gebhart/patrepeval huggingface dataset:
Vapor Pressure Osmometry Studies of Osmolyte−Protein Interactions:  Implications for the Action of Osmoprotectants in Vivo and for the Interpretation of “Osmotic Stress” Experiments in Vitro (2000)

To interpret or to predict the responses of biopolymer processes in vivo and in vitro to changes in solute concentration and to coupled changes in water activity (osmotic stress), a quantitative understanding of the thermodynamic consequences of interactions of solutes and water with biopolymer surfaces is required. To this end, we report isoosmolal preferential interaction coefficients (Gamma(mu1) determined by vapor pressure osmometry (VPO) over a wide range of concentrations for interactions between native bovine serum albumin (BSA) and six small solutes. These include Escherichia coli cytoplasmic osmolytes [potassium glutamate (K(+)Glu(-)), trehalose], E. coli osmoprotectants (proline, glycine betaine), and also glycerol and trimethylamine N-oxide (TMAO). For all six solutes, Gamma(mu1) and the corresponding dialysis preferential interaction coefficient Gamma(mu1),(mu3) (both calculated from the VPO data) are negative; Gamma(mu1), (mu3) is proportional to bulk solute molality (m(bulk)3) at least up to 1 m (molal). Negative values of Gamma(mu1),(mu3) indicate preferential exclusion of these solutes from a BSA solution at dialysis equilibrium and correspond to local concentrations of these solutes in the vicinity of BSA which are lower than their bulk concentrations. Of the solutes investigated, betaine is the most excluded (Gamma(mu1),(mu3)/m(bulk)3 = -49 +/- 1 m(-1)); glycerol is the least excluded (Gamma(mu1),(mu3)/m(bulk)3 = -10 +/- 1 m(-1)). Between these extremes, the magnitude of Gamma(mu1),(mu3)/m(bulk)3 decreases in the order glycine betaine >> proline >TMAO > trehalose approximately K(+)Glu(-) > glycerol. The order of exclusion of E. coli osmolytes from BSA surface correlates with their effectiveness as osmoprotectants, which increase the growth rate of E. coli at high external osmolality. For the most excluded solute (betaine), Gamma(mu1),(mu3) provides a minimum estimate of the hydration of native BSA of approximately 2.8 x 10(3) H(2)O/BSA, which corresponds to slightly less than a monolayer (estimated to be approximately 3.2 x 10(3) H(2)O). Consequently, of the solutes investigated here, only betaine might be suitable for use in osmotic stress experiments in vitro as a direct probe to quantify changes in hydration of protein surface in biopolymer processes. More generally, however, our results and analysis lead to the proposal that any of these solutes can be used to quantify changes in water-accessible surface area (ASA) in biopolymer processes once preferential interactions of the solute with biopolymer surface are properly taken into account.
Correlation between terminal restriction fragments and flow‐FISH measures in samples over wide range telomere lengths (2014)

The reviewed FF protocol appeared at least as suitable as the TRF method. Measures obtained by TRF can be affected by chromosome end variability, DNA fragmentation, incomplete digestion and unsuitable electrophoresis. In contrast, the FF technique analyses telomeric sequences confined to preserved nuclei thus overcome most previous limitations. As yet, however, the FF telomere measure cannot be performed together with immunophenotyping and/or generation study by the dye dilution method.
Mixed conducting ceramic hollow‐fiber membranes for air separation (2005)

Abstract Mixed conducting ceramic hollow‐fiber membranes, which possess an asymmetric structure, were prepared by a combined phase inversion and sintering technique where precursors of the hollow fibers were first spun using a polymer solution containing suspended LSCF powders and were then sintered at elevated temperature. By controlling the weight ratio of the LSCF powder to the polymer binder, sintering temperature, and time, the LSCF hollow fibers with gastight properties have been prepared and evaluated using an apparatus developed during the course of this study. Using the gastight LSCF hollow fibers, a membrane module was assembled for air separation. The performances of the module for air separation have been studied under various operating modes and at different temperatures and feed flow rates both experimentally and theoretically. The results reveal that the surface exchange reaction at the downstream side is much more important than that at the upstream side, especially for lower operating temperatures. The porous inner surface of the prepared LSCF hollow‐fiber membranes substantially favors the oxygen permeation when air is fed in the shell side of the membrane module. At high operating temperatures, oxygen permeation can be enhanced by the countercurrent flow operation. Vacuum operation favors the oxygen permeation kinetically in the LSCF hollow‐fiber membrane modules. © 2005 American Institute of Chemical Engineers AIChE J, 2005
Direct laser manipulation reveals the mechanics of cell contacts in vivo (2015)

