gebhart/patrepeval huggingface dataset:
Abstract IA-16: Control of growth by mTOR signaling (2009)

Abstract mTOR is the target of the immunosuppressive drug rapamycin and the central component of a nutrient- and hormone-sensitive signaling pathway that regulates cell growth and proliferation. We now appreciate that this pathway becomes deregulated in many human cancers. We have identified two distinct mTOR-containing proteins complexes, one of which regulates growth through S6K and another that regulates cell survival through Akt. These complexes, mTORC1 and mTORC2, define both rapamycin-sensitive and insensitive branches of the mTOR pathway. I will discuss new results from our lab on the regulation of the mTORC1 and mTORC2 pathways. I will provide an overview of mTOR signaling as well as discuss the regulation of mTORC1 by insulin and nutrients and the role of mTORC2 in cancer. We have recently identified new upstream components of the mTORC1 pathway that are involved in amino acid sensing and are starting to understand some of the molecular mechanisms involved in this process. Current evidence suggests that amino acids regulate the mTORC1 pathway by controlling the intracellular localization of mTORC1. Specifically, amino acids promote the movement of mTORC1 to a part of the endomembrane system that also contains its activator Rheb. Amino acids signal through the conserved Rag family of small GTPases that directly interact with the raptor component of mTORC1 in fashion that depends on the GTP-loaded status of the Rags. In addition, I will present evidence that inhibition of mTORC1 by the novel mTOR-interacting protein Deptor is a mechanism for hyperactivating PI3K signaling in multiple myeloma. Citation Information: Cancer Res 2009;69(23 Suppl):IA-16.
High-speed ultrawideband photonically enabled compressed sensing of sparse radio frequency signals (2013)

We demonstrate a new architecture for high-speed compressed sensing using chirp processing with ultrafast laser pulses, presently applied to the measurement of sparse-frequency microwave signals. We spectrally encode highly chirped ultrafast laser pulses with pseudorandom bit sequences such that every laser pulse acquires a unique spectral pattern. The pulses are partially compressed in time, extending the effective sampling rate beyond the electronic limit, and then modulated with a sparse microwave signal. Finally the pulses are fully compressed and detected, effectively integrating the measurement. We achieve 100 usable features per pattern allowing for 100 points in the reconstructed microwave spectra and experimentally demonstrate reconstruction of two- and three-tone microwave signals spanning from 900 MHz to 14.76 GHz. These spectra are reconstructed by measuring the energy of only 23 to 38 consecutive laser pulses acquired in a single shot with a 500 MHz real-time oscilloscope.
Untersuchungen über Pyrimidine, II. Darstellung und Eigenschaften von 2.6‐Dichlor‐5‐chlormethyl‐pyrimidin (1966)

Abstract Aus 5‐Hydroxymethyl‐uracil ( 1 ) entsteht bei der Chlorierung mit einer Mischung von Phosphoroxidchlorid und Phosphorpentachlorid in guter Ausbeute 2.6‐Dichlor‐5‐chlormethyl‐pyrimidin ( 2 ). Dieses reagiert mit den verschiedensten Verbindungen, die nucleophile Gruppen enthalten. Die drei Chlor‐Atome besitzen eine deutlich abgestufte Reaktionsfähigkeit: Cl‐aliphatisch (allylständig) > Cl an C‐6 > Cl an C‐2. So lassen sich gezielt mono‐, di‐ und trisubstituierte Derivate, z. B. Alkyläther, Phenoläther, Thioäther, Amine und Azide darstellen. Einige dieser Verbindungen besitzen beträchtliche bakteriostatische und fungistatische Wirksamkeit. Die Glykolyse von Tumorzellen wird gehemmt, die Transplantierbarkeit gewisser Tumorarten aufgehoben.
THE PREPARATION AND REACTIONS OF SOME SIMPLE 2,8-DISUBSTITUTED PURINES AND RELATED DERIVATIVES (1963)

