gebhart/patrepeval huggingface dataset:
Compartmentalization of cAMP-Dependent Signaling by Phosphodiesterase-4D Is Involved in the Regulation of Vasopressin-Mediated Water Reabsorption in Renal Principal Cells (2006)

The cAMP/protein kinase A (PKA)-dependent insertion of water channel aquaporin-2 (AQP2)-bearing vesicles into the plasma membrane in renal collecting duct principal cells (AQP2 shuttle) constitutes the molecular basis of arginine vasopressin (AVP)-regulated water reabsorption. cAMP/PKA signaling systems are compartmentalized by A kinase anchoring proteins (AKAP) that tether PKA to subcellular sites and by phosphodiesterases (PDE) that terminate PKA signaling through hydrolysis of localized cAMP. In primary cultured principal cells, AVP causes focal activation of PKA. PKA and cAMP-specific phosphodiesterase-4D (PDE4D) are located on AQP2-bearing vesicles. The selective PDE4 inhibitor rolipram increases AKAP-tethered PKA activity on AQP2-bearing vesicles and enhances the AQP2 shuttle and thereby the osmotic water permeability. AKAP18delta, which is located on AQP2-bearing vesicles, directly interacts with PDE4D and PKA. In response to AVP, PDE4D and AQP2 translocate to the plasma membrane. Here PDE4D is activated through PKA phosphorylation and reduces the osmotic water permeability. Taken together, a novel, compartmentalized, and physiologically relevant cAMP-dependent signal transduction module on AQP2-bearing vesicles, comprising anchored PDE4D, AKAP18delta, and PKA, has been identified.
Automatic partial loop summarization in dynamic test generation (2011)

Whitebox fuzzing extends dynamic test generation based on symbolic execution and constraint solving from unit testing to whole-application security testing. Unfortunately, input-dependent loops may cause an explosion in the number of constraints to be solved and in the number of execution paths to be explored. In practice, whitebox fuzzers arbitrarily bound the number of constraints and paths due to input-dependent loops, at the risk of missing code and bugs.
Local anaesthetic effect of antiarrhythmic drugs and human sperm immobilization: mechanism and application of the interrelationship. (1984)

Sperm immobilizing activity of three class I antiarrhythmic drugs, quinidine, procainamide, mexiletine, one adrenoceptor blocking drug, labetalol and one calcium channel blocking drug, diltiazem was measured with a trans-membrane migration method. All these drugs immobilized human sperm. Local anaesthetic effect is the underlying mechanism for these drugs to inhibit sperm motility. Sperm immobilization could be a screening test for the local anaesthetic effect of antiarrhythmic drugs.
Effect of twist on fused couplers (1988)

The effect of twist on fused couplers is discussed theoretically. We find that the twist, large or small, introduced unintentionally in fused couplers may deteriorate the extinction ratio of polarization splitting when devices are used as polarization beam splitters, and that the modulation period of the spectral response of fused couplers can be tuned by controlling the twist rate when they are used as wavelength filters.
Interactive artificial life based on behavior and perception in a virtual environment (2002)

A cyber character is a kind of artificial life inhabiting a virtual world. To be a life form in the virtual world, cyber characters need sensors and control systems. The sensor system enables the cyber character to recognize not only the virtual world but also the real world in such a manner that it can respond to user commands. The control system provides the cyber character with life-like behavior by generating goals and plans, selecting appropriate actions, and finally by animating the character. Users may feel the cyber character to be alive because of its close interaction and smart performance. A cyber character system designed to provide users with a realistic feeling of an artificial life is discussed.
Wideband MIMO Mobile-to-Mobile Channels: Geometry-Based Statistical Modeling With Experimental Verification (2009)

A 3-D reference model for wideband multiple-input multiple-output (MIMO) mobile-to-mobile (M-to-M) channels is reviewed along with its corresponding first- and second-order channel statistics. To validate the reference model, an experimental MIMO M-to-M channel-sounding campaign was conducted for M-to-M vehicular communication with vehicles that travel along surface streets and expressways in a metropolitan area. To compare the first- and second-order channel statistics that were obtained from the reference model with those obtained from the empirical measurements, a new maximum-likelihood-based stochastic estimator is derived to extract the relevant model parameters from the measured data. The measured data is processed and compared with the analytical results. The close agreement between the analytically and empirically obtained channel statistics confirms the utility of the proposed reference model and the method for estimating the model parameters.
Development of an ultraflex-based thin film solar array for space applications (2003)

