gebhart/patrepeval huggingface dataset:
Tumorigenic conversion of p53-deficient colon epithelial cells by an activated Ki-ras gene. (1998)

Distinct genetic abnormalities (loss-of-function mutations of APC and p53 and oncogenic activation of Ki-ras) are associated with specific stages of the sporadic, most common types of colorectal tumors. However, the inability to maintain primary colon epithelial cells in culture has hindered the analysis of the pathogenetic role of these abnormalities in colorectal tumorigenesis. We have now established primary cultures of epithelial cells from the colon crypts of p53-deficient mice; these cells are nontumorigenic as indicated by their failure to form colonies in soft agar and to grow as tumors in immunodeficient SCID mice and in immunocompetent syngeneic hosts. Upon ectopic expression of an activated Ki-ras gene, p53-deficient colon epithelial cells form colonies in soft agar and highly invasive subcutaneous tumors in both immunodeficient and immunocompetent mice. Ectopic expression of wild-type p53, but not of a DNA-binding-deficient mutant, markedly suppressed the colony-forming ability of the Ki-ras-transformed p53-deficient epithelial cells. Together, these findings establish a functional synergism in colorectal tumorigenesis dependent on the effects of an oncogenic Ki-ras in a p53-deficient background. This model of tumorigenic conversion of colon epithelial cells might be useful to identify genetic changes associated with disease progression and to evaluate the therapeutic response to conventional and novel anticancer drugs.
Ab initio inversion of structure and the lattice dynamics of a metallic glass: the case of Pd 40 Ni 40 P 20 (2019)

Abstract In this paper we infer the structure of Pd 40 Ni 40 P 20 from experimental diffraction data and ab initio interactions using ‘force enhanced atomic refinement’. Our model accurately reproduces known experimental signatures of the system and is more efficient than conventional melt-quench schemes. We critically evaluate the local order, carry out detailed comparisons to extended x-ray absorption fine structure experiments and also discuss the electronic structure. We thoroughly explore the lattice dynamics of the system, and describe a vibrational localized-to-extended transition and discuss the special role of P dynamics. At low energies P is fully contributing to extended modes, but at higher frequencies executes local motion reminiscent of a ‘rattler’ inside a cage of metal atoms. These highly localized vibrational states suggest a possible utility of these materials for thermoelectric applications.
Biodegradation of ionic liquids – a critical review (2015)

The importance of biodegradation data as part of the design of safer chemicals is presented using ionic liquids (ILs) as a model study. Structural features that promote/impede IL biodegradation, IL design strategies, methods of biodegradation analysis, properties of IL/surfactant derivatives and computational methods of predicting biodegradation are discussed. The importance of metabolite studies as part of biodegradation assays is highlighted. The relevance of applying the lessons learned developing biodegradable ILs to other chemical classes is proposed. A comprehensive appendix of IL biodegradation data published since 2010 (∼300 ILs) has been compiled.
Computational Analysis of Biochemical Systems: A Practical Guide for Biochemists and Molecular Biologists (2000)

Preface Introduction 1. Graphical representation of biochemical systems 2. Models of biochemical systems 3. From maps to equations 4. Computer simulation 5. Parameter estimation 6. Analytical steady-state evaluation 7. Sensitivity analysis 8. Case study 1 - Anaerobic fermentation pathway in Saccharomyces cerevisiae 9. Case study 2 - diagnosis and refinement of a model of the tricarboxylic acid cycle in Dictyostelium discoideum 10. Case study 3 - A sequence of models describing purine metabolism 11. Case study 4 - Algebraic analysis of the initial steps of the Glycolytic-Glycogenolytic pathway in perfused rat liver 12. Epilogue-Canonical modeling beyond biochemistry Appendix Hints and solutions References Author index Subject index.
Safety and efficacy of ketorolac tromethamine 0.4% ophthalmic solution in post-photorefractive keratectomy patients (2004)

Ketorolac 0.4% ophthalmic solution is safe and effective in reducing ocular pain when used 4 times daily for up to 4 days post PRK.
Overproduction, purification and characterization of the Escherichia coli ferritin (1993)

