gebhart/patrepeval huggingface dataset:
Privacy preserving origin-destination flow measurement in vehicular cyber-physical systems (2013)

Traffic volume measurement is one of the most basic functions of road planning and management. In this paper, we investigate an important problem of privacy preserving “point-to-point” traffic volume measurement. We formalize “point-to-point” traffic as an origin-destination (O-D) flow, which represents the set of vehicles traveling from one geographical location (origin) to another location (destination). We take advantage of vehicular cyber-physical systems (VCPS) to exploit the potential for a fundamental shift in the way how O-D data are collected. The challenge is to allow the collection of statistical O-D flow information, yet protect identities of individual vehicles. To address that, we design two novel schemes which utilize both the latest technological advance in VCPS and the nice properties of a family of commutative one-way hash functions. Furthermore, we adopt statistical methodology and use sampling to achieve far better efficiency with graceful degradation in measurement accuracy. We perform simulations to demonstrate the feasibility and scalability of our schemes.
Generation of Highly Selective VPAC2 Receptor Agonists by High Throughput Mutagenesis of Vasoactive Intestinal Peptide and Pituitary Adenylate Cyclase-activating Peptide (2003)

Pituitary adenylate cyclase-activating peptide (PACAP) has a specific receptor PAC1 and shares two receptors VPAC1 and VPAC2 with vasoactive intestinal peptide (VIP). VPAC2 activation enhances glucose-induced insulin release while VPAC1 activation elevates glucose output. To generate a large pool of VPAC2 selective agonists for the treatment of type 2 diabetes, structure-activity relationship studies were performed on PACAP, VIP, and a VPAC2 selective VIP analog. Chemical modifications on this analog that prevent recombinant expression were sequentially removed to show that a recombinant peptide would retain VPAC2 selectivity. An efficient recombinant expression system was then developed to produce and screen hundreds of mutant peptides. The 11 mutations found on the VIP analog were systematically replaced with VIP or PACAP sequences. Three of these mutations, V19A, L27K, and N28K, were sufficient to provide most of the VPAC2 selectivity. C-terminal extension with the KRY sequence from PACAP38 led to potent VPAC2 agonists with improved selectivity (100-1000-fold). Saturation mutagenesis at positions 19, 27, 29, and 30 of VIP and charge-scanning mutagenesis of PACAP27 generated additional VPAC2 selective agonists. We have generated the first set of recombinant VPAC2 selective agonists described, which exhibit activity profiles that suggest therapeutic utility in the treatment of diabetes.
Acetyl-CoA carboxylase from Escherichia coli: gene organization and nucleotide sequence of the biotin carboxylase subunit. (1991)

Biotin carboxylase [biotin-carboxyl-carrier-protein:carbon-dioxide ligase (ADP-forming), EC 6.3.4.14] is the enzyme mediating the first step of the acetyl-CoA carboxylase [acetyl-CoA:carbon-dioxide ligase (ADP-forming), EC 6.4.1.2] reaction. We screened an Escherichia coli DNA library and a DNA fragment carrying the biotin carboxylase gene fabG, and its flanking regions were cloned. The gene for biotin carboxyl carrier protein was found 13 base pairs upstream of the fabG gene. Nucleotide sequencing of the recombinant plasmids revealed that the fabG codes for a 449-amino acid residue protein with a calculated molecular weight of 49,320, a value in good agreement with that of 51,000 determined by SDS/polyacrylamide gel electrophoresis of the purified enzyme. The deduced amino acid sequence of biotin carboxylase is also consistent with the partial amino acid sequence determined by Edman degradation. The primary structure of this enzyme exhibits a high homology with those of other biotin-dependent enzymes and carbamoyl-phosphate synthetase [carbon-dioxide:L-glutamine amino-ligase (ADP-forming, carbamate-phosphorylating), EC 6.3.5.5]; therefore, all these enzymes probably function through the same mechanism of reaction.
The Spread of Contrast media in Splanchnic Nerve Block (1989)

