gebhart/patrepeval huggingface dataset:
The gene encoding Escherichia coli acyl carrier protein lies within a cluster of fatty acid biosynthetic genes. (1992)

The gene encoding Escherichia coli acyl carrier protein (ACP) has been isolated and sequenced. The ACP gene (called acpP) was located on the genetic map between fabF and fabD which encode two fatty acid biosynthetic enzymes, 3-ketoacyl-ACP synthase II and malonyl CoA-ACP transacylase, respectively. An open reading frame between acpP and fabD encodes a 26.5-kDa protein that has significant sequence identity (greater than 40%) with two acetoacetyl-CoA reductases and thus is believed to encode a 3-ketoacyl-ACP reductase. This gene (called fabG) is cotranscribed with acpP. Thus, the gene encoding ACP, the key carrier protein of fatty acid synthesis, is located within a cluster of fatty acid biosynthetic genes.
T cell growth without serum. (1987)

Most in vitro T cell proliferation experiments are performed by using serum-supplemented medium, yet the actual contributions of serum components to cell cycle progression remain ill-defined, thus complicating attempts to fully define requirements for cell division. By utilizing a functional separation between T cell receptor-triggered "competence" and IL 2-promoted "progression" to independently assess serum requirements during each cell cycle stage, it was shown that serum serves an essential, active role only during the early events of the competence phase (G0-G1 transition) of T cell activation. Serum is required for optimal IL 2 production and the cell surface expression of IL 2 receptors after the stimulation of the T3/Ti antigen receptor complex. In contrast, serum does not function actively during IL 2-mediated progression through the G1 phase of the cycle. Serum proteins serve only a passive role at this stage, preventing the adsorption of IL 2. This same effect can be provided by any number of proteins including IL 2 itself, or even a high cell concentration. Supplementation of serum-free T cell cultures solely with IL 2 and transferrin is sufficient for maximal T cell proliferation, although the time of the peak response is delayed owing to a suboptimal rate of IL 2 receptor expression. Accordingly, the realization that serum is only necessary for the earliest stage of T cell activation will now enable studies designed to identify the critical individual serum components and to define their mechanism of action.
Identification of the Hepatitis C Virus E2 Glycoprotein Binding Site on the Large Extracellular Loop of CD81 (2002)

The binding of hepatitis C virus glycoprotein E2 to the large extracellular loop (LEL) of CD81 has been shown to modulate human T-cell and NK cell activity in vitro. Using random mutagenesis of a chimera of maltose-binding protein and LEL residues 113 to 201, we have determined that the E2-binding site on CD81 comprises residues Ile(182), Phe(186), Asn(184), and Leu(162). These findings reveal an E2-binding surface of approximately 806 A(2) and potential target sites for the development of small-molecule inhibitors of E2 binding.
Small cationic antimicrobial peptides delocalize peripheral membrane proteins (2014)

Short antimicrobial peptides rich in arginine (R) and tryptophan (W) interact with membranes. To learn how this interaction leads to bacterial death, we characterized the effects of the minimal pharmacophore RWRWRW-NH2. A ruthenium-substituted derivative of this peptide localized to the membrane in vivo, and the peptide also integrated readily into mixed phospholipid bilayers that resemble Gram-positive membranes. Proteome and Western blot analyses showed that integration of the peptide caused delocalization of peripheral membrane proteins essential for respiration and cell-wall biosynthesis, limiting cellular energy and undermining cell-wall integrity. This delocalization phenomenon also was observed with the cyclic peptide gramicidin S, indicating the generality of the mechanism. Exogenous glutamate increases tolerance to the peptide, indicating that osmotic destabilization also contributes to antibacterial efficacy. Bacillus subtilis responds to peptide stress by releasing osmoprotective amino acids, in part via mechanosensitive channels. This response is triggered by membrane-targeting bacteriolytic peptides of different structural classes as well as by hypoosmotic conditions.
Conditional DC depletion does not affect priming of encephalitogenic Th cells in EAE (2012)

