gebhart/patrepeval huggingface dataset:
Preparation of His-Tagged Armored RNA Phage Particles as a Control for Real-Time Reverse Transcription-PCR Detection of Severe Acute Respiratory Syndrome Coronavirus (2006)

Armored RNA has been increasingly used as both an external and internal positive control in nucleic acid-based assays for RNA virus. In order to facilitate armored RNA purification, a His6 tag was introduced into the loop region of the MS2 coat protein, which allows the exposure of multiple His tags on the surface during armored RNA assembly. The His-tagged armored RNA particles were purified to homogeneity and verified to be free of DNA contamination in a single run of affinity chromatography. A fragment of severe acute respiratory syndrome coronavirus (SARS-CoV) genome targeted for SARS-CoV detection was chosen for an external positive control preparation. A plant-specific gene sequence was chosen for a universal noncompetitive internal positive control preparation. Both controls were purified by Co2+ affinity chromatography and were included in a real-time reverse transcription-PCR assay for SARS-CoV. The noncompetitive internal positive control can be added to clinical samples before RNA extraction and enables the identification of potential inhibitive effects without interfering with target amplification. The external control could be used for the quantification of viral loads in clinical samples.
ChemInform Abstract: POLYCYCLIC FUSED AMIDINES. III. UNEXPECTED MODE OF CYCLIZATION OF 2‐PHENYLACYLISOQUINOLINIUM BROMIDE (1976)

Abstract Entgegen früheren Angaben von Kröhnke und Zecher entstehen bei der Cyclisierung des Isochinoliniumsalzes (I) das Imidazoisochinolin (II) und bei der Cyclisierung des Chinoliniumsalzes (III) das Imidazochinolin (IV).
Review of Acanthamoeba keratitis associated with contact lenses in Hong Kong Chinese people (2009)

Aim: To review the management and outcomes of Acanthamoeba keratitis associated with contact lenses in Hong Kong Chinese people. Methods: This was a retrospective review performed at the subspecialty eye clinics at a tertiary hospital. Con- secutive patients with presumed Acanthamoeba keratitis who were treated at the Prince of Wales Hospital, Hong Kong, from August 2005 to August 2007 were included. Medical interventions included corneal scraping, confo- cal microscopy, and intensive anti- Acanthamoeba eye drops. Surgical intervention included corneal gluing. Risk factors, clinical features, culture results, confocal microscopy results, treatment responses, and visual outcomes were analyzed. Results: Nine eyes of seven patients with clinical Acanthamoeba keratitis were identified. The use of Complete® MoisturePlus™ solution, overnight contact lens wear, and swimming with contact lenses were found to be risk factors for Acanthamoeba keratitis. Ocular pain and perineural infiltrates were important clinical features of Acanthamoeba corneal ulcer. The culture-positive rate for Acanthamoeba was 22.2%. Confocal microscopy was positive for 44.4% of eyes. Eight (88.9%) of the treated eyes had improvement of vision after medical treatment. Eight eyes had vision better than 20/50 and 6 eyes had vision better than 20/30. Conclusions: Contact with contaminated fluids was a n important risk factor for contact lens–related Acan- thamoeba keratitis. The recognition of clinical features, acquisition of corneal specimens for Acanthamoeba culture, and identification of intrastromal cysts by confocal microscopy were important for early diagnosis and subsequent treatment. Prompt initiation of a com- bination anti- Acanthamoeba treatment regimen was conducive to good visual recovery.
Insertional mutagenesis by theTol2transposon-mediated enhancer trap approach generated mutations in two developmental genes:tcf7andsynembryn-like (2007)