Splanchnic nerve block is performed to relieve intractable upper abdominal pain caused by carcinoma of the pancreas, stomach, liver, or colon; and upper abdominal metastasis of tumors having more distant origins. We have performed splanchnic nerve blocks under control of X-ray fluoroscopy, for all cases of alcohol splanchnic nerve block at vertebra, to determine both the position of the needle tips and the spread of contrast media. During the period from December 1987 to August 1988, this method was used in 40 cases of malignancy at Severance Hospital and we clinically evaluated the location of the needle tip and the spread of contrast media. The results were as follows: 1) Our method was a retrocrural approach, the splanchnic nerve block, in all cases. 2) Most of the inserted needle points were located in the upper and anterolateral part of the vertebra on the antero posterior roentagenogram and in the upper quarter anteriorly on the lateral roentgenogram. 3) There was no specific relationship between the location of the needle and the spread of the contrast media. 4) The contrast media was spread around the needle and then upward along the anterior margin of the vertebral body in most of the cases. 5) Pain relief was obtained immediately in 37 cases (92.5%), but in 3 cases only after a second splanchnic nerve block.
T Cells as Vehicles for Cancer Vaccination (2011)

The success of cancer vaccines is dependent on the delivery of tumor-associated antigens (TAAs) within lymphoid tissue in the context of costimulatory molecules and immune stimulatory cytokines. Dendritic cells (DCs) are commonly utilized to elicit antitumor immune responses due to their attractive costimulatory molecule and cytokine expression profile. However, the efficacy of DC-based vaccines is limited by the poor viability and lymph-node migration of exogenously generated DCs in vivo. Alternatively, adoptively transferred T cells persist for long periods of time in vivo and readily migrate between the lymphoid and vascular compartments. In addition, T cells may be genetically modified to express both TAA and DC-activating molecules, suggesting that T cells may be ideal candidates to serve as cellular vehicles for antigen delivery to lymph node-resident DCs in vivo. This paper discusses the concept of using T cells to induce tumor-specific immunity for vaccination against cancer.
α-Adrenergic Stimulation by Clonidine Increases Plasma Concentrations of Immunoreactive β-Endorphin in Rats (1981)

Peripheral administration of the alpha-adrenergic agonist clonidine (0.5 mg/kg, sc) evoked a 2- to 3-fold rise (0.22 +/- 0.03 to 0.59 +/- 0.05 ng/ml) in plasma levels of beta-endorphin-like immunoreactivity (beta-END-LI) 15-30 min later in intact, but not hypophysectomized, rats. This rise in plasma beta-END-LI, which was dose dependent up to 0.5 mg/kg clonidine, appeared to be mediated by activation of alpha-adrenergic receptors, since pretreatment with the alpha-adrenergic antagonists yohimbine (1 mg/kg, ip), phentolamine (1, 3, or 10 mg/kg, kp), or phenoxybenzamine (2 and 10 mg/kg, ip) partially or fully blocked clonidine's effect. By contrast, the beta-adrenergic antagonist propranolol (1 and 5 mg/kg, ip) did not modify the clonidine-induced increased in plasma beta-END-LI. Given alone, the adrenergic blocking drugs were generally without effect on plasma levels of beta-END-LI. Clonidine appeared to be acting on the brain (or pituitary), since the intracerebroventricular injection of phenoxybenzamine (20 microgram) blocked the drug-induced rise in plasma beta-END-LI. These data suggest an alpha-adrenergic mechanism influences the release of pituitary beta-END in the rat.
Mesenchymal Stem Cells: Roles and Relationships in Vascularization (2014)

One of the primary challenges in translating tissue engineering to clinical applicability is adequate, functional vascularization of tissue constructs. Vascularization is necessary for the long-term viability of implanted tissue expanded and differentiated in vitro. Such tissues may be derived from various cell sources, including mesenchymal stem cells (MSCs). MSCs, able to differentiate down several lineages, have been extensively researched for their therapeutic capabilities. In addition, MSCs have a variety of roles in the vascularization of tissue, both through direct contact and indirect signaling. The studied relationships between MSCs and vascularization have been utilized to further the necessary advancement of vascularization in tissue engineering concepts. This review aims to provide a summary of relevant relationships between MSCs, vascularization, and other relevant cell types, along with an overview discussing applications and challenges related to the roles and relationships of MSCs and vascular tissues.
Analysis and design of a fast response three phase fixed frequency static power supply (2002)

Pulse width modulated voltage source inverters (PWM VSI) for uninterruptible power supply (UPS), parallel redundant system applications require fast acting inverter output current and voltage control. This paper describes a predictive current control method and a multivariable output state feedback voltage regulator for a proposed power supply system. The control methods provide a fast response and robust control (insensitive to plant parameter variations) of the load voltage in the presence of load/line disturbances. Analysis and design of the proposed power supply system is presented and digital simulations are carried out which demonstrate the excellent dynamic performance of the power supply.
Peripheral kisspeptin reverses short photoperiod-induced gonadal regression in Syrian hamsters by promoting GNRH release (2011)

In seasonal breeders, reproduction is synchronised by day length via the pineal hormone melatonin. In short winter days (short day, SD), the Syrian hamster displays a complete gonadal atrophy together with a marked reduction in expression of kisspeptins (Kp), a family of potent hypothalamic stimulators of GNRH neurons. Both central and peripheral acute injections of Kp have been reported to activate the gonadotropic axis in mammals. The aim of this study was to determine if and how peripheral administration of Kp54 could restore gonadal function in photo-inhibited hamsters. Testicular activity of hamsters kept in SD was reactivated by two daily i.p. injections of Kp54 but not by chronic subcutaneous delivery of the same peptide via mini-pumps. Acute i.p. injection of Kp54-induced FOS (c-Fos) expression in a large number of GNRH neurons and pituitary gonadotrophs together with a strong increase in circulating testosterone. The activation of pituitary cells by Kp was inhibited by preadministration of the GNRH receptor antagonist acyline. Altogether, our results demonstrate that peripheral Kp54 activates the gonadotropic axis by stimulating GNRH release and indicate that an appropriate protocol of long-term systemic Kp administration can recrudesce a photo-inhibited reproductive axis.
Structural investigation of the alpha‐1‐antichymotrypsin: Prostate‐specific antigen complex by comparative model building (1996)

Prostate-specific antigen (PSA), produced by prostate cells, provides an excellent serum marker for prostate cancer. It belongs to the human kallikrein family of enzymes, a second prostate-derived member of which is human glandular kallikrein-1 (hK2). Active PSA and hK2 are both 237-residue kallikrein-like proteases, based on sequence homology. An hK2 model structure based on the serine protease fold is presented and compared to PSA and six other serine proteases in order to analyze in depth the role of the surface-accessible loops surrounding the active site. The results show that PSA and hK2 share extensive structural similarity and that most amino acid replacements are centered on the loops surrounding the active site. Furthermore, the electrostatic potential surfaces are very similar for PSA and hK2. PSA interacts with at least two serine protease inhibitors (serpins): alpha-1-antichymotrypsin (ACT) and protein C inhibitor (PCI). Three-dimensional model structures of the uncleaved ACT molecule were developed based upon the recent X-ray structure of uncleaved antithrombin. The serpin was docked both to PSA and hK2. Amino acid replacements and electrostatic complementarities indicate that the overall orientation of the proteins in these complexes is reasonable. In order to investigate PSA's heparin interaction sites, electrostatic computations were carried out on PSA, hK2, protein C, ACT, and PCI. Two heparin binding sites are suggested on the PSA surface and could explain the enhanced complex formation between PSA and PCI, while inhibiting the formation of the ACT-PSA complex, PSA, hK2, and their preliminary complexes with ACT should facilitate the understanding and prediction of structural and functional properties for these important proteins also with respect to prostate diseases.
Monolithic white light emitting diodes using a (Ga,In)N/GaN multiple quantum well light converter (2008)

A monolithic white light emitting diode using a (Ga,In)N/GaN multiple quantum well (MQW) light converter is demonstrated. Blue photons emitted under electrical injection by (Ga,In)N/GaN QWs located inside a GaN p-n junction are partly absorbed by another (Ga,In)N/GaN MQW situated outside the junction which emits yellow-green light. The combination of the blue and yellow-green components results in white light emission.
Fundamentals of tracer kinetics for dynamic contrast‐enhanced MRI (2011)

Tracer kinetic methods employed for quantitative analysis of dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) share common roots with earlier tracer studies involving arterial-venous sampling and other dynamic imaging modalities. This article reviews the essential foundation concepts and principles in tracer kinetics that are relevant to DCE MRI, including the notions of impulse response and convolution, which are central to the analysis of DCE MRI data. We further examine the formulation and solutions of various compartmental models frequently used in the literature. Topics of recent interest in the processing of DCE MRI data, such as the account of water exchange and the use of reference tissue methods to obviate the measurement of an arterial input, are also discussed. Although the primary focus of this review is on the tracer models and methods for T(1) -weighted DCE MRI, some of these concepts and methods are also applicable for analysis of dynamic susceptibility contrast-enhanced MRI data.
[Prokaryotic expression of human calcyclin-binding protein and preparation of mouse polyclonal antibody against hCacyBP]. (2004)

CacyBP expressed widespreadly in varied tissues. Polyclonal antibody against hCacyBP that we prepared has high specificity, which provides a powerful tool for studying the function of hCacyBP.
Localized fault-tolerant event boundary detection in sensor networks (2005)

This paper targets the identification of faulty sensors and detection of the reach of events in sensor networks with faulty sensors. Typical applications include the detection of the transportation front line of a contamination and the diagnosis of network health. We propose and analyze two novel algorithms for faulty sensor identification and fault-tolerant event boundary detection. These algorithms are purely localized and thus scale well to large sensor networks. Their computational overhead is low, since only simple numerical operations are involved. Simulation results indicate that these algorithms can clearly detect the event boundary and can identify faulty sensors with a high accuracy and a low false alarm rate when as many as 20% sensors become faulty. Our work is exploratory in that the proposed algorithms can accept any kind of scalar values as inputs, a dramatic improvement over existing works that take only 0/1 decision predicates. Therefore, our algorithms are generic. They can be applied as long as the "events" can be modelled by numerical numbers. Though designed for sensor networks, our algorithms can be applied to the outlier detection and regional data analysis in spatial data mining.
Interactions of non‐detergent sulfobetaines with early folding intermediates facilitate <i>in vitro</i> protein renaturation (1998)

Non-detergent sulfobetaines (NDSB) are a family of solubilizing and stabilizing agents for proteins. In a previous study [Goldberg, M. E., Expert-Bezancon, N., Vuillard, L. & Rabilloud, T. (1996) Folding & Design 1, 21-27] we showed that the amount of active protein recovered in in vitro folding experiments could be significantly increased by some NDSBS. In this work we investigated the mechanisms by which these molecules facilitate protein renaturation. Stopped-flow and manual-mixing fluorescence and enzyme activity measurements were used to compare the kinetics of protein folding in the presence and absence of N-phenyl-methyl-N,N-dimethylammonium-propane-sulfonate (NDSB 256). Hen lysozyme and the beta2 subunit of Escherichia coli tryptophan synthase were chosen as model systems since their folding pathways had been previously investigated in detail. It is shown that, massive aggregation of tryptophan synthase occurs within less than 2.5 s after dilution in the renaturation buffer, but can be prevented by NDSB 256; only very early folding phases (such as the formation of a loosely packed hydrophobic core able to bind 8-anilino-1-naphthalenesulphonic acid, and the initial burying of tryptophan 177) are significantly altered by NDSB 256; none of the later phases is affected. Furthermore, NDSB 256 did not significantly affect any of the kinetic phases observed during the refolding of denatured lysozyme retaining intact disulphide bonds. This shows that NDSB 256 only interferes with very early steps in the folding process and acts by limiting the abortive interactions that could lead to the formation of inactive aggregates.
The levels and kinetics of oxygen tension detectable at the surface of human dermal fibroblast cultures (2000)

Low oxygen tension has recently been shown to stimulate cell growth and clonal expansion, as well as synthesis and transcription of certain growth factors and extracellular matrix components. These results have been obtained by exposing cell cultures to a hypoxic environment. Using an oxygen probe, we have now studied how experimental conditions affect the oxygen tension detectable at the cell surface. Dissolved oxygen tension was directly related to the height of the medium above the cell surface (r = 0.8793, P = 0.021), but was constant when no cells were present in the flask (r = -0. 9732, P = 0.001). In both human dermal fibroblasts and NIH/3T3 cultures, oxygen tension decreased linearly as cell density increased (r = -0.835, P < 0.0001; r = -0.916, P < 0.0001, respectively). When human dermal fibroblasts were exposed to 2% O(2), maximum hypoxic levels (0 mmHg) were achieved within approximately 15 min, and the recovery time was within a similar time frame. The addition of rotenone, an inhibitor of cellular respiration, blocked this decrease in oxygen tension at the cell surface, suggesting that cellular consumption of oxygen is responsible for the decline. Finally, we examined the cell-surface oxygen tension in control and acutely wounded human skin equivalents (HSE), consisting of a keratinocyte layer over a type I collagen matrix containing fibroblasts. We found that oxygen tension dropped significantly (P < 0.0001) in acutely wounded areas of HSE as compared to unwounded areas of HSE and that this drop was prevented by the addition of mitomycin C. These results indicate that cell-surface oxygen tension is indirectly related to cell density, and that the amount of detectable oxygen at the cell surface is a function of cell density, the oxygen tension in the incubator, and increased cellular activity, as occurs after injury.
Color bar coding the <i>BRCA1</i> gene on combed DNA: A useful strategy for detecting large gene rearrangements (2001)

Genetic linkage data have shown that alterations of the BRCA1 gene are responsible for the majority of hereditary breast and ovarian cancers. BRCA1 germline mutations, however, are found less frequently than expected. Mutation detection strategies, which are generally based on the polymerase chain reaction, therefore focus on point and small gene alterations. These approaches do not allow for the detection of large gene rearrangements, which also can be involved in BRCA1 alterations. Indeed, a few of them, spread over the entire BRCA1 gene, have been detected recently by Southern blotting or transcript analysis. We have developed an alternative strategy allowing a panoramic view of the BRCA1 gene, based on dynamic molecular combing and the design of a full four-color bar code of the BRCA1 region. The strategy was tested with the study of four large BRCA1 rearrangements previously reported. In addition, when screening a series of 10 breast and ovarian cancer families negatively tested for point mutation in BRCA1/2, we found an unreported 17-kb BRCA1 duplication encompassing exons 3 to 8. The detection of rearrangements as small as 2 to 6 kb with respect to the normal size of the studied fragment is achieved when the BRCA1 region is divided into 10 fragments. In addition, as the BRCA1 bar code is a morphologic approach, the direct observation of complex and likely underreported rearrangements, such as inversions and insertions, becomes possible.
MCL-1-independent mechanisms of synergy between dual PI3K/mTOR and BCL-2 inhibition in diffuse large B cell lymphoma (2015)

The PI3K/AKT/mTOR axis promotes survival and is a frequently mutated pathway in cancer. Yet, inhibitors targeting this pathway are insufficient to induce cancer cell death as single agents in some contexts, including diffuse large B cell lymphoma (DLBCL). In these situations, combinations with inhibitors targeting BCL-2 survival proteins (ABT-199 and ABT-263) may hold potential. Indeed, studies have demonstrated marked synergy in contexts where PI3K/mTOR inhibitors suppress expression of the pro-survival protein, MCL-1. In this study, we use BH3 profiling to confirm that BCL-2 and BCL-XL support survival following PI3K pathway inhibition, and that the dual PI3K/mTOR inhibitor BEZ235 strongly synergizes with BCL-2 antagonists in DLBCL. However, we identify an alternative mechanism of synergy between PI3K/mTOR and BCL-2 inhibitors, independent of MCL-1 down-regulation. Instead, we show that suppression of AKT activation by BEZ235 can induce the mitochondrial accumulation of pro-apoptotic BAD and BIM, and that expression of a constitutively active form of AKT prevents sensitization to BCL-2 antagonism. Thus, our work identifies an additional mechanism of synergy between PI3K pathway inhibitors and BCL-2 antagonists that strengthens the rationale for testing this combination in DLBCL.