gebhart/patrepeval huggingface dataset:
MapIt: a case study for location driven knowledge discovery and mining (2013)

In the present world scenario, everybody is on the lookout for suitable housing options, each having different needs (e.g., the elderly are looking for safe, quiet neighbourhood, while students are looking for affordable apartments close to the university/school). For e.g., Craigslist currently does not have a map version, making the process of apartment searching a very long and laborious process. This creates a need for software that is significantly superior to current web search tools. We demonstrate the development of a tool which takes the Craigslist apartment listings on Google Maps. MapIt then integrates this functionality with the information collected from location based extraction of various web sources such as the city police blotter which makes apartment searching simpler and faster, helping the user to make a better decision. The paper also discusses the challenges that are faced in the development process, the raw and unstructured nature of the documents, the existence of geo/non-geo and geo-geo disambiguities and our approach in identifying the location of the apartment from informal text (geo-parsing and geo-tagging of content) to ensure maximum coverage of the listings.
New Insights into the Biosynthesis of Mycobacterial Lipomannan Arising from Deletion of a Conserved Gene (2007)

Genetic construction of a mutant strain (designated MSMEG4245) of Mycobacterium smegmatis, defective in a broadly conserved gene for a putative glycosyltransferase of the glycosyltransferase-C superfamily, results in a phenotype marked by the virtual absence of the phosphatidylinositol-containing lipomannan and lipoarabinomannan, replaced instead by a novel truncated form of lipomannan. The normal spectrum of phosphatidylinositol mannosides, long presumed precursors of these lipoglycans, was retained. Matrix-assisted laser desorption/ionization-time of flight/mass spectrometry of the mutated form of lipomannan shows a family of phosphatidylinositol-anchored lipomannans with from only 5 to 20 Manp residues as compared with lipomannan from the wild type strain consisting of 21-34 Manp residues but with few changes in the branching pattern. Thus, MSMEG4245 is apparently a key mannosyltransferase, required for the proper elongation of lipomannan to its normal state and subsequent synthesis of lipoarabinomannan. The corresponding ortholog in Mycobacterium tuberculosis H37Rv has been identified as Rv2174. This previously unrecognized feature of the biosynthesis of lipomannan/lipoarabinomannan allows a significant revision of structural and biosynthetic schemata and provides a molecular basis of selectivity in biosynthesis, as conferred by the MSMEG4245 gene.
A zero TCF band 13 SAW duplexer (2015)

RF spectrum is becoming a very sparse resource and several systems have to coexist while separated by small frequency gaps. For example, public safety band NS07 is 2.5 MHz below the LTE band 13 TX band. Standard SAW and typical Temperature Compensated SAW (TC-SAW) filters do not provide enough rejection in this band, especially within the required operating temperature range. The only way, when not using an NS07 compliant duplexer, to avoid noise radiation into the public safety band is to reduce their transmitted power when the public safety network is activated. To be compliant with NS07, the band 13 TX filter needs to have a very steep transition. Therefore, high quality factors as well as low temperature coefficient of frequency (TCF) are required. To reduce the TCF, the current standard approach is to bury the electrodes inside a silicon oxide overlay. Since silicon oxide has a positive TCF while piezoelectric substrates have negative TCFs, compensation is possible. Usually, TC-SAW filters on lithium niobate substrates have a TCF in the range of -20 to -25 ppm/°C. This corresponds to a frequency shift of 2 MHz at 800 MHz for a temperature range of 100°C. This is too large for applications requiring steep transitions bands. A band 13 duplexer meeting the NS07 rejection requirement is presented. The substrate utilized is lithium niobate with an orientation close to Y+128°. The oxide thickness is increased enough to obtain full temperature compensation. Piston mode transducers are used in order to suppress the transverse modes and to reduce the losses. By increasing the silicon oxide thickness, it is possible to reduce TCF toward some targeted ppm/degC value. The drawback is a reduction by about 40% of the coupling factor and thus, of the possible relative bandwidth. However, band 13 is narrow enough to be compatible with this approach. The resulting temperature compensation produces a frequency shift smaller than 200 kHz p.p. within the 100°C temperature range. Quality factors in the 1500 range are obtained. Typical results are a rejection of 25dB in the NS07 band within the temperature range with an insertion loss better than 3dB. It is understood that this duplexer is the first band 13 SAW duplexer meeting the NS07 rejection specification.
Vibrio harveyi NADPH-flavin oxidoreductase: cloning, sequencing and overexpression of the gene and purification and characterization of the cloned enzyme (1994)