Gene trap and enhancer trap methods using transposon or retrovirus have been recently described in zebrafish. However, insertional mutants using these methods have not been reported. We report here development of an enhancer trap method by using the Tol2 transposable element and identification and characterization of insertional mutants. We created 73 fish lines that carried single copy insertions of an enhancer trap construct, which contained the zebrafish hsp70 promoter and the GFP gene, in their genome and expressed GFP in specific cells, tissues and organs, indicating that the hsp70 promoter is highly capable of responding to chromosomal enhancers. First, we analyzed genomic DNA surrounding these insertions. Fifty-one of them were mapped onto the current version of the genomic sequence and 43% (22/51) were located within transcribed regions, either exons or introns. Then, we crossed heterozygous fish carrying the same insertions and identified two insertions that caused recessive mutant phenotypes. One disrupted the tcf7 gene, which encodes a transcription factor of the Tcf/Lef family mediating Wnt signaling, and caused shorter and wavy median fin folds and pectoral fins. We knocked down Lef1, another member of the Tcf/Lef family also expressed in the fin bud, in the tcf7 mutant, and revealed functional redundancy of these factors and their essential role in establishment of the apical ectodermal ridge (AER). The other disrupted the synembryn-like gene (synbl), a homolog of the C. elegans synembryn gene, and caused embryonic lethality and small pigment spots. The pigment phenotype was rescued by application of forskolin, an activator of adenylyl cyclase, suggesting that the synbl gene activates the Galpha(S) pathway leading to activation of adenylyl cyclase. We thus demonstrated that the transposon-mediated enhancer trap approach can indeed create insertional mutations in developmental genes. Our present study provides a basis for the development of efficient transposon-mediated insertional mutagenesis in a vertebrate.
Optimal Signal Processing in Ground-Based Forward Scatter Micro Radars (2012)

The received signal in forward scatter radar (FSR) depends on the target's electrical size and trajectory, which are unknown a priori. As a result, in practical situations, it is impossible to obtain the accurate reference function at the reception side, and adaptation of optimal filtering is therefore proposed for this case. This paper presents a signal processing algorithm for ground target detection using FSR, which includes the construction of the adaptive reference functions and the identification of target velocity and its observation time. Furthermore, the algorithm performance is analytically determined under practical motion trajectories such as different motion directions and baseline crossing points, which indicate the effectiveness of the proposed algorithm in a practical case for FSR. The effectiveness of the algorithm is shown using both simulated and experimental data. Finally, the resolution in convoy targets in ground-based FSR is analytically obtained for the first time; the resolution is totally different from the resolution in conventional radar theory because of the target signature characteristics in ground-based FSR. The majority of the analytical results are verified experimentally.
Strassen's Matrix Multiplication on GPUs (2011)

We provide efficient single-precision and integer GPU implementations of Strassen's algorithm as well as of Winograd's variant. On an NVIDIA C1060 GPU, a speedup of 32% (35%) is obtained for Strassen's 4-level implementation and 33% (36%) for Winograd's variant relative to the sgemm (integer version of sgemm) code in CUBLAS 3.0 when multiplying 16384×16384 matrices. The maximum numerical error for the single-precision implementations is about 2 orders of magnitude higher than those for sgemm when n = 16384 and is zero for the integer implementations.
Cultura de seguridad del paciente en practicas médicas con radiaciones ionizantes: una revisión conceptual (2018)

Introducción: La cultura de seguridad del paciente implica un compromiso de pacientes y familiares, personal de salud, directivos y responsables de desarrollar e implementar las políticas sanitarias. Su fortalecimiento aumenta la seguridad de todos los involucrados en las prácticas con radiaciones ionizantes, minimizando los riesgos que atentan contra la salud individual, colectiva y ambiental. Objetivos: Introducir el concepto de cultura de seguridad del paciente aplicado a prácticas que utilizan radiaciones ionizantes en el ámbito de la salud pública. Método: Revisión bibliográfica para investigar las experiencias relacionadas con la cultura de seguridad en las prácticas médicas que utilizan fuentes de radiación ionizante, en sentido general. Resultados: Se precisaron los conceptos de cultura, cultura de seguridad y cultura de seguridad del paciente, enfatizando la necesidad de crear un ambiente propicio para reducir la probabilidad de incidentes y accidentes. Conclusiones: El compromiso con la seguridad del paciente y la cultura de seguridad del paciente debe estar lo suficientemente consolidado como para aceptar la responsabilidad y el desafío de garantizar que los pacientes estén y se sientan seguros. Las instituciones que realizan actividades con fuentes de radiación tienen la responsabilidad de alcanzar y sostener el más alto nivel de cultura de seguridad.
Syntheses of amphiphilic block copolymers of epsilon-caprolactone of ABA type (2009)

