gebhart/patrepeval huggingface dataset:
Screening and selection of <b><i>Lactobacillus</i></b> strains for use as adjunct cultures in production of semi-hard cheese (2002)

Thirty-three Lactobacillus strains were tested as adjuncts in a cheese model system. Eighteen strains originated from cheese (nine Lactobacillus spp. and nine Lb. paracasei/casei) and 15 from human intestinal mucosa (11 Lb. rhamnosus; three Lb. paracasei; one Lb. plantarum). Model cheeses weighing 120 g were made of cheese grains from full-scale production of washed curd semi-hard cheese (Herrgård). The model system was reproducible and similar to full-scale production with respect to moisture, salt content, pH and microbial flora. The model cheeses were sampled for aerobic and anaerobic plate count and viable counts of Lactobacillus and Lactococcus. The presence of adjuncts in the model cheeses was confirmed by typing isolates with Randomly Amplified Polymorphic DNA (RAPD). The sensory properties of model cheeses were described. In a first trial 23 of the 33 adjuncts were re-isolated from the corresponding model cheeses after 9 or 13 weeks. Adjuncts of Lb. paracasei were re-isolated more frequently than adjuncts of Lb. rhamnosus. Nine strains were selected, on the basis of their ability to grow and be a dominating part of the microflora of model cheese with interesting sensory properties. These strains were further studied together with two commercial cultures. The sensory influences on model cheeses of six of the adjuncts were confirmed, and flavour scores were in the range of 2.9-7.1 for model cheeses with different adjuncts while the control had a flavour score of 5.6 (0-10 scale). Survival and growth of seven out of the nine strains correlated with the results of the first trial. Growth and influence on flavour of four adjunct cultures were confirmed in experimental cheese manufactured in a 400-1 open vat.
Recent advances in the stereoselective synthesis of <scp>L</scp>‐phosphinothricin (1994)

Abstract L ‐Phosphinothricin, the parent α‐amino acid of the herbicide glufosinate‐ammonium, has been obtained in high enantiomeric purity by three different methods. The stereoselective alkylation of a D ‐valine‐derived bis‐lactim ether, followed by the hydrolysis of the heterocyclic intermediate, represents an attractive approach for gram‐scale quantities in the laboratory. Another very efficient access to L ‐phosphinothricin consists of the asymmetric hydrogenation of a prochiral α‐acylamido acrylate with a chiral bis‐phosphine‐rhodium catalyst, while the reaction of chiral pre‐built C‐4‐fragments, like L ‐vinylglycine or L ‐2‐amino‐4‐halobutyric acid, which can be obtained from the inexpensive starting materials L ‐aspartic acid and L ‐glutamic acid, with (methyl)phosphinic acid derivatives represents a third route which allows the production of nearly enantiomerically pure L ‐phosphinothricin.
Photonic bandgap fibers: theory and experiments (2002)

We will in this presentation address, show how the fiber cladding structure influences the resulting waveguiding properties. The core may be introduced by breaking the periodicity of the air holes at the center of the fiber. It has been demonstrated experimentally that this makes it possible to localize modes in the core region by the photonic band gap (PBG) effect. The photonic crystal fibers (PCFs) were first proposed for a high-index-core region, surrounded by a periodic dielectric structure consisting of a matrix of microscopic holes placed in a silica-glass-base material.
Human immunodeficiency virus type 1 (HIV-1) inhibition, DNA-binding, RNA-binding, and ribosome inactivation activities in the N-terminal segments of the plant anti-HIV protein GAP31. (1994)