Several previously unknown, simple 2,8-disubstituted purines have been prepared. The readily available (see H. Ballweg, Ann. 649, 114 (1961); and A. G. Beaman and R. K. Robins, J. Appl. Chem. (London), 12, 432 (1962)) 2,8-dichloropurine proved to be a most valuable synthetic intermediate in this work. The chemical reactivity of 2,8-dichloropurine toward nucleophilic substitution has been studied.
Memory-Based Dependency Parsing (2004)

Abstract. This paper describes experiments on using inductive machine learning to guide a deterinistic dependency parser for unrestricted natural language text. Using data from a small treebank of Swedish, an eager probabilistic learning algorithm is used to induce context-sensitive parse tables. Evaluation shows a significant improvement over the baseline, which uses a table without contextual information. 1
Hydrophobin Fusion of an Influenza Virus Hemagglutinin Allows High Transient Expression in Nicotiana benthamiana, Easy Purification and Immune Response with Neutralizing Activity (2014)

The expression of recombinant hemagglutinin in plants is a promising alternative to the current egg-based production system for the influenza vaccines. Protein-stabilizing fusion partners have been developed to overcome the low production yields and the high downstream process costs associated with the plant expression system. In this context, we tested the fusion of hydrophobin I to the hemagglutinin ectodomain of the influenza A (H1N1)pdm09 virus controlled by the hybrid En2PMA4 transcriptional promoter to rapidly produce high levels of recombinant antigen by transient expression in agro-infiltrated Nicotiana benthamiana leaves. The fusion increased the expression level by a factor of ∼ 2.5 compared to the unfused protein allowing a high accumulation level of 8.6% of the total soluble proteins. Hemagglutinin was located in ER-derived protein bodies and was successfully purified by combining an aqueous-two phase partition system and a salting out step. Hydrophobin interactions allowed the formation of high molecular weight hemagglutinin structures, while unfused proteins were produced as monomers. Purified protein was shown to be biologically active and to induce neutralizing antibodies after mice immunization. Hydrophobin fusion to influenza hemagglutinin might therefore be a promising approach for rapid, easy, and low cost production of seasonal or pandemic influenza vaccines in plants.
Effects of target identity and collision energy on the fragmentation of some mass‐selected protonated neuropeptides (1993)

A number of protonated neuropetides formed by 10 keV Cs+ ion bombardment are mass selected and their collision-induced dissociations (CID) with helium, argon, xenon and isobutane are monitored using a collision energy of 200 eV. Data obtained by fixing the collision gas and using translational energies in the range 50-250 eV are also presented. The present data imply that optimization of the CID spectra presented can be achieved through a judicious choice of both the target gas and the translational energy of the mass-selected ion. The combined effect of the two experimental parameters on the relative abundances of the major sequence ions and on the loss of side-chain moieties is discussed.
<i>Anaplasma phagocytophilum</i> MSP2(P44)-18 Predominates and Is Modified into Multiple Isoforms in Human Myeloid Cells (2008)

Anaplasma phagocytophilum is the etiologic agent of human granulocytic anaplasmosis. MSP2(P44), the bacterium's major surface protein, is encoded by a paralogous gene family and has been implicated in a variety of pathobiological processes, including antigenic variation, host adaptation, adhesion, porin activity, and structural integrity. The consensus among several studies performed at the DNA and RNA levels is that a heterogeneous mix of a limited number of msp2(p44) transcripts is expressed by A. phagocytophilum during in vitro cultivation. Such analyses have yet to be extended to the protein level. In this study, we used proteomic and molecular approaches to determine that MSP2(P44)-18 is the predominant if not the only paralog expressed and is modified into multiple 42- to 44-kDa isoforms by A. phagocytophilum strain HGE1 during infection of HL-60 cells. The msp2(p44) expression profile was homogeneous for msp2(p44)-18. Thus, MSP2(P44)-18 may have a fitness advantage in HL-60 cell culture in the absence of selective immune pressure. Several novel 22- to 27-kDa MSP2 isoforms lacking most of the N-terminal conserved region were also identified. A. phagocytophilum MSP2(P44) orthologs expressed by other pathogens in the family Anaplasmataceae are glycosylated. Gas chromatography revealed that recombinant MSP2(P44)-18 is modified by glucose, galactose, xylose, mannose, and trace amounts of other glycosyl residues. These data are the first to confirm differential modification of any A. phagocytophilum MSP2(P44) paralog and the first to provide evidence for expression of truncated versions of such proteins.
Design of a miniaturized ultrasonic bladder volume monitor and subsequent preliminary evaluation on 41 enuretic patients (1998)

