gebhart/patrepeval huggingface dataset:
Influence of Metal Coordination on the Mismatch Tolerance of Ligand-Modified PNA Duplexes (2005)

Recent studies on metal incorporation in ligand-modified nucleic acids have focused on the effect of metal coordination on the stability of metal-containing duplexes or triplexes and on the metal binding selectivity but did not address the effect of the sequence of the nucleic acid in which the ligands are incorporated. We have introduced 8-hydroxyquinoline Q in 10-mer PNA strands with various sequences and have investigated the properties of the duplexes formed from these strands upon binding of Cu(2+). Variable-temperature UV-vis spectroscopy shows that, in the presence of Cu(2+), duplexes are formed even from ligand-modified Q-PNA strands that have a large number of mismatches. Spectrophotometric titrations demonstrate that at any temperature, one Cu(2+) ion binds a pair of Q-PNA strands that each contain one 8-hydroxyquinoline, but below the melting temperature, the PNA duplex exerts a supramolecular chelate effect, which prevents the transformation in the presence of excess Cu(2+) of the 1:2 Cu(2+):Q-PNA complexes into 1:1 complexes. EPR spectroscopy gives further support for the existence in the duplexes of [CuQ(2)] moieties that are similar to the corresponding square planar synthetic complex formed between Cu(2+) and 8-hydroxyquinoline. As PNA duplexes show a preferred handedness due to the chiral induction effect of a C-terminal l-lysine, which is transmitted through stacking interactions within the duplex, only if the metal-containing duplex has complementary strands, does it show a chiral excess measured by CD spectroscopy. The strong effect of the metal-ligand moiety is suggestive of an increased correlation length in PNA duplexes that contain such moieties. These results indicate that strong metal-ligand alternative base pairs significantly diminish the importance of Watson-Crick base pairing for the formation of a stable PNA duplex and lead to high mismatch tolerance, a principle that can be used in the construction of hybrid inorganic-nucleic acid nanostructures.
Effects of IL-3 on promoter usage, attenuation and antisense transcription of the c-myc oncogene in the IL-3-dependent Ba/F3 early pre-B cell line. (1991)

The c-myc gene uses two major promoters, P1 and P2, for production of mRNA. In most proliferating normal cells, transcripts initiated from P2 predominate over the ones from P1. Furthermore, transcription of normal and translocated c-myc genes is bidirectional and overlapping. In this study, we have measured the effects of interleukin 3 (IL-3) deprivation and restimulation on c-myc promoter usage in the IL-3-dependent pre-B cell line Ba/F3. The rapid drop in c-myc mRNA expression observed in Ba/F3 cells upon IL-3 deprivation is reversible upon restimulation with interleukin. The use of P1 and P2 promoters, as judged by P1/P2 ratio, shifted from 0.2 in cells in exponential growth or in quiescence to 1.3 following IL-3 stimulation. This change was not due to selective instability of one of the two myc transcripts. In vitro nuclear run-on experiments indicated that IL-3 addition resulted in a large release of transcriptional attenuation, as well as a significant increase in transcriptional initiation. These results are consistent with the hypothesis that P1/P2 promoter usage is involved in the control of transcriptional elongation. Furthermore, deprivation of IL-3 resulted in a dramatic increase in antisense transcription, whereas little change was observed in the rate of initiation of elongation of c-myc mRNA precursors. This correlation suggests a negative role for antisense transcription in expression of c-myc mRNA levels in IL-3-deprived Ba/F3 cells.
3D localization based on parametric loop division and subdivision surfaces for wireless sensor networks (2016)

Precise location information is crucial for many wireless sensor network (WSN) applications. Location aware WSN sensor nodes can normally exchange information by knowing each other coordinates. In this paper we study and evaluate an algorithm based on parametric loop division (PLD), where anchor nodes form a triangle which uses coordinate of anchor nodes for three-dimensional (3D) nodes localization. Proposed method utilizes triangulation to find the centre node as well as two consecutive control nodes from ring control matrix which generates parametric nodes. Then the RSSI power at each parametric node has been compared with threshold value to find the localized nodes. Accuracy and stability of proposed solution have good impact on today's range free localization algorithms. With taking advantage of triangulation and grid system of nodes as similar to APIT and MDS this scheme of PLD shows less error if anchor nodes have uniform distribution in indoor deployed networks.
A New Approach Measuring Users' QoE in the IPTV (2009)