GAP31 (gelonium anti-HIV protein of 31 kDa) is an anti-HIV protein which we have identified and purified from a medicinal plant, Gelonium multiflorum. It is capable of inhibiting HIV-1 infection and replication. GAP31 also exhibits DNA topoisomerase inhibitor activity and RNA N-glycosidase activity. The ability of GAP31 to interrupt both DNA and RNA functions may be related to its multiple antiviral actions. To define the roles of these activities in the anti-HIV action of GAP31, a series of peptides corresponding to the N-terminal segment of GAP31 were synthesized and assayed for the aforementioned activities of the parent molecule. A 33-aa segment (KGATYITYVNFLNELRVKTKPEGNSHGIPSLRK) designated as K10-K42 is the shortest peptide necessary and sufficient for HIV-1 inhibition, DNA and RNA binding, and ribosome inactivation. The peptides were 2-5 orders of magnitude less active than GAP31. Truncation of 19 aa from the C terminus of K10-K42 resulted in the loss of all of these activities. On the other hand, deletion of N-terminal residues to give E23-K42 did not alter ribosome-inactivation activity but eliminated the other activities. These findings permit identification of a 7-aa sequence, KGATYIT, at the N terminus of K10-K42 that is critical for DNA binding and RNA binding, whereas a 9-aa sequence, SHGIPSLRK, at the C terminus is important to ribosome inactivation. Both regions contribute to anti-HIV activity. Histidine at position 35 is critical for all of these activities. The disparity of sequence requirements for inhibition of HIV infection and replication and for ribosome-inactivation activity suggests that the anti-HIV activity of most ribosome-inactivating proteins may not be the result of N-glycosidase activity alone. Mapping the minimal domain of GAP31 offers insights into the rational design of molecular mimetics of anti-HIV drugs.
Comparative Evaluation of Sloppy Molecular Beacon and Dual-Labeled Probe Melting Temperature Assays to Identify Mutations in Mycobacterium tuberculosis Resulting in Rifampin, Fluoroquinolone and Aminoglycoside Resistance (2015)

Several molecular assays to detect resistance to Rifampin, the Fluoroquinolones, and Aminoglycosides in Mycobacterium tuberculosis (M. tuberculosis) have been recently described. A systematic approach for comparing these assays in the laboratory is needed in order to determine the relative advantage of each assay and to decide which ones should be advanced to evaluation. We performed an analytic comparison of a Sloppy Molecular Beacon (SMB) melting temperature (Tm) assay and a Dual labeled probe (DLP) Tm assay. Both assays targeted the M. tuberculosis rpoB, gyrA, rrs genes and the eis promoter region. The sensitivity and specificity to detect mutations, analytic limit of detection (LOD) and the detection of heteroresistance were tested using a panel of 56 clinical DNA samples from drug resistant M. tuberculosis strains. Both SMB and DLP assays detected 29/29 (100%) samples with rpoB RRDR mutations and 3/3 (100%) samples with eis promoter mutations correctly. The SMB assay detected all 17/17 gyrA mutants and 22/22 rrs mutants, while the DLP assay detected 16/17 (94%) gyrA mutants and 12/22 (55%) rrs mutants. Both assays showed comparable LODs for detecting rpoB and eis mutations; however, the SMB assay LODs were at least two logs better for detecting wild type and mutants in gyrA and rrs targets. The SMB assay was also moderately better at detecting heteroresistance. In summary, both assays appeared to be promising methods to detect drug resistance associated mutations in M. tuberculosis; however, the relative advantage of each assay varied under each test condition.
Direct Hydrogenation of Carboxylic Acids to Corresponding Aldehydes Catalyzed by Palladium Complexes in the Presence of Pivalic Anhydride (1998)

Abstract Carboxylic acids are catalytically hydrogenated into corresponding aldehydes by palladium complexes in the presence of pivalic (trimethylacetic) anhydride under H2. Less hindered aliphatic and aromatic acids are reduced to aldehydes in high yields. The method is also applicable to hydrogenation of dibasic carboxylic acids and carboxylic acids containing heterocyclic groups.
Controlled-Phase Gate Using Dynamically Coupled Cavities and Optical Nonlinearities (2020)

We show that relatively simple integrated photonic circuits have the potential to realize a high fidelity deterministic controlled-phase gate between photonic qubits using bulk optical nonlinearities. The gate is enabled by converting travelling continuous-mode photons into stationary cavity modes using strong classical control fields that dynamically change the effective cavity-waveguide coupling rate. This architecture succeeds because it reduces the wave packet distortions that otherwise accompany the action of optical nonlinearities [J. Shapiro, Phys. Rev. A 73, 062305 (2006)PLRAAN1050-294710.1103/PhysRevA.73.062305; J. Gea-Banacloche, Phys. Rev. A 81, 043823 (2010)PLRAAN1050-294710.1103/PhysRevA.81.043823]. We show that high-fidelity gates can be achieved with self-phase modulation in χ^{(3)} materials as well as second-harmonic generation in χ^{(2)} materials. The gate fidelity asymptotically approaches unity with increasing storage time for an incident photon wave packet with fixed duration. We also show that dynamically coupled cavities enable a trade-off between errors due to loss and wave packet distortion. Our proposed architecture represents a new approach to practical implementation of quantum gates that is room-temperature compatible and only relies on components that have been individually demonstrated.
Manipulation of <i>Arabidopsis</i> fatty acid amide hydrolase expression modifies plant growth and sensitivity to <i>N</i> -acylethanolamines (2006)

