gebhart/patrepeval huggingface dataset:
Analysis of the Plasmodium and Anopheles Transcriptional Repertoire during Ookinete Development and Midgut Invasion (2004)

Plasmodium, the causative agent of malaria, has to undergo sexual differentiation and development in anopheline mosquitoes for transmission to occur. To isolate genes specifically induced in both organisms during the early stages of Plasmodium differentiation in the mosquito, two cDNA libraries were constructed, one enriched for sequences expressed in differentiating Plasmodium berghei ookinetes and another enriched for sequences expressed in Anopheles stephensi guts containing invading ookinetes and early oocysts. Sequencing of 457 ookinete library clones and 652 early oocyst clones represented 175 and 346 unique expressed sequence tags, respectively. Nine of 13 Plasmodium and four of the five Anopheles novel expressed sequence tags analyzed on Northern blots were induced during ookinete differentiation and mosquito gut invasion. Ancaspase-7, an Anopheles effector caspase, is proteolytically activated during Plasmodium invasion of the midgut. WARP, a gene encoding a Plasmodium surface protein with a von Willebrand factor A-like adhesive domain, is expressed only in ookinetes and early oocysts. An anti-WARP polyclonal antibody strongly inhibits (70-92%) Plasmodium development in the mosquito, making it a candidate antigen for transmission blocking vaccines. The present results and those of an accompanying report (Srinivasan, P., Abraham, E. G., Ghosh, A. K., Valenzuela, J., Ribeiro, J. M. C., Dimopoulos G., Kafatos, F. C., Adams, J. H., and Jacobs-Lorena, M. (2004) J. Biol. Chem. 279, 5581-5587) provide the foundation for further analysis of Plasmodium differentiation in the mosquito and of mosquito responses to the parasite.
Applications of conducting polymers and their issues in biomedical engineering (2010)

Conducting polymers (CPs) have attracted much interest as suitable matrices of biomolecules and have been used to enhance the stability, speed and sensitivity of various biomedical devices. Moreover, CPs are inexpensive, easy to synthesize and versatile because their properties can be readily modulated by (i) surface functionalization techniques and (ii) the use of a wide range of molecules that can be entrapped or used as dopants. This paper discusses the various surface modifications of the CP that can be employed in order to impart physico-chemical and biological guidance cues that promote cell adhesion/proliferation at the polymer-tissue interface. This ability of the CP to induce various cellular mechanisms widens its applications in medical fields and bioengineering.
Intercloud Architecture Framework for Heterogeneous Cloud Based Infrastructure Services Provisioning On-Demand (2013)

This paper presents on-going research to develop the Intercloud Architecture Framework (ICAF) that addresses problems in multi-provider multi-domain heterogeneous cloud based infrastructure services and applications integration and interoperability, to allow their on-demand provisioning. The paper refers to existing standards and ongoing standardisation activity in Cloud Computing, in particular, recently published NIST Cloud Computing Reference Architecture (CCRA) and ITU-T JCA-Cloud activity. The proposed ICAF defines four complementary components addressing Intercloud integration and interoperability: multi-layer Cloud Services Model that combines commonly adopted cloud service models, such as IaaS, PaaS, SaaS, in one multilayer model with corresponding inter-layer interfaces, Intercloud Control and Management Plane that supports cloud based applications interaction, Intercloud Federation Framework, and Intercloud Operations Framework. The paper briefly describes the Service delivery and lifecycle management as an important ICAF component that provides a basis for consistent management and security of the provisioned on-demand complex cloud based services. The paper describes an implementation of the Intercloud Control and Management Plane in the GEYSERS project to allow optimal provisioning of the combined Network+IT resources in the inter-cloud environment. The proposed architecture is intended to provide an architectural model for developing Intercloud middleware and in this way will facilitate clouds interoperability and integration.
Comparison of articular and auricular cartilage as a cell source for the autologous chondrocyte implantation (2008)