Recent studies have indicated that Escherichia coli possesses at least two iron-storage proteins, the haem-containing bacterioferritin and ferritin. The ferritin protein has been amplified 600-fold to 11-14% of total cell protein in a bfr mutant and purified to homogeneity with an overall yield of 13%. The cellular ferritin content remained relatively constant throughout the growth cycle and amplification was accompanied by a 2.5-fold increase in cellular iron content. The isolated ferritin contained 5-20 non-haem iron atoms/holomer and resembled the eukaryotic ferritins rather than the prokaryotic bacterioferritins in containing no haem. The 24 subunits of this ferritin (M(r) 19,400) assemble into a spherical protein shell (12 +/- 1 nm diameter, M(r) 465,000) which sequesters at least 2000 iron atoms in vitro to form an electron-dense iron core of 7.9 +/- 1 nm diameter. Electron-microscopic and Mössbauer spectroscopic studies with iron-loaded ferritin showed that the core can be either crystalline (ferrihydrite) or amorphous, depending on the absence or presence of phosphate, respectively. Mössbauer spectroscopy with intact E. coli revealed a novel-high spin Fe(II) component which is enhanced in bacteria amplified for ferritin but not in the parental strain. Western blotting showed that ferritin and bacterioferritin are immunologically distinct proteins. E. coli is thus an organism containing both a ferritin and a bacterioferritin and the relative roles of the two iron-storage proteins are discussed in this study.
Automatic high-precision self-calibration of camera-robot systems (2009)

In this article a new method is presented to obtain a full and precise calibration of camera-robot systems with eye-in-hand cameras. It achieves a simultaneous and numerically stable calibration of intrinsic and extrinsic camera parameters by analysing the image coordinates of a single point marker placed in the environment of the robot. The method works by first determining a rough initial estimate of the camera pose in the tool coordinate frame. This estimate is then used to generate a set of uniformly distributed calibration poses from which the object is visible. The measurements obtained in these poses are then used to obtain the exact parameters with CMA-ES (Covariance Matrix Adaptation Evolution Strategy), a derandomised variant of an evolution strategy optimiser. Minimal claims on the surrounding area and flexible handling of environmental and kinematical limitations make this method applicable to a range of robot setups and camera models. The algorithm runs autonomously without supervision and does not need manual adjustments. Our problem formulation is directly in the 3D space which helps in minimising the resulting calibration errors in the robot's task space. Both simulations and experimental results with a real robot show a very good convergence and high repeatability of calibration results without requiring user-supplied initial estimates of the calibration parameters.
Composition and Variation of the Gel Electrophoretic Fractions of Plasma, Cerebrospinal Fluid and Urine (1972)

The electrophoretic distribution of the 14 plasma components of decisive influence on the normal gel electrophoretic plasma patterns are presented. The genetic variants and aquired shifts in disease are outlined with comments on blurred and displaced bands as a result of intercation phenomenon of individual proteins. The common electrophoretic band patterns of cerebrospinal fluid and urine in health and disease are analysed.
Crushed cartilage in nasal recontruction (1986)

Experience when using crushed cartilage for restoration of the dorsal nasal contour is presented. The septal cartilage is used as fresh autogenous grafts and as preserved septal cartilage. Implantation of autogenous grafts is preferable. Bank cartilage, however, has the advantage of being easily available and of causing very little reaction in the host organism. Normally, it is absorbed very slowly and replaced by connective tissue, which retains most of the bulk and shape of the implant. The crushed material is pushed in over the undermined nasal dorsum by means of a syringe connected to a plastic tube. When the piston of the loaded syringe is depressed, the cartilage is injected and the crushed cartilage can be moulded under the skin and the shape maintained by a tight dressing. The cartilage serves as a padding, which covers bony defects, smooths out the irregularities of the bone and avoids the open roof syndrome as well as retracted scar formation between skin and bone.
Effect of dietary supplements on lean mass and strength gains with resistance exercise: a meta-analysis (2003)