In vertebrates, the endocannabinoid signaling pathway is an important lipid regulatory pathway that modulates a variety of physiological and behavioral processes. N-Acylethanolamines (NAEs) comprise a group of fatty acid derivatives that function within this pathway, and their signaling activity is terminated by an enzyme called fatty acid amide hydrolase (FAAH), which hydrolyzes NAEs to ethanolamine and their corresponding free fatty acids. Bioinformatic approaches led to the identification of plant homologues of FAAH that are capable of hydrolyzing NAEs in vitro. To better understand the role of NAEs in plants, we identified T-DNA knockouts to Arabidopsis FAAH (AtFAAH; At5g64440) and generated plants overexpressing AtFAAH. Here we show that seeds of AtFAAH knockouts had elevated levels of endogenous NAEs, and seedling growth was hypersensitive to exogenously applied NAE. On the other hand, seeds and seedlings of AtFAAH overexpressors had lower endogenous NAE content, and seedlings were less sensitive to exogenous NAE. Moreover, AtFAAH overexpressors displayed enhanced seedling growth and increased cell size. AtFAAH expression and FAAH catalytic activity increased during seed germination and seedling growth, consistent with the timing of NAE depletion during seedling establishment. Collectively, our results show that AtFAAH is one, but not the only, modulator of endogenous NAE levels in plants, and that NAE depletion likely participates in the regulation of plant growth.
TrkB Agonists Ameliorate Obesity and Associated Metabolic Conditions in Mice (2007)

Mutations in the tyrosine kinase receptor trkB or in one of its natural ligands, brain-derived neurotrophic factor (BDNF), lead to severe hyperphagia and obesity in rodents and/or humans. Here, we show that peripheral administration of neurotrophin-4 (NT4), the second natural ligand for trkB, suppresses appetite and body weight in a dose-dependent manner in several murine models of obesity. NT4 treatment increased lipolysis, reduced body fat content and leptin, and elicited long-lasting amelioration of hypertriglyceridemia and hyperglycemia. After treatment termination, body weight gradually recovered to control levels in obese mice with functional leptin receptor. A single intrahypothalamic application of minute amounts of NT4 or an agonist trkB antibody also reduced food intake and body weight in mice. Taken together with the genetic evidence, our findings support the concept that trkB signaling, which originates in the hypothalamus, directly modulates appetite, metabolism, and taste preference downstream of the leptin and melanocortin 4 receptor. The trkB agonists mediate anorexic and weight-reducing effects independent of stress induction, visceral discomfort, or pain sensitization and thus emerge as a potential therapeutic for metabolic disorders.
High Energy Density Electrode Materials for Rechargeable Magnesium Batteries (2015)

Rechargeable magnesium batteries are drawing increasing interest as a future alternative to lithium-based batteries due to their high energy density, low environmental impact and low cost. However, the sluggish diffusion of Mg 2+ and incompatibility between magnesium anode and traditional electrolytes are hindering the realization of practical magnesium batteries. In this report, we present the preparation, characterization and magnesium electrochemistry of a cathode material, Mg x V 2 O 5, and a novel bismuth based composite anode material, Bi-CNT. The Mg x V 2 O 5 cathode material was developed via sol-gel route, and it is shown here that the material is of high capacity and favorable for Mg 2+ diffusion. The Bi-CNT composite electrode was prepared by electrodeposition, and it shows quasi-reversible electrochemistry and compatibility with non-corrosive electrolyte. The deposition of Bi via a cyclic voltammetry technique was systematically studied, establishing a paradigm for future development of electrodeposited-Bi electrodes.
Rotation scheme of V <sub>1</sub> -motor is different from that of F <sub>1</sub> -motor (2005)