Articular (medial femoral condyle) and auricular cartilage (anithelix) was compared as a cell source for the autologous joint repair. Cells isolated from five human cadaveric donors were cultured parallel in the monolayer cultures and in the 3D alginate hydrogel constructs for 1 week. Cell morphology was controlled by the fluorescent microscopy and gene expressions of type I collagen (COL1), type II collagen (COL2), aggrecan (AGR), versican (VER), and elastin (ELS) were analyzed by the real-time polymerase chain reaction. COL1 and ELS, predominant in the phenotype of auricular biopsy, were statistically lower in the articular biopsies. Even though COL2 and AGR decreased in monolayers of both cell sources, the dedifferentiation process affected auricular cells intensely. Cells embedded in the alginate hydrogel directly after the isolation did not exhibit the dedifferentiated phenotype. Additionally, COL1, COL2, AGR, and VER were comparable between the two sources. ELS however, remained higher in the auricular cells regardless of the culture type. The study indicates that auricular chondrocytes cultured in a 3D environment immediately after the isolation have a neo-cartilage potential for the articular surface reconstruction.
DNA methylation: A promising target for the twenty-first century (2008)

Despite side effects, data obtained to date still support the vision that DNA-methylation, possibly associated with the use of histone deacetylases (HDACs) and/or artificial transcription factors (ATFs), is a promising target for improving anticancer therapy in the 21st century.
The Spectra of Tropical Cyclone Generated Waves (1999)

An extensive data base of one-dimensional spectra observed during the passage of tropical cyclones is examined. Spectra recorded within 8 times the radius to maximum winds of the centers of tropical cyclones are uni-modal and remarkably similar to previously recorded fetch limited spectra. Parametric spectral forms such as JONSWAP (Hasselmann et al., 1973) and that of Donelan et al. (1985) approximate the data well. In addition, the functional dependence of the spectral parameters a and 7 on the inverse wave age is consistent with that observed under fetch limited conditions. It is concluded that the similarity of the tropical cyclone wave spectra to those observed for simpler fetch limited spectra is largely due to the effects of nonlinear interactions. The shape stabilizing effects of the nonlinear interactions re-shape spectra consisting of a mix of swell and wind-sea to conform with typical one-dimensional fetch limited wind-sea forms.
Antiviral treatment for preventing postherpetic neuralgia (2014)

There is high quality evidence that oral aciclovir does not reduce the incidence of PHN significantly. In addition, there is insufficient evidence to determine the effect of other antiviral treatments; therefore, further well-designed RCTs are needed to investigate famciclovir or other new antiviral agents in preventing PHN. Future trials should pay more attention to the severity of pain and quality of life of participants, and should be conducted among different subgroups of people, such as people who are immunocompromised.
Colicin M Exerts Its Bacteriolytic Effect via Enzymatic Degradation of Undecaprenyl Phosphate-linked Peptidoglycan Precursors (2006)

Colicin M was earlier demonstrated to provoke Escherichia coli cell lysis via inhibition of cell wall peptidoglycan (murein) biosynthesis. As the formation of the O-antigen moiety of lipopolysaccharides was concomitantly blocked, it was hypothesized that the metabolism of undecaprenyl phosphate, an essential carrier lipid shared by these two pathways, should be the target of this colicin. However, the exact target and mechanism of action of colicin M was unknown. Colicin M was now purified to near homogeneity, and its effects on cell wall peptidoglycan metabolism reinvestigated. It is demonstrated that colicin M exhibits both in vitro and in vivo enzymatic properties of degradation of lipid I and lipid II peptidoglycan intermediates. Free undecaprenol and either 1-pyrophospho-MurNAc-pentapeptide or 1-pyrophospho-MurNAc-(pentapeptide)-Glc-NAc were identified as the lipid I and lipid II degradation products, respectively, showing that the cleavage occurred between the lipid moiety and the pyrophosphoryl group. This is the first time such an activity is described. Neither undecaprenyl pyrophosphate nor the peptidoglycan nucleotide precursors were substrates of colicin M, indicating that both undecaprenyl and sugar moieties were essential for activity. The bacteriolytic effect of colicin M therefore appears to be the consequence of an arrest of peptidoglycan polymerization steps provoked by enzymatic degradation of the undecaprenyl phosphate-linked peptidoglycan precursors.
PDE1B2 regulates cGMP and a subset of the phenotypic characteristics acquired upon macrophage differentiation from a monocyte (2006)