Cell-generated forces produce a variety of tissue movements and tissue shape changes. The cytoskeletal elements that underlie these dynamics act at cell-cell and cell-ECM contacts to apply local forces on adhesive structures. In epithelia, force imbalance at cell contacts induces cell shape changes, such as apical constriction or polarized junction remodeling, driving tissue morphogenesis. The dynamics of these processes are well-characterized; however, the mechanical basis of cell shape changes is largely unknown because of a lack of mechanical measurements in vivo. We have developed an approach combining optical tweezers with light-sheet microscopy to probe the mechanical properties of epithelial cell junctions in the early Drosophila embryo. We show that optical trapping can efficiently deform cell-cell interfaces and measure tension at cell junctions, which is on the order of 100 pN. We show that tension at cell junctions equilibrates over a few seconds, a short timescale compared with the contractile events that drive morphogenetic movements. We also show that tension increases along cell interfaces during early tissue morphogenesis and becomes anisotropic as cells intercalate during germ-band extension. By performing pull-and-release experiments, we identify time-dependent properties of junctional mechanics consistent with a simple viscoelastic model. Integrating this constitutive law into a tissue-scale model, we predict quantitatively how local deformations propagate throughout the tissue.
Characterization of a cancer/testis (CT) antigen gene family capable of eliciting humoral response in cancer patients (2006)

Cancer/testis (CT) antigens are immunogenic proteins expressed in normal gametogenic tissues and in different types of tumors. CT antigens are promising candidates for cancer immunotherapy, and the identification of novel CT antigens is a prerequisite for the development of cancer vaccines. We have identified a CT antigen, named CTSP-1, with partial similarity to the breast differentiation antigen NY-BR-1. CTSP-1 presents several splicing and polyadenylation variants and has a very restricted expression pattern among normal tissues. CTSP-1 is exclusively expressed in normal testis and is aberrantly expressed in 47.6% (10 of 21) of tumor cell lines and in 44.4% (75 of 169) of tumors from different histological types. The highest percentages of positive expression were observed in melanomas (59.0%) followed by prostate (58.0%) and lung (57.0%) tumors. CTSP-1 is part of a highly conserved gene family, and members of this family also have a restricted expression pattern and similar protein structure. Antibodies against members of this gene family were detected in 10% (14 of 141) of plasma samples from patients with a wide spectrum of tumors. The highest percentages of antibody response were observed in patients with prostate (20.8%), thyroid (20.0%), and breast (16.6%) tumors. Because of its very restricted expression pattern in normal tissues and immunogenicity in different types of tumors, CTSP-1 should be considered a promising candidate for cancer immunotherapy.
Simultaneous amplitude-contrast and quantitative phase-contrast microscopy by numerical reconstruction of Fresnel off-axis holograms (1999)

We present a digital method for holographic microscopy involving a CCD camera as a recording device. Off-axis holograms recorded with a magnified image of microscopic objects are numerically reconstructed in amplitude and phase by calculation of scalar diffraction in the Fresnel approximation. For phase-contrast imaging the reconstruction method involves the computation of a digital replica of the reference wave. A digital method for the correction of the phase aberrations is presented. We present a detailed description of the reconstruction procedure and show that the transverse resolution is equal to the diffraction limit of the imaging system.
Lipopeptides as main ingredients for inhibition of fungal phytopathogens by B acillus subtilis/amyloliquefaciens (2014)

