gebhart/patrepeval huggingface dataset:
Structural determinants for transcriptional activation by cAMP-responsive DNA elements. (1988)

A transcriptional cAMP-responsive enhancer element (CRE) consisting of the 8-base pair (bp) palindrome, 5' TGACGTCA 3', is found in several eukaryotic genes. We analyzed the effects on gene transcription of point mutations within the CRE, the influence of the bases surrounding the CRE, and the requirements for transcriptional synergism of tandemly repeated CREs. When inserted as an oligonucleotide with restriction enzyme linker sites, the 8-bp CRE itself is as active in conferring cAMP responsivity on an enhancerless chloramphenicol acetyltransferase reporter plasmid as is a single copy of the choriogonadotropin alpha (CG alpha), twice repeated 18-bp sequence containing the CRE. Point mutations in the first (T to A), fourth (C to G), or eighth (A to T) positions of the CRE, when contained within the CG alpha 18-bp sequence, each inhibited transcriptional activity greater than 90%. However, the identical eighth position A to T mutation occurs in the cAMP-responsive sequence of the vasoactive intestinal peptide (VIP) gene, and that mutant sequence in the context of the adjacent bases of the native VIP sequence is maximally cAMP responsive when inserted in the reporter plasmid. The substantially reduced activity of the core 8-bp CRE when synthesized as a cassette including the adjacent bases of the rat glucagon or bovine parathyroid hormone gene further emphasizes the restrictive influence of particular surrounding sequences. Active oligonucleotides containing the 8-bp palindrome and different but equally permissive contexts have comparable properties in transfected reporter genes and gel mobility-shift assays. The pair of tandemly repeated 18-bp elements containing the CRE in the CG alpha gene synergistically stimulate transcription either with paired native CREs or when one native CRE is paired with one mutant CRE, suggesting the presence of cooperative interactions. Tandem insertion of more than two 18-bp sequences, or insertion of additional sequences between the two CREs, inhibits transcription. These observations indicate that the contexts of the bases adjacent to CREs exert profound influences on the transcriptional activities mediated by the cAMP-responsive elements.
Implication of PBP74/mortalin/GRP75 in the radio-adaptive response (2002)

The results support the view that while PBP74 is necessary to the adaptive response, it may not by itself be sufficient for the adaptive response to occur.
Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution (2008)

Protein dynamics are essential for protein function, and yet it has been challenging to access the underlying atomic motions in solution on nanosecond-to-microsecond time scales. We present a structural ensemble of ubiquitin, refined against residual dipolar couplings (RDCs), comprising solution dynamics up to microseconds. The ensemble covers the complete structural heterogeneity observed in 46 ubiquitin crystal structures, most of which are complexes with other proteins. Conformational selection, rather than induced-fit motion, thus suffices to explain the molecular recognition dynamics of ubiquitin. Marked correlations are seen between the flexibility of the ensemble and contacts formed in ubiquitin complexes. A large part of the solution dynamics is concentrated in one concerted mode, which accounts for most of ubiquitin's molecular recognition heterogeneity and ensures a low entropic complex formation cost.
Analysis of Nucleotide Sequences at 3' Termini of Duplex Deoxyribonucleic Acid with the Use of the T4 Deoxyribonucleic Acid Polymerase (1971)

Abstract The T4 DNA polymerase catalyzes extensive exonucleolytic degradation of linear duplex DNA starting at the 3' ends. However, the enzyme will release only a few nucleotides from each DNA molecule if the degradation is run in the presence of a single deoxynucleoside triphosphate. Several experiments suggested that the polymerase degrades a chain only until a nucleotide is released which can be replaced by transfer from the triphosphate. Subsequent reaction consists only of alternating removal and replacement of that nucleotide, without net degradation of the DNA. Because only a few nucleotides are released in the presence of a single triphosphate, it seemed possible that the polymerase could be used for analysis of nucleotide sequences at 3' termini of duplex DNA. This possibility was verified by the analysis of the 3'-terminal sequence of fragments of bacteriophage T7 DNA produced by endonuclease R, the Hemophilus influenzae restriction endonuclease. This terminal sequence had been previously identified by Kelly and Smith (J. Mol. Biol., 51, 393 (1970)). The method used in this analysis, which should also be applicable to other DNAs, was to degrade 32P-labeled DNA by the T4 polymerase in the presence of each of the four triphosphates. The nucleotides released in each case were identified and quantitatively determined by thin layer chromatography, and were consistent with the previously determined terminal sequence.
Survival in Primary Pulmonary Hypertension (2002)