Monocyte-to-macrophage differentiation with the cytokine granulocyte-macrophage colony-stimulating factor induces expression of the cyclic nucleotide phosphodiesterase PDE1B2. However, what role PDE1B2 plays in macrophage biology has not been elucidated. We have addressed this question by inhibiting PDE1B2 induction by using RNA interference. Using a retrovirus-based system, we created HL-60 stable cell lines that express a short-hairpin RNA targeting PDE1B2. HL-60 cells treated with phorbol-12-myristate-13-acetate differentiate to a macrophage-like phenotype and up-regulate PDE1B2. However, expression of PDE1B2 short hairpin RNA effectively suppresses PDE1B2 mRNA, protein, and activity up-regulation. Using the HL-60 PDE1B2 knockdown cells and agonists for either adenylyl or guanylyl cyclase, it was found that PDE1B2 predominantly regulates cGMP and plays a lesser role in cAMP regulation in response to cyclase agonists. Furthermore, in intact HL-60 cells, PDE1B2 activity can be regulated by changes in Ca+2 levels. Inhibiting PDE1B2 up-regulation does not prevent HL-60 cell differentiation, because several markers of macrophage differentiation are unaffected. However, suppression of PDE1B2 expression alters some aspects of the macrophage-like phenotype, because cell spreading, phagocytic ability, and CD11b expression are augmented. The cAMP analog 8-Bromo-cAMP reverses the changes caused by PDE1B2 knockdown. Also, PDE1B2 knockdown cells have lower basal levels of cAMP and alterations in the phosphorylation state of several probable PKA substrate proteins. Thus, the effects of PDE1B2 on differentiation may ultimately be mediated through decreased cAMP. In conclusion, PDE1B2 regulates a subset of phenotypic changes that occur upon phorbol-12-myristate-13-acetate-induced differentiation and likely also plays a role in differentiated macrophages by regulating agonist-stimulated cGMP levels.
Speciation and Mechanistic Studies of Chiral Copper(I) Schiff Base Precursors Mediating Asymmetric Carbenoid Insertion Reactions of Diazoacetates into the Si−H Bond of Silanes (2000)

[Cu(CH3CN)4](PF6) and the chiral C2-symmetric diimine ligand (1R,2R)-bis((2,6-dichlorobenzylidene)diamino)cyclohexane (R,R-1) (1.2 equiv) mediate asymmetric carbenoid insertion of aryl diazoesters into the Si−H bond of silanes in good to high yields and levels of enantiocontrol. Dichloromethane solutions of [Cu(CH3CN)4](PF6)/R,R-1 afford yellow crystals of [CuI(R,R-1)(CH3CN)·CuI(R,R-1)(CH3CN)2·CuI2(R,R-1)3](PF6)4·2CH2Cl2·3Et2O, which feature three distinct copper complexes in the crystal lattice. 1H NMR and electrospray ionization MS (ESI-MS) studies establish that only [CuI(R,R-1)(CH3CN)]+ is present in solution in high yields. Upon addition of stoichiometric PhC(N2)CO2Me, cations [CuI(R,R-1)(C(CO2Me)Ph)]+ and [CuI(R,R-1)(C(CO2Me)Ph)(CH3CN)]+ are detected by ESI-MS, consistent with the presence of a copper−carbenoid moiety. The catalytically active precursor is most likely a mononuclear unit of the type [CuI(R,R-1)(CH3CN)n]+, as suggested by the linearity of plots relating the enantiomeric excess (ee) of product to that of the ligand (Kagan's analysis). Hammett plots correlate enhanced catalytic reactivities with stabilization of a sizable positive charge on the carbenoid carbon and a smaller positive charge on the silicon atom, but the corresponding enantioselectivities are insensitive to these electronic properties. The kinetic isotope effect for carbenoid insertion into PhMe2Si−H(D) varies from 2.12 (−40 °C) to 1.08 (25 °C), in agreement with other small KIE values observed for processes in which Si−H activation is involved in the turnover-limiting step. A linear Eyring plot of ln(k(major enantiomer)/k(minor enantiomer)) over a range of 80 K supports the notion of a single step controlling the levels of enantioselection. No H/D scrambling is observed in competitive carbenoid insertions into PhMe2Si-D/Ph2MeSi-H, indicating that the insertion reaction takes place in a concerted fashion. These results are discussed in light of an early transition state, characterized by hydrogen-first penetration of the Si−H bond into the copper−carbenoid cavity, which is assumed to impart high levels of enantioselectivity due to intrinsic preorganization under the influence of the specific ligand and aryl diazoesters employed.
Instrumented composite turbine blade for health monitoring (2012)