EAE, an animal model for multiple sclerosis, is a Th17- and Th1-cell-mediated auto-immune disease, but the mechanisms leading to priming of encephalitogenic T cells in autoimmune neuroinflammation are poorly understood. To investigate the role of dendritic cells (DCs) in the initiation of autoimmune Th17- and Th1-cell responses and EAE, we used mice transgenic for a simian diphtheria toxin receptor (DTR) expressed under the control of the murine CD11c promoter (CD11c-DTR mice o nC57BL/6 background).EAE was induced by immunization with myelin oligodendrocyte glycoprotein (MOG) protein in CFA. DCs were depleted on the day before and 8 days after MOG immunization. The mean clinical EAE score was only mildly reduced in DC-depleted mice when DCs were ablated before EAE induction. The frequency of activated Th cells was not altered, and MOG-induced Th17 or Th1-cell responses were not altered, in the spleens of DC-depleted mice. Similar results were obtained if DCs were ablated the first 10 days after MOG immunization with repeated DC depletions. Unexpectedly, transient depletion of DCs did not affect priming or differentiation of MOG-induced Th17 and Th1-cell responses or the incidence of EAE. Thus, the mechanism of priming of Th cells in EAE remains to be elucidated.
RET as a Diagnostic and Therapeutic Target in Sporadic and Hereditary Endocrine Tumors (2006)

The RET gene encodes a receptor tyrosine kinase that is expressed in neural crest-derived cell lineages. The RET receptor plays a crucial role in regulating cell proliferation, migration, differentiation, and survival through embryogenesis. Activating mutations in RET lead to the development of several inherited and noninherited diseases. Germline point mutations are found in the cancer syndromes multiple endocrine neoplasia (MEN) type 2, including MEN 2A and 2B, and familial medullary thyroid carcinoma. These syndromes are autosomal dominantly inherited. The identification of mutations associated with these syndromes has led to genetic testing to identify patients at risk for MEN 2 and familial medullary thyroid carcinoma and subsequent implementation of prophylactic thyroidectomy in mutation carriers. In addition, more than 10 somatic rearrangements of RET have been identified from papillary thyroid carcinomas. These mutations, as those found in MEN 2, induce oncogenic activation of the RET tyrosine kinase domain via different mechanisms, making RET an excellent candidate for the design of molecular targeted therapy. Recently, various kinds of therapeutic approaches, such as tyrosine kinase inhibition, gene therapy with dominant negative RET mutants, monoclonal antibodies against oncogene products, and nuclease-resistant aptamers that recognize and inhibit RET have been developed. The use of these strategies in preclinical models has provided evidence that RET is indeed a potential target for selective cancer therapy. However, a clinically useful therapeutic option for treating patients with RET-associated cancer is still not available.
Quality of service and bandwidth efficiency of cellular mobile radio with variable-bit-rate speech transmission (1983)

We have investigated the performance of an adjustable source/channel codec in a cellular mobile-radio environment. The speech transmission rate and the amount of forward error correction change in response to changing channel conditions. The channel rate is constant at 32 kb/s and when the channel is good all of these bits are used for speech transmission. In intermediate and poor channels the speech rate is 24 or 16 kb/s and the remaining channel symbols are used for forward error correction. Relative to conventional transmission this approach offers an improved grade of service. For example, the outage rate (the proportion of "poor or worse" communications) goes from 9% with fixed-rate to 3% with variable-rate transmission. Alternatively, this improved grade of service can be exchanged for higher bandwidth efficiency. The fixed-rate system (with 9% outage) has 23 users per cell. With 52 users per cell the outage of the variable-rate system is only 6%.
Bringing Augmented Reality to Mobile Phones (2007)