Some isolates of the Bacillus subtilis/amyloliquefaciens species are known for their plant protective activity against fungal phytopathogens. It is notably due to their genetic potential to form an impressive array of antibiotics including non-ribosomal lipopeptides (LPs). In the work presented here, we wanted to gain further insights into the relative role of these LPs in the global antifungal activity of B. subtilis/amyloliquefaciens. To that end, a comparative study was conducted involving multiple strains that were tested against four different phytopathogens. We combined various approaches to further exemplify that secretion of those LPs is a crucial trait in direct pathogen ward off and this can actually be generalized to all members of these species. Our data illustrate that for each LP family, the fungitoxic activity varies in function of the target species and that the production of iturins and fengycins is modulated by the presence of pathogens. Our data on the relative involvement of these LPs in the biocontrol activity and modulation of their production are discussed in the context of natural conditions in the rhizosphere.
Adapting side effects analysis for modular program model checking (2003)

There is a widely held belief that whole program analysis is intractable for large complex software systems, and there can be little doubt that this is true for program analyses based on model checking. Model checking selected program components that comprise a cohesive unit, however, can be an effective way of uncovering subtle coding errors, especially for components of multi-threaded programs. In this setting, one of the chief problems is how to safely approximate the behavior of the rest of the application as it relates to the unit being analyzed.Non-unit application components are collectively referred to as the environment. In this paper, we describe how points-to and side-effects analyses can be adapted to support generation of summaries of environment behavior that can be reified into Java code using special modeling primitives. The resulting abstract models of the environment can be combined with the code of the unit and then model checked against unit properties. We present our analysis framework, illustrate its flexibility in generating several types of models, and present experience that provides evidence of the scalability of the approach.
In ovarian cancer the prognostic influence of HER2/neu is not dependent on the CXCR4/SDF-1 signalling pathway (2007)

HER2/neu overexpression is a driving force in the carcinogenesis of several human cancers. In breast cancer the prognostic influence of HER2/neu was shown to be at least partly based on increased metastatic potential mediated by the chemokine-chemokine receptor pair SDF-1(CXCL12)/CXCR4. We wanted to evaluate the influence of HER2/neu on ovarian cancer prognosis and to investigate whether compromised survival would correlate with CXCR4 expression and/or SDF-1 abundance. Therefore, we analysed HER2/neu, CXCR4, and SDF-1 in 148 ovarian tumour samples by means of immunohistochemistry on tissue microarrays. Overexpression of HER2/neu was found in 27.6% of ovarian cancer tissues and in 15% of ovarian borderline tumours. In ovarian cancer patients, overexpression of HER2/neu correlated closely with overall survival (univariate hazard ratio (HR) 2.59, P=0.005; multiple corrected HR 1.92, P=0.074). In contrast, CXCR4 expression and SDF-1 abundance had no impact on overall survival, and both parameters were not correlated with HER2/neu expression. As expected, cytoplasmic CXCR4 expression and SDF-1 abundance correlated closely (P<0.0001). Our results confirm a univariate influence of HER2/neu expression on overall survival, which was completely independent of the expression of CXCR4 and the abundance of SDF-1, implying significant differences between the HER2/neu downstream pathways in ovarian cancer compared with breast cancer.
Supercoil Sequencing: A Fast and Simple Method for Sequencing Plasmid DNA (1985)

A method for obtaining sequence information directly from plasmid DNA is presented. The procedure involves the rapid preparation of clean supercoiled plasmid DNA from small bacterial cultures, its complete denaturation by alkali, and sequence determination using oligodeoxyribonucleotide-primed enzymatic DNA synthesis in the presence of dideoxynucleoside triphosphates. The advantages of the method include speed, simplicity, avoidance of additional cloning steps into single-stranded phage M13 vectors, and hence applicability to sequencing large numbers of samples.
Reverse Temperature Dependence of Circuit Performance in High- $\kappa$/Metal-Gate Technology (2009)

The temperature dependence of ring-oscillator delay of high-kappa /metal-gate (HKMG) and poly-Si/SiON technologies are analyzed. HKMG gate stacks drive significantly stronger threshold temperature dependence over poly-Si/SiON. This effect, together with the reduced mobility temperature sensitivity, result in higher drive current at elevated temperature for HKMG devices. This is in contrast to poly-Si/SiON technology where the low-driven current performance-limiting corner is typically at high temperature.
Long-term resource variation and group size: A large-sample field test of the Resource Dispersion Hypothesis (2001)

This is, we believe, the largest ever test of the RDH and builds on the long-term project that initiated part of the thinking behind the hypothesis. Support for predictions were mixed and depended on year and the method used to map territory borders. We suggest that within-habitat patchiness, as well as model assumptions, should be further investigated for improved tests of the RDH in the future.
Field emission from dense, sparse, and patterned arrays of carbon nanofibers (2002)

We compare the field emission characteristics of dense (109 nanofibers/cm2), sparse (107 nanofibers/cm2), and patterned arrays (106 nanofibers/cm2) of vertically aligned carbon nanofibers on silicon substrates. The carbon nanofibers were prepared using plasma-enhanced chemical vapor deposition of acetylene and ammonia gases in the presence of a nickel catalyst. We demonstrate how the density of carbon nanofibers can be varied by reducing the deposition yield through nickel interaction with a diffusion layer or by direct lithographic patterning of the nickel catalyst to precisely position each nanofiber. The patterned array of individual vertically aligned nanofibers had the most desirable field emission characteristics, highest apparent field enhancement factor, and emission site density.
Josephson current and proximity effect in Luttinger liquids (1996)

A theory describing a one-dimensional Luttinger liquid in contact with a superconductor is developed. Boundary conditions for the fermion fields describing Andreev reflection at the contacts are derived and used to construct a bosonic representation of the fermions. The Josephson current through a superconductor/Luttinger liquid/superconductor junction is considered for both perfectly and poorly transmitting interfaces. In the former case, the Josephson current at low temperatures is found to be essentially unaffected by electron-electron interactions. In the latter case, significant renormalization of the Josephson current occurs. The profile of the (induced) condensate wave function in a semi-infinite Luttinger liquid in contact with a superconductor is shown to decay as a power law, the exponent depending on the sign and strength of the interactions. In the case of repulsive (attractive) interactions the decay is faster (slower) than in their absence. An equivalent method of calculating the Josephson current through a Luttinger liquid, which employs the bosonization of the system as a whole (i.e., superconductor, as well as Luttinger liquid) is developed and shown to give the results equivalent to those obtained via boundary conditions describing Andreev reflection. \textcopyright{} 1996 The American Physical Society.
InP/InGaAs pin photodiode structure maximising bandwidth and efficiency (2003)

A new photodiode design that combines depleted and neutral absorption layers to minimise carrier travelling delay time for a given total absorption layer thickness is proposed. The fabricated photodiode has a thick (0.8 µm) InGaAs absorption layer and achieves a responsivity of 0.98 A/W at λ=1.55 µm while still maintaining a high bandwidth of 50 GHz.
Behavioral and Cerebellar Transmission Deficits in Mice Lacking the Autism-Linked Gene Islet Brain-2 (2010)

Deletion of the human SHANK3 gene near the terminus of chromosome 22q is associated with Phelan-McDermid syndrome and autism spectrum disorders. Nearly all such deletions also span the tightly linked IB2 gene. We show here that IB2 protein is broadly expressed in the brain and is highly enriched within postsynaptic densities. Experimental disruption of the IB2 gene in mice reduces AMPA and enhances NMDA receptor-mediated glutamatergic transmission in cerebellum, changes the morphology of Purkinje cell dendritic arbors, and induces motor and cognitive deficits suggesting an autism phenotype. These findings support a role for human IB2 mutation as a contributing genetic factor in Chr22qter-associated cognitive disorders.
The Drosophila GMII gene encodes a Golgi α-mannosidase II (1999)

In this paper we show the organisation of the Drosophila gene encoding a Golgi alpha-mannosidase II. We demonstrate that it encodes a functional homologue of the mouse Golgi alpha-mannosidase II. The Drosophila and mouse cDNA sequences translate into amino acid sequences which show 41% identity and 61% similarity. Expression of the Drosophila GMII sequence in CHOP cells produces an enzyme which has mannosidase activity and is inhibited by swainsonine and by CuSO(4.) In cultured Drosophila cells and in Drosophila embryos, antibodies raised against a C-terminal peptide localise this product mainly to the Golgi apparatus as identified by cryo-immuno electron microscopy studies and by antibodies raised against known mammalian Golgi proteins. We discuss these results in terms of the possible use of dGMII as a Drosophila Golgi marker.
Anti-CD16/CD30 bispecific antibody treatment for Hodgkin's disease: role of infusion schedule and costimulation with cytokines. (2001)

The natural killer cell-activating anti-CD16/CD30 bispecific monoclonal antibody (BiMAb) had shown efficacy in a Phase I/II trial of refractory Hodgkin's disease (HD). To gain additional information on clinical efficacy and to investigate the effects of different application schedules and the concomitant application of cytokines, we performed a second randomized pilot trial using this BiMAb in patients with refractory HD. Patients received 4 x 25 mg HRS-3/A9 either as a continuous infusion for 4 days or as a 1-h infusion every other day. In case of an objective response, retreatment was attempted after 4 weeks; in case of stable disease (SD), a second course was given after prestimulation with interleukin 2 and followed by granulocyte macrophage colony-stimulating factor s.c. A total of 16 heavily pretreated patients received one to four BiMAb courses. Overall, we observed one complete remission and three partial remissions lasting 5-9 months (three of four of these responses occurred after continuous BiMAb infusion) and four cases of SD for 3 to >6 months. Interleukin 2 pretreatment before the second BiMAb course resulted in a significant increase of circulating natural killer cells in all five patients treated. This coincided with the conversion of two cases of SD into one complete remission and one partial remission. HRS-3/A9-related side effects consisted of mild fever in only six patients. In summary, this second trial confirmed the antitumor efficacy of this BiMAb against HD and the minor toxicity of this BiMAb. Coadministration of cytokines might contribute to an augmented antitumor activity, and additional clinical trials are warranted to optimize this novel treatment modality.
Backlash compensation in discrete time nonlinear systems using dynamic inversion by neural networks (2002)

A dynamics inversion compensation scheme is designed for control of nonlinear discrete-time systems with input backlash. The compensator uses the backstepping technique with neural networks (NN) for inverting the backlash nonlinearity in the feedforward path. The technique provides a general procedure for using NN to determine the dynamics pre-inverse of an invertible discrete time dynamical system. A discrete-time tuning algorithm is given for the NN weights so that the backlash compensation scheme becomes adaptive, guaranteeing bounded tracking and backlash errors, and also bounded parameter estimates. A rigorous proof of stability and performance is given and a simulation example verifies the performance. Unlike standard discrete-time adaptive control techniques, no certainty equivalence assumption is needed.
Regions of High Antigenicity within the Hypothetical PPE Major Polymorphic Tandem Repeat Open‐Reading Frame, Rv2608, Show a Differential Humoral Response and a Low T Cell Response in Various Categories of Patients with Tuberculosis (2004)

The function of the PE/PPE families of proteins, which represent approximately 10% of the coding capacity of the Mycobacterium tuberculosis genome, has remained relatively unknown. We earlier described a PPE family member, Rv2430c, as an immunodominant antigen. We now report another PPE family gene, Rv2608, a member of the major polymorphic tandem repeat subfamily, for its ability to elicit a high humoral and a low T cell response. Rv2608 was also found to be polymorphic in different clinical isolates of M. tuberculosis, as determined by polymerase chain reaction-restriction fragment-length polymorphism analysis. A total of 51 clinically confirmed patients with tuberculosis (TB), belonging to 3 different categories--fresh infection (n=22), relapsed infection (n=21), and extrapulmonary infection (n=8)--and 10 healthy control subjects were included in the study. Recombinant Rv2608 protein showed positive reactivity to patients' serum samples. Enzyme-linked immunosorbent assays and T cell-proliferation assays with synthetic peptides corresponding to predicted regions of high antigenicity showed a predominantly humoral response in patients with relapsed TB. We additionally identified the Gly-X-Gly-Asn-X-Gly repeat motifs as being primarily responsible for eliciting a humoral immune response.
Didemnins: Antiviral and Antitumor Depsipeptides from a Caribbean Tunicate (1981)

Extracts of samples of a Caribbean tunicate (ascidian, sea squirt) of the family Didemnidae inhibit in vitro at low concentrations the growth of DNA and RNA viruses as well as L1210 leukemic cells. The active compounds isolated from the tunicate, didemnins A, B, and C, are depsipeptides, and didemnin B (a derivative of didemnin A) is the component active at the lowest concentration in inhibiting viral replication in vitro and P388 leukemia in vivo.