A health monitoring approach is investigated for hydrokinetic turbine blade applications. In-service monitoring is critical due to the difficult environment for blade inspection and the cost of inspection downtime. Composite blade designs have advantages that include long life in marine environments and great control over mechanical properties. Experimental strain characteristics are determined for static loads and free-vibration loads. These experiments are designed to simulate the dynamic characteristics of hydrokinetic turbine blades. Carbon/epoxy symmetric composite laminates are manufactured using an autoclave process. Four-layer composite beams, eight-layer composite beams, and two-dimensional eight-layer composite blades are instrumented for strain. Experimental results for strain measurements from electrical resistance gages are validated with theoretical characteristics obtained from in-house finite-element analysis for all sample cases. These preliminary tests on the composite samples show good correlation between experimental and finite-element strain results. A health monitoring system is proposed in which damage to a composite structure, e.g. delamination and fiber breakage, causes changes in the strain signature behavior. The system is based on embedded strain sensors and embedded motes in which strain information is demodulated for wireless transmission.
Robotics: Theory and applications (1986)

This book presents the papers given at a conference on the computer-aspects of robots. Topics considered at the conference included robot system control theory, the adaptive control of robotic manipulators, feedback control, position and impulsive force at collision for the control of two coordinated robots in motion, robust control of a robotic manipulator with joint variable feedback, the modeling and control of elastic joint robots, and stability of feedback control with gravity compensation for a robot manipulator.
Brain-Inspired Motion Learning in Recurrent Neural Network With Emotion Modulation (2018)

Based on basic emotion modulation theory and the neural mechanisms of generating complex motor patterns, we introduce a novel emotion-modulated learning rule to train a recurrent neural network, which enables a complex musculoskeletal arm and a robotic arm to perform goal-directed tasks with high accuracy and learning efficiency. Specifically, inspired by the fact that emotions can modulate the process of learning and decision making through neuromodulatory system, we present a model of emotion generation and modulation to adjust the parameters of learning adaptively, including the reward prediction error, the speed of learning, and the randomness in action selection. Additionally, we use Oja learning rule to adjust the recurrent weights in delayed-reinforcement tasks, which outperforms the Hebbian update rule in terms of stability and accuracy. In the experimental section, we use a musculoskeletal model of the human upper limb and a robotic arm to perform goal-directed tasks through trial-and-reward learning, respectively. The results show that emotion-based methods are able to control the arm with higher accuracy and a faster learning rate. Meanwhile, emotional Oja agent is superior to emotional Hebbian one in term of performance.
Kaposi's sarcoma‐associated herpesvirus infection in Chinese patients with chronic hepatitis B (2011)

The seroprevalence of Kaposi's sarcoma-associated herpesvirus (KSHV) in Chinese patients with chronic hepatitis B, the relationship between KSHV and hepatitis B virus (HBV) infection, and the influence of glycyrrhizic acid on KSHV replication in vivo are undefined. Plasma was collected from 211 patients with chronic hepatitis B. Antibody to KSHV ORF65 was evaluated by ELISA, and real-time PCR was used to quantify KSHV DNA and HBV DNA. The KSHV ORF65 positivity rate in patients with chronic hepatitis B was found to be 28% (59/211): 27.3% (44/161) in males and 30% (15/50) in females (P > 0.05). The seroprevalence of KSHV increased with age until reaching the highest rate (37.1%) in the 31-40 years age group. HBV DNA loads in patients with chronic hepatitis B infected with KSHV were higher than those without KSHV infection (9.2 log (10) IU/ml vs. 7.8 log (10) IU/ml, P < 0.05). The average KSHV DNA loads in patients with HBV genotype B, C, and mixed (B/C) were 409.1, 484.5, and 352 copies/ml, respectively (P > 0.05). Patients treated with glycyrrhizic acid had lower KSHV DNA levels than those without therapy (204.7 copies/ml vs. 533.9 copies/ml, P < 0.05). The KSHV ORF65 positivity rates tended to increase with age, but were not related to gender or HBV genotypes. The data indicated the interaction between KSHV and HBV, and the inhibiting effect of glycyrrhizic acid on KSHV replication in patients with chronic hepatitis B.
Experiences with X in a wireless environment (1993)

Wireless computing is all the rage; the X Window System seems to be inescapable. We have been experimenting with the cross-product, and have had mixed results. The network may not be the computer any more, but it certainly influences the way the computer performs, and adding a fairly atypical network layer cannot help but expose some underlying assumptions. We discuss a few that we found and go on to speculate about how to best push X in the direction of mobile and location-independent computing.
Recovery of cardiac calcium release is controlled by sarcoplasmic reticulum refilling and ryanodine receptor sensitivity (2011)