The purpose of this study was to quantify which dietary supplements augment lean mass and strength gains during resistance training. Peer-reviewed studies between the years 1967 and 2001 were included in the analysis if they met a predetermined set of experimental criteria, among which were at least 3-wk duration and resistance-training 2 or more times a week. Lean mass and strength were normalized for meta-analysis by conversion to percent change per week and by calculating the effect size for each variable. Of the 250 supplements examined, only 6 had more than 2 studies that met the criteria for inclusion in the meta-analysis. Creatine and beta-hydroxy-beta-methylbutyrate (HMB) were found to significantly increase net lean mass gains of 0.36 and 0.28%/wk and strength gains of 1.09 and 1.40%/wk (P < 0.05), respectively. Chromium, dehydroepiandrosterone, androstenedione, and protein did not significantly affect lean gain or strength. In conclusion, two supplements, creatine and HMB, have data supporting their use to augment lean mass and strength gains with resistance training.
Broadband wavelength conversion in a silicon vertical-dual-slot waveguide (2017)

We propose a silicon waveguide structure employing silica-filled vertical-dual slots for broadband wavelength conversion, which can be fabricated using simple silicon-on-insulator technology. We demonstrate group-velocity dispersion tailoring by varying the width of the core, the slots and the side strips, and put forward a method to achieve spectrally-flattened near-zero anomalous group-velocity dispersion at telecom wavelengths. A proposed structure provides a group-velocity dispersion parameter β2 of −60 ps2/km with an e ective mode area Aeff of 0.075 µm2 at 1550 nm. This structure is predicted to significantly broaden the bandwidth of wavelength conversion via four-wave mixing, which is validated with experimentally measured 3 dB bandwidth of 76 nm.
<title>Image-based registration of ultrasound and magnetic resonance images: a preliminary study</title> (2000)

A number of surgical procedures are planned and executed based on medical images. Typically, x-ray computed tomography (CT) and magnetic resonance (MR) images are acquired preoperatively for diagnosis and surgical planning. In the operating room, execution of the surgical plan becomes feasible due to registration between preoperative images and surgical space where patient anatomy lies. In this paper, we present a new automatic algorithm where we use ultrasound (US) 2D B-mode images to register the preoperative MR image coordinate system with the surgical space which in our experiments is represented by the reference coordinate system of a DC magnetic position sensor. The position sensor is also used for tracking the position and orientation of the US images. Furthermore, we simulated patient anatomy by using custom-built phantoms. Our registration algorithm is a hybrid between fiducial- based and image-based registration algorithms. Initially, we perform a fiducial-based rigid-body registration between MR and position sensor space. Then, by changing various parameters of the rigid-body fiducial-based transformation, we produce an MR-sensor misregistration in order to simulate potential movements of the skin fiducials and/or the organs. The perturbed transformation serves as the initial estimate for the image-based registration algorithm, which uses normalized mutual information as a similarity measure, where one or more US images of the phantom are automatically matched with the MR image data set. By using the fiducial- based registration as the gold standard, we could compute the accuracy of the image-based registration algorithm in registering MR and sensor spaces. The registration error varied depending on the number of 2D US images used for registration. A good compromise between accuracy and computation time was the use of 3 US slices. In this case, the registration error had a mean value of 1.88 mm and standard deviation of 0.42 mm, whereas the required computation time was approximately 52 sec. Subsampling the US data by a factor of 4 X 4 and reducing the number of histogram bins to 128 reduced the computation time to approximately 6 sec. with a small increase in the registration error.
Retinal degeneration is slowed in transgenic rats by AAV-mediated delivery of FGF-2. (2000)

Transduction of retinal cells with AAV-FGF-2 reduces the rate of photoreceptor degeneration in an S334ter-4 animal model. Despite the lack of significantly increased ERG amplitudes from eyes expressing FGF-2, a greater number of surviving photoreceptors was demonstrated. Delivery of FGF-2 using recombinant AAV has potential as a therapy for retinal degeneration.
Prognostic significance of vascular endothelial cell growth factors -A, -C and -D in breast cancer and their relationship with angio- and lymphangiogenesis (2007)

