gebhart/patrepeval huggingface dataset:
Genome-Wide Screening for Genes Associated with FK506 Sensitivity in Fission Yeast (2011)

We have been studying calcineurin signal transduction pathway in fission yeast Schizosaccharomyces pombe (S. pombe) by developing a genetic screen for mutants that show hypersensitivity to the immunosuppressive calcineurin inhibitor FK506 (tacrolimus). In the present study, to identify nonessential genes that are functionally related to the calcineurin signaling pathway, we performed a genome-wide screen of 3004 haploid deletion strains and confirmed 72 deletion strains to be FK506 sensitive. These 72 genes are classified into nine functional groups to include membrane trafficking (16 genes), signal transduction (10 genes), ubiquitination (8 genes), chromatin remodeling (6 genes), cytokinesis (4 genes), ribosomal protein (3 genes), RNA binding protein (3 genes), and a variety of other known functions (17 genes) or still unknown functions (5 genes) in the biological system. In our previous screening of FK506-sensitive mutants we isolated several membrane-trafficking mutants showing defective cell wall integrity. Here, we further examined the vacuolar fusion, the v-SNARE synaptobrevin Syb1 localization, and the sensitivity to the β-glucan synthase inhibitor micafungin in these 72 FK506-sensitive strains. Results showed that 25 deletion strains exhibited abnormal vacuole fusion, 19 deletion strains exhibited Syb1 mislocalization, and 14 deletion strains exhibited both abnormal vacuole fusion and Syb1 mislocalization, while 42 deletion strains showed both normal vacuole fusion and Syb1 localization. Likewise, 16 deletion strains showed sensitivity to micafungin. Altogether, our present study indicates that calcineurin mediates a plethora of physiological processes in fission yeast, and that calcineurin is extensively involved in cross-talk between signaling pathways.
Biomolecular resource utilization in elementary cell-free gene circuits (2013)

We present a detailed dynamical model of the behavior of transcription-translation circuits in vitro that makes explicit the roles played by essential molecular resources. A set of simple two-gene test circuits operating in a cell-free biochemical `breadboard' validate this model and highlight the consequences of limited resource availability. In particular, we are able to confirm the existence of biomolecular `crosstalk' and isolate its individual sources. The implications of crosstalk for biomolecular circuit design and function are discussed.
Animal Model of Depression (1969)

THIS PAPER has three major purposes: (1) to present the need for an experimental animal model of "depression," ie, why the creation of such a model would be useful; (2) to review pertinent evidence from a variety of fields which points to the feasibility of such a model; and (3) to discuss possible research strategies which could be used to create an experimental animal model of depression. Depression in man is a poorly defined entity. As Lehmann<sup>1</sup>points out, the term may refer to a symptom, a syndrome, or a nosological entity. We are interested in the depressive syndrome which is often defined as consisting of both primary and secondary symptoms. The primary symptoms in man consist of a despairing emotional state and the depressive mood. The secondary symptoms vary and are less regularly found. They may include such things as social withdrawal, psychomotor retardation, an
Tremor frequency based filter to extract voluntary movement of patients with essential tremor (2012)

Essential Tremor (ET) refers to involuntary oscillations of a part of the body. ET patients face serious difficulties in performing daily living activities. Our motivation is to develop a system that can enable ET patients to perform their daily living activities; hence we have been developing a myoelectric controlled exoskeletal robot for ET patients. However, the EMG signal of ET patients contains not only voluntary movement signals but also tremor signals. Accordingly, to control this robot correctly, tremor signals must be removed from the EMG signal of ET patients. To date, we have been developing a filter to remove tremor signals, which has been largely effective in this. However, tremor signals are generated both while voluntary movement is being performed and while a posture is being maintained, and the filter ended up attenuating both these signals. But, to control this robot accurately, the signal generated during performance of voluntary movement is expected not to be attenuated. Therefore, in this paper, we propose a method that attenuates only tremor signals arising during maintenance of a posture. To accomplish this objective, we focus on the frequency of tremor signals. From the experiment, we confirmed the characteristic that the frequency of tremor signals changed depending on the state of the patient's movement. We then used frequency as a switch to activate the previously proposed filter by setting a threshold. As an evaluation, signals processed by the proposed method were input to a time delay neural network. The proposed method succeeded in partly improving recognition due to reduction of attenuation during performance of voluntary movement. However, the proposed method failed recognition in cases where the frequency of tremor signals varied widely. As a future work we will review the method to calculate the frequency of tremor signals and improve recognition.
Design and Synthesis of Highly Luminescent Near-Infrared-Emitting Water-Soluble CdTe/CdSe/ZnS Core/Shell/Shell Quantum Dots (2009)