Series of amphiphilic block copolymers of poly(?-caprolactone) (PCL) and poly(oxy)ethylene glycol monomethyl ether (MPEG) of ABA type were synthesized in two-stage process. At first stage the isocyanate prepolymers (PCLpre) were prepared in the reactions of polyesterdiols (PCLdiol) of various molecular weights with either hexamethylene diisocyanate (HDI) or isophorone diisocyanate (IPDI) carried out in the presence of dibutyltin dilaurate (DBTL). PCLpre coupling with MPEG in the presence of the same catalyst was the other stage of synthesis. The products (PCLpre and MPEG-PCL-MPEG) were characterized by 1H NMR, IR and DSC methods (Fig. 1-4, Table 1 and 2). It was found in solubility tests in water of triblock copolymers obtained that aggregates were formed in aqueous solutions (Fig. 5).
Long-term inflammation increases risk of common mental disorder: a cohort study (2013)

. Dichotomizing the material according to CSF T-tau or P-tau did not change the ORs as compared with clinical diagnosis only (Figure Even though the OR for the ratio P-tau/Ab42 (6.50 (95% CI 5.07-8.35)) was slightly higher than for Ab42 alone, the difference was not statistically significant.
An exploratory study of awareness interests about software modifications (2011)

As software engineers collaboratively develop software, they need to often analyze past and present program modifications implemented by other developers. While several techniques focus on tool support for investigating past and present software modifications, do these techniques indeed address developers' awareness interests that are important to them? We conducted an initial focus group study and a web survey to understand in which task contexts and how often particular types of awareness-interests arise. Our preliminary study results indicate that developers have daily information needs about code changes that affect or interfere with their code, yet it is extremely challenging for them to identify relevant events out of a large number of change-events.
Serverless OpenHealth at data commons scale - traversing the 20 million patient records of New York's SPARCS dataset in real-time (2018)

In a previous report, we explored the serverless OpenHealth approach to the Web as a Global Compute space. That approach relies on the modern browser full stack, and, in particular, its configuration for application assembly by code injection. The opportunity, and need, to expand this approach has since increased markedly, reflecting a wider adoption of Open Data policies by Public Health Agencies. Here, we describe how the serverless scaling challenge can be achieved by the isomorphic mapping between the remote data layer API and a local (client-side, in-browser) operator. This solution is validated with an accompanying interactive web application (bit.ly/loadsparcs) capable of real-time traversal of New York’s 20 million patient records of the Statewide Planning and Research Cooperative System (SPARCS), and is compared with alternative approaches. The results obtained strengthen the argument that the FAIR reproducibility needed for Population Science applications in the age of P4 Medicine is particularly well served by the Web platform.
Coherent radar receiver that comprises a sigma delta modulator (2023)

Described herein are various technologies relating to processing a coherent signal. A receiver is configured to receive an analog signal, and process the analog signal to generate an input analog signal. The input analog signal has been modulated according to a suitable modulation sequence. A coherent signal sampler coherently samples the modulation sequence, and the result of such sampling is in turn used to demodulate the input analog signal. The resultant signal is then passed to a sigma delta modulator, where it is converted to digital form.
Energy levels of neutral and singly ionized berkelium, ^249Bk i and ^249Bk ii (1987)