IPTV is a system where a digital television service is delivered by using IP packets over broadband network infrastructure. IPTV can be operated through telephone line that is installed almost in all houses. Transmitted video streams take bandwidth and also need priority running in queue with other services in the providerpsilas network. Such has in the effect implementation the quality of service (QoS) into network. QoS mechanisms allow the best way to transfer for different traffics through the network. Consumers want their IPTV programs to be smooth and visually excellent. From this perspective, it is specified as userpsilas quality of experience (QoE) that is the most important parameter for IPTV provider. Hence, network equipment must be rigorously tested that they fulfill QoE. In this paper, we present a new approach to estimate the userspsila QoE, which uses the full reference model. We have implemented and evaluated a trail system, and the results show the relationship between userspsila QoE and objective QoS.
The Majority of Patients With Achilles Tendinopathy Recover Fully When Treated With Exercise Alone (2010)

The majority of patients with Achilles tendinopathy in this study fully recovered in regard to both symptoms and function when treated with exercise alone. Increased fear of movement might have a negative effect on the effectiveness of exercise treatment; therefore, a pain-monitoring model should be used when patients are treated with exercise.
A correctness proof of a cache coherence protocol (2002)

SCI, Scalable Coherent Interface, is a new IEEE standard for specifying communication between multiprocessors in a shared memory model. We model part of SCI by a program written in a UNITY like programming language. This part of SCI is formally specified in Z. Manna and A. Pnueli's (1991) linear time temporal logic (LTL). We prove that the program satisfies its specification. The proof is carried out within LTL and uses history variables. Structuring of the proof is achieved by means of auxiliary predicates.
Increased hippocampal accumulation of autophagosomes predicts short-term recognition memory impairment in aged mice (2011)

Constitutive macroautophagy involved in the turnover of defective long-lived proteins and organelles is crucial for neuronal homeostasis. We hypothesized that macroautophagic dysregulation in selective brain regions was associated with memory impairment in aged mice. We used the single-trial object recognition test to measure short-term memory in 18 aged mice compared to 22 young mice and employed immunohistochemistry to assess cellular distribution of proteins involved in the selective degradation of ubiquitinated proteins via macroautophagy. Values of the discrimination ratio (DR, a measure of short-term recognition memory performance) in aged mice were significantly lower than those in young mice (median, 0.54 vs. 0.67; p = 0.005, U test). Almost exclusively in aged mice, there were clusters of puncta immunoreactive for microtubule-associated protein 1 light chain 3 (LC3), ubiquitin- and LC3-binding protein p62, and ubiquitin in neuronal processes predominantly in the hippocampal formation, olfactory bulb/tubercle, and cerebellar cortex. The hippocampal burden of clustered puncta immunoreactive for LC3 and p62 exhibited inverse linear correlations with DR in aged mice (ρ = -0.48 and -0.55, p = 0.044 and 0.018, respectively, Spearman's rank correlation). These findings suggest that increased accumulation of autophagosomes within neuronal processes in selective brain regions is characteristic of aging. The dysregulation of macroautophagy can adversely affect the turnover of aggregate-prone proteins and defective organelles, which may contribute to memory impairment in aged mice.
Schedule-dependent sphinganine potentiation of retinoic acid-induced differentiation, cell growth inhibition, and nucleophosmin translocation in a human leukemia cell line (HL-60). (1992)