V(1), a water-soluble portion of vacuole-type ATPase (V-ATPase), is an ATP-driven rotary motor, similar to F(1)-ATPase. Hydrolysis of ATP is coupled to unidirectional rotation of the central rotor D and F subunits relative to the A(3)B(3) cylinder. In this study, we analyzed the rotation kinetics of V(1) in detail. At low ATP concentrations, the D subunit rotated stepwise, pausing every 120 degrees . The dwell time between steps revealed that V(1) consumes one ATP per 120 degrees step. V(1) generated torque of approximately 35 pN nm, slightly lower than the approximately 46 pN nm measured for F(1). Noticeably, the angles for both ATP cleavage and binding were apparently the same in V(1), in sharp contrast to F(1), which cleaves ATP at 80 degrees posterior to the binding of ATP. Thus, the mechanochemical cycle of V(1) has marked differences to that of F(1).
Radio frequency-driven proton source with a back-streaming electron dump (2010)

This article describes an rf ion source with a back-streaming electron dump. A quartz tube, brazed to a metal plug at one end, is fused in the center of a flat quartz plate. rf power (at 13.6 MHz) is coupled to generate hydrogen plasma using a planar external antenna bonded to the window. Bonding the water-cooled rf antenna to the quartz window significantly lowers its temperature. The water-cooled metal plug serves as the back-streaming electron dump. At 1800 W, the current density of extracted hydrogen ions reaches approximately 125 mA/cm2.
High transport critical current density obtained for powder-in-tube-processed MgB2 tapes and wires using stainless steel and Cu–Ni tubes (2001)

MgB 2 tapes and wires were fabricated by the powder-in-tube method. Stainless steel and Cu–Ni tubes were used as sheath materials, and no heat treatment was applied. The tapes made of stainless steel showed transport critical current density Jc of about 10 000 A/cm2 at 4.2 K and 5 T. A high Jc of about 300 000 A/cm2 was obtained by extrapolating the Jc–B curves to zero field. Multifilamentary (seven-core) MgB2 wire was successfully fabricated using Cu–Ni tubes. For both tapes and wires, the grain connectivity of MgB2 was as good as a high-pressure sintered bulk sample. However, the Jc of the Cu–Ni sheathed wire was lower than the stainless steel sheathed tape due to the lower packing density of MgB2.
Sweep-free distributed Brillouin sensing using multiple pump and probe tones (2011)

Using multiple pump and probe tones, a frequency-sweep-free method for distributed Brillouin sensing, is proposed, having the potential for fast dynamic strain measurements. Experimentally, a spatial resolution on the order of 1-meter is demonstrated.
Cloning and physical mapping of a gene fragment coding for a 64-kilodalton major late antigen of human cytomegalovirus. (1984)

We have isolated a clone containing a gene fragment coding for a 64-kilodalton glycoprotein that is the major late antigen of human cytomegalovirus (HCMV). Based upon the amino acid sequence of a tryptic peptide of this glycoprotein (HCMVgp64), two sets of mixed-sequence probes, one consisting of a mixture of 16 heptadecadeoxyribonucleotides and the other a mixture of 32 icosadeoxyribonucleotides, were synthesized. A subgenomic library of HCMV (Towne strain) DNA was constructed in plasmid pBR327 and transformants were screened with 32P-labeled aliquots of these synthetic oligodeoxyribonucleotide probes. Two clones among 15,000 gave strong positive signals. Plasmid DNA was isolated from the positive clones and characterized by restriction mapping and Southern blot analysis using both probes. The plasmid DNA contained a 2.3-kilobase insert, which yielded an 800-base-pair and a 1500-base-pair fragment after Sau3A digestion. Only the 800-base-pair fragment hybridized to the mixed probes, and DNA sequence analysis revealed that it contains nucleotide sequences compatible with amino acid sequences of tryptic peptides of HCMVgp64. Restriction mapping studies of HCMV DNA using this 32P-labeled 800-base-pair cloned DNA have allowed us to locate this gene fragment in the long unique region of HCMV (Towne strain) genome at approximately equal to 0.5-0.51 map unit.
Watermark based access control to copyrighted content (2013)