Energy-level analyses of the observed emission spectrum of berkelium have yielded 179 odd and 186 even levels of neutral berkelium, Bk i, and 42 odd and 117 even levels of singly ionized berkelium, Bk ii. The levels are tabulated with the J value, the g value, the configuration and hyperfine constants A and B, and the width given for many of the levels. The ground states of Bk i and Bk ii are [Rn]5f79s2 H615/2∘ and [Rn]5f79s H78∘, respectively. A table lists the lowest level of each identified electronic configuration of Bk i and Bk ii.
Investigation of Polymer and Nanoparticle Properties with Nicotinic Acid and p-Aminobenzoic Acid Grafted on Poly(ε-caprolactone)-Poly(ethylene glycol)-Poly(ε-caprolactone) via Click Chemistry (2011)

In this study, the grafting of nicotinic acid and p-aminobenzoic acid (PABA) onto poly(ε-caprolactone)-poly(ethylene glycol)-poly(ε-caprolactone) was performed by Huisgen's 1,3-dipolar cycloaddition, also known as click chemistry. Concentrations used for grafting were 0.10, 0.20, and 0.30 molar ratios with respect to caproyl units. The grafted copolymers were successfully obtained at all ratios as confirmed by NMR, GPC, and FT-IR. According to the DSC results, the polymorphisms of these grafted copolymers were mostly changed from semicrystalline to amorphous depending on the type and the amount of grafting compounds. TGA thermograms showed different thermal stabilities of the grafted copolymers compared to the original copolymers. Cytotoxicity results from HUVEC models suggested that the toxicity of grafted nanoparticles increased with the molar ratios of grafting units. Due to differences in molecular structure between nicotinic acid and PABA, physicochemical properties (particle size and surface charge) of grafted copolymer nanoparticles were substantially different. With increasing molar ratio of the grafting units, the particle size of blank nanoparticles tended to increase, resulting from an increase in the hydrophobic fragments of the grafted copolymer. Ibuprofen was chosen as a model drug to evaluate the interaction between grafted copolymers and loaded drug. After ibuprofen loading, the particle size of the loaded nanoparticles of both grafted copolymers increased compared to that of the blank nanoparticles. Significant differences in loading capacity between nicotinic acid and PABA grafted copolymer nanoparticles were clearly shown. This is most likely a result of different compatibility between each grafting compound and ibuprofen, including hydrogen bond interaction, π-π stacking interaction, and steric hindrance.
Management of neurodegenerative disorders: Parkinson's disease and Alzheimer's disease. (2005)

Neurodegenerative disorders result from premature progressive degeneration of specific neurons, and manifest as diseases or syndromes with varied combinations of cognitive, motor, sensory and autonomic dysfunctions. The management involves pharmacotherapy as well as non-pharmacological measures and also to lessen the burden of the care-givers. The medications available for medical treatment are: Levodopa, dopamine agonists, amantadine, anticholinergics, enzyme inhibitors, etc. Advanced Parkinson's disease is concerned with management of motor complications and non-motor complications. Recently surgical treatment is a great option for managing motor complication. Orthostatic hypotension, gait distiurbances, emotional and psychiatric problems, sleep disturbances can be managed and had been discussed in brief. Currently there is no medication available for the cure of Alzheimer's disease. The specific medications claimed to improve patient's well being and cognition include cholinesterase inhibitors, N-methyl-D-aspartate receptor antagonist, anti-oxidants, and anti-amyloid therapy. While medical and surgical treatments for Parkinson's disease have revolutionised the management, still drug therapy for Alzheimer's disease is dismal.
Effect of Polymer Amphiphilicity on Loading of a Therapeutic Enzyme into Protective Filamentous and Spherical Polymer Nanocarriers (2007)