Induction of differentiation, inhibition of cell growth, and localization of nucleophosmin in HL-60 cells under the treatment of retinoic acid (RA) were studied. Bright nucleolar fluorescence was observed in control promyelocytic growing cells. The addition of RA in the culture system resulted in time- and dose-dependent induction of differentiation, cell growth inhibition, and nucleophosmin translocation from nucleoli to nucleoplasm. Unlike the control cells, many fewer nucleophosmin-associated preribosomal ribonucleoprotein particles (pre-rRNPs) could be obtained from nucleoli of RA-treated cells. Addition of sphinganine, an inhibitor of protein kinase C, facilitated the RA-induced differentiation, nucleophosmin translocation, and cell growth inhibition. Cells treated with sphinganine were more responsive to RA. Differentiation, translocation of nucleophosmin, and inhibition of cell growth occurred with lesser doses of RA or in shorter incubation times in the presence of sphinganine. Significant numbers of HL-60 cells could be rescued from the effects of RA upon the removal of RA after 2-h drug exposure. Pretreatment but not posttreatment of HL-60 cells with sphinganine, however, modulated the reversibility of the effects induced by short-exposure RA treatment. These results indicated that RA therapy can be improved by the pretreatment or the concurrent use of a modulator of protein kinase C activity. Nucleophosmin translocation as observed by immunofluorescence may be a simple and rapid method for assessing inhibition of cellular growth in response to differentiation inducers such as RA in cancer chemotherapy.
Understanding the Molecular Aspects of Tetrahydrocannabinol and Cannabidiol as Antioxidants (2013)

An antioxidant mechanism of tetrahydrocannabinol (THC) and cannabidiol (CBD) were compared with a simplified model of α-tocopherol, butylhydroxytoluene and hydroxytoluene in order to understand the antioxidant nature of THC and CBD molecules using DFT. The following electronic properties were evaluated: frontier orbitals nature, ionization potential, O-H bond dissociation energy (BDEOH), stabilization energy, and spin density distribution. An important factor that shows an influence in the antioxidant property of THC is the electron abstraction at the phenol position. Our data indicate that the decrease of the HOMO values and the highest ionization potential values are related to phenol, ether, and alkyl moieties. On the other hand, BDEOH in molecules with the cyclohexenyl group at ortho position of phenol are formed from lower energies than the molecules with an ether group at the meta position. In the light of our results, the properties calculated here predict that THC has a sightly higher antioxidant potential than CBD.
Computer-Assisted Resection and Reconstruction of Pelvic Tumor Sarcoma (2010)

Pelvic sarcoma is associated with a relatively poor prognosis, due to the difficulty in obtaining an adequate surgical margin given the complex pelvic anatomy. Magnetic resonance imaging and computerized tomography allow valuable surgical resection planning, but intraoperative localization remains hazardous. Surgical navigation systems could be of great benefit in surgical oncology, especially in difficult tumor location; however, no commercial surgical oncology software is currently available. A customized navigation software was developed and used to perform a synovial sarcoma resection and allograft reconstruction. The software permitted preoperative planning with defined target planes and intraoperative navigation with a free-hand saw blade. The allograft was cut according to the same planes. Histological examination revealed tumor-free resection margins. Allograft fitting to the pelvis of the patient was excellent and allowed stable osteosynthesis. We believe this to be the first case of combined computer-assisted tumor resection and reconstruction with an allograft.
MazeBase: A Sandbox for Learning from Games (2015)

This paper introduces MazeBase: an environment for simple 2D games, designed as a sandbox for machine learning approaches to reasoning and planning. Within it, we create 10 simple games embodying a range of algorithmic tasks (e.g. if-then statements or set negation). A variety of neural models (fully connected, convolutional network, memory network) are deployed via reinforcement learning on these games, with and without a procedurally generated curriculum. Despite the tasks' simplicity, the performance of the models is far from optimal, suggesting directions for future development. We also demonstrate the versatility of MazeBase by using it to emulate small combat scenarios from StarCraft. Models trained on the MazeBase version can be directly applied to StarCraft, where they consistently beat the in-game AI.
Learning attack strategies through attack sequence mining method (2006)

