior is a useful data source, with clicks being the best-known implicit signal. However, it is possible for a non-clicking user to be satisfied and a clicking user to be dissatisfied. Here we study additional implicit signals based on the relationship between the user's current query and the next query, such as their textual similarity and the inter-query time. Using a large unlabeled dataset, a labeled dataset of queries and a labeled dataset of user tasks, we analyze the relationship between these signals. We identify an easily-implemented rule that indicates dissatisfaction: that a similar query issued within a time interval that is short enough (such as five minutes) implies dissatisfaction. By incorporating additional query-based features in the model, we show that a query-based model (with no click information) can indicate satisfaction more accurately than click-based models. The best model uses both query and click features. In addition, by comparing query sequences in successful tasks and unsuccessful tasks, we observe that search success is an incremental process for successful tasks with multiple queries.
Treating intermittent allergic rhinitis: a prospective, randomized, placebo and antihistamine‐controlled study of Butterbur extract Ze 339 (2005)

Butterbur Ze 339 and Fexofenadine are comparably efficacious relative to placebo. Despite being a herbal drug, Butterbur Ze 339 has now been subject to a series of well controlled trials and should be considered as an alternative treatment for IAR.