NAD(P)H-flavin oxidoreductases (flavin reductases) from luminous bacteria catalyze the reduction of flavin by NAD(P)H and are believed to provide the reduced form of flavin mononucleotide (FMN) for luciferase in the bioluminescence reaction. By using an oligonucleotide probe based on the partial N-terminal amino acid sequence of the Vibrio harveyi NADPH-FMN oxidoreductase (flavin reductase P), a recombinant plasmid, pFRP1, was obtained which contained the frp gene encoding this enzyme. The DNA sequence of the frp gene was determined; the deduced amino acid sequence for flavin reductase P consists of 240 amino acid residues with a molecular weight of 26,312. The frp gene was overexpressed, apparently through induction, in Escherichia coli JM109 cells harboring pFRP1. The cloned flavin reductase P was purified to homogeneity by following a new and simple procedure involving FMN-agarose chromatography as a key step. The same chromatography material was also highly effective in concentrating diluted flavin reductase P. The purified enzyme is a monomer and is unusual in having a tightly bound FMN cofactor. Distinct from the free FMN, the bound FMN cofactor showed a diminished A375 peak and a slightly increased 8-nm red-shifted A453 peak and was completely or nearly nonfluorescent. The Kms for FMN and NADPH and the turnover number of this flavin reductase were determined. In comparison with other flavin reductases and homologous proteins, this flavin reductase P shows a number of distinct features with respect to primary sequence, redox center, and/or kinetic mechanism.
Production of Insulin-Like Growth Factors and Their Binding Proteins by Rabbit Articular Chondrocytes: Relationships with Cell Multiplication* (1989)

Articular chondrocytes from 2- to 3-month-old rabbits were cultured in serum-free medium supplemented with fibroblast growth factor. The effects were studied of GH, insulin-like growth factors (IGFs), and insulin on the production of IGF-I, IGF-II, and their binding proteins (BPs) and on cell multiplication. In the control culture medium, IGF-I levels were about one fifth those of IGF-II. Western blot analysis of the BPs revealed a predominant 30K form and 24K and 20K forms which appeared inconsistently and in small quantities. Ten to 100 ng/ml human GH had no mitogenic effect, and even had a slightly inhibitory effect. IGF-I at 10 ng/ml stimulated cell multiplication above the control level by 41% and at 50 ng/ml by 74%, whereas the mean increase obtained with IGF-II (10 and 50 ng/ml) was only 19%. At the same doses, insulin had no effect, but at 5 micrograms/ml it stimulated cell multiplication by a mean of 67%. There was a positive correlation between cell number and release into the medium of both IGF-I (r = 0.86) and IGF-II (r = 0.77). Neither IGF-I nor IGF-II production was affected by GH. Insulin (5 micrograms/ml) increased IGF-I production by a factor of 2.6, but increased IGF-II production by a factor of only 1.4. Under the various conditions of culture with different doses of GH and insulin, cell multiplication, relative to the control value was positively correlated to the IGF-I/IGF-II production ratio (r = 0.77). It would, therefore, seem that IGF-I secreted by the chondrocytes may stimulate their own proliferation. When IGFs or insulin were added to the culture medium, changes in the electrophoretic profiles of the BPs included an increase in the 30K form and an increase in or the appearance of the 24K and 20K forms. Ten and 50 ng/ml IGF-I or IGF-II had effects equal to or greater than those induced by 5 micrograms/ml insulin. These results indicate that the syntheses of BPs and IGFs are coordinated and that IGFs may be implicated in the control of the synthesis of their BPs.
Polarity of Binary Liquid Mixtures (1982)