Since security audit data increased so dramatically, management and analysis of these security data become a challenge issue. In our system SATA (Security Alerts and Threat Analysis), we proposed a new method of learning multi-stage attack strategies through attack sequence mining method to recognize attacker's high-level strategies and predicting upcoming attack intentions. We first apply an attack sequence mining algorithm to mine attack behavior sequence patterns from alarm database. We then correlate the attack behaviors matched with certain attack sequence pattern to identify potential attack intentions. Our technique is easy to implement and it can be used to detect novel multi-stage attack strategies. The primary experiments show that our approach is effective and practical.
The Frequency and Suppressor Function of CD4+CD25highFoxp3+ T Cells in the Circulation of Patients with Squamous Cell Carcinoma of the Head and Neck (2007)

The frequency of T cells with suppressor phenotype and function (Treg) was significantly greater in HNSCC patients who were NED after oncologic therapy relative to those with AD. This finding suggests that oncologic therapy favors expansion of Treg.
Analysis and design of vertical N-channel IGBT (2002)

Steady-state operation of a vertical n-channel IGBT has been investigated by means of analytical models and simulations. P-I-N diode, bipolar transistor and MOSFET models have been applied to gain physical insight into the structure. A design approach has been formulated for blocking voltage capability, forward current density, forward voltage drop and latching current density, which is crucial to device operation. Based on this approach, a 1000 V, 20 A n-channel vertical IGBT has been designed. Various structural parameters such as W, L/sub n//sup +/, L/sub C/, L/sub CH/ and process parameters X/sub j/, /spl rho//spl square/, t/sub ox/, t/sub poly/, impurity concentration, etc. have been computed. Trade-offs curves for J/sub c/-V/sub a/, V/sub F/-d/L/sub a/, J/sub CL/-L/sub n//sup +/, L/sub CL/-C/sub BS/ have been obtained from design and simulation. The calculated values of various design parameters are N/sub d/=2.35/spl times/10/sup 14/ atoms/cm/sup 3/, W=100 /spl mu/m, p-base surface concentration=1/spl times/10/sup 17/ atoms/cm/sup 3/, p-base depth=4 /spl mu/m, L/sub n//sup +/=6 /spl mu/m, n/sup +/ depth=1 /spl mu/m, L/sub CH/=2 /spl mu/m and t/sub ox/=9000 /spl Aring/, with poly-Si gate. Unit cell size is 40 /spl mu/m/spl times/40 /spl mu/m. The results presented provide guidelines for designing high-voltage and high-current bipolar transistors for various applications.
Xanthine oxidase activity and free radical generation in patients with sepsis syndrome (1996)

Patients with sepsis have xanthine oxidase activation, high free-radical concentrations, and evidence of free radical damage. The finding that xanthine oxidase activity was lower in those patients who died, coupled with increased lactate concentrations implies more severe ischemia with incomplete reperfusion resulting in less xanthine oxidase "wash out" into the circulation. Increased ascorbyl radical concentrations may be due to an increased radical generation and oxidant scavenging, but appears to be unrelated to xanthine oxidase activity within the circulation.
Security and trust issues in ubiquitous environments - the business-to-employee dimension (2004)

Ubiquitous applications and services combined with mobile business applications define a challenging context for security and trust. Besides the basic security requirements for controlled access, confidentiality, data integrity and accountability, it is essential to know whether devices surrounding a user are trusted and to distribute application tasks between those devices. We propose a development framework that combines security policies, certificates and an enforcement protocol as a solution to provide security and trust in ubiquitous applications and services. Security policies define the constraints when, how and which mobile devices can be use in a mobile business application. Enforcement of policies makes use of certificates, defined for users and devices, which determine delegable application tasks and trustworthiness of devices. Our proposed framework is flexible - can be dynamically changed, is adaptable - can be dynamically extended, and is scalable - policies and certificates are evaluated on demand and in a distributed fashion.
Too late to coordinate: Contextual influences on behavioral synchrony (2009)

