gebhart/patrepeval huggingface dataset:
The small Rho GTPase Cdc42 regulates neutrophil polarity via CD11b integrin signaling (2009)

Neutrophil migration to sites of infection is the first line of cellular defense. A key event of migration is the maintenance of a polarized morphology, which is characterized by a single leading edge of filamentous actin and a contractile uropod devoid of filamentous actin protrusions. Using a mouse model of high Cdc42 activity, we previously demonstrated the importance of Cdc42 activity in neutrophil migration. However, the specific functions of Cdc42 in this process remain to be understood. Using neutrophils genetically deficient in Cdc42, we show that Cdc42 regulates directed migration by maintaining neutrophil polarity. Although it is known to be activated at the front, Cdc42 suppresses protrusions at the uropod. Interestingly, Cdc42 makes use of the integrin CD11b during this process. Cdc42 determines the redistribution of CD11b at the uropod. In turn, using CD11b-null cells and CD11b crosslinking experiments, we show that CD11b modulates myosin light chain phosphorylation to suppress lateral protrusions. Our results uncover a new mechanism in which Cdc42 regulates the uropod through CD11b signaling to maintain polarity in migrating neutrophils. It also reveals new functions for CD11b in neutrophil polarity.
Disease resistance conferred by expression of a gene encoding H2O2-generating glucose oxidase in transgenic potato plants. (1995)

Plant defense responses to pathogen infection involve the production of active oxygen species, including hydrogen peroxide (H2O2). We obtained transgenic potato plants expressing a fungal gene encoding glucose oxidase, which generates H2O2 when glucose is oxidized. H2O2 levels were elevated in both leaf and tuber tissues of these plants. Transgenic potato tubers exhibited strong resistance to a bacterial soft rot disease caused by Erwinia carotovora subsp carotovora, and disease resistance was sustained under both aerobic and anaerobic conditions of bacterial infection. This resistance to soft rot was apparently mediated by elevated levels of H2O2, because the resistance could be counteracted by exogenously added H2O2-degrading catalase. The transgenic plants with increased levels of H2O2 also exhibited enhanced resistance to potato late blight caused by Phytophthora infestans. The development of lesions resulting from infection by P. infestans was significantly delayed in leaves of these plants. Thus, the expression of an active oxygen species-generating enzyme in transgenic plants represents a novel approach for engineering broad-spectrum disease resistance in plants.
Hand-off analysis for an integrated satellite and terrestrial mobile system over a fading channel (2003)

An integrated satellite and terrestrial mobile system enables the satellite mobile terminal (MT) to access the land mobile satellite system (LMSS) inside the coverage of a terrestrial network. When the MT operates inside an urban area, base stations of the terrestrial network will act as relay stations for the LMSS. The hand-off analysis for the two systems is an important issue. A mathematical model is developed to simulate the received signals at the MT over a Rayleigh fading channel. By using this model, the effects of level-crossing rate (LCR) on hand-off criteria for the integrated system are also discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Dda Helicase Tightly Couples Translocation on Single-Stranded DNA to Unwinding of Duplex DNA: Dda Is an Optimally Active Helicase (2012)

Helicases utilize the energy of ATP hydrolysis to unwind double-stranded DNA while translocating on the DNA. Mechanisms for melting the duplex have been characterized as active or passive, depending on whether the enzyme actively separates the base pairs or simply sequesters single-stranded DNA (ssDNA) that forms due to thermal fraying. Here, we show that Dda translocates unidirectionally on ssDNA at the same rate at which it unwinds double-stranded DNA in both ensemble and single-molecule experiments. Further, the unwinding rate is largely insensitive to the duplex stability and to the applied force. Thus, Dda transduces all of its translocase activity into DNA unwinding activity so that the rate of unwinding is limited by the rate of translocation and that the enzyme actively separates the duplex. Active and passive helicases have been characterized by dividing the velocity of DNA unwinding in base pairs per second (V(un)) by the velocity of translocation on ssDNA in nucleotides per second (V(trans)). If the resulting fraction is 0.25, then a helicase is considered to be at the lower end of the "active" range. In the case of Dda, the average DNA unwinding velocity was 257±42 bp/s, and the average translocation velocity was 267±15 nt/s. The V(un)/V(trans) value of 0.96 places Dda in a unique category of being an essentially "perfectly" active helicase.
POU‐specific domain of Oct‐2 factor confers ‘octamer’ motif DNA binding specificity on heterologous Antennapedia homeodomain (1992)

The bipartite DNA binding domain of the POU family of transcription factors contains a 'POU-specific' domain unique to this class of factors and a 'POU homeodomain' homologous to other homeodomains. We compared DNA binding of the Oct-2 factor POU domain and the Antennapedia (Antp) homeodomain with a chimeric Oct-2/Antp protein in which the distantly related Antp homeodomain was substituted for the Oct-2 POU homeodomain. The Oct-2/Antp chimeric protein bound both the octamer and the Antp sites efficiently, indicating that DNA binding specificity is contributed by both components of the POU domain.
Estolides: From structure and function to structured and functionalized (2008)

Abstract Oligomeric fatty acid esters, known as estolides, have been studied for close to a century. It has only been in the last few years, however, that efficient methods for preparing estolides have been developed that also allow some control over their molecular structures. By varying the bio‐based feedstocks and reaction conditions, the functional properties, particularly those geared toward lubrication, can be modified. More recently, synthetic advances have permitted stepwise construction of estolides with functional groups (hydrophilic or reactive) positioned at specific sites within the chain.
Integrin alphavbeta5 participates in the binding of photoreceptor rod outer segments during phagocytosis by cultured human retinal pigment epithelium. (1998)

The integrin alphavbeta5 vitronectin receptor is expressed on the apical membrane of human RPE and participates in the binding of photoreceptor ROS during phagocytosis by cultured human RPE.
Model of autism: increased ratio of excitation/inhibition in key neural systems (2003)

Autism is a severe neurobehavioral syndrome, arising largely as an inherited disorder, which can arise from several diseases. Despite recent advances in identifying some genes that can cause autism, its underlying neurological mechanisms are uncertain. Autism is best conceptualized by considering the neural systems that may be defective in autistic individuals. Recent advances in understanding neural systems that process sensory information, various types of memories and social and emotional behaviors are reviewed and compared with known abnormalities in autism. Then, specific genetic abnormalities that are linked with autism are examined. Synthesis of this information leads to a model that postulates that some forms of autism are caused by an increased ratio of excitation/inhibition in sensory, mnemonic, social and emotional systems. The model further postulates that the increased ratio of excitation/inhibition can be caused by combinatorial effects of genetic and environmental variables that impinge upon a given neural system. Furthermore, the model suggests potential therapeutic interventions.
7.1: Invited Paper : Novel Diffractive Optical Components for Near to Eye Displays (2006)

Abstract Diffractive Optical Elements (DOE's) on planar waveguides can be used to miniaturize the optics of a Virtual Reality Display (VRD). A biocular VRD that uses the diffractive planar waveguide as an Exit Pupil Expander (EPE) is ergonomically excellent but suffers from low efficiency and from uneven light distribution in the perceived virtual image. Using novel diffractive structures the efficiency of the system can be dramatically improved and an excellent performance over a wide Field of View (FOV) can be achieved. In this paper it is shown that with deep slanted grating profiles more than 90% diffraction efficiency can be reached and that etendue of the system is improved. It is also shown that the binary sub‐wavelength gratings with a proper groove shape are not polarization sensitive. The performance of the EPE plate can be optimized using the filling ratio, the grating depth and the slanting angle as tuning parameters. The volume production methods of the deep slanted grating structures are discussed and some experimental results are shown.
Hippocampal and entorhinal cortex atrophy in frontotemporal dementia and Alzheimer’s disease (1999)

At variance with AD, detectable in vivo atrophy of the hippocampus might not be an early event in FTD. Differential patterns of atrophy might help in the diagnostic process of the degenerative dementias.
EFFECT OF BENTONITE ON SKIN WOUND HEALING: EXPERIMENTAL STUDY IN THE RAT MODEL (2014)

Abstract- Wound healing in the skin depends upon the availability of appropriate trace metals as enzyme cofactors and structural components in tissue repair. The present study is a part of a series of experimental investigations to examine the influence of Bentonite on skin wound healing. Surgically induced skin wounds in 48 young adult male rats were exposed topically to Bentonite (12 round wound and 12 incisional wound) and control wounds (12 round wound and 12 incisional wound) received de-ionized water only. Skin wounds (round and incisional) treated with Bentonite exhibited no significant difference in margins with erythema and edematous changes. Scab and wound debris was more extensive and persisted for at least 7 days after surgery in control group (P &amp;lt; 0.05). Skin wounds exposed to Bentonite exhibited a mild retarded re-epithelialization, the treatment wounds were characterized by a prominent central mass of inflammatory cells, cell debris and wound exudate. The intense infiltrate of lymphocytes, macrophages, monocytes and fibroblasts extended from the wound margin into the region of the panniculus carnosus muscle and hypodermis. Vascular dilatation and dermal oedema were prominent features of these wounds. External utilization of Bentonite for wound healing is safe and feasible, and we finalized that macroscopic healing of wound that treated by Bentonite was superior versus control group.
Photochemical stroke model: flunarizine prevents sensorimotor deficits after neocortical infarcts in rats. (1989)

We produced unilateral photochemical infarcts in the hindlimb sensorimotor neocortex of 186 rats by intravenous injection of the fluorescein derivative rose bengal and focal illumination of the intact skull surface. Infarcted rats showed specific, long-lasting deficits in tactile and proprioceptive placing reactions of the contralateral limbs, mostly the hindlimb. Placing deficits were most prominent during transition to immobility and/or when independent limb movements were required. Administration of flunarizine, a Class IV calcium antagonist, 30 minutes after infarction resulted in marked sparing of sensorimotor function in 30 rats. In contrast to 20 vehicle-treated rats, which remained deficient for at least 21 days, 15 (75%) of the rats treated with 1.25 mg/kg i.v. flunarizine showed normal placing on Day 1 after infarction, whereas the remaining five (25%) recovered within 5 days. Oral treatment of 10 rats with 40 mg/kg flunarizine was also effective. Neocortical infarct volume and thalamic gliosis, assessed 21 days after infarction, did not differ between 30 flunarizine- and 30 vehicle-treated rats. However, when 4-hour-old infarcts were measured in 16 rats, posttreatment with intravenous flunarizine reduced infarct size by 31%. In combination with appropriate behavioral analyses, photochemical thrombosis may constitute a relevant stroke model, in which flunarizine preserved behavioral function during a critical period, corresponding to the spread of ischemic damage.
Fast Disinfecting Antimicrobial Surfaces (2008)

Silicon wafers and glass surfaces were functionalized with facially amphiphilic antimicrobial copolymers using the "grafting from" technique. Surface-initiated atom transfer radical polymerization (ATRP) was used to grow poly(butylmethacrylate)-co-poly(Boc-aminoethyl methacrylate) from the surfaces. Upon Boc-deprotection, these surfaces became highly antimicrobial and killed S. aureus and E. coli 100% in less than 5 min. The molecular weight and grafting density of the polymer were controlled by varying the polymerization time and initiator surface density. Antimicrobial studies showed that the killing efficiency of these surfaces was independent of polymer layer thickness or grafting density within the range of surfaces studied.
Plumbagin, a novel Nrf2/ARE activator, protects against cerebral ischemia (2009)

Many phytochemicals function as noxious agents that protect plants against insects and other damaging organisms. However, at subtoxic doses, the same phytochemicals may activate adaptive cellular stress response pathways that can protect cells against a variety of adverse conditions. We screened a panel of botanical pesticides using cultured human and rodent neuronal cell models, and identified plumbagin as a novel potent activator of the nuclear factor E2-related factor 2 (Nrf2)/antioxidant response element (ARE) pathway. In vitro, plumbagin increases nuclear localization and transcriptional activity of Nrf2, and induces the expression of the Nrf2/ARE-dependent genes, such as heme oxygenase 1 in human neuroblastoma cells. Plumbagin specifically activates the Nrf2/ARE pathway in primary mixed cultures from ARE-human placental alkaline phosphatase reporter mice. Exposure of neuroblastoma cells and primary cortical neurons to plumbagin provides protection against subsequent oxidative and metabolic insults. The neuroprotective effects of plumbagin are abolished by RNA interference-mediated knockdown of Nrf2 expression. In vivo, administration of plumbagin significantly reduces the amount of brain damage and ameliorates-associated neurological deficits in a mouse model of focal ischemic stroke. Our findings establish precedence for the identification and characterization of neuroprotective phytochemicals based upon their ability to activate adaptive cellular stress response pathways.
virG, a plasmid-coded virulence gene of Shigella flexneri: identification of the virG protein and determination of the complete coding sequence (1989)

On the 230-kilobase-pair (kb) virulence plasmid of Shigella flexneri 2a strain YSH6000, at least seven separate genetic determinants have been identified. One of them, an approximately 4-kb region, virG, that is required for the Sereny reaction, was extensively studied to examine the role of the virG region. The phenotype of a VirG- mutant (M94) of YSH6000 in the cytoplasm of cultured MK cells was characterized by a kinetic study of the invading shigellae. The observed phenotype of M94 in the cytoplasm indicated that the virG locus is not required for multiplication of the invading shigellae, but is essential for their spread to adjacent cells. The DNA region necessary for the VirG function was localized to a 3.6-kb DNA sequence on the 230-kb plasmid. A 130-kilodalton polypeptide was confirmed to be the virG product. External labeling of bacteria with 125I indicated that the 130-kilodalton virG protein is exposed on the bacterial surface. The nucleotide sequence of 4,472 bp, which contains the functional virG gene and its own regulatory sequence, was determined, and a large open reading frame encoding 1,102 amino acid residues was identified.
Large area ITO-free flexible white OLEDs with Orgacon PEDOT:PSS and printed metal shunting lines (2009)

We demonstrate the feasibility of white organic light-emitting diodes that exclude the transparent conductor indium-tinoxide. Instead, a highly conductive Orgacon<sup>TM</sup> PEDOT:PSS material in combination with a metal support structure is used as transparent anode and hole-injection layer. The PEDOT:PSS exhibits a conductivity of 460&plusmn;20 S/cm and a work function of 5.35&plusmn;0.05 eV. On ITO-free OLEDs on glass with an active area of ~6 cm<sup>2</sup> the inclusion of 120 nm thick printed metal lines reduces the variation in brightness from 35% to 20%. The ITO-free concept based on PEDOT:PSS with printed metal structures is scaled up to large flexible OLEDs with a size of 150 cm<sup>2</sup> on a heat-stabilized Teonex&#174; Polyethylene Naphtalate foil. The voltage distribution across the various electrodes was verified by a finite element model, allowing a prediction of the OLED brightness and homogeneity over large areas.
Functionalization of Carbon Nanotubes via Cleavable Disulfide Bonds for Efficient Intracellular Delivery of siRNA and Potent Gene Silencing (2005)

We present a novel functionalization scheme for single-walled carbon nanotubes (SWNTs) to afford nanotube-biomolecule conjugates with the incorporation of cleavable bonds to enable controlled molecular releasing from nanotube surfaces, thus creating "smart" nanomaterials with high potential for chemical and biological applications. With this versatile functionalization, we demonstrate transporting, enzymatic cleaving and releasing of DNA from SWNT transporters, and subsequent nuclear translocation of DNA oligonucleotides in mammalian cells. We further show highly efficient delivery of siRNA by SWNTs and achieving more potent RNAi functionality than a widely used conventional transfection agent. Thus, the novel functionalization of SWNTs with cleavable bonds is highly promising for a wide range of applications including gene and protein therapy.
Study of Humidification Potential of a Heat and Moisture Exchanger in Tracheotomized Dogs (1988)

Though a heat and moisture exchanger (HME) has been used in clinical practice following a tracheotomy on a limited basis, no work has been done to document the humidification potential of an HME in this situation. Eighteen dogs underwent tracheotomy and were killed at either 1 day (nine dogs) or 10 days (nine dogs) postoperatively. Following the tracheotomy, the animals were divided into three groups according to the type of humidification received: ambient conditions, warm mist, or HME. The tracheal mucosa was studied for histologic changes in the cilia, the epithelium, submucosal reaction, and mucus production at the level of the carina. The results were significant (p = .02) for the interaction of the experimental type and method of treatment in their effect on the histologic changes noted at the carina. The study supports the use of an HME as an alternative for long-term humidification in a patient with a tracheotomy.
Effect of Major Deletions in the V1 and V2 Loops of a Macrophage-Tropic HIV Type 1 Isolate on Viral Envelope Structure, Cell Entry, and Replication (1998)

Two HIV-1 envelope mutant proteins were generated by introducing deletions in the first and second hypervariable gp120 regions (V1 and V2 loops, respectively) of a macrophage-tropic primary HIV-1 isolate, SF162, to study the effect of the deleted sequences on envelope structure, viral entry, and replication potentials. The first mutant lacked 17 amino acids of the V1 loop and the latter 30 amino acids of the V2 loop. A comparison of the immunochemical structure of the wild-type and mutant monomeric and virion-associated gp120 molecules revealed that the V1 and V2 loop deletions differentially altered the structure of the V3 loop, the CD4-binding site, and epitopes within conserved regions of gp120. Regardless of differences in structure, both mutated envelope proteins supported viral replication into peripheral blood mononuclear cells to levels comparable to those of the wild-type SF162 virus. However, they decreased the viral replication potential in macrophages, even though they did not alter the coreceptor usage of the viruses. These studies support and extend previous observations that a complex structural interaction between the V1, V2, and V3 loops and elements of the CD4-binding site of gp120 controls entry of virus into cells. The present studies, however, suggest that the effect of the V1 and V2 loops in viral entry is cell dependent.
Non-Homogeneous Stochastic Model for Cyber Security Predictions (2017)

Any computer system with known vulnerabilities can be presented using attack graphs. An attacker generally has a mission to reach a goal state that he expects to achieve. Expected Path Length (EPL) [1] in the context of an attack graph describes the length or number of steps that the attacker has to take in achieving the goal state. However, EPL varies and it is based on the “state of vulnerabilities” [2] [3] in a given computer system. Any vulnerability throughout its life cycle passes through several stages that we identify as “states of the vulnerability life cycle” [2] [3]. In our previous studies we have developed mathematical models using Markovian theory to estimate the probability of a given vulnerability being in a particular state of its life cycle. There, we have considered a typical model of a computer network system with two computers subject to three vulnerabilities, and developed a method driven by an algorithm to estimate the EPL of this network system as a function of time. This approach is important because it allows us to monitor a computer system during the process of being exploited. Proposed non-homogeneous model in this study estimates the behavior of the EPL as a function of time and therefore act as an index of the risk associated with the network system getting exploited.
Fishing for gene function – endocrine modelling in the zebrafish (2006)

The use of zebrafish (Danio rerio) in scientific research is growing rapidly. It initially became popular as a model of vertebrate development because zebrafish embryos develop rapidly and are transparent. In the past 5 years, the sequencing of the zebrafish genome has increased the profile of zebrafish research even further, expanding into other areas such as pharmacology, cancer research and drug discovery. The use of zebrafish in endocrine research has mainly been confined to the study of the development of endocrine organs. However, it is likely to be a useful model in other areas of endocrinology, as there are a wide variety of both forward and reverse genetic techniques that can be employed in the zebrafish to decipher gene function in disease states. In this review, we compare the endocrine system of the zebrafish to mouse and human, demonstrating that the systems are sufficiently similar for zebrafish to be employed as a model for endocrine research. We subsequently review the repertoire of genetic techniques commonly employed in the zebrafish model to understand gene function in vertebrate development and disease. We anticipate that the use of these techniques will make the zebrafish a prominent model in endocrine research in the coming years.