Vascular endothelial cell growth factors (VEGF)-A, -C and -D have potent angio and lymphangiogenic functions in experimental models, although their role in the progression of human breast cancer is unclear. The aims of the current study were to examine the relationship between the expression of the aforementioned growth factors with the angio and lymphangiogenic characteristics of breast cancer, and to assess their suitability as potential prognostic factors. Paraffin-embedded sections of 177 primary invasive breast cancer, with complete clinical follow-up information for 10 years, were stained for VEGF-A, -C, -D, podoplanin and CD34 using standard immunohistochemical approaches. The expression of the growth factors was correlated with clinicopathological criteria and patients' survival. Lymph vessel density (LVD) and microvessel density (MVD) were assessed and correlated with expression of the growth factors. Vascular endothelial cell growth factor-A, -C and -D were highly expressed in 40, 37 and 42% of specimens, respectively. High expression of VEGF-A and - C, but not of -D, was associated with a higher LVD (P=0.013 and P=0.014, respectively), a higher MVD (P<0.001 and P=0.002, respectively), the presence of lymph node metastasis (P<0.001 and P<0.001, respectively), distant metastasis (P=0.010 and P=0.008, respectively) and a shorter Overall Survival (P=0.029 and 0.028, respectively). In conclusion, breast cancers that express high levels of VEGF-A and -C are characterised by a poor prognosis, likely through the induction of angio and lymphangiogenesis. Examination of expression of VEGF-A and -C in breast cancer may be beneficial in the identification of a subset of tumours that have a higher probability of recurrence and metastatic spread.
Recombinant FIXFc: a novel therapy for the royal disease? (2011)

Genetically engineered recombinant FIX fused to the Fc portion of immunoglobulin significantly extends FIX half-life, thereby decreasing the frequency of prophylactic infusions. This in turn may increase the adoption of, and adherence to, prophylaxis, leading to better outcomes for hemophilia B patients.
Cytokine profiles in spontaneously regressing basal cell carcinomas (2000)

These findings support a role for T-helper 1 type cytokines in mediating spontaneous regression of BCCs.
Genomic Signature-Based Identification of Influenza A Viruses Using RT-PCR/Electro-Spray Ionization Mass Spectrometry (ESI-MS) Technology (2010)

The emergence and rapid spread of the 2009 H1N1 pandemic influenza A virus (H1N1pdm) in humans highlights the importance of enhancing the capability of existing influenza surveillance systems with tools for rapid identification of emerging and re-emerging viruses. One of the new approaches is the RT-PCR electrospray ionization mass spectrometry (RT-PCR/ESI-MS) technology, which is based on analysis of base composition (BC) of RT-PCR amplicons from influenza ''core'' genes. Combination of the BC signatures represents a ''genomic print'' of an influenza A virus.
Biochemical sensors based on polymer microrings with sharp asymmetrical resonance (2003)

Photonic microresonators have great potential in the application of highly sensitive sensors due to high Q-factor resonances and steep slopes between zero and unity transmission. A microring resonator with increased resonance slopes is proposed by introducing two partially reflecting elements implemented by waveguide offsets. This configuration produces a Fano-resonant line shape and can greatly enhance the sensitivity of the sensor. Polystyrene microring resonators were fabricated by the nanoimprinting technique, and the optical spectra were measured in glucose solutions of different concentrations. The shift in resonant wavelength and variation of the normalized transmitted intensity are linearly related to the concentration of the glucose solution.
Directed evolution of glucose oxidase from Aspergillus niger for ferrocenemethanol‐mediated electron transfer (2007)

A directed evolution protocol was developed for glucose oxidase (GOx) from Aspergillus niger that mimics applications conditions and employs a well-known mediator, oxidized ferrocenemethanol, in a medium throughput screen (96-well plate format). Upon reduction, oxidized ferrocenemethanol shows a color change from blue to pale yellow that can be recorded at 625 nm. Under optimized screening conditions, a CV of less than 20% was achieved in 96-well microtiter plates. For validating the screening system, two mutant libraries of GOx were generated by standard error-prone PCR conditions (0.04 mM MnCl(2)) and Saccharomyces cerevisiae was employed as host for secreted GOx expression. Two screening of approximately 2000 GOx mutants yielded a double mutant (T30S I94V) with improved pH and thermal resistance. Thermal resistance at a residual activity of 50% was increased from 58 degrees C (wild type, WT) to 62 degrees C (T30S I94V) and pH stability was improved at basic pH (pH 8-11). K(m) for glucose remained nearly unchanged (20.8 mM WT; 21.3 mM T30S I94V) and k(cat) increased (69.5/s WT; 137.7/s T30S I94V).
Human H+ATPase a4 subunit mutations causing renal tubular acidosis reveal a role for interaction with phosphofructokinase-1 (2008)