One application of digital watermarks deals with control of copying, playback, transmission and other uses of copyrighted content. In this application, the watermark extractor is typically in user-controlled devices, which means that an attacker could mount the oracle attack, or attempt reverse engineering of the watermarking technology. Furthermore, the watermark extractor has to use limited device resources in order to maintain low implementation cost. On the other hand, in this application the payload is relatively small, and watermarks are typically embedded redundantly. In this paper, we describe methods to utilize the embedding redundancy to maximize robustness and security of the system while maintaining low implementation cost. Some of the proposed techniques include iterative extraction process based on initial sparse and random sampling of the distortion space, followed by partial or tentative watermark extraction that triggers extractor adjustment to estimated distortion parameters. Distortion estimation is based on partial watermark matching to pre-distorted templates which can be preselected using experimental approach based on pilot signals. Upon detection of one or more partial or tentative watermarks a new selection of pre-distorted templates is designed to improve distortion resolution and extraction reliability. Extrapolation of watermark segments in the vicinity of partial or tentative watermark extraction is done in view of estimated distortion and an algorithm for combining results of multiple extrapolation segments is proposed. The techniques proposed here allow reduction in processing load and reduction in false positive rates, which in turn can be used to increase watermark robustness to distortion and improved overall security of the system.
Fast multiple-antenna differential decoding (2001)

We present an algorithm based on lattice reduction for the fast decoding of diagonal differential modulation across multiple antenna. While the complexity of the maximum-likelihood (ML) algorithm is exponential both in the number of antenna and the rate, the complexity of our approximate lattice algorithm is polynomial in the number of antennas and the rate. We show that the error performance of our lattice algorithm is very close to the ML algorithm.
Secure de-identification and re-identification. (2003)

Today's healthcare organizations have both an ethical and legal responsibility for protecting patient privacy. However, the HIPAA privacy rule allows for the release of de-identified patient data for certain purposes. Secure encryption technology can be used to encrypt patient identified data so only the owners of the original data can re-identify the patient. It further allows consistent de-identification over episodic collection events.
RRED indices: Reduced reference entropic differencing framework for image quality assessment (2011)

We study the problem of automatic "reduced reference" image quality assessment algorithms from the point of view of image information change. Algorithms that measure differences between the entropies of wavelet coefficients of reference and distorted images are designed. A family of algorithms are presented, each differing in the amount of data on which information change is predicted and ranging from al most full reference to almost no reference. A special case of this are algorithms that require just a single number from the reference for quality assessment. The algorithms are shown to correlate very well with subjective quality scores as demonstrated on the LIVE Image Quality Assessment Database.
Design and development of thin film materials for 157-nm and VUV wavelengths: APSM, binary masking, and optical coatings applications (1999)

As optical lithography below 193 nm is explored, materials issues become more challenging. Thin film coatings that are sufficient for use at wavelengths near or above 200 nm are more likely than not to be problematic at 157 nm, 126 nm, or other potential VUV wavelengths. The situation is a concern for optical coatings, masking films, and for resist/substrate reflectivity control. Potential solutions for several film types are presented, which have been deposited and optically characterized for use as attenuated phase shift masking films, binary masking films, and optical coatings for use at 157 nm.
Remission and Survival Following Monthly Intraarterial Cisplatinum in Nonresectable Hepatoma (2002)

Hepatic intraarterial cisplatinum at 50 mg/m2 is a well-tolerated monthly regimen for patients with nonresectable hepatoma.
Neutron capture therapy (NCT) enhancement of fast neutron radiotherapy: Application to non-small cell lung cancer (2001)

Fast neutron radiotherapy utilizes neutrons in the energy range of several millions to several tens of millions of eV to treat human malignancies. These fast neutron beams produce a small cloud of “slow” neutrons as they penetrate the body. If one can selectively attach isotopes having large neutron capture cross sections (such as 10B) to cancer cells, these “slow” neutrons can be used to enhance the killing of tumors. We describe a multidisciplinary effort to apply this technique to the treatment of patients with inoperable, non-small cell lung cancers. Problems in target design, compound development, beam optimization, and radiobiological experiments are discussed.