With its mixing of real and virtual, Augmented Reality (AR) is a technology that has attracted lots of attention from the science community and is seen as a perfect way to visualize context-related information. Computer generated graphics is presented to the user overlaid and registered with the real world and hence augmenting it. Promising intelligence amplification and higher productivity, AR has been intensively researched over several decades but has yet to reach a broad audience. This thesis presents efforts in bringing Augmented Reality to mobile phones and thus to the general public. Implementing technologies on limited devices, such as mobile phones, poses a number of challenges that differ from traditional research directions. These include: limited computational resources with little or no possibility to upgrade or add hardware, limited input and output capabilities for interactive 3D graphics. The research presented in this thesis addresses these challenges and makes contributions in the following areas: Mobile Phone Computer Vision-Based Tracking The first contribution of thesis has been to migrate computer vision algorithms for tracking the mobile phone camera in a real world reference frame - a key enabling technology for AR. To tackle performance issues, low-level optimized code, using fixed-point algorithms, has been developed. Mobile Phone 3D Interaction Techniques Another contribution of this thesis has been to research interaction techniques for manipulating virtual content. This is in part realized by exploiting camera tracking for position-controlled interaction where motion of the device is used as input. Gesture input, made possible by a separate front camera, is another approach that is investigated. The obtained results are not unique to AR and could also be applicable to general mobile 3D graphics. Novel Single User AR Applications With short range communication technologies, mobile phones can exchange data not only with other phones but also with an intelligent environment. Data can be obtained for tracking or visualization; displays can be used to render graphics with the tracked mobile phone acting as an interaction device. Work is presented where a mobile phone harvests a sensor-network to use AR to visualize live data in context. Novel Collaboration AR Applications One of the most promising areas for mobile phone based AR is enhancing face-to-face computer supported cooperative work. This is because the AR display permits non-verbal cues to be used to a larger extent. In this thesis, face-to-face collaboration has been researched to examine whether AR increases awareness of collaboration partners even on small devices such as mobile phones. User feedback indicates that this is the case, confirming the hypothesis that mobile phones are increasingly able to deliver an AR experience to a large audience.
Murine Plasmacytoid Dendritic Cells Initiate the Immunosuppressive Pathway of Tryptophan Catabolism in Response to CD200 Receptor Engagement (2004)

In this study, using a soluble CD200-Ig fusion protein, we provide evidence that murine dendritic cells (DCs) possess a functional CD200R, whose engagement results in the reinforcement or appearance of immunosuppressive properties in these cells. In particular, the plasmacytoid subset (CD11c+B220+120G8+) of splenic DCs (pDCs) is induced by CD200-Ig to express the enzyme IDO, which initiates the tolerogenic pathway of tryptophan catabolism. As a result, pDCs are capable of suppressing Ag-specific responses in vivo when transferred into recipient hosts after treatment with CD200-Ig. IDO induction in pDCs through CD200R engagement requires type I IFNR signaling. Although the release of IFN-alpha may contribute to the full expression of CD200-Ig activity, autocrine IFN-alpha is unlikely to mediate alone the effects of CD200R engagement. These data prospect novel functions for both pDCs and the CD200-CD200R pair in the mouse. At the same time, these data underscore the possible unifying role of the IDO mechanism in immune tolerance.
In vivo Anti‐tumor Efficacy of Polyethylene Glycol‐modified Tumor Necrosis Factor‐α against Tumor Necrosis Factor‐resistant Tumors (1996)

We previously reported that the optimally PEGylated tumor necrosis factor-alpha (MPEG-TNF-alpha), in which 56% of the TNF-alpha-lysine amino groups were coupled with polyethylene glycol (PEG), had about 100-fold greater anti-tumor effect than native TNF-alpha. Here, we assessed the usefulness of MPEG-TNF-alpha as a systemic anti-tumor therapeutic drug, using B16-BL6 melanoma and colon-26 adenocarcinoma, which have been reported to be resistant to TNF-alpha in vivo, as compared with Meth-A fibrosarcoma. MPEG-TNF-alpha markedly inhibited the growth of both tumors without causing any TNF-alpha-mediated side-effects, whereas native TNF-alpha had no anti-tumor effects and caused adverse side-effects. In addition, MPEG-TNF-alpha drastically inhibited the metastatic colony formation of B16-BL6 melanoma. MPEG-TNF-alpha may, thus, be a potential systemic anti-tumor therapeutic agent.
Stable inhibitory activity of regulatory T cells requires the transcription factor Helios (2015)

The maintenance of immune homeostasis requires regulatory T cells (T(regs)). Given their intrinsic self-reactivity, T(regs) must stably maintain a suppressive phenotype to avoid autoimmunity. We report that impaired expression of the transcription factor (TF) Helios by FoxP3(+) CD4 and Qa-1-restricted CD8 T(regs) results in defective regulatory activity and autoimmunity in mice. Helios-deficient T(regs) develop an unstable phenotype during inflammatory responses characterized by reduced FoxP3 expression and increased effector cytokine expression secondary to diminished activation of the STAT5 pathway. CD8 T(regs) also require Helios-dependent STAT5 activation for survival and to prevent terminal T cell differentiation. The definition of Helios as a key transcription factor that stabilizes T(regs) in the face of inflammatory responses provides a genetic explanation for a core property of T(regs).
Design of organizational decision support systems: the use of a data extraction scheme to facilitate model-database communication (2002)

The concept of organizational decision support and the criteria for designing such support systems (ODSS) have recently received a great deal of attention. While the organizational decision processes differ considerably from individual and group decision making, the requirements for securing data from the corporate database in an ODSS are not much different. The computer and communication technologies that integrate the subsystems of knowledge, data, and models are still essential for ODSS. The authors examine the issues of integrating models and databases through the use of a data extraction scheme. In particular, they describe certain aspects of the query generation algorithms that allow the user or model to view the database as a single relation. The generated query is then translated into TQUEL, a temporal query language reflecting the historical nature of corporate databases.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Glycine Substitution at Helix-to-Coil Transitions Facilitates the Structural Determination of a Stabilized Subtype C HIV Envelope Glycoprotein (2017)

Advances in HIV-1 envelope glycoprotein (Env) design generate native-like trimers and high-resolution clade A, B, and G structures and elicit neutralizing antibodies. However, a high-resolution clade C structure is critical, as this subtype accounts for the majority of HIV infections worldwide, but well-ordered clade C Env trimers are more challenging to produce due to their instability. Based on targeted glycine substitutions in the Env fusion machinery, we defined a general approach that disfavors helical transitions leading to post-fusion conformations, thereby favoring the pre-fusion state. We generated a stabilized, soluble clade C Env (16055 NFL) and determined its crystal structure at 3.9 Å. Its overall conformation is similar to SOSIP.664 and native Env trimers but includes a covalent linker between gp120 and gp41, an engineered 201-433 disulfide bond, and density corresponding to 22 N-glycans. Env-structure-guided design strategies resulted in multiple homogeneous cross-clade immunogens with the potential to advance HIV vaccine development.
Localization of thrombospondin and its cysteine-serine-valine-threonine-cysteine-glycine-specific receptor in human breast carcinoma. (1994)

Our results indicate that increasing expression of stromal TSP and the CSVTCG-specific TSP receptor in ductal epithelium correlates with neoplastic transformation. In addition, our results indicate that both malignant and benign breast tissue can stimulate surrounding capillaries to express the TSP receptor, whereas only carcinoma has the capacity to stimulate surrounding nonendothelial stromal cells, such as myofibroblasts, to secrete a TSP-rich matrix that may contribute to the desmoplastic stromal reaction characteristic of ductal carcinoma tumor. The TSP-rich matrix may then promote tumor cell attachment, migration, and angiogenesis, factors important in tumor growth. The receptor-rich capillary endothelium may promote the cell adhesive interactions important in tumor intravasation. Taken together the results of this study provide a rational basis for a role of TSP in tumor angiogenesis and metastasis.
Vignette and exposure calibration and compensation (2005)

We discuss calibration and removal of "vignetting" (radial falloff) and exposure (gain) variations from sequences of images. Unique solutions for vignetting, exposure and scene radiances are possible when the response curve is known. When the response curve is unknown, an exponential ambiguity prevents us from recovering these parameters uniquely. However, the vignetting and exposure variations can nonetheless be removed from the images without resolving this ambiguity. Applications include panoramic image mosaics, photometry for material reconstruction, image-based rendering, and preprocessing for correlation-based vision algorithms.
Scalable read-mostly synchronization using passive reader-writer locks (2014)