Applications of water-dispersible near-infrared (NIR)-emitting quantum dots (QDs) have been hampered by their instability and low photoluminescence (PL) efficiencies. In this paper, water-soluble highly luminescent NIR-emitting QDs were developed through constructing CdTe/CdSe/ZnS core/shell/shell nanostructure. The CdTe/CdSe type-II structure yields the QDs with NIR emission. By varying the size of CdTe cores and the thickness of the CdSe shell, the emission wavelength of the obtained nanostructure can span from 540 to 825 nm. In addition, the passivation of the ZnS shell with a substantially wide bandgap confines the excitons within the CdTe/CdSe interface and isolates them from the solution environment and consequently improves the stability of the nanostructure, especially in aqueous media. An effective shell-coating route was developed for the preparation of CdTe/CdSe core/shell nanostructures by selecting capping reagents with a strong coordinating capacity and adopting a low temperature for shell deposition. An additional ZnS shell was deposited around the outer layer of CdTe/CdSe QDs to form the core/shell/shell nanostructure through the decomposition of single molecular precursor zinc diethyldithiocarbamate in the crude CdTe/CdSe reaction solution. The water solubilization of the initially oil-soluble CdTe/CdSe/ZnS QDs was achieved through ligand replacement by 3-mercaptopropionic acid. The as-prepared water-soluble CdTe/CdSe/ZnS QDs possess PL quantum yields as high as 84% in aqueous media, which is one of the best results for the luminescent semiconductor nanocrystals.
A pairing algorithm of range information between multiple IR-UWB radar sensors (2016)

In this paper, a pairing algorithm of range information between multiple IR-UWB radar sensors is proposed to localize multiple targets. The IR-UWB radar sensors measure the distance of multiple targets anonymously, so that the range information of multiple sensors is needed to be paired to find a position of a specific target. The number of pairing cases increases with the increasing of the number of radars and targets. Algorithms to find the pair of the measured distances based on the cost function or segmentation of the received signal are proposed before, however, if the multiple targets are positioned in ambiguous positions which make multiple equally likeable fake locations besides the true position, the conventional algorithms fail to pair the distance information. To handle the problem, a new pairing algorithm of the distance information between the multiple IR-UWB radar sensors is proposed in this paper. The algorithm basically uses the information of variations in magnitude and distance invoked by a movement of a specific target. Using the proposed algorithm, the wrong pairing could be avoided with high probability. The performance of the proposed algorithm is proved by experiments using the two IR-UWB radar sensors.
La autoevaluacion, camino hacia la excelencia. (1999)

Tras obtener la certificacion ISO 9000 a finales de 1996, en Novotec Consultores sentimos la necesidad de potenciar un proceso de mejora continua mediante la aplicacion de criterios y metodologias de gestion de la Calidad Total. Se tomo la decision de aplicar el Modelo Europeo por lo que supone de herramienta que determina los puntos fuertes y las areas de mejora de la organizacion a traves de la autoevaluacion, como conocimiento de la propia organizacion; y por su mayor adaptacion al entorno y la cultura europea en que nos movemos.
Simplified screening for the detection of soluble fusion constructs expressed in E. coli using a modular set of vectors (2005)