Intravenous epoprostenol improves long-term survival in PPH.
Comparison of DNA-lipid complexes and DNA alone for gene transfer to cystic fibrosis airway epithelia in vivo. (1997)

Cationic lipids show promise as vectors for transfer of CFTR cDNA to airway epithelia of patients with cystic fibrosis (CF). However, previous studies have not compared the effect of DNA-lipid to DNA alone. Recently, we developed a formulation of plasmid encoding CFTR (pCF1-CFTR) and cationic lipid (GL-67:DOPE) that generated greater gene transfer in mouse lung than previously described DNA-lipid vectors. Therefore, we tested the hypothesis that DNA-lipid complexes were more effective than DNA alone at transferring CFTR cDNA to airway epithelia in vivo. We administered complexes of DNA-lipid to one nostril and DNA alone to the other nostril in a randomized, double-blind study. Electrophysiologic measurements showed that DNA-lipid complexes partially corrected the Cl- transport defect. Importantly, the pCF1-CFTR plasmid alone was at least as effective as complexes of DNA with lipid. Measurements of vector-specific CFTR transcripts also showed gene transfer with both DNA-lipid and DNA alone. These results indicate that nonviral vectors can transfer CFTR cDNA to airway epithelia and at least partially restore the Cl- transport defect characteristic of CF. However, improvements in the overall efficacy of gene transfer are required to develop a treatment for CF.
Discrete Distributions of Adenosine Receptors in Mammalian Retina (1990)

Binding sites for both the adenosine A1 receptor agonists [3H]phenylisopropyladenosine and [3H]cyclohexyladenosine and the mixed A1-A2 agonist N-[3H]ethylcarboxamidoadenosine [( 3H]NECA) were localized in rabbit and mouse retinas using autoradiographic techniques. These two classes of agonists bound to very different regions of mammalian retinas. A1 agonist binding was localized to the inner retina, particularly over the inner plexiform layer. The binding of [3H]NECA was observed primarily over the retinal pigmented epithelium and the outer and inner segments of photoreceptors. [3H]NECA labeling was not affected either by including a low concentration of unlabeled A1 agonist or by pretreating tissue with N-ethylmaleimide to inhibit ligand binding at A1 sites. While virtually all of the [3H]NECA binding was displaced by an excess of unlabeled NECA, displacement with antagonist or a large excess of cyclohexyladenosine revealed that approximately 30% of the [3H]NECA binding was at non-A1,A2 sites. The majority of the binding in the outer retina thus labeled A2 receptor sites. The unique localizations of the two classes of adenosine receptors suggest different functions in visual processing.
Normalized Switch Schemes for Low Density Parity Check Codes (2006)

This paper addresses switch schemes for switch type hybrid hard decision iterative algorithms decoding finite length low density parity check (LDPC) codes. After piecewise analysis for extrinsic transfer information (EXIT) chart family and exploration of fixed points, one general switch scheme named normalized switch scheme, for which majority based (MB) algorithms and Gallager's decoding algorithm B (GB) are extreme cases, is proposed. Several specific normalized switch scheme, named expanded optimal switch scheme and tail-cut (TC) optimal switch scheme, are given and their convergence properties are analyzed. Simulation shows that compared with GB that holds optimality for infinity length codes, proposed switch schemes show performance improvements while enjoying less sensitivity to channel parameter underestimations for finite length codes
Non-alcoholic fatty liver disease, to struggle with the strangle: Oxygen availability in fatty livers (2017)