As flexible thin film photovoltaic (FTFPV) cell technology is developed for space applications, integration into a viable solar array structure that optimizes the attributes of this cell technology is critical. An advanced version of ABLE's UltraFlex solar array platform represents a near-term, low-risk approach to demonstrating outstanding array performance with the implementation of FTFPV technology. Recent studies indicate that an advanced UltraFlex solar array populated with 15% efficient thin film cells can achieve over 250 W/kg BOL. An overview of the status of hardware development and the future potential of this technology is presented.
Fluorescence and Electronic Action Spectroscopy of Mass-Selected Gas-Phase Fluorescein, 2′,7′-Dichlorofluorescein, and 2′,7′-Difluorofluorescein Ions (2013)

2',7'-Dichloro- and 2',7'-difluorofluoresceins are superior alternatives to underivatized fluorescein. Although several studies characterizing their condensed-phase photophysical properties have been reported, little is known about their intrinsic characteristics. Here, the gas-phase properties of three charge states of each fluorescein are characterized using a quadrupole ion trap mass spectrometer which has been modified for spectroscopy. Electronic action spectra, constructed by monitoring the extent of photodissociation as a function of excitation wavelength, indicate that the gaseous dianions and cations resemble their solution-phase counterparts. In contrast, a large shift in the electronic action spectra of the monoanions indicates the presence of a different tautomer in the gas phase than that present in solution. The gaseous monoanion is deprotonated on the xanthene ring, rather than being deprotonated on the pendant group as found in soluion. The dianions and cations do not emit detectable fluorescence in the gas phase. In contrast, the monoanions do fluoresce, but the emission intensity is low and the spectra are broad. This work illustrates the effect of halogenation on the intrinsic properties of the dyes and provides useful fundamental understanding that promises to aid the development more robust fluorescent dyes.
Cooperatives, Agriculture and Rural Development: Role, Issues and Policy Implications (2013)

Cooperatives, credit cooperatives in particular, are an integral part of the Indian rural economy.
Contamination specification for dimensional metrology SEMs (2008)

Electron beam-induced contamination is one of the most bothersome problems encountered in the use of the scanning electron microscope (SEM). Even in "clean-vacuum" instruments it is possible that the image gradually darkens because a polymerized hydrocarbon layer with low secondary electron yield is deposited. This contamination layer can get so thick that it noticeably changes the size and shape of the small structures of current and future state-of-the art integrated circuits (ICs). Contamination greatly disturbs or hinders the measurement process and the erroneous results can lead to wrong process control decisions. NIST has developed cleaning procedures and a contamination specification that offer an effective and viable solution for this problem. By the acceptance, implementation and regular use of these methods it is possible to get rid of electron beam induced contamination.
Pptc7 is an essential phosphatase for promoting mammalian mitochondrial metabolism and biogenesis (2019)

Mitochondrial proteins are replete with phosphorylation, yet its functional relevance remains largely unclear. The presence of multiple resident mitochondrial phosphatases, however, suggests that protein dephosphorylation may be broadly important for calibrating mitochondrial activities. To explore this, we deleted the poorly characterized matrix phosphatase Pptc7 from mice using CRISPR-Cas9 technology. Strikingly, Pptc7<sup>-/-</sup> mice exhibit hypoketotic hypoglycemia, elevated acylcarnitines and serum lactate, and die soon after birth. Pptc7<sup>-/-</sup> tissues have markedly diminished mitochondrial size and protein content despite normal transcript levels, and aberrantly elevated phosphorylation on select mitochondrial proteins. Among these, we identify the protein translocase complex subunit Timm50 as a putative Pptc7 substrate whose phosphorylation reduces import activity. We further find that phosphorylation within or near the mitochondrial targeting sequences of multiple proteins could disrupt their import rates and matrix processing. Overall, our data define Pptc7 as a protein phosphatase essential for proper mitochondrial function and biogenesis during the extrauterine transition.
Chronic Exposure of Renal Stem Cells to Inorganic Arsenic Induces a Cancer Phenotype (2012)