The experiments showed that the set of pETM vectors could be used for the rapid production of a large array of different constructs with specific yield, stability, and cleavage features. Their comparison allowed the identification of the optimal constructs to use for the large-scale expression. We expect that the approach outlined in this paper, i.e. the possibility to obtain in parallel fusion products of the target protein with different partners for a preliminary evaluation, would be highly beneficial for all them who are interested in the rapid identification of the optimal conditions for protein expression.
Kinetics and mechanism of the cyclisation of 2′,6′-dihydroxychalcone and derivatives (1989)

pH–Rate profiles are reported for the cyclisation in water to 5-hydroxyflavanones of 2′,6′-dihydroxychalcone (1) and its 4-methoxy (2), 3,4-dimethoxy (3), 3,4,5-trimethoxy (4), 2,4,6-trimethoxy (5), 4-chloro (6), and 3,4,4′-trimethoxy (8) derivatives. As for the previously studied 2′,6′-dihydroxy-4,4′-dimethoxychalcone (7), rate coefficients are established for acid-catalysed cyclisation of neutral chalcone, for unimolecular cyclisation of the neutral, monoanionic, and dianionic chalcone, and for the base-catalysed reverse ring-opening reaction. Cyclisation of the monoanion of 2′,6′-dihydroxychalcone is almost 40 times faster than that of the monoanion of the 2′-hydroxy-6′-methoxychalcone (10) and is also estimated to be about ten times faster than that of the reactive monoanion of 2′,4′-dihydroxychalcone. These are the first calculations of the enhancement of rate of monoanion cyclisation by the 6′-OH group. The effect is only small, and is suggested to arise largely from stabilisation of the transition state for ketonisation by hydrogen bonding to enolate oxygen. Other reactivity differences amongst the chalcone monoanions are also discussed. Enthalpy and entropy of activation data are reported for monoanion cyclisation of (1), (2), and (4)–(6). Rate coefficients for the cyclisation of the chalcone monoanions are almost identical for (1)–(4) and (6) in water but not in deuterium oxide: kinetic hydrogen isotope effect (KIE) values are 3.4 (1), 5.7 (2), 4.9 (3), 3.0 (4), 7.5 (5), 2.9 (6), and 5.0 (8). For chalcones (2) and (7), the KIE values of which are both 5.7, the amounts of H versus D incorporation at the flavanone 3-carbon for monoanion cyclisation in H2O/D2O mixtures were established by mass spectroscopy. This gave product (or ‘discrimination’) isotope effect (PIE) values of 7.9 for (2) and 3.8 for (7), suggesting for (2) but not (7) an inverse isotope effect contribution to KIE from sources other than rate-limiting proton transfer to carbon. Monoanion cyclisation of (1) in D2O was established by 1H n.m.r. as involving almost equal amounts of anti and syn addition of 2′-O– to the enone double bond. Reactivity differences amongst the chalcones for reactions other than monoanion cyclisation are only briefly considered.
Optical QPSK Signal Quality Degradation due to Phase Error of Pump Light in Optical Parametric Phase-Sensitive Amplifier Repeaters (2018)

The influence of pump phase error on phase-sensitive optical amplifier (PSA) repeaters and the waveform degradation due to chromatic dispersion and fiber nonlinearities in the optical multi-relay transmission of quadrature phase-shift keying phase-conjugated twin waves are considered theoretically. First, the influence of noise from the pump phase error, optical local oscillator, receiver, and the amplified spontaneous-emission (ASE) in PSA repeaters is investigated with the assumption that transmission fibers are linear lossy channels. The bit-error rate (BER) is estimated as a function of the signal-to-noise ratio, and the relationship between the number of transmission relays and the fiber launch power is clarified. Waveform degradation due to chromatic dispersion and the optical fiber nonlinearities in transmission fibers are investigated with the noiseless condition, and the maximum repeatable number as a function of the fiber launch power is calculated. Finally, we show the relationship among the maximum repeatable number, standard deviation of pump phase error in PSA repeaters, and the fiber launch power to clarify the optimum transmission condition with consideration of the noise and the waveform degradation.
Color Sonagrams: A New Dimension In Seismic Data Interpretation (1971)