Nocturnal incontinence (enuresis) affects 20% of children over four years old, and this figure typically decreases by 15% each year. At the age of 18, 1% of those people remain enuretic. Nocturnal enuresis can be treated by means of a conditioning device that awakens the patient once the urine level has reached a preestablished threshold of the capacity of his or her bladder. We have designed and implemented a portable miniaturized ultrasonic monitor, which permits estimation of the urine volume with an accuracy of 75%. Prototypes have been completed and validated on 41 patients (children) at Ste. Justine Hospital (Montréal). On the first group of 33 patients, we used a hand-held transducer to determine the volume detection range, which is accurate for volumes between 40 and 400 mL. With the second group of 8 patients, the device was mounted on an elastic belt around the abdomen. Measurements were taken in order to validate the accuracy of urine threshold detection and the activation of the corresponding alarm.
Injection locking of oscillators (1965)

An oscillator can be locked in frequency by an external signal which is injected into the oscillator. In the oscillator model developed by Adler [1], the mechanism of the locking process depends upon the following. 1) The initial frequency difference between the oscillator and external signals. 2) The relative amplitude between the injected and the oscillator signals. 3) The circuit parameters. There are cases when the time required for locking must be known, particularly when an oscillator is being locked to a pulsed signal. In this paper, the work of Adler is extended to develop an equation which is useful for higher levels of locking signal, a case often encountered when an oscillator is being injection locked by a pulsed signal. Because the solution of this equation is unwieldy and difficult to understand intuitively, except in very special cases, curves describing the locking mechanism were obtained using a digital computer. These curves enable a designer to construct oscillators which will provide a desired performance. The curves were checked experimentally and showed a close agreement between predicted and measured results. The experimental data indicates that the theory describes the locking time remarkably well even at high levels of locking signal.
Proliferative arrest and rapid turnover of thymic epithelial cells expressing Aire (2007)

Expression of autoimmune regulator (Aire) by thymic medullary epithelial cells (MECs) is critical for central tolerance of self. To explore the mechanism by which such a rare cell population imposes tolerance on the large repertoire of differentiating thymocytes, we examined the proliferation and turnover of Aire(+) and Aire(-) MEC subsets through flow cytometric analysis of 5-bromo-2'deoxyuridine (BrdU) incorporation. The Aire(+) MEC subset was almost entirely postmitotic and derived from cycling Aire(-) precursors. Experiments using reaggregate thymic organ cultures revealed the presence of such precursors among Aire(-) MECs expressing low levels of major histocompatibility complex class II and CD80. The kinetics of BrdU decay showed the Aire(+) population to have a high turnover. Aire did not have a direct impact on the division of MECs in vitro or in vivo but, rather, induced their apoptosis. We argue that these properties strongly favor a "terminal differentiation" model for Aire function in MECs, placing strict temporal limits on the operation of any individual Aire(+) MEC in central tolerance induction. We further speculate that the speedy apoptosis of Aire-expressing MECs may be a mechanism to promote cross-presentation of the array of peripheral-tissue antigens they produce.
The temporal relationship of the onsets of alcohol dependence and major depression: using a genetically informative study design (2006)

Risk for developing AD was substantially increased by a prior episode of MD. The association was only partially accounted for by familial factors, providing support for a direct causal effect such as self-medication. The etiologic path from AD to MD was insignificant.
A visual wikipedia for satellite imagery (2018)