Inorganic arsenic in the drinking water is a multisite human carcinogen that potentially targets the kidney. Recent evidence also indicates that developmental arsenic exposure impacts renal carcinogenesis in humans and mice. Emerging theory indicates that cancer may be a disease of stem cells (SCs) and that there are abundant active SCs during early life. Therefore, we hypothesized that inorganic arsenic targets SCs, or partially differentiated progenitor cells (PCs), for oncogenic transformation. Thus, a rat kidney SC/PC cell line, RIMM-18, was chronically exposed to low-level arsenite (500 nM) for up to 28 weeks. Multiple markers of acquired cancer phenotype were assessed biweekly during arsenic exposure, including secreted matrix metalloproteinase (MMP) activity, proliferation rate, colony formation in soft agar, and cellular invasiveness. Arsenic exposure by 10 weeks and after also induced marked and sustained increases in colony formation, indicative of the loss of contact inhibition, and increased invasiveness, both cancer cell characteristics. Compared to the passage-matched control, chronic arsenic exposure caused exposure-duration dependent increases in secreted MMP-2 and MMP-9 activity, Cox-2 expression, and more rapid proliferation (all >2-fold), characteristics typical of cancer cells. Dysregulation of SC maintenance genes and signaling pathways are common during oncogenesis. During arsenite exposure, expression of several genes associated with normal kidney development and SC regulation and differentiation (i.e., Wt-1, Wnt-4, Bmp-7, etc.) were aberrantly altered. Arsenic-exposed renal SCs produced more nonadherent spheroid bodies that grew much more aggressively in Matrigel, typical of cancer SCs (CSCs). The transformed cells also showed gene overexpression typical of renal SCs/CSCs (CD24, Osr1, Ncam) and arsenic adaptation such as overexpression of Mt-1, Mt2, Sod-1, and Abcc2. These data suggest that inorganic arsenic induced an acquired cancer phenotype in vitro in these rat kidney SCs potentially forming CSCs and, consistent with data in vivo, indicate that these multipotent SCs may be targets of arsenic during renal carcinogenesis.
Role of IKK and oscillatory NFκB kinetics in MMP‐9 gene expression and chemoresistance to 5‐fluorouracil in RKO colorectal cancer cells (2006)

Nuclear factor kappa B (NFkappaB) is a central participant in the metastasis and chemoresistance of colorectal cancer (CRC). However, it is not fully understood to what extent NFkappaB contributes to induction of the metastasis-associated matrix metalloprotease-9 (MMP-9) gene and sensitivity to the commonly used chemotherapeutic 5-fluorouracil (5-Fu) in CRC. Using the RKO human CRC cell line and two NFkappaB signaling deficient RKO mutants, we investigated NFkappaB's role in the induction of MMP-9 and 5-Fu sensitivity in RKO CRC cells. NFkappaB plays a predominant role in MMP-9 gene induction in RKO cells, as evidenced by the failure of tumor necrosis factor alpha (TNFalpha) to induce MMP-9 in either of the NFkappaB signaling mutants. RKO cells exhibit a robust, oscillatory NFkappaB activity in response to TNFalpha not seen in either of the NFkappaB mutant cell lines, which instead demonstrate diminished, nonoscillatory NFkappaB activation. Analysis of TNFalpha-induced phosphorylation and MMP-9 promoter recruitment of the p65 NFkappaB subunit revealed a significant reduction in p65 phosphorylation as well as reduced and altered recruitment of p65 to the MMP-9 gene promoter in the mutants compared to the parental RKO cell line. 5-Fu only activated NFkappaB in the parental RKO cells through induction of IkappaB-kinase (IKK) activity and increased sensitivity to 5-Fu is observed in both NFkappaB mutant lines. Our results suggest that TNFalpha-dependent induction of MMP-9 gene expression is tightly regulated by oscillatory/cumulative activation of NFkappaB and that 5-Fu stimulates NFkappaB and RKO CRC cell survival through induction of IKK activity.
Identification of a gene required for maturation of an extracellular lactococcal serine proteinase (1989)