The vacuolar-type ATPase (H+ATPase) is a ubiquitously expressed multisubunit pump whose regulation is poorly understood. Its membrane-integral a-subunit is involved in proton translocation and in humans has four forms, a1-a4. This study investigated two naturally occurring point mutations in a4's COOH terminus that cause recessive distal renal tubular acidosis (dRTA), R807Q and G820R. Both lie within a domain that binds the glycolytic enzyme phosphofructokinase-1 (PFK-1). We recreated these disease mutations in yeast to investigate effects on protein expression, H+ATPase assembly, targeting and activity, and performed in vitro PFK-1 binding and activity studies of mammalian proteins. Mammalian studies revealed complete loss of binding between the COOH terminus of a4 containing the G-to-R mutant and PFK-1, without affecting PFK-1's catalytic activity. In yeast expression studies, protein levels, H+ATPase assembly, and targeting of this mutant were all preserved. However, severe (78%) loss of proton transport but less decrease in ATPase activity (36%) were observed in mutant vacuoles, suggesting a requirement for the a-subunit/PFK-1 binding to couple these two functions. This role for PFK in H+ATPase function was supported by similar functional losses and uncoupling ratio between the two proton pump domains observed in vacuoles from a PFK-null strain, which was also unable to grow at alkaline pH. In contrast, the R-to-Q mutation dramatically reduced a-subunit production, abolishing H+ATPase function completely. Thus in the context of dRTA, stability and function of the metabolon composed of H+ATPase and glycolytic components can be compromised by either loss of required PFK-1 binding (G820R) or loss of pump protein (R807Q).
A novel pressure balanced microfluidic valve (2003)

A microfluidic valve capable of driving fluids under high (up to 10 atm) pressure is presented. The valve actuation is based on a principle of pressure compensation by means of an air chamber that supports a moving membrane. The air balances the fluid pressure, and then an electrostatic actuator can open the valve. This valve is designed with valve arrays in mind. In such configurations, it is useful for analysis, biology and medicine applications.
Evidence for efficacy of drugs affecting bone metabolism in preventing hip fracture. (1992)

Oestrogen, calcium, and calcitonins significantly decrease the risk of hip fracture. Short term intervention late in the natural course of osteoporosis may have significant effects on the incidence of hip fracture.
Development and Evaluation of a Combined WLAN and Inertial Indoor Pedestrian Positioning System (2009)

In this paper we have presented an indoor positioning system for pedestrians combining Wireless LAN fingerprinting with foot mounted inertial and magnetometer sensors. To achieve a system capable of real-time processing we have employed a hierarchical Bayesian filtering approach using cascaded extended Kalman filters. The accuracy of the combined system was quantitatively evaluated in a real building against ground-truth. Our results show that accuracy is much higher than using Wireless LAN fingerprinting alone; in our experiment we achieved a positioning error (standard deviation) of roughly 1.6 meters. The approach requires only minimal fingerprinting effort since the high accuracy is achieved by the support of the inertial-based step estimation in the overall estimation process.
Plant Molecular Biology Labfax (1993)

Plant Anatomy And Taxonomy Plant Nucleic Acids Plant Gene Index Plant Transformation Vectors Plant Selectable And Reporter Genes Plant Introns And Transposable Elements Plant Tissue Culture And Transformation Plant Organellar Targeting Sequences Chloroplast Molecular Biology Culture Methodology Gene Expression And PCR Techniques Appendix 1: Plant Molecular Biology Journals Appendix 2: General Molecular Biology Data Appendix 3: Molecular Biology Software
A new optimization based approach to experimental combination chemotherapy. (1995)

A new approach towards the design of optimal multiple drug experimental cancer chemotherapy is presented. Once an adequate model is specified, an optimization procedure is used in order to achieve an optimal compromise between after treatment tumor size and toxic effects on healthy tissues. In our approach we consider a model including cancer cell population growth and pharmacokinetic dynamics. These elements of the model are essential in order to allow less empirical relationships between multiple drug delivery policies, and their effects on cancer and normal cells. The desired multiple drug dosage schedule is computed by minimizing a customizable cost function subject to dynamic constraints expressed by the model. However, this additional dynamic wealth increases the complexity of the problem which, in general, cannot be solved in a closed form. Therefore, we propose an iterative optimization algorithm of the projected gradient type where the Maximum Principle of Pontryagin is used to select the optimal control policy.