Abstract In contrast to the thoroughly studied plarity properties of pure liquids, only little is known about the polarity of mixtures of liquids, although the majority of machanistic and preparative work is not carried out in pure phases. Using a widely applicable two‐parameter equation, polar behavior of binary liquid mixtues can be described quantitatively as a function of their composition. Based on this equation, satisfactory explanations are found for deviations observed for binary solvent mixtures from the linear correaltion of polarity scales, as well as for the unusual activation parameters estimated by Winstein for solvolysis of tert ‐butyl chloride. Applications of the equation range from a rapid test for determining water contents of solvents, the study of reaction mechanisms, to polymer chemistry.
Planar Directional Contributions to Optic Flow Responses in MST Neurons (1997)

Many neurons in the dorsal region of the medial superior temporal area (MSTd) of monkey cerebral cortex respond to optic flow stimuli in which the center of motion is shifted off the center of the visual field. Each shifted-center-of-motion stimulus presents both different directions of planar motion throughout the visual field and a unique pattern of global motion across the visual field. We investigated the contribution of planar motion to the responses of these neurons in two experiments. In the first, we compared the responses of 243 neurons to planar motion and to shifted-center-of-motion stimuli created by vector summation of planar motion and radial or circular motion. We found that many neurons preferred the same directions of motion in the combined stimuli as in the planar stimuli, but other neurons did not. When we divided our sample into one group with stronger directionality to both planar and vector combination stimuli and one group with weaker directionality, we found that the neurons with the stronger directionality were those that showed the greatest similarity in the preferred direction of motion for both the planar and combined stimuli. In a second set of experiments, we overlapped planar motion and radial or circular motion to create transparent stimuli with the same motion components as the vector combination stimuli, but without the shifted centers of motion. We found that the neurons that responded most strongly to the planar motion when it was combined with radial or circular motion also responded best when the planar motion was overlapped by a transparent motion stimulus. We conclude that the responses of those neurons with stronger directional responses to both the motion of planar and vector combination stimuli are most readily understood as responding to the total planar motion in the stimulus, a planar motion mechanism. Other neurons that had weaker directional responses showed no such similarity in the preferred directions of planar motion in the vector combination and the transparent overlap stimuli and fit best with a mechanism dependent on the global motion pattern. We also found that neurons having significant responses to both radial and circular motion also responded to the spiral stimuli that result from a vector combination of radial and circular motion. The preferred planar-spiral vector combination stimulus was frequently the one containing that neurons' preferred direction of planar motion, which makes them similar to other MSTd neurons.
Regulation of the araC gene of Escherichia coli: catabolite repression, autoregulation, and effect on araBAD expression. (1984)

The araC gene encodes a positive regulatory protein required for L-arabinose utilization in Escherichia coli. Transcription from the araC promoter has been shown to be under positive control by cAMP receptor protein and under negative control by its protein product (autoregulation). This work describes the identification of the region of the araC promoter that interacts with the cAMP receptor protein to mediate catabolite repression. A 3-base-pair deletion centered 60 base pairs from the transcriptional initiation site results in a mutant araC promoter that, in the absence of araC protein, reduces transcriptional activity when compared with the wild-type promoter and is unresponsive to various concentrations of intracellular cAMP in vivo. The same deletion results in a lowered affinity of the araC promoter for cAMP receptor protein in vitro. However, this lowered affinity for the mutant araC promoter does not result in substantial reduction of intracellular araC protein because autoregulation of the araC gene dominates catabolite repression. The 3-base-pair deletion in the cAMP receptor protein binding site of the araC promoter does not affect catabolite repression of the adjacent araBAD operon. The implications of these results on current models for expression of the araBAD operon and the araC gene are discussed.
Building, Testing and Evaluating Database Clusters : OSA project (2014)