Directly upstream of the Lactococcus lactis subsp. cremoris Wg2 proteinase gene is an oppositely directed open reading frame (ORF1). The complete nucleotide sequence of ORF1, encoding a 33-kilodalton protein, was determined. A protein of approximately 32 kilodaltons was synthesized when ORF1 was expressed in Escherichia coli by using a T7 RNA polymerase-specific promoter. L. lactis subsp. lactis MG1363 transformants carrying the proteinase gene but lacking ORF1 were phenotypically proteinase deficient, unlike transformants carrying both the proteinase gene and ORF1. Synthesis and secretion of proteinase antigen by L. lactis could be detected with proteinase-directed monoclonal antibodies regardless of whether ORF1 was present. The requirement of ORF1 for proteinase activation was reflected in a reduction in the molecular weight of the secreted proteinase. Furthermore, deletion of the 130 C-terminal amino acids of the Wg2 proteinase prevented attachment of the enzyme to lactococcal cells.
Bulk universality of sparse random matrices (2015)

We consider the adjacency matrix of the ensemble of Erdős-Rényi random graphs which consists of graphs on N vertices in which each edge occurs independently with probability p. We prove that in the regime pN ≫ 1, these matrices exhibit bulk universality in the sense that both the averaged n-point correlation functions and distribution of a single eigenvalue gap coincide with those of the GOE. Our methods extend to a class of random matrices which includes sparse ensembles whose entries have different variances.
Probing plasma clearance of the thrombin–antithrombin complex with a monoclonal antibody against the putative serpin–enzyme complex receptor‐binding site (2003)

A high-affinity monoclonal antibody (M27), raised against the human thrombin-antithrombin complex, has been identified and characterized. The epitope recognized by M27 was located to the linear sequence FIREVP (residues 411-416), located in the C-terminal cleavage peptide of antithrombin. This region overlaps, by two residues, the putative binding site of antithrombin for the serpin-enzyme complex receptor. Studies in rats and with HepG2 cells in culture indicated that the Fab fragment of M27 does not block binding and uptake of the thrombin-antithrombin complex, suggesting that this region does not play a major role in the recognition and clearance of the thrombin-antithrombin complex. M27 blocked the ability of antithrombin to inhibit thrombin as well as antithrombin cleavage, both in the presence and absence of heparin.
Network-level synchronization in decentralized social ad-hoc networks (2010)

Social ad-hoc networks can be composed of a large number of tiny, wireless, battery-powered nodes, and exhibit arbitrary mobility. We aim to enable the execution of distributed applications that depend on capturing network dynamics across large-scale social ad-hoc networks. Conservation of the nodes' fixed energy budget is the chief concern in all design decisions, and necessitates that wireless communication is kept to a minimum. In this paper we present GMAC <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> : a gossiping TOMA MAC layer created to address these problems. We analyze its efficiency in achieving and maintaining a tight network-layer synchronization with respect to the active periods of node radios.
FreeMAC: Implementing a Multi-Channel TDMA MAC on 802.11 Hardware (2008)

Modern wireless devices offer increased software control over radio communication parameters. In the future, the trend of making the hardware more programmable is expected to grow due to the emergence of cognitive and software defined radio networking. Since a large portion of the MAC protocol is implemented in software, with the firmware providing a set of functional primitives, it is possible to d esign and implement alternate MAC protocols in real testbeds equipped with commodity 802.11 devices [1, 2, 3]. Validation of protocols on real testbeds helps characterize the ad ditional system constraints that are difficult to capture in a simulated environment. This work demonstrates FreeMAC ‐ a framework that enables the design and implementation of a general class of multi-channel MAC protocols, with strict timing requirements, on a typical Linux system. Multi-channel MAC protocols aim to improve the capacity of a wireless network by time-multiplexing the operation of nodes on orthogonal channels. Generally such protocols rely on precise time scheduling of channel switch operations, usually every 20-80 ms to limit latency. TDMA based MAC protocols require that packets are transmitted during designated time slots. However, implementing such MAC protocols on a Linux system using commodity 802.11 hardware involves several systems challenges. The focus of the FreeMAC platform lies on enabling the primitives for the deployment of such MAC protocols on existing systems. FreeMAC allows tight control over several radio parameters using API functions. We also propose a novel approach of programming the beacon interval to invoke periodic hardware interrupts that can be used to bound the latency in scheduling of time-sensitive MAC functions using kernel timers. We use the FreeMAC framework to implement a simple proof of concept multi-channel TDMA based MAC on a testbed of 4 laptops, each running kernel 2.6.15.7 on the Ubuntu Linux distribution. Each laptop is equipped with an AR5212 chipset-based LinkSys 802.11 a/b/g PCMCIA card. We use the OpenHAL port of MadWiFi - an open source driver for Atheros chipset-based commodity 802.11 wireless devices. In our testbed setup, as shown in Figure , we demonstrate the capability of the FreeMAC framework to implement both single-channel (for nodes 2 and 3) as well as multi-channel (for nodes 1 and 4) TDMA-style MAC protocols. The TDMA schedule of our testbed comprises of four 50ms timeslots (the slot duration is reconfigurable), operating on two orthogonal channels. Each node transmits in two of these slots and receives on the remaining two. We eliminate per-packet acknowledgements and reduce the contention period to a minimum to ensure a TDMA style MAC implementation.
Women in War: Operational Issues of Menstruation and Unintended Pregnancy (2007)