Together, the results strongly suggest that: (i) local SR refilling controls Ca(2+) spark amplitude recovery; (ii) Ca(2+) spark triggering depends on both refilling and RyR sensitivity; and (iii) β-adrenergic stimulation influences both processes.
Aurora A, Meiosis and Mitosis (2004)

The Aurora family kinases are pivotal to the successful execution of cell division. Together they ensure the formation of a bipolar mitotic spindle, accurate segregation of chromosomes and the completion of cytokinesis. They are also attractive drug targets, being frequently deregulated in cancer and able to transform cells in vitro. In this review, we summarize current knowledge about the three family members, Aur-A, Aur-B and Aur-C. We then focus on Aur-A, its roles in mitotic progression, and its emerging roles in checkpoint control pathways. Aur-A activity can be controlled at several levels, including phosphorylation, ubiquitin-dependent proteolysis and interaction with both positive regulators, such as TPX2, and negative ones, like the tumor suppressor protein p53. In addition, work in Xenopus oocytes and early embryos has revealed a second role for Aur-A, directing the polyadenylation-dependent translation of specific mRNAs important for cell cycle progression. This function extends to post-mitotic neurons, and perhaps even to cycling somatic cells.
Telemedicine using mobile satellite communication (1994)

With a view to providing paramedical care within moving vehicles, a telemedicine technique using mobile satellite communication was proposed. With this technique, the diagnosis from a specialist and the emergency care under his/her instructions would be available on the spot without unnecessary delay. The characteristic problems of this technique were identified as: channel capacity, size of the system, reliability of vital sign transmission, real-time operation and electromagnetic interference. Measures against these problems were devised, and their effectiveness was analyzed. A data format was designed and an experimental system was developed. The system can simultaneously transmit a color image, an audio signal, 3 channels ECG and blood pressures from a mobile station to a ground station. It can transmit an audio signal and error control signals from a ground station to a mobile station in a full duplex mode. Fundamental transmission characteristics were measured in a fixed station. Finally, experiments of medical data transmission were conducted with a navigating ship and an aircraft flying an international route. The measured threshold values of C/N(o) to guarantee satisfactory data reception were well below the lower boundary of C/N(o) of the communication link. Consequently, the feasibility of this technique was verified.
Biomechanically Induced Gene <i>iex-1</i> Inhibits Vascular Smooth Muscle Cell Proliferation and Neointima Formation (2003)

Mechanotransduction plays a prominent role in vascular pathophysiology but is incompletely understood. In this study, we report the biomechanical induction of the immediate early response gene iex-1 in vascular smooth muscle cells (SMCs). Mechanical induction of iex-1 was confirmed by Northern (30-fold induction after 2 hours) and Western (6-fold induction after 24 hours) analyses. Expression of iex-1 was regulated by mechanical activation of nuclear factor (NF)-kappaB and abolished by overexpression of IkappaB in SMCs. The function of iex-1 in SMCs was explored by gene transfer using adenoviral vectors overexpressing iex-1. After 48 hours of 4% cyclic mechanical strain, adenoviral vectors overexpressing iex-1-infected cells had lower 3[H]-thymidine incorporation compared with AdGFP-infected controls (71.3+/-8.5% versus 180.2+/-19.4% in controls; P<0.001). Overexpression of iex-1 suppressed mitogenesis induced by platelet-derived growth factor (208.1+/-108.3% versus 290.0+/-120.5% in controls; P<0.05). This was accompanied by reduced degradation of p27kip1, inhibition of Rb hyperphosphorylation, and reduced cell cycle progression. To investigate functional effects of iex-1 in vivo, we performed carotid artery mechanical injury and endothelial denudation in low-density lipoprotein receptor-deficient mice followed by intraluminal injection of adenoviral vectors (3x10(9) pfu in 50 microL) for overexpression of iex-1 or gfp (control). Vascular overexpression of iex-1 reduced neointima formation 2 weeks after injury (intima/media ratio, 0.23+/-0.04 versus 0.5+/-0.24 in controls; P<0.05). Our findings demonstrate that biomechanical strain induces iex-1 with subsequent antiproliferative effects in SMCs and that selective gene transfer of iex-1 inhibits the local vascular response after injury. These findings suggest that the induction of iex-1 represents a novel negative biomechanical feedback mechanism limiting the vascular response to injury.