Abstract We have developed a computer-graphic-photographic system which uses color mimicry to display the frequency spectra of seismic events simultaneously with their time-varying waveforms. Mimicking the visible light spectrum, we have used red for the low frequencies and violet for the highs. The output of our system is a variable-area-wiggle-trace seismic cross-section. The waveforms are the same as those on a conventional section; however, the variable-area part of the section appears in color. The color represents the frequency spectrum of the wavelets. Lateral changes in rock attenuation show up as color shifts on this type of display. Faults often stand out as interrupted color bands. Fault diffractions sometimes have a characteristic color signature. The cancellation of high frequencies due to misalignment of events on constant-velocity stacks can show up in color. Loss of high frequencies due to slight lateral changes in moveout velocity, and consequent trace misalignment, is often indicated by a shift toward red on a color seismic section.
An Over-Cell Gate Array Channel Router (1983)

A gate array router that utilizes horizontal and vertical over-cell routing channels to increase cell density is described. Logic macros, with fixed intraconnect metal that may span several cell columns, are mapped onto the array producing partially filled routing channels. Macro interconnects are loosely assigned to the partially filled horizontal and vertical routing channels during global routing. Each loose horizontal channel segment is assigned to a channel track using a maze router. Vertical channel segments are completed by a modified dogleg channel router.
Magnesium, Zinc and Copper Status in Osteoporotic, Osteopenic and Normal Post-menopausal Women (2007)

Serum concentrations of magnesium, zinc and copper were measured in postmenopausal women with osteoporosis (n = 40), osteopenia (n = 40) or normal bone mineral density (n = 40) as classified on the basis of the T-score of the femur neck and dual energy X-ray absorptiometry results. Mean concentrations of magnesium and zinc were significantly lower in osteoporotic women than in both osteopenic women and normal women. In addition, magnesium and zinc concentrations in osteopenic women were significantly lower than in normal women. There were no statistically significant differences observed between the osteopenic, osteoporotic and control groups with respect to copper levels. The clinical significance of these changes needs further elucidation, but trace element supplementation, especially with magnesium and zinc and perhaps copper, may have beneficial effects on bone density.
Studies on an acetate-fermenting strain of Methanosarcina (1978)

An acetate-fermenting strain of Methanosarcina was isolated from an acetate enrichment culture inoculated with anaerobic sludge from a waste treatment digestor. In pure culture, this organism fermented acetate in the absence of added hydrogen at rates comparable in magnitude to those found in digestor systems. This rate was significantly higher than previously obtained for pure cultures of this genus. Mineral components of yeast extract were highly stimulatory for cultures growing on methanol. Comparable stimulation was not observed for cultures growing on acetate. Labeling studies indicated that acetate was converted to methane and CO2 as predicted by previous studies on mixed cultures. Total oxidation or reduction of acetate was not the mechanism of conversion of acetate to methane by the pure culture. The ability of this strain to form colonies or to produce methane from acetate was apparently influenced by the choice of substrate and conditions used for growing the inoculum.
Minutiae location and direction adjustment for nonlinear distorted fingerprint image matching (2010)

Nonlinear distorted fingerprint image matching is a challenge task in most computer-based Auto Fingerprint Identification Systems. Especially for minutiae-based matching algorithm, which is most widely adopted, both the location and direction of the minutiae are changed because of distortion. We carefully observe many distorted fingerprint images, find out some useful characteristics of minutiae' deviation on nonlinear distorted image, and try to use them to improve the matching accuracy. In this paper, we propose a method to adjust the minutiae position and direction on the basis of some landmark minutiae pairs got in pre-processing step. As a result, the minutiae deviation caused by nonlinear distortion can be recovered to a certain extent. Experimental results on FVC2004 DB2 show that our method can improve the matching performance clearly. Also this method can be deployed in most existing minutiae-based Auto Fingerprint Identification Systems easily.
Selective-area epitaxy and etching by chemical beam epitaxy (1993)