With rapid and frequent deployments around the world, the current high level of military operations demands combat readiness of every military member. In the U.S. Armed Forces, women represent 15% of active duty troops and 17% of reserve and Guard troops and are a critical component for mission accomplishment. The operational issues of menstruation and unintended pregnancy, unique to this population, can decrease a female member's military readiness and affect her ability to deploy. Strategies to mitigate and even eliminate these concerns include the optional use of hormonal medications to induce reversible menstrual cycle suppression. These medications, traditionally indicated for contraception, should be considered essential for female troops during training and deployment. This article, tailored specifically for military women, provides valuable information regarding the risks and benefits, as well as the various options available for menstrual cycle suppression.
Endophthalmitis After Keratoprosthesis (2001)

The most important risk factor for endophthalmitis after these keratoprostheses was found to be preoperative diagnosis. The rate of infection was very high in Stevens-Johnson syndrome and ocular cicatricial pemphigoid, moderate in chemical burns, and low in noncicatrizing corneal disease.
Effect of Temperature Downshift on the Transcriptomic Responses of Chinese Hamster Ovary Cells Using Recombinant Human Tissue Plasminogen Activator Production Culture (2016)

Recombinant proteins are widely used as biopharmaceuticals, but their production by mammalian cell culture is expensive. Hence, improvement of bioprocess productivity is greatly needed. A temperature downshift (TDS) from 37°C to 28-34°C is an effective strategy to expand the productive life period of cells and increase their productivity (qp). Here, TDS in Chinese hamster ovary (CHO) cell cultures, initially grown at 37°C and switched to 30°C during the exponential growth phase, resulted in a 1.6-fold increase in the qp of recombinant human tissue plasminogen activator (rh-tPA). The transcriptomic response using next-generation sequencing (NGS) was assessed to characterize the cellular behavior associated with TDS. A total of 416 (q > 0.8) and 3,472 (q > 0.9) differentially expressed transcripts, with more than a 1.6-fold change at 24 and 48 h post TDS, respectively, were observed in cultures with TDS compared to those at constant 37°C. In agreement with the extended cell survival resulting from TDS, transcripts related to cell growth arrest that controlled cell proliferation without the activation of the DNA damage response, were differentially expressed. Most upregulated genes were related to energy metabolism in mitochondria, mitochondrial biogenesis, central metabolism, and avoidance of apoptotic cell death. The gene coding for rh-tPA was not differentially expressed, but fluctuations were detected in the transcripts encoding proteins involved in the secretory machinery, particularly in glycosylation. Through NGS the dynamic processes caused by TDS were assessed in this biological system.
Adaptive intensity models for probabilistic tracking of 3D vasculature (2010)

The segmentation of vascular structures in 3D medical images is of great importance for many clinical applications, ranging from the detection and measurement of vascular disease to providing information for surgical intervention. Accurate and robust vascular segmentation is made difficult by variations in the vessel's contrast enhancement and its surrounding background, both within the same patient and across the patient population. This paper introduces a technique that first creates a patient-specific vessel intensity model and then adaptively varies this model during tracking as a function of vessel radius. The intensity model is used for estimating the likelihood of the observed intensity distribution within a sequential Monte Carlo tracking framework. We apply the proposed method to coronary artery segmentation from Computed Tomography Angiography 3D volumes and present results demonstrating the improved segmentation results achieved using the approach.