Reader-writer locks (rwlocks) aim to maximize parallelism among readers, but many existing rwlocks either cause readers to contend, or significantly extend writer latency, or both. Further, some scalable rwlocks cannot cope with OS semantics like sleeping inside critical sections, preemption and conditional wait. Though truly scalable rwlocks exist, some of them cannot handle preemption, sleeping inside critical sections, or other important functions required inside OS kernels. This paper describes a new rwlock called the passive reader-writer lock (prwlock) that provides scalable read-side performance as well as small writer latency for TSO architectures. The key of prwlock is a version-based consensus protocol between multiple non-communicating readers and a pending writer. Prwlock leverages bounded staleness of memory consistency to avoid atomic instructions and memory barriers in readers' common paths, and uses message-passing (e.g., IPI) for straggling readers so that writer lock acquisition latency can be bounded. Evaluation on a 64-core machine shows that prwlock significantly boosts the performance of the Linux virtual memory subsystem, a concurrent hashtable and an in-memory database.
A newly designed planar stacked capacitor cell with high dielectric constant film for 256 Mbit DRAM (2002)

Thin film of (Ba/sub 0.75/Sr/sub 0.25/)TiO/sub 3/ with equivalent SiO/sub 2/ thickness of 0.47 nm has been developed for capacitor dielectric film of 256 Mbit DRAM. A novel cell design named FOGOS (FOlded Global and Open Segment bit-line cell) structure is also proposed for 256 Mbit DRAM. By combining high dielectric constant film and FOGOS design, we have succeeded in making a practical and integrated cell that has sufficient cell capacitance with planar stacked capacitor, small bitline parasitic capacitance and large lithographic tolerance of alignment and DOF. 0.72 /spl mu/m/sup 2/ cell size based on 0.25 /spl mu/m process technology is realized.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Acute Upper Airway Responses to Hypoglossal Nerve Stimulation during Sleep in Obstructive Sleep Apnea (2011)

HGNS produced marked dose-related increases in airflow without arousing patients from sleep. Increases in airflow were of sufficient magnitude to eliminate IFL in most patients and IFL and non-IFL subgroups achieved normal or near-normal levels of flow, suggesting potential HGNS efficacy across a broad range of sleep apnea severity.
Hybrid Nanorod-Polymer Solar Cells (2002)

We demonstrate that semiconductor nanorods can be used to fabricate readily processed and efficient hybrid solar cells together with polymers. By controlling nanorod length, we can change the distance on which electrons are transported directly through the thin film device. Tuning the band gap by altering the nanorod radius enabled us to optimize the overlap between the absorption spectrum of the cell and the solar emission spectrum. A photovoltaic device consisting of 7-nanometer by 60-nanometer CdSe nanorods and the conjugated polymer poly-3(hexylthiophene) was assembled from solution with an external quantum efficiency of over 54% and a monochromatic power conversion efficiency of 6.9% under 0.1 milliwatt per square centimeter illumination at 515 nanometers. Under Air Mass (A.M.) 1.5 Global solar conditions, we obtained a power conversion efficiency of 1.7%.
Conservation Voltage Reduction Potential In The Pacific Northwest (2005)

This paper summarizes a study performed by Pacific Northwest Laboratory (PNL) indicating that the region-wide implementation of conservation voltage reduction (CVR) would provide a significant level of electric energy conservation in the Bonneville Power Administration (BPA) service area. This resource was estimated by developing supply curves showing the magnitude of energy savings as a function of CVR implementation cost. Energy savings were estimated for residential, commercial, agricultural irrigation, and industrial consumer classes. Using the convention of expressing energy conservation in average megawatts (AMW), the CVR conservation resource in the Pacific Northwest was estimated to be between 170 and 268 AMW at a cost of 5 cents/kWh. Estimates were also made for the contribution of major load sectors to the total CVR resource. Approximately 55% of the total was estimated to be available in the residential sector. Contributions by the other sectors considered were as follows: commercial, 29%; industrial, 14%; and agricultural irrigation, 3%. A large portion (142 to 230 AMW) of the conservation resource would be available at less than 1 cent/kWh. a median estimate of the regional CVR resource at 1 cent/kWh (179 AMW) exceeds the conservation potential (150 AMW) expected from possible implementation of major efficiency improvements onmore » Pacific Northwest transmission and distribution systems. This paper also shows that CVR can be more effective than conventional demand-side management measures in reducing system peak load. 9 refs., 2 figs., 5 tabs.« less