Rapid clearance and proteolysis limit delivery and efficacy of protein therapeutics. Loading into biodegradable polymer nanocarriers (PNC) might protect proteins, extending therapeutic duration, but loading can be complicated by protein unfolding and inactivation. We encapsulated active enzymes into methoxy-poly(ethylene glycol- block-lactic acid) (mPEG-PLA) PNC with a freeze-thaw double emulsion ( J. Controlled Release 2005, 102 (2), 427-439). On the basis of concepts of amphiphile self-assembly, we hypothesized that the copolymer block ratio that controls spontaneous curvature would influence PNC morphology and loading. We examined PNC yield, shape, stability, loading, activity, and protease resistance of the antioxidant enzyme, catalase. PNC transitioned from spherical to filamentous shapes with increasing hydrophobic polymer fraction, consistent with trends for self-assembly of lower MW amphiphiles. Importantly, one diblock copolymer formed filamentous particles loaded with significant levels of protease-resistant enzyme, demonstrating for the first time encapsulation of an active therapeutic enzyme into filamentous carriers. PNC morphology also greatly influenced its degradation, offering a new means of controlled delivery.
Rapid and High‐Throughput Forensic Short Tandem Repeat Typing Using a 96‐Lane Microfabricated Capillary Array Electrophoresis Microdevice* (2006)

A 96-channel microfabricated capillary array electrophoresis (muCAE) device was evaluated for forensic short tandem repeat (STR) typing using PowerPlex 16 and AmpFlSTR Profiler Plus multiplex PCR systems. The high-throughput muCAE system produced high-speed <30-min parallel sample separations with single-base resolution. Forty-eight previously analyzed single-source samples were accurately typed, as confirmed on an ABI Prism 310 and/or the Hitachi FMBIO II. Minor alleles in 3:1 mixture samples containing female and male DNA were reliably typed as well. The instrument produced full profiles from sample DNA down to 0.17 ng, a threshold similar to that found for the ABI 310. Seventeen nonprobative samples from various evidentiary biological stains were also correctly typed. The successful application of the muCAE device to actual forensic STR typing samples is a significant step toward the development of a completely integrated STR analysis microdevice.
Closed-form Expressions for the Moments of the Binomial Probability Distribution (2008)

This work develops closed-form expressions for the raw and central moments of the binomial probability distribution. For this I first derive a recursive formula for the raw moments from the moment generating function. Then it is shown that the recursion involved is essentially the same as for the Stirling numbers of the second kind. From this fact it is then possible to derive the closed formulae. Finally, I discuss an application of these formulae to the analysis of neural associative memory.
Extensions of the Chalmers nonlinear HEMT and MESFET model (1996)

The ability to simulate temperature, dispersion, and soft-breakdown effects as well as a new /spl alpha/ dependence was added to the Chalmers nonlinear model for high electron mobility transistor (HEMT's) and metal semiconductor field-effect transistor (MESFET's). DC, pulsed dc, low frequency (10 Hz-10 MHz), RF, and small signal S-parameter measurements (1-18 GHz) have been made on a large number of commercial HEMT and MESFET devices from different manufacturers in the temperature range 17-400 K in order to evaluate the validity of the model extensions.
The Effect of Commencing Combination Antiretroviral Therapy Soon after Human Immunodeficiency Virus Type 1 Infection on Viral Replication and Antiviral Immune Responses (1999)

Twelve subjects were treated with zidovudine, lamivudine, and ritonavir within 90 days of onset of symptoms of acute infection to determine whether human immunodeficiency virus type 1 (HIV-1) infection could be eradicated from an infected host. In adherent subjects, with or without modifications due to intolerance, viral replication was suppressed during the 24-month treatment period. Durable suppression reduced levels of HIV-1-specific antibodies and cytotoxic T lymphocyte responses in selected subjects. Proviral DNA in mononuclear cells uniformly persisted. The persistence of HIV-1 RNA expression in lymphoid tissues and peripheral blood mononuclear cells suggests that elimination of this residual pool of virus should be achieved before considering adjustments in antiretroviral therapeutