gebhart/patrepeval huggingface dataset:
Tuning hydrogel properties for applications in tissue engineering (2009)

Biomaterial design is an important component towards tissue engineering applications. There are many parameters that may be adjusted including physical properties (i.e., degradation and mechanics) and chemical properties (e.g., adhesion and cellular interactions). These design components may dictate the success or failure of a tissue engineering approach. Our group is particularly interested in the use of swollen hydrogels as cell carriers. One material that is used to fabricate hydrogels is hyaluronic acid (HA), which is found in many tissues in the body. Here, we show the control over hydrogel degradation, both in the bulk and locally to cells to control both the distribution of extracellular matrix by cells and whether or not a cell spreads in the hydrogels. These signals are important in the final structure and mechanical properties of engineered tissues, and potentially the differentiation of encapsulated stem cells.
Genetic CNN (2017)

The deep convolutional neural network (CNN) is the state-of-the-art solution for large-scale visual recognition. Following some basic principles such as increasing network depth and constructing highway connections, researchers have manually designed a lot of fixed network architectures and verified their effectiveness.,,In this paper, we discuss the possibility of learning deep network structures automatically. Note that the number of possible network structures increases exponentially with the number of layers in the network, which motivates us to adopt the genetic algorithm to efficiently explore this large search space. The core idea is to propose an encoding method to represent each network structure in a fixed-length binary string. The genetic algorithm is initialized by generating a set of randomized individuals. In each generation, we define standard genetic operations, e.g., selection, mutation and crossover, to generate competitive individuals and eliminate weak ones. The competitiveness of each individual is defined as its recognition accuracy, which is obtained via a standalone training process on a reference dataset. We run the genetic process on CIFAR10, a small-scale dataset, demonstrating its ability to find high-quality structures which are little studied before. The learned powerful structures are also transferrable to the ILSVRC2012 dataset for large-scale visual recognition.
IMU-RGBD camera 3D pose estimation and extrinsic calibration: Observability analysis and consistency improvement (2013)

In this paper, we address the problem of extrinsically calibrating an inertial measurement unit (IMU) with respect to an RGBD sensor. In particular, we study the observability of the nonlinear IMU-RGBD calibration system and prove that the calibration parameters are observable given observations to a single point feature. Moreover, we show that the system has four unobservable directions corresponding to the global translation and rotations about the gravity vector. Based on the results of the observability analysis, we design a consistency-improved, observability constrained (OC) extended Kalman filter (EKF)-based estimator for calibrating the sensor pair while at the same time tracking its pose and creating a 3D map of the environment. Finally, we validate the key findings of the observability analysis and assess the performance of the OC-EKF estimator both in simulation and experimentally.
Rho activation is apically restricted by Arhgap1 in neural crest cells and drives epithelial-to-mesenchymal transition (2013)

Epithelial-to-mesenchymal transitions (EMTs) are crucial for morphogenesis and carcinoma metastasis, yet mechanisms controlling the underlying cell behaviors are poorly understood. RhoGTPase signaling has been implicated in EMT; however, previous studies have yielded conflicting results regarding Rho function, and its role in EMT remains poorly understood. Elucidation of precise Rho functions has been challenging because Rho signaling is highly context dependent and its activity is tightly regulated spatiotemporally within the cell. To date, few studies have examined how Rho affects cell motility in intact organisms, and the pattern of Rho activity during motile cell behaviors of EMT has not been determined in any system. Here, we image endogenous active Rho during EMT in vivo, and analyze effects of Rho and Rho-kinase (ROCK) manipulation on cell motility in vivo. We show that Rho is activated in a discrete apical region of premigratory neural crest cells during EMT, and Rho-ROCK signaling is essential for apical detachment and generation of motility within the neuroepithelium, a process that has been poorly understood. Furthermore, we find that Arhgap1 restricts Rho activation to apical areas, and this restriction is necessary for detachment. Our results provide new insight into mechanisms controlling local Rho activation and how it affects dynamic cell behaviors and actomyosin contraction during key steps of EMT in an intact living organism.
Update of the Standard Numbering Scheme for Class B β-Lactamases (2004)

peer reviewed
5-HT1A Receptor hypersensitivity in migraine is suggested by the m-chlorophenylpiperazine test (1998)

Involvement of the cerebral serotoninergic system has been invoked to explain the origin of the pain and the vascular phenomena in migraine. To further investigate the type of cerebral serotonin receptors that may be altered in migraine, the prolactin (PRL) and cortisol responses to m-chlorophenylpiperazine (mCPP), a selective 5-HT1A,-5-HT(2A/C) receptor agonist, were monitored in 12 patients suffering from migraine without aura and in 14 matched healthy controls. Each subject underwent two challenges, one with mCPP (0.5 mg/kg) and the other with placebo (orally) using a double-blind crossover design. Anxiety level was measured by the State Trait Anxiety Inventory. Migraine patients had a greater PRL response to mCPP (p = 0.05) and greater anxiety (p < 0.01) than controls; cortisol response to mCPP did not differ suggesting that 5-HT2C receptors are normal in migraine. Augmented PRL response to mCPP could derive from 5-HT1A receptor hypersensitivity, perhaps as as a consequence of anxiety due to pain expectation. Cerebral 5-HT1A hypersensitivity could also explain the increased occurrence of migraine attacks during anxiety.
Improved Antigen Yield in Pandemic H1N1 (2009) Candidate Vaccine Viruses with Chimeric Hemagglutinin Molecules (2011)

The candidate pandemic H1N1 vaccine virus NIBRG-121 was derived by reverse genetics and comprises the hemagglutinin (HA) and neuraminidase (NA) genes from A/California/7/2009 (CAL) on an A/Puerto Rico/8/34 (PR8) backbone. NIBRG-121 was found to grow poorly in eggs, compared to seasonal H1N1 candidate vaccine viruses. Based on our previous study with H5N1 candidate vaccine viruses, we generated two new viruses with chimeric PR8/CAL HA genes. Here we show that these new viruses have considerably improved growth in eggs and are therefore better candidate vaccine viruses for use in production of pandemic H1N1 (2009) vaccine.
In Vitro Evaluation of the Heparin‐Coated Gyro C1E3 Blood Pump (2001)

Abstract: The blood‐contacting surface, mainly composed of polycarbonate, of the Gyro C1E3 pump was modified using plasma glow discharge to introduce a carboxyl functional group, coated with a base layer of polyethyleneimine as a linker, and coupled with heparin by multi‐ionic binding to enhance blood compatibility. A relative surface content of 3.7% sulfur, which demonstrated heparin immobilization on the polycarbonate substrate, was observed on x‐ray photoelectron spectroscopy, and a initial bioactivity of approximately 88.5 ± 7.3 mIU/cm 2 was obtained by the chromogenic method for antifactor Xa assay. Furthermore, in vitro observation of platelet and fibrin adherence using bovine blood under dynamic flow conditions for 6 h revealed that the multi‐ionically heparinized Gyro C1E3 had significantly stronger antithrombogenecity than the noncoated original type which was evaluated as a good hemocompatible blood pump for clinical use. Not only the Gyro C1E3 but also the ionically heparin‐coated Gyro pump are expected to be thromboresistant in clinical use.
A Broadly Neutralizing Human Monoclonal Antibody against gp41 of Human Immunodeficiency Virus Type 1 (1994)

We have established a hybridoma clone, designated 2F5, secreting a neutralizing human monoclonal antibody (MAb) specific for gp41 of human immunodeficiency virus type 1 (HIV-1). The epitope of MAb 2F5 was mapped to amino acid sequence Glu-Leu-Asp-Lys-Trp-Ala on the ectodomain of gp41. In this study different in vitro test systems were used to characterize the neutralizing properties of MAb 2F5. In syncytium inhibition assays, fusion inhibition experiments, and neutralization assays on different HIV-susceptible cells (H9, U937, and peripheral blood mononuclear cells) MAb 2F5 showed broad-spectrum neutralizing capacity against HIV-1 laboratory isolates IIIB, MN, RF, and SF2. In addition, primary isolates from AIDS patients were also neutralized.
Recombinant protein expression and solubility screening in Escherichia coli: a comparative study (2006)

Producing soluble proteins in Escherichia coli is still a major bottleneck for structural proteomics. Therefore, screening for soluble expression on a small scale is an attractive way of identifying constructs that are likely to be amenable to structural analysis. A variety of expression-screening methods have been developed within the Structural Proteomics In Europe (SPINE) consortium and to assist the further refinement of such approaches, eight laboratories participating in the network have benchmarked their protocols. For this study, the solubility profiles of a common set of 96 His(6)-tagged proteins were assessed by expression screening in E. coli. The level of soluble expression for each target was scored according to estimated protein yield. By reference to a subset of the proteins, it is demonstrated that the small-scale result can provide a useful indicator of the amount of soluble protein likely to be produced on a large scale (i.e. sufficient for structural studies). In general, there was agreement between the different groups as to which targets were not soluble and which were the most soluble. However, for a large number of the targets there were wide discrepancies in the results reported from the different screening methods, which is correlated with variations in the procedures and the range of parameters explored. Given finite resources, it appears that the question of how to most effectively explore ;expression space' is similar to several other multi-parameter problems faced by crystallographers, such as crystallization.
Morphological and electrical properties of rf sputtered Y2O3-doped ZrO2 thin films (1976)

The structural, compositional, and electrical properties of rf sputter-deposited Y2O3-doped ZrO2 films have been investigated as a function of sputtering conditions. The results show that the application of an rf substrate bias during deposition has a large effect on both the morphological and electrical properties of the films. Auger electron spectroscopy, electron diffraction, and scanning-electron-fractography results show that films deposited at P=20 mTorr (2.67 Pa), VT=−500 V, and VS=−40 V are nearly stoichiometric, have a cubic crystal structure, and a relatively equiaxed microstructure. The results of electrical measurements indicate that films grown under these sputtering conditions have an ionic transference number which is nearly zero below 100 °C and rises to approximately 0.4 at 200 °C.
Fermi level and surface barrier of GaxIn1−xAs alloys (1981)

The surface Fermi level of n-type GaxIn1−xAs alloys is displaced as a function of x from above the conduction band minimum of InAs to the lower half of the band gap of GaAs. Fermi-level pinning is attributed to an As vacancy-related energy level located ∼0.5 eV above the valence band and invariant with x.
Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote (2013)

Some microbial eukaryotes, such as the extremophilic red alga Galdieria sulphuraria, live in hot, toxic metal-rich, acidic environments. To elucidate the underlying molecular mechanisms of adaptation, we sequenced the 13.7-megabase genome of G. sulphuraria. This alga shows an enormous metabolic flexibility, growing either photoautotrophically or heterotrophically on more than 50 carbon sources. Environmental adaptation seems to have been facilitated by horizontal gene transfer from various bacteria and archaea, often followed by gene family expansion. At least 5% of protein-coding genes of G. sulphuraria were probably acquired horizontally. These proteins are involved in ecologically important processes ranging from heavy-metal detoxification to glycerol uptake and metabolism. Thus, our findings show that a pan-domain gene pool has facilitated environmental adaptation in this unicellular eukaryote.
A Digital Telecine Processing Channel (1979)

Digital processing of signals has advantages of improved stability, accuracy, and reliability. There are two problems that might arise in a digital processing channel. One is that gamma correction increases the visibility of contouring due to quantizing in dark areas of the picture so that more than the usual eight bits per sample are needed. The other is that nonlinear processing in gamma correctors and clippers may give rise to beats causing coarse moire patterns on the output picture. A digital telecine processing channel was built to examine these problems. It incorporates a range-changing analog-to-digital converter which gives improved coding resolution for low level signals. The channel performs the operations of gamma correction, color masking, and aperture correction. A subjective test has shown that ten bits per sample are needed in the green channel when signals are digitally coded before gamma correction. The generation of moire patterns due to nonlinear processing has been shown not to be significant in practice.
A phase II trial of IPI-504 (retaspimycin hydrochloride), a novel Hsp90 inhibitor, in patients with relapsed and/or refractory stage IIIb or stage IV non-small cell lung cancer (NSCLC) stratified by EGFR mutation status (2009)

8073 Background: IPI-504 (retaspimycin hydrochloride) is a potent, water-soluble heat shock protein 90 (Hsp90) inhibitor. IPI-504 causes the degradation of mutated epidermal growth factor receptor (mtEGFR) kinase and cMET in NSCLC cell lines. IPI-504 also significantly reduces tumor growth in murine xenograft models, including tumors resistant to tyrosine kinase inhibitors (TKIs). Methods: This phase II trial is investigating the safety and antitumor activity of intravenous (IV) 400 mg/m 2 IPI-504 given twice weekly for 2 out of 3 weeks. Eligible patients (pts) had stage IIIb (w/ malignant effusion) or stage IV NSCLC that progressed after TKI treatment. EGFR mutation analysis was performed on all pts. Two cohorts (n=10 each) were initially enrolled and stratified by EGFR status (mtEGFR or wtEGFR). Planned cohort expansion to 29 pts occurred if ≥ 1 pt from that cohort had a best response of stable disease (SD) ≥12 wks or partial response (PR). Pts were evaluated for safety and RECIST response every 6 weeks. Central, independent radiology review was performed for all imaging studies. Results: 43 pts have been enrolled: 10 mtEGFR, 17 wtEGFR, 12 pending analysis, and 4 EGFR-failed samples. 19 pts are currently on study. Median age is 62 yrs (range 31–77). Median no. of prior therapies is 3. Common related adverse events are fatigue, nausea, and diarrhea. Anti-tumor activity has been observed, see table. Both cohorts have been expanded. Conclusions: IPI-504 monotherapy has been well tolerated, with evidence of anti-tumor activity, particularly and unexpectedly in the wtEGFR cohort. These data suggest that IPI-504 may have antitumor activity in heavily pretreated pts with advanced NSCLC. Further evaluation continues in the expansion phase of the trial. [Table: see text] [Table: see text]
A 0.72 mu m/sup 2/ recessed STC (RSTC) technology for 256 Mbit DRAMs using quarter-micron phase-shift lithography (2003)

A recessed stacked capacitor (RSTC) structure to achieve both fine-pattern delineation and high cell capacitance is presented. Using a RSTC structure, an experimental memory array with 0.25 mu m phase-shift lithography and CVD-W plate technology has been fabricated. A 25-fF/cell capacitance was obtained in a 0.72 mu m/sup 2/ cell.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Anti-sense phosphorothioate oligonucleotides have both specific and non-specific effects on cells containing human papillomavirus type 16 (1991)

A range of specific nuclease resistant phosphorothioate oligodeoxynucleotides (S-oligos) complementary to mRNA of human papillomavirus type 16 (HPV16), were tested for their ability to inhibit cell proliferation and to alter the level of HPV-specific mRNA and proteins in CaSki cells, a human cervical carcinoma cell line containing HPV16 DNA. Only certain of the S-oligos to the viral upstream regulatory region (URR) and the early viral open reading frames (ORF), E6 and E7, were found to display any activity on the cells. These S-oligos were found to exhibit potent anti-proliferative activity at concentrations between 0.25 microM and 20 microM, inhibiting the uptake of [3H]-thymidine into CaSki cells by up to 90% at higher concentrations. The rate of synthesis of E6 and E7 proteins and the steady state level of the E7 protein however remained largely unchanged. E7 protein exhibited a greater decrease in phosphorylation in the presence of only one of the antisense oligos. Other S-oligos including a random sequence, unmodified sequences or O-methylphosphonate modified oligos, had no specific effect on the cells. The results imply that the anti-sense S-oligonucleotides had both specific anti-HPV16 and other non-specific effects on cell proliferation and synthesis of virally encoded proteins.
A Family of Well-Clear Boundary Models for the Integration of UAS in the NAS (2014)

The FAA-sponsored Sense and Avoid Workshop for Unmanned Aircraft Systems (UAS) defines the concept of sense and avoid for remote pilots as "the capability of a UAS to remain well clear from and avoid collisions with other airborne traffic." Hence, a rigorous definition of well clear is fundamental to any separation assurance concept for the integration of UAS into civil airspace. This paper presents a family of well-clear boundary models based on the TCAS II Resolution Advisory logic. For these models, algorithms that predict well-clear violations along aircraft current trajectories are provided. These algorithms are analogous to conflict detection algorithms but instead of predicting loss of separation, they predict whether well-clear violations will occur during a given lookahead time interval. Analytical techniques are used to study the properties and relationships satisfied by the models.
IL-1 induction-capacity of defined lipopolysaccharide partial structures. (1989)

Natural and synthetic lipid A as well as natural and synthetic oligosaccharide partial structures of LPS were examined in dose-response experiments to define the minimal structure necessary for IL-1 induction and release in cultures of human mononuclear cells. Wild type LPS (S. abortus equi) and rough mutant LPS was active in minimal-doses of 1 to 100 pg/ml, whereas synthetic heptaacyl and hexaacyl lipid A (Salmonella minnesota and Escherichia coli lipid A, respectively) induced IL-1 in minimal-doses of 100 to 1,000 pg/ml and 10 to 1,000 pg/ml, respectively. Nanogram amounts (0.1 to 10 ng/ml) of synthetic monodephospho partial structures of E. coli lipid A were necessary for IL-1 induction. Synthetic pentaacyl partial structures induced IL-1 very weakly. Synthetic tetraacyl and bisacyl partial structures lacking non-hydroxylated fatty acids were not active. Compared to LPS million-fold higher doses of natural and synthetic 3-deoxy-D-manno-octulosonic acid containing core oligosaccharides were necessary for IL-1 induction. Dose-response investigations with LPS and natural or synthetic partial structures established the following hierarchy in IL-1 induction-capacity: LPS greater than lipid A much greater than lipid A partial structures greater than core oligosaccharides greater than oligoacyl lipid A. Lipid A was shown here to be the portion of LPS mainly responsible for induction of IL-1 activity. The high potency of lipid A in inducing IL-1 release and the failure of the precursor Ia of lipid A to induce IL-1 production and release was also observed measuring intracellular IL-1 activity after freeze-thawing the cells. Levels of IL-1 beta mRNA in extracts of mononuclear cells correlated with biologic activity. In co-incubation experiments, precursor Ia of lipid A produced dose-dependent inhibition of production and release of IL-1 activity induced by lipid A or LPS, but not by Staphylococcus epidermidis or PHA. Incubation of cells with precursor Ia for 1h, followed by a medium change and further incubation of stimulus without precursor Ia of lipid A also resulted in inhibition. We conclude that lipid A is the main portion of LPS responsible for induction of IL-1, and that specific activation- and/or binding-mechanisms are involved in stimulation of cells with LPS and/or lipid A.
The cell biology ofListeria monocytogenesinfection (2002)

Listeria monocytogenes has emerged as a remarkably tractable pathogen to dissect basic aspects of cell biology, intracellular pathogenesis, and innate and acquired immunity. In order to maintain its intracellular lifestyle, L. monocytogenes has evolved a number of mechanisms to exploit host processes to grow and spread cell to cell without damaging the host cell. The pore-forming protein listeriolysin O mediates escape from host vacuoles and utilizes multiple fail-safe mechanisms to avoid causing toxicity to infected cells. Once in the cytosol, the L. monocytogenes ActA protein recruits host cell Arp2/3 complexes and enabled/vasodilator-stimulated phosphoprotein family members to mediate efficient actin-based motility, thereby propelling the bacteria into neighboring cells. Alteration in any of these processes dramatically reduces the ability of the bacteria to establish a productive infection in vivo.