Nonalcoholic fatty liver diseases (NAFLD) is one of the most common chronic liver disease in Western countries. Oxygen is a central component of the cellular microenvironment, which participate in the regulation of cell survival, differentiation, functions and energy metabolism. Accordingly, sufficient oxygen supply is an important factor for tissue durability, mainly in highly metabolic tissues, such as the liver. Accumulating evidence from the past few decades provides strong support for the existence of interruptions in oxygen availability in fatty livers. This outcome may be the consequence of both, impaired systemic microcirculation and cellular membrane modifications which occur under steatotic conditions. This review summarizes current knowledge regarding the main factors which can affect oxygen supply in fatty liver.
Breakdown voltage and reverse recovery characteristics of free-standing GaN Schottky rectifiers (2002)

Schottky rectifiers with implanted p/sup +/ guard ring edge termination fabricated on free-standing GaN substrates show reverse breakdown voltages up to 160 V in vertical geometry devices. The specific on-state resistance was in the range 1.7-3.0 /spl Omega//spl middot/cm/sup 2/, while the turn-on voltage was /spl sim/1.8 V. The switching performance was analyzed using the reverse recovery current transient waveform, producing an approximate high-injection, level hole lifetime of /spl sim/15 ns. The bulk GaN rectifiers show significant improvement in forward current density and on-state resistance over previous heteroepitaxial devices.
Palladium-Catalysed Synthesis of Alkyl Alkenylmethyl-and Alkenylphenylphosphinates (1986)

Alkyl Alkenylmethyl- and alkenylphenylphosphinates were synthesized stereospecifically by the palladium-catalysed reaction of a monoalkyl methane- or benzenephosphonite with an alkenyl bromide in the presence of triethylamine with moderate to good yields.
Digital Opportunities for Outcomes in Recovery Services (DOORS): A Pragmatic Hands-On Group Approach Toward Increasing Digital Health and Smartphone Competencies, Autonomy, Relatedness, and Alliance for Those With Serious Mental Illness (2020)

Digital health technologies such as smartphones present the potential for increased access to care and on-demand services. However, many patients with serious mental illnesses (eg, schizophrenia) have not been offered the digital health training necessary to fully utilize these innovative approaches. To bridge this digital divide in knowledge and skills, we created a hands-on and interactive training program grounded in self-determination theory, technology use cases, and the therapeutic alliance. This article introduces the need and theoretical foundation for and the experience of running the resulting Digital Opportunities for Outcomes in Recovery Services (DOORS) group in the setting of 2 programs: a first-episode psychosis program and a clubhouse for individuals with serious mental illness. The experience of running these 2 DOORS groups resulted in 2 publicly available, free training manuals to empower others to run such groups and adapt them for local needs. Future work on DOORS will expand the curriculum to best support digital health needs and increase equity of access to and knowledge and skills related to technology use in serious mental illness.
Design and characterization of a photometer-colorimeter standard (2004)

A photometer and tristimulus colorimeter has been developed at the National Institute of Standards and Technology (NIST) to realize a color scale. A novel construction was developed to implement the spectral-responsivity-based scale with small uncertainty. The new device can be used as a reference illuminance and luminance meter as well. Temperature-controlled filter combinations, with 5-8 layers in one package, are used to match the responsivity of a silicon tunnel-trap detector to the CIE color-matching functions with small spectral mismatch values (f1'). Design considerations to extend the tunnel-trap detector with replaceable single and double apertures and changeable filter combinations are described. The design and fabrication of the filter packages and the dependence of the f1' values on the thickness of the filter layers are discussed. The colorimeter was characterized for angular, spatial, and spectral responsivity. An improved preamplifier can convert current to voltage in an 11-decade dynamic range with 0.01% uncertainty.
Formation of Gilgai and Soil Wedges in South Dakota 1 (1997)