The purpose of this study was to research idea and functionality of clustered database systems. Since relational databases started to lose their functionality in modern data size and manipulation a new solution had to be found to overcome the limitations. On one side the relational databases started to support clustered implementations, which made the database more reliable and helped to achieve better performance. On the other side, a totally new data store structure came with NoSQL movement. From the beginning NoSQL was developed as a system which can be spread across multiple servers therefore it supports clustering in its structure.\n\nAnother aim of the study was to give ideas and guidance for OSA project. It is an Open Source Archive project carried in MAMK, which goal is to create a functional long term data store – dark archive with open source tools. For the project this thesis presents guidance for building and designing clustered database system.\n\nThe thesis research was carried out with practical implementation of different clustered solutions. There have been viewed and analysed four different systems presenting SQL and NoSQL cluster types. From relational databases MariaDB Replication and Galera clusters were built and for NoSQL side document-oriented MongoDB Replica Set and Sharded cluster. All the systems for testing and evaluation have been built independently from their initial state. Tests were mainly focused on cluster implementation, failover solution, availability, backup system and performance.\n\nThe results of the project have shown that clustered database proves to be a way for a system to support massive data, high user access and data recovery. Although in an open source environment building and configuring a cluster can bring challenges and take time to implement it.\n\nThis work has cleared out some points for MariaDB and MongoDB clusters implementation solutions. However there lots more elements to consider for cluster building and in future for NoSQL into SQL implementation.
Estimated conformation, orientation, and accumulation of dynorphin A-(1-13)-tridecapeptide on the surface of neutral lipid membranes (1986)

Equilibrium thermodynamic and kinetic estimations were used to confirm the rather unusual conformation, orientation, and accumulation of dynorphin A-(1-13)-tridecapeptide (dynorphin1-13) on the surface of neutral lipid membranes, as observed by Erne et al. [Erne, D., Sargent, D. F., & Schwyzer, R. (1985) Biochemistry 24, 4261-4263]. I started from the premise that the most stable conformation of molecularly disperse peptides in contact with the hydrophobic phase of a membrane is helical [Henderson, R. (1979) Soc. Gen. Physiol. Ser. 33, 3-15]. Calculation of the Gibbs free energy difference for the transfer of increasing numbers m of N-terminal residues of dynorphin1-13 from their random-coil conformation in water to their alpha-helical conformation in a hydrophobic phase, with the values provided by Von Heijne and Blomberg [Von Heijne, G., & Blomberg, C. (1979) Eur. J. Biochem. 97, 175-181], showed an energy minimum at m = 9 that corresponded to the observed apparent association constant of 9 X 10(4) L/mol. This confirmed our experimental observations. The orientation of dynorphin1-13 in the interphase was estimated by calculation of the molecular amphiphilic moment A. This force vector was defined in analogy to the "helical" and "structural" hydrophobic moments of Eisenberg et al. [Eisenberg, D., Weiss, R. M., & Terwilliger, T. C. (1982) Nature (London) 299, 371-374]. It takes into account the segregation of hydrophobic and hydrophilic residues with respect to the center of the alpha-helix. A peptide located in a hydrophobic-hydrophilic gradient experiences a torque that tends to orient A in a direction perpendicular to the surfaces of equal hydrophobicity.(ABSTRACT TRUNCATED AT 250 WORDS)
MR imaging of Parkinson disease with spin-echo and gradient-echo sequences (1989)

MR imaging of Parkinson disease with spin-echo and gradient-echo sequencesBH Braffman, RI Grossman, HI Goldberg, MB Stern, HI Hurtig, DB Hackney, LT Bilaniuk and RA ZimmermanAudio Available | Share
Polarized light-scattering matrix elements for select perfect and perturbed optical surfaces (1987)

The angular distribution of scattered light depends on the electromagnetic properties (refractive index, absorptivity), the geometrical properties (size, shape, and distribution) of the scatterer(s), as well as the polarization and illumination angle of the incident light. To study the total information content, we measured the entire experimental sixteen-element Mueller scattering matrix for a smooth reflecting aluminum surface illuminated with lambda = 4416-A light at various angles of incidence alpha. In comparison, we also measured the scattering matrix for a degraded surface of identical material. This paper discusses the experimental procedure and compares the scattering results obtained from these two types of surface.
Electrical Conductivity of Silver Sulfide (1952)

Mixed electronic and ionic conduction in silver sulfide is examined. The importance of terminal conditions which may affect the ratio of ionic to electronic currents in experimental measurements is emphasized. In particular, either the electronic or ionic components can be completely suppressed. This is the basis of a new method of measuring the ionic and electronic conductivities independently, as functions of the chemical potential ζ of the silver component. The electronic conductivity is found to vary as expBζ both above and below the transition at 177°C. However, the coefficient B changes abruptly from e/kT below the transition to e/2kT above. This result can be understood theoretically in terms of the following picture: Excess silver is present mainly as dissolved atoms below the transition and as dissociated ions and electrons above. In the former case, only the electrons contribute to ζ, whereas in the latter there is a contribution both from the electrons and the ions.
Functional GLP-1R antibodies identified from a synthetic GPCR-focused library demonstrate potent blood glucose control (2021)

G protein-coupled receptors (GPCRs) are a group of seven-transmembrane receptor proteins that have proven to be successful drug targets. Antibodies are becoming an increasingly promising modality to target these receptors due to their unique properties, such as exquisite specificity, long half-life, and fewer side effects, and their improved pharmacokinetic and pharmacodynamic profiles compared to peptides and small molecules, which results from their more favorable biodistribution. To date, there are only two US Food and Drug Administration-approved GPCR antibody drugs, namely erenumab and mogamulizumab, and this highlights the challenges encountered in identifying functional antibodies against GPCRs. Utilizing Twist's precision DNA writing technologies, we have created a GPCR-focused phage display library with 1 × 10<sup>10</sup> diversity. Specifically, we mined endogenous GPCR binding ligand and peptide sequences and incorporated these binding motifs into the heavy chain complementarity-determining region 3 in a synthetic antibody library. Glucagon-like peptide-1 receptor (GLP-1 R) is a class B GPCR that acts as the receptor for the incretin GLP-1, which is released to regulate insulin levels in response to food intake. GLP-1 R agonists have been widely used to increase insulin secretion to lower blood glucose levels for the treatment of type 1 and type 2 diabetes, whereas GLP-1 R antagonists have applications in the treatment of severe hypoglycemia associated with bariatric surgery and hyperinsulinomic hypoglycemia. Here we present the discovery and creation of both antagonistic and agonistic GLP-1 R antibodies by panning this GPCR-focused phage display library on a GLP-1 R-overexpressing Chinese hamster ovary cell line and demonstrate their in vitro and in vivo functional activity.
Measurements of Engine Torque with the Intra-Bearing Torque Sensor (1987)

<div class="htmlview paragraph">A miniature noncontact torque sensor has been developed to be mounted on an engine for use in engine control systems. The sensor is installed in a last main bearing of the engine crankshaft. The principle is based on the measurement of torque-induced change in magnetic properties of a crankshaft due to the magneto-strictive effect.</div> <div class="htmlview paragraph">A new signal processing has also been developed. The method is very superior in linearity and stability of the output signal. Performance of the sensor examined on an engine-dynamometer arrangement is described.</div>
Prime editing for functional repair in patient-derived disease models (2020)

Prime editing is a recent genome editing technology using fusion proteins of Cas9-nickase and reverse transcriptase, that holds promise to correct the vast majority of genetic defects. Here, we develop prime editing for primary adult stem cells grown in organoid culture models. First, we generate precise in-frame deletions in the gene encoding β-catenin (CTNNB1) that result in proliferation independent of Wnt-stimuli, mimicking a mechanism of the development of liver cancer. Moreover, prime editing functionally recovers disease-causing mutations in intestinal organoids from patients with DGAT1-deficiency and liver organoids from a patient with Wilson disease (ATP7B). Prime editing is as efficient in 3D grown organoids as in 2D grown cell lines and offers greater precision than Cas9-mediated homology directed repair (HDR). Base editing remains more reliable than prime editing but is restricted to a subgroup of pathogenic mutations. Whole-genome sequencing of four prime-edited clonal organoid lines reveals absence of genome-wide off-target effects underscoring therapeutic potential of this versatile and precise gene editing strategy.