This paper reviews the unique characteristics of selective-area epitaxy by chemical beam epitaxy (CBE) using either shadow masks for dielectric masks. The beam nature permits the use of shadow masks. The high-vacuum environment results in no residual deposits on the dielectric masks. By injecting a gaseous etching beam, e.g. PCl3, directly into the CBE growth chamber, selective reactive chemical beam etching of InP was also demonstrated. This permits instant switching from etching to growth (and vice versa) in the same run for the first time in CBE, etching at high substrate temperatures, and improved morphology.
Concise Synthesis of Both Enantiomers of Pilocarpine (2021)

Furan-2-carboxylic acid was used as a starting material for the synthesis of dehydro-homopilopic acid. Esterification, hydrogenation and enzymatic hydrolysis followed by the reduction of Weinreb amides and a single-step attachment of a 1-methyl-imidazole residue allowed for the concise synthesis of both enantiomers of pilocarpine.
Gel Electrophoresis - Principles and Basics (2012)

Most will agree that gel electrophoresis is one of the basic pillars of molecular biology. This coined terminology covers a myriad of gel-based separation approaches that rely mainly on fractionating biomolecules under electrophoretic current based mainly on the molecular weight. In this book, the authors try to present simplified fundamentals of gel-based separation together with exemplarily applications of this versatile technique. We try to keep the contents of the book crisp and comprehensive, and hope that it will receive overwhelming interest and deliver benefits and valuable information to the readers.
Implementation of the notch technique as an RF peak pulse power standard (1976)

The theory and operation of a standard for measuring rf peak pulse power is described.
Effect of Mineralogy on Initial Wettability and Oil Recovery from Silica-containing Chalk (2019)

Summary Carbonate rock wettability is influenced by polar components in the crude oil, rock mineralogy and brine composition. Previous studies on chalk suggest that exposure of a large amount of acidic crude oil to core material reduces water wetness, thus affecting the ultimate oil recovery achieved during waterflooding. Presence of silica in the pore space appears to affect the wetting state of chalk toward more water-wet conditions. This study evaluates the wetting effect of crude oil exposure on the silica-rich Aalborg chalk, and its impact on oil recovery. Spontaneous imbibition and forced imbibition tests have been conducted at 50 °C to evaluate initial wetting and its effect on oil recovery from three silica-rich (6.8 At%) outcrop Aalborg chalk cores. Various amounts of crude oil was injected during core preparation, and it was observed that as the amount of crude oil injected increased, less water-wet conditions were obtained. A higher degree of water wetness in the Aalborg chalk core promoted higher ultimate oil recovery under forced imbibition than that previously reported for Stevns Klint chalk, containing low silica content. It was concluded that the silica content in the core induced a more water-wet wetting state in the core.
Broad Spectrum Thiopeptide Recognition Specificity of theStreptomyces lividans TipAL Protein and Its Role in Regulating Gene Expression (1999)

Microbial metabolites isolated in screening programs for their ability to activate transcription of the tipA promoter (ptipA) in Streptomyces lividans define a class of cyclic thiopeptide antibiotics having dehydroalanine side chains ("tails"). Here we show that such compounds of heterogeneous primary structure (representatives tested: thiostrepton, nosiheptide, berninamycin, promothiocin) are all recognized by TipAS and TipAL, two in-frame translation products of the tipA gene. The N-terminal helix-turn-helix DNA binding motif of TipAL is homologous to the MerR family of transcriptional activators, while the C terminus forms a novel ligand-binding domain. ptipA inducers formed irreversible complexes in vitro and in vivo (presumably covalent) with TipAS by reacting with the second of the two C-terminal cysteine residues. Promothiocin and thiostrepton derivatives in which the dehydroalanine side chains were removed lost the ability to modify TipAS. They were able to induce expression of ptipA as well as the tipA gene, although with reduced activity. Thus, TipA required the thiopeptide ring structure for recognition, while the tail served either as a dispensable part of the recognition domain and/or locked thiopeptides onto TipA proteins, thus leading to an irreversible transcriptional activation. Construction and analysis of a disruption mutant showed that tipA was autogenously regulated and conferred thiopeptide resistance. Thiostrepton induced the synthesis of other proteins, some of which did not require tipA.