gebhart/patrepeval huggingface dataset:
Yeast metabolic chassis designs for diverse biotechnological products (2016)

The diversity of industrially important molecules for which microbial production routes have been experimentally demonstrated is rapidly increasing. The development of economically viable producer cells is, however, lagging behind, as it requires substantial engineering of the host metabolism. A chassis strain suitable for production of a range of molecules is therefore highly sought after but remains elusive. Here, we propose a genome-scale metabolic modeling approach to design chassis strains of Saccharomyces cerevisiae - a widely used microbial cell factory. For a group of 29 products covering a broad range of biochemistry and applications, we identified modular metabolic engineering strategies for re-routing carbon flux towards the desired product. We find distinct product families with shared targets forming the basis for the corresponding chassis cells. The design strategies include overexpression targets that group products by similarity in precursor and cofactor requirements, as well as gene deletion strategies for growth-product coupling that lead to non-intuitive product groups. Our results reveal the extent and the nature of flux re-routing necessary for producing a diverse range of products in a widely used cell factory and provide blueprints for constructing pre-optimized chassis strains.
Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin. (1986)

Model calculations are performed to evaluate the utility of molecular dynamics with NMR interproton distance restraints for determining the three-dimensional structure of proteins. The system used for testing the method is the 1.5-A resolution crystal structure of crambin (a protein of 46 residues) from which a set of 240 approximate interproton distances of less than 4 A are derived. The convergence properties of the method are examined by using different dynamics protocols and starting from two initial structures; one is a completely extended beta-strand, and the other has residues 7-19 and 23-30 in the form of alpha-helices (as in the crystal structure) with the remaining residues in the form of extended beta-strands. In both cases global and local convergence to the correct final structure is achieved with rms atomic differences between the restrained dynamics structures and the crystal structure of 1.5-2.1 A for the backbone atoms and 2.1-2.8 A for all atoms; the averaged structure has backbone and all atom rms deviations of 1.3 and 1.9 A, respectively. Further, it is shown that a restrained dynamics structure with significantly larger deviations (i.e., 5.7 A for the backbone atoms) can be characterized as incorrect, independent of a knowledge of the crystal structure.
ACCURACY ANALYSIS OF KINECT DEPTH DATA (2012)

Abstract. This paper presents an investigation of the geometric quality of depth data obtained by the Kinect sensor. Based on the mathematical model of depth measurement by the sensor a theoretical error analysis is presented, which provides an insight into the factors influencing the accuracy of the data. Experimental results show that the random error of depth measurement increases with increasing distance to the sensor, and ranges from a few millimetres up to about 4 cm at the maximum range of the sensor. The accuracy of the data is also found to be influenced by the low resolution of the depth measurements.
Yield pressure: a new concept in the evaluation of GERD? (1996)

This study evaluates the yield pressure at the gastroesophageal junction in a group of 73 patients undergoing diagnostic endoscopy and in another group of 82 patients during the course of manometry for suspected GERD. The group included 17 patients who had previously undergone a successful Nissen fundoplication and eight patients who had a failed Nissen fundoplication. Air is insufflated into the stomach, and a water perfused pressure transducer is used to detect intragastric pressure. The pressure at which the cardia was seen to open at endoscopy, or when a common cavity phenomenon was detected at manometry, was taken as the opening pressure. Yield pressure was calculated as the difference between the opening pressure of the cardia and the resting gastric pressure. Results indicated a significant decrease in yield pressure in 65 patients with esophagitis compared with 65 patients with no evidence of reflux or esophagitis. A significant inverse correlation was found between yield pressure and the size of the hiatus hernia noted in these patients. There was also a correlation between valvular appearance of the cardia at endoscopy and the yield pressure. A progressive decrease in yield pressure occurred with an increasing deterioration in the physical appearance of the valve. There was no significant relationship found between yield pressure and lower esophageal sphincter (LES) pressure or intra-abdominal length. A small but significant relationship was found between yield pressure and acid exposure of the lower esophagus. The 17 patients with a successful Nissen showed a significantly increased yield pressure to supranormal values. In contrast, the eight patients with a failed Nissen had yield pressures within the range of the patients with esophagitis. In eight patients, yield pressure was measured by both manometry and endoscopy and showed no significant differences between the two methods.
Comparative effects of dietary nucleoside-nucleotide mixture and its components on endotoxin induced bacterial translocation and small intestinal injury in protein deficient mice. (1996)

These results suggest that dietary nucleosides and nucleotides are essential nutrients for intestinal repair; nucleotides or cytidine provide a better response.
DR-Scan: Dual-Rail Asynchronous Scan DfT and ATPG (2018)

Due to many state-holding elements in asynchronous circuits, many faults need two-pattern tests. This paper presents a test methodology (DR-scan) for dual-rail asynchronous circuits. Our design for testability is a full-scan, clock-less technique that supports both one-pattern and two-pattern tests for single stuck-at faults. DR-scan is able to test memory elements in dual-rail logic without breaking local feedback loops. To reduce test time, we choose a minimum set of selected test configurations (TCs). If there are more than one selected TCs, we need to split scan latches into multiple scan chains. To apply two-pattern tests, we partition the circuit using vertex coloring. With our test methodology, we can apply traditional full-scan automatic test pattern generation (ATPG) to generate two-pattern tests with high test coverage. Experimental results show our methodology can achieve test coverage up to nearly 94% for various asynchronous circuits.
Advanced techniques for target discrimination using laser speckle (1992)

II A new high-resolution imaging technique known as wavelength decorrelation is demonstrated in the laboratory for measuring target shape and estimating surface-scattering properties. In these demonstrations, the target is flood illuminated with a frequency-scanning Ti:sapphire ring laser. As the laser frequency changes, the speckle pattern in the backscattered light appears to boil; the time-varying intensity at a point in this pattern carries information about the target&apos;s range-resolved laser radar cross section U(z). A range resolution of better than 1 mm is demonstrated. A theoretical analysis ofwavelength decorre1ation is also presented, including the mathematical framework for predicting wavelength-decorrelation signatures. An additional technique known as speckle tracking is described for measuring a target&apos;s angular dynamics. THE LASER SPECKLE LABORATORY at Lincoln Laboratory was established in 1990 to study high-resolution discrimination techniques based on laser speckle. These techniques allow us to
Triple negative breast cancer - current status and prospective targeted treatment based on HER1 (EGFR), TOP2A and C-MYC gene assessment (2009)

HER1 belonging to the HER family of receptors plays an important role in cell proliferation, migration and protection against apoptosis. HER1 protein could be targeted by monoclonal antibodies and/or tyrosine kinase inhibitors (TKIs). Given signal pathway complexity and HER family member cooperation, it may be better to simultaneously target a number of these receptors (e.g. HER1/HER2 by lapatinib). Thus, HER1 assessment could reveal a particular breast cancer patient group with probably good response to HER1 targeted therapy. TOP2A gene, encoding topoisomerase II alpha (target for anthracyclines) is predictive of response to anthracycline therapy. TOP2A aberrations (amplification, deletion) are found in up to approximately 30-90 % of HER2 amplified breast cancer and amplifications are more common than deletions. Recent publications describe TOP2A amplification also in 2.7-8.8 % HER2 nonamplified breast cancers. Patients with a pathologic complete response to anthracycline based neoadjuvant chemotherapy had a good overall prognosis regardless of molecular subtype of breast cancer. These results suggest that particularly tumors with a complete pathological response to anthracyclines could have TOP2A amplification. C-MYC encodes nuclear DNA binding proteins that regulate proliferation and apoptosis; amplification is associated with poor prognosis and hormonally negative breast carcinoma.
A Method of Measurement of the Pitch and Refractive Indices of Cholesteric Liquid Crystals Using Selective Reflections and Total Reflections (1975)

It is proposed that the pitch of the spiral structure and the refractive indices of cholesteric liquid crystals can be determined separately by using selective reflections and total reflections. This method is effective when the pitch is comparable with or shorter than the wavelength of visible light. In such a case, the "Cano wedge" method is difficult. Using the values of the pitch and refractive indices obtained by this method, the incident angle dependence of light transmission was calculated and compared with experimental results in order to examine the effectiveness of this method.
Biological characterization of a novel antitumor quinolone. (1995)

A-84441, a potent new antitumor quinolone, was active in vitro and in vivo against murine and human tumors. A-84441, a prodrug, was comparable in potency to the parent compound with an IC50 range of 0.03-0.49 microgram/ml against a panel of murine and human tumor cell lines. The parent compound bound mammalian DNA in a magnesium-dependent manner and caused inhibition of DNA and RNA synthesis. A-84441 produced a significant increased life span and cures in three lines of i.p. implanted murine tumors. A-84441 was active against seven of nine solid tumors including s.c. murine tumors and human tumor xenografts. The compound appeared to be more active when administered i.v. compared to i.p. injection. Antitumor efficacy was little effected by treatment schedule, although multiple divided dosing was generally more effective than single dose treatment. A-84441 was over 10-fold-more active against murine leukemic cells than against normal murine bone marrow cells. The acute toxicity of A-84441 following single or multiple dosing ranged between 11 and 50 mg/kg dependent on schedule of administration when given by i.v. or i.p. route. The agent had no apparent toxicity or efficacy when administered p.o.
Mapping the Epitope in Cadherin-like Receptors Involved inBacillus thuringiensis Cry1A Toxin Interaction Using Phage Display (2001)

In susceptible lepidopteran insects, aminopeptidase N and cadherin-like proteins are the putative receptors for Bacillus thuringiensis (Bt) toxins. Using phage display, we identified a key epitope that is involved in toxin-receptor interaction. Three different scFv molecules that bind Cry1Ab toxin were obtained, and these scFv proteins have different amino acid sequences in the complementary determinant region 3 (CDR3). Binding analysis of these scFv molecules to different members of the Cry1A toxin family and to Escherichia coli clones expressing different Cry1A toxin domains showed that the three selected scFv molecules recognized only domain II. Heterologous binding competition of Cry1Ab toxin to midgut membrane vesicles from susceptible Manduca sexta larvae using the selected scFv molecules showed that scFv73 competed with Cry1Ab binding to the receptor. The calculated binding affinities (K(d)) of scFv73 to Cry1Aa, Cry1Ab, and Cry1Ac toxins are in the range of 20-51 nm. Sequence analysis showed this scFv73 molecule has a CDR3 significantly homologous to a region present in the cadherin-like protein from M. sexta (Bt-R(1)), Bombyx mori (Bt-R(175)), and Lymantria dispar. We demonstrated that peptides of 8 amino acids corresponding to the CDR3 from scFv73 or to the corresponding regions of Bt-R(1) or Bt-R(175) are also able to compete with the binding of Cry1Ab and Cry1Aa toxins to the Bt-R(1) or Bt-R(175) receptors. Finally, we showed that synthetic peptides homologous to Bt-R(1) and scFv73 CDR3 and the scFv73 antibody decreased the in vivo toxicity of Cry1Ab to M. sexta larvae. These results show that we have identified the amino acid region of Bt-R(1) and Bt-R(175) involved in Cry1A toxin interaction.
Purification and Characterization of Cinnamyl Alcohol Dehydrogenase from Tobacco Stems (1992)

Cinnamyl alcohol dehydrogenase (CAD) is an enzyme involved in lignin biosynthesis. In this paper, we report the purification of CAD to homogeneity from tobacco (Nicotiana tabacum) stems. The enzyme is low in abundance, comprising approximately 0.05% of total soluble cell protein. A simple and efficient purification procedure for CAD was developed. It employs three chromatography steps, including two affinity matrices, Blue Sepharose and 2'5' ADP-Sepharose. The purified enzyme has a specific cofactor requirement for NADP and has high affinity for coniferyl alcohol (K(m) = 12 micromolar) and coniferaldehyde (K(m) = 0.3 micromolar). Two different sized polypeptide subunits of 42.5 and 44 kilodaltons were identified and separated by reverse-phase HPLC. Peptide mapping and amino acid composition analysis of the polypeptides showed that they are closely related, although not identical.
Experiments on eliminating spherical aberration in electron guns using aspherical mesh lenses (1986)

Experiments on electron lenses incorporating aspherical meshes are described. Two guns with adjustable position of the aspherical mesh were constructed. In the first, the gap between the mesh and the focus electrode was variable; in the second, the gap was fixed and the mesh could be positioned relative to this gap. It was possible to change the spherical aberration from the usually positive value to zero or even to a negative value. This was verified by calculations. Spot size reductions by a factor of 3 were observed at the highest currents around 5 mA. The minimum spot sizes were obtained for a negative spherical aberration of the lens, which compensates the positive aberration of the object.
Protein Disulphide‐Isomerase Activity in Various Cells Synthesizing Collagen (1983)

A high correlation was found between the activities of protein disulphide isomerase and prolyl 4-hydroxylase when assayed in cells synthesizing various collagen types or the same type at markedly different rates. The highest activities of both enzymes were found in freshly isolated chick-embryo tendon and cartilage cells, intermediate activities in confluent cultures of human skin and lung fibroblasts and mouse 3T6 fibroblasts, and the lowest values in three human sarcoma cell lines, the difference in protein disulphide isomerase activity between the freshly isolated tendon cells and confluent simian-virus-40-transformed human lung fibroblasts being about 25-fold. All these differences are in good agreement with differences reported between the various cells in their rates of collagen synthesis. A great similarity was also found between the changes in the two enzyme activities measured per cell during the growth of 3T6 fibroblast cultures from the early logarithmic phase to the stationary phase. No correlation was found between protein disulphide isomerase activity and the type of collagen synthesized. The data suggest that protein disulphide isomerase may be involved in the formation of intra-chain and inter-chain disulphide bonds in procollagens, but there is no collagen type-related variation in this enzyme activity of a magnitude that would explain the marked differences in the rates of formation of inter-chain disulphide bonds between the various collagen types.
Functionalization of Deuterium- and Hydrogen-Terminated Diamond Particles with Mono- and Multilayers using Di-<i>tert</i>-Amyl Peroxide and Their Use in Solid Phase Extraction (2009)

In spite of an earlier report to the contrary and a different attempt that appears to have been unsuccessful, here we show an improved method that allows functionalization of hydrogen- and deuterium-terminated diamond with a dialkyl peroxide. In particular, hydrogen-/deuterium-terminated diamond particles were treated with neat di-tert-amyl peroxide (DTAP, C2H5C(CH3)2OOC(CH3)2C2H5) at elevated temperature. Surface changes were followed by X-ray photoelectron spectroscopy (XPS), diffuse reflectance Fourier transform infrared spectroscopy (DRIFT), and time-of-flight secondary ion mass spectroscopy (ToF-SIMS). After these reactions, the oxygen signal in the XPS spectra increased, the deuterium peak in the negative ToF-SIMS spectra decreased, and DRIFT showed C−H stretches, which were not previously present and which were similar to those of the precursor. In the C−H stretching region, the IR spectrum of adsorbed di-tert-amyl peroxide shows features that are red-shifted with respect to the IR spectrum of the precursor molecule. These trends are supported by density functional theory (DFT) calculations. These data are consistent with the chemisorption of fragments of di-tert-amyl peroxide primarily through ether linkages. The threshold for this reaction was determined by DRIFT to be ca. 95 °C. Multilayers of DTAP could be prepared by repeated exposure of the substrate to this reagent. Functionalized diamond particles were used in solid phase extraction.
The Merits of Different Units (1965)

As an industrial physicist I am not normally involved in arguments on the merits of teaching in m.k.s. or c.g.s. units. Recently, however, I was amazed to learn that, in at least one of our universities, students have to change back from the m.k.s. system of their schooldays to c.g.s. units. One of the principal reasons for the international adoption of the m.k.s. system in 1950 was that it would ease the problems of teachers and students.
Human Myeloid-derived Suppressor Cells are Associated With Chronic Immune Suppression After Severe Sepsis/Septic Shock (2016)

After SS/SS in humans, circulating MDSCs are persistently increased, functionally immunosuppressive, and associated with adverse outcomes. This novel observation warrants further studies. As observed in cancer immunotherapy, MDSCs could be a novel component in multimodality immunotherapy targeting detrimental inflammation and immunosuppression after SS/SS to improve currently observed dismal long-term outcomes.
A real-time digital signal processing system for bioelectric control of music (2003)

A new approach to creating music is described in which bioelectric signals detected by small disk electrodes placed on the skin are digitally processed and subsequently used to generate musical control sequences in the form of standard musical instrument digital interface, (MIDI) code. Several algorithms for the TMS320C25 are described in which signals from the muscles, the eyes, and the brain are processed and then used to control sound generation, localization, and timbre. Algorithm design focuses on extracting appropriate properties of the bioelectric signal to afford the user maximum control over the desired musical outcome. As a consequence, properties such as the long-term spectral content and the overall amplitude envelope of the signals are found to be more important than the stochastic short-term amplitude information. Applications of this device are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
<i>KiSS-1</i>/G Protein-Coupled Receptor 54 Metastasis Suppressor Pathway Increases Myocyte-Enriched Calcineurin Interacting Protein 1 Expression and Chronically Inhibits Calcineurin Activity (2005)

These data suggest a role for MCIP-1 and calcineurin inhibition in GPR54-mediated metastasis suppression in human cancers.
Aminosäuren, I. Darstellung von Aminosäuren aus Halogencarbonsäure‐Alkylestern mit Alkalimetallcyanaten<sup>1)</sup> (1981)

Abstract α‐ und ω‐Halogen‐ sowie α,ω‐Dihalogencarbonsäure‐alkylester reagieren mit Kaliumcyanat in Gegenwart von Alkoholen in dipolaren aprotischen Lösungsmitteln bei 80–120°C in guten Ausbeuten zu α‐ und ω‐(Alkoxycarbonylamino)‐ bzw. α,ω‐Bis(alkoxycarbonylamino)carbonsäurealkylestern (Mono‐ bzw. Diuerthane). Die hydrolytische Spaltung dieser Verbindungen mit einem wäßrigen Salzsäure/Ameisensäure‐Gemisch führt in meist quantitativen Ausbeuten zu den entsprechenden Aminosäure‐hydrochloriden.
"JaamSim" open-source simulation software (2013)

JaamSim is a free, open-source simulation package written in the Java programming language. It is a general-purpose dynamic simulator that supports discrete-event logic, continuous variables, and agent-based model design. A modern graphical user interface is provided that is comparable to commercial software, including drag-and-drop model building, an Input Editor, Output Viewer, and 3D graphics. Users are able to create their own palettes of high-level objects using standard Java and modern programming tools such as Eclipse. If you are writing hundreds or thousands of lines of code in a proprietary programming language provided with your commercial software, you would be far better off to write your code in Java and use JaamSim.
Human induced pluripotent stem cell region recognition in microscopy images using Convolutional Neural Networks (2017)

We present a deep learning architecture Convolutional Neural Networks (CNNs) for automatic classification and recognition of reprogramming and reprogrammed human Induced Pluripotent Stem (iPS) cell regions in microscopy images. The differentiated cells that possibly undergo reprogramming to iPS cells can be detected by this method for screening reagents or culture conditions in iPS induction. The learning results demonstrate that our CNNs can achieve the Top-1 and Top-2 error rates of 9.2% and 0.84%, respectively, to produce probability maps for the automatic analysis. The implementation results show that this automatic method can successfully detect and localize the human iPS cell formation, thereby yield a potential tool for helping iPS cell culture.