Abstract The temporal coupling of behavior serves as a foundation for effective social exchange with synchronized actions moderating core components of social‐cognitive functioning. Questions remain, however, regarding the precise conditions under which this form of behavioral coordination emerges. In particular, do social factors moderate the extent to which people synchronize their movements with others? Given that synchrony serves as an important non‐verbal route through which interpersonal connections can be forged, the current investigation considered whether contextual influences moderate the emergence of behavioral coupling. To explore this issue, movements were recorded while participants performed a repetitive activity (i.e., stepping) with an interaction partner who either turned up for the experiment on time or was 15 minutes late. Results revealed that coordination (i.e., in‐phase synchrony) was substantially reduced when participants interacted with a tardy partner, a finding that highlights the impact that social factors exert on the spontaneous emergence of behavioral synchrony. Copyright © 2009 John Wiley & Sons, Ltd.
Comparative studies on bioavailability and tissue uptake of two intraruminally or intraperitoneally administered esters of alpha-tocopherol in sheep. (1991)

An experiment was conducted to compare the bioavailability of dl-alpha-tocopherol acetate (TA) with that of dl-alpha-tocopherol nicotinate (TN) when administered to sheep, as a single dose, either into the rumen or the peritoneal cavity. A total of 16 sheep were used in a factorial design, with 4 sheep/treatment at the interaction level. In addition, 5 sheep that received no supplemental alpha-tocopherol, were euthanatized at the end of the trial to provide base-line data for tissue alpha-tocopherol concentrations. Curves were fitted to the plasma alpha-tocopherol concentration values, taken over 180 hours after administration of the esters. Availability of TA was greater than TN, as evidenced by the significantly higher curve parameter values (P less than 0.05) and tissue concentrations (P less than 0.05). Route of administration had a marked effect on availability of TA (P less than 0.001), but not of TN.
Phase IIB Multicenter Trial of Vorinostat in Patients With Persistent, Progressive, or Treatment Refractory Cutaneous T-Cell Lymphoma (2007)

Oral vorinostat was effective in treatment refractory MF/SS with an acceptable safety profile.
Expression of Drosophila Trehalose-Phosphate Synthase in HEK-293 Cells Increases Hypoxia Tolerance (2003)

Increasing hypoxia tolerance in mammalian cells is potentially of major importance, but it has not been feasible thus far. The disaccharide trehalose, which accumulates dramatically during heat shock, enhances thermotolerance and reduces aggregation of denatured proteins. Previous studies from our laboratory showed that over-expression of Drosophila trehalose-phosphate synthase (dtps1) increases the trehalose level and anoxia tolerance in flies. To determine whether trehalose can protect against anoxic injury in mammalian cells, we transfected the dtps1 gene into human HEK-293 cells using the recombinant plasmid pcDNA3.1(-)-dtps1 and obtained more than 20 stable cell strains. Glucose starvation in culture showed that HEK-293 cells transfected with pcDNA3.1(-)-dtps1 (HEK-dtps1) do not metabolize intracellular trehalose, and, interestingly, these cells accumulated intracellular trehalose during hypoxic exposure. In contrast to HEK-293 cells transfected with pcDNA3.1(-) (HEK-v), cells with trehalose were more resistant to low oxygen stress (1% O2). To elucidate how trehalose protects cells from anoxic injury, we assayed protein solubility and the amount of ubiquitinated proteins. There was three times more insoluble protein in HEK-v than in HEK-dtps1 after 3 days of exposure to low O2. The amount of Na+-K+ ATPase present in the insoluble proteins dramatically increased in HEK-v cells after 2 and 3 days of exposure, whereas there was no significant change in HEK-dtps1 cells. Ubiquitinated proteins increased dramatically in HEK-v cells after 2 and 3 days of exposure but not in HEK-dtps1 cells over the same period. Our results indicate that increased trehalose in mammalian cells following transfection by the Drosophila tps1 gene protects cells from hypoxic injury. The mechanism of this protection is likely related to a decrease in protein denaturation, through protein-trehalose interactions, resulting in enhanced cellular recovery from hypoxic stress.
ON PHYSICAL HEAT REGULATION AND THE SENSE OF TEMPERATURE IN MAN (1959)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.