Soil microrelief forms where the subsoils are usually dry, have vertical desiccation cracks, and the percentage volume change divided by the percentage weight change as water is added to dry clods ranges from about 1.3 to 1.6. The microrelief, often called gilgai, consists of microdepressions and microknolls on level slopes and of microvalleys and microridges oriented in the slope direction on sloping areas. The microhighs are generally S to 15 ft apart and a few inches high. Gilgai microlows receive runoff from microhighs so their subsoils moisten first, swell, and close cracks in the microhigh subsoils. Microhigh subsoils swell upward when moistened to enlarge the microhigh. Distance between microhighs increases as the depth of wetting and drying increases. Subsoils can have giant desiccation cracks 8 to 12 in. (20–30 cm) wide and extend downward 6.5 to 10 ft (2–3 m). These large cracks form where the lower subsoil is usually dry but the upper subsoil is wetted and dried annually over several years. Soil wedges form where vertical desiccation cracks are stable so surface soils can enter the cracks as the soil wets and dries. Gilgai and soil wedges occur where droughts of several years duration are frequent. Soil volume changes caused by water content changes are necessary in their formation (Hallsworth et al., 1955). Surface microrelief and soil wedges are similar in permafrost and in gilgai (Washburn, 1980). Both occur where soil volumes change because either the temperature or water content changes. Gilgai occur in the semiarid part of South Dakota on fine‐textured soils that have vertic characteristics. Soil wedges can form in soils with stable subsoil prisms. The discussion of the formation of gilgai and soil wedges in South Dakota will be based on published material and over 40 yr of field observation. Discussions on South Dakota' climate, soil drying and cracking, and water movement into soils permit the reader to apply the proposed mechanisms in similar soil areas.
Soluble cytokine receptors: novel immunotherapeutic agents (2000)

Being mediators of immune and inflammatory reactions, abnormal or excessive production of cytokines is often the main cause of the pathology in many types of disease. Targeting cytokines by means of inhibitory drugs may thus offer a valid therapeutic approach in particular diseases. Soluble forms of cytokine receptors (sCR) normally participate in the control of cytokine activity in vivo by inhibiting the ability of cytokines to bind their membrane receptors and from generating a biological response. The ability of sCR to act as cytokine inhibitors, coupled to their specificity, high affinities and low immunogenicities have prompted considerable interest in their use as immunotherapeutic agents. In fact, many types of sCR have been shown to inhibit the biological activity of their cytokines in vitro and in different experimental models. Several sCR, particularly the soluble TNF receptors sTNFR-I (p55) and sTNFR-II (p75), have been modified by linking them to the Fc portion of human immunoglobulin (e.g., 'immunoadhesins') or by the addition of polyethylene-glycol (PEG) (e.g., 'PEGylation'), in order to enhance their affinity and/or biological half-life. These agents have shown significant therapeutic value in clinical trials of patients with rheumatoid arthritis (RA). Indeed, a sTNFR-II:Fc hybrid molecule (etanercept), the first sCR-derived therapeutic agent to receive approval for human use, is already utilised for the treatment of some forms of RA. Additional applications of this drug in other inflammatory conditions are currently being evaluated, while another sCR-derived agent, a human sIL-4R, is undergoing trials for the treatment of asthma. Many other sCR, such as sIL-1R, sIL-5R, sIFNgammaR, may also have significant potential for the treatment of a wide variety of human diseases.
Study on Rural Living Environment and Satisfaction by Improving Rural Hosing Renewal Project (2003)

The aim of this study is to analyze the improvement of housing renewal project and suggest the conditions of rural housing environment filled with the resident's desire, requirements concerning about characteristics of a rural environment and temporal and social requirements. The project for improvement of rural housing environment has been executed in a few ways: reform of the rural housing environment and the development of territories for settlement of a desolate region. To analyze and assess the accomplishments, we considered codes and process related to the project for improvement of rural housing environment and analyzed present conditions and problems through many reference books and administrative data. According to these results, devices in future business for improvement of rural housing environment are as follows; It should required a rational allocation of working space, living space, cultural activity space suitable for rural area characteristics and changed into uniformed system in various projects governed by different institutions.
Orthodontic Treatment Acceleration with Corticotomy-assisted Exposure of Palatally Impacted Canines (2007)

This preliminary study supports the concept that a corticotomy-assisted surgical technique helps reduce orthodontic treatment time for palatally impacted canines.
The Synthesis of 2-Aminobenzophenones (1980)

Methods for the preparation of 2-aminobenzophenone and its derivatives published from 1945 through 1979 are reviewed. The various synthetic schemes developed to date for 2-aminobenzophenones allow most derivatives to be prepared readily and in good yield. The review is completed by tables of mono- and di-substituted 2-aminobenzophenones. 1. Introduction 2. Syntheses from 2-Benzoylbenzoic Acids 3. Syntheses from 3-Arylindoles 4. Syntheses from 2,1-Benzisoxazoles 5. Syntheses from Nitroaryl Substrates 5.1. From 2-Nitrobenzyl Chloride 5.2. From 2-Nitrobenzoyl Chloride 5.3. From 2-Nitrobenzoic Acid 5.4. From 2-Chloronitrobenzene 6. Syntheses from Anthranilic Acids 6.1. From 2-Aminobenzonitrile 6.2. From 3,1-Benzoxazin-4-one 6.3. From Isatoic Anhydride 6.4. From Formamidine 6.5. From Arylsulfonamide 7. Syntheses from Anilines 7.1. para-Substitution 7.2. Boron Trichloride Complex 7.3. ortho-Lithiation 7.4. 2-Benzylaniline 8. Syntheses from Halobenzophenones 9. Syntheses of N-Alkyl Derivatives 10. Tables of Derivatives
Acoustic scattering in dispersions: Improvements in the calculation of single particle scattering coefficients (2007)

Measurements of ultrasound speed and attenuation can be related to the properties of dispersed systems by applying a scattering model. Rayleigh's method for scattering of sound by a spherical object, and its subsequent developments to include viscous, thermal, and other effects (known as the ECAH model) has been widely adopted. The ECAH method has difficulties, including numerical ill-conditioning, calculation of Bessel functions at large arguments, and inclusion of thermal effects in all cases. The present work develops techniques for improving the ECAH calculations to allow its use in instrumentation. It is shown that thermal terms can be neglected in some boundary equations up to approximately 100 GHz in water, and several simplified solutions result. An analytical solution for the zero-order coefficient is presented, with separate nonthermal and thermal parts, allowing estimation of the thermal contribution. Higher orders have been simplified by estimating the small shear contribution as the inertial limit is approached. The condition of the matrix solutions have been greatly improved by these techniques and by including appropriate scaling factors. A method is presented for calculating the required Bessel functions when the argument is large (high frequency or large particle size). The required number of partial wave orders is also considered.
Systematic Review of Lumbar ProvocationDiscography in Asymptomatic Subjectswith a Meta-analysis of False-positive Rates (2008)

Strength of evidence is level II-2 based on the Agency for Healthcare Research Quality (USPSTF) for the diagnostic accuracy of discography. Contrary to recently published studies, discography has a low false-positive rate for the diagnosis of discogenic pain.
Experience with vero cells at Pasteur Mérieux Connaught. (1999)

The Vero cell line has been used by Pasteur-Merieux-Connaught (PMC) since 1982 with the Cell Bank's system to produce, at the 142nd passage, inactivated polio vaccine (IPV), oral polio vaccine (OPV) and rabies vaccines. The safety of the cell line has been regularly validated at the WCB level according to the WHO and European Pharmacopeia requirements for absence of bacteria, fungi, mycoplasma and viruses. Special emphasis was devoted to establishing the absence of simian viruses (SV40, SIV, Retro-D virus, simian CMV). Reverse Transcriptase (RT) activity was also negative. At low level of passage, the Vero cells are not tumorigenic. Vaccines have been prepared in low passage level Vero cells and, together with the excellent downstream purification, has resulted in excellent safety as attested by pharmacovigilance of more than 100 million doses of IPV during 12 years, more than 20 million doses of rabies vaccine during 10 years and more than one billion of OPV during six years.
Parallel video decoding in the emerging HEVC standard (2012)

In this paper we propose and evaluate a parallelization strategy for the emerging HEVC video coding standard. The proposed strategy is based on entropy slices which allows exploiting parallelism in the entropy decoding stage while maintaining high coding efficiency. Our approach requires to encode videos with one entropy slice per LCU row in order to decode multiple LCU rows in a wavefront parallel manner. Evaluations performed on a PC with 12 Intel Xeon cores running at 3.3 GHz show that it is possible to achieve real-time performance for 1920×1080p50 (53.1 fps) and 2560×1600 (29.5fps) video resolutions with speedups of 5.2× and 6.3× compared to sequential execution, respectively.