GeoVisipedia (Geospatial Visual Wikipedia) is a new and novel approach to sharing knowledge about complex geospatial entities such as facilities. Facilities are composed of interconnected objects such as buildings, chemical processing units, electrical generation equipment and similar structures. Satellite imagery of a facility reveals a great deal about the organization and visual appearance of objects in a facility, but very little about the identity or function of the object. For example, given a satellite imagery of an oil refinery, an expert in refining readily identifies distillation units and can explain how they work. A non-expert would have a very difficult time identifying these objects let alone explaining how they function. To make highly complex information accessible to non-experts, GeoVisipedia associates a wiki page with objects in satellite imagery. A user selects an object in the image and a wiki page appears that provides the user with detailed information about the object. Experts can author information into the wiki and this information is shared with other users. Additionally, GeoVisipedia automatically transfers all wiki pages from one image of a facility to other imagery of the facility. Consequentially, knowledge about objects in the facility integrates over time as new imagery becomes available and as new wiki pages are created and additional information is added to existing wiki pages. In this respect, satellite imagery becomes a portal to expert knowledge and insight about objects in a facility.
A METHODOLOGY FOR THE PLANNING OF THE INTEGRATED E-BUSINESS SYSTEM ARCHITECTURE (2004)

This research investigates the procedure for the design of an integrated e-Business system architecture from the viewpoint to support the fulfillment of the business strategic goals and to minimize the total system life-cycle cost. A model for describing the relationship between the e-Business information architecture and the corporate objectives was developed first. This model was then used for the resolution of design problems of the integrated e-Business information system architecture. These problems include defining corporate e-Business strategic objectives, developing the business process model and identifying core processes, establishing the e-Business common architecture, mapping core processes to e-Business common architecture components, mapping the e-Business common architecture to the specific commercial e-Business system. Finally, a model for the design of an integrated e-Business architecture is proposed, which includes: (1) the e-Business knowledge library; and (2) the design procedure of the integrated architecture. A case study of a domestic electronic company is presented to illustrate the construction of the integrated e-Business architecture.
A CMOS Instrumentation Amplifier With 90-dB CMRR at 2-MHz Using Capacitive Neutralization: Analysis, Design Considerations, and Implementation (2010)

The benefits of using “current feedback” in instrumentation amplifier (IA) design are well known. In this paper, we analyze the mismatch mechanisms, both random and systematic types, which influence the common-mode rejection ratio (CMRR) performance of the local current feedback IA topology. We derive analytical expressions for the common-mode gain frequency response due to random mismatches (transconductance, drain-source conductance and parasitic capacitance) and verify the integrity of the analysis through simulation. To address the systematic mismatch in the drain capacitance of the input pair transistors, we employ capacitive neutralization and verify its effectiveness in practice from the fabricated IA chip samples in a 0.35- CMOS process technology. The measured average common-mode gain improvement for the 20 fabricated samples employing our neutralization technique is about 20 dB at 2 MHz ( 3 dB bandwidth). When taking into account the differential gain response (33.7 dB), the average CMRR of the neutralized IA at 2 MHz exceeds 90 dB. The IA occupies an area of 0.068 and dissipates 0.85 mW from a 3-V power supply. The circuit is intended for a wideband bioimpedance spectroscopy application.
Addition of Catfish Gonadotropin-Releasing Hormone (GnRH) Receptor Intracellular Carboxyl-Terminal Tail to Rat GnRH Receptor Alters Receptor Expression and Regulation (1998)

Mammalian GnRH receptor (GnRHR) is unique among G protein-coupled seven-transmembrane segment receptors due to the absence of an intracellular C-terminal tail frequently important for internalization and/or desensitization of other G protein-coupled receptors. The recent cloning of nonmammalian (i.e. catfish, goldfish, frog, and chicken) GnRHRs shows that these contain an intracellular C terminus. Addition of the 51-amino acid intracellular C terminus from catfish GnRHR (cfGnRHR) to rat GnRHR (rGnRHR) did not affect rGnRHR binding affinity but elevated receptor expression by about 5-fold. Truncation of the added C terminus impaired the elevated receptor-binding sites by 3- to 8-fold, depending on the truncation site. In addition, introducing the C terminus to rGnRHR altered the pattern of receptor regulation from biphasic down-regulation and recovery to monophasic down-regulation. The extent of down-regulation was also enhanced. The alteration in receptor regulation due to the addition of a C terminus was reversed by truncation of the added C terminus. Furthermore, addition of the cfGnRHR C terminus to rGnRHR significantly augmented the inositol phospholipid (IP) response of transfected cells to Buserelin, but this did not result from the elevation of receptor-binding sites. Addition of the C terminus did not affect Buserelin-stimulated cAMP and PRL release. GH3 cells transfected with wild-type cfGnRHR did not show measurable Buserelin binding or significant stimulation of IP, cAMP, or PRL in response to Buserelin (10[-13]-10[-9] M). GH3 cells transfected with C terminus-truncated cfGnRHR showed no IP response to Buserelin (10[-13]-10[-7] M). These results suggest that addition of the cfGnRHR intracellular C terminus to rGnRHR has a significant impact on rGnRHR expression and regulation and efficiency of differential receptor coupling to G proteins.
Photobioreactor cultivation strategies for microalgae and cyanobacteria (2018)

The current burden on fossil-derived chemicals and fuels combined with the rapidly increasing global population has led to a crucial need to develop renewable and sustainable sources of chemicals and biofuels. Photoautotrophic microorganisms, including cyanobacteria and microalgae, have garnered a great deal of attention for their capability to produce these chemicals from carbon dioxide, mineralized water, and solar energy. While there have been substantial amounts of research directed at scaling-up production from these microorganisms, several factors have proven difficult to overcome, including high costs associated with cultivation, photobioreactor construction, and artificial lighting. Decreasing these costs will substantially increase the economic feasibility of these production processes. Thus, the purpose of this review is to describe various photobioreactor designs, and then provide an overview on lighting systems, mixing, gas transfer, and the hydrodynamics of bubbles. These factors must be considered when the goal of a production process is economic feasibility. Targets for improving microalgae and cyanobacteria cultivation media, including water reduction strategies will also be described. As fossil fuel reserves continue to be depleted and the world population continues to increase, it is imperative that renewable chemical and biofuel production processes be developed toward becoming economically feasible. Thus, it is essential that future research is directed toward improving these processes. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:811-827, 2018.
Towards a rule model for self-adaptive software (2005)

Most self-adaptive software use rules explicitly or implicitly to decide how to react to monitored events. Meanwhile, rules are usually scattered in different procedures, which makes procedures more complex. This paper proposes a Rule Model, which is used to extract scattered rules from different procedures, so as to enhance the self-adaptive ability of software. The paper presents what is Rule Model, including: three key concepts (event, parameter, and rule), hierarchical organization, role in application, and XML-based representation. The paper also introduces how to map declarative rules inside one deployable application to executable rules inside one rule engine, based on one J2EE-compliant application server.
Ursa Minor: Versatile Cluster-based Storage (CMU-PDL-05-104) (2018)

No single encoding scheme or fault model is optimal for all data. A versatile storage system allows them to be matched to access patterns, reliability requirements, and cost goals on a per-data item basis. Ursa Minor is a cluster-based storage system that allows data-specific selection of, and on-line changes to, encoding schemes and fault models. Thus, different data types can share a scalable storage infrastructure and still enjoy specialized choices, rather than suffering from “one size fits all.” Experiments with Ursa Minor show performance benefits of 2–3× when using specialized choices as opposed to a single, more general, configuration. Experiments also show that a single cluster supporting multiple workloads simultaneously is much more efficient when the choices are specialized for each distribution rather than forced to use a “one size fits all” configuration. When using the specialized distributions, aggregate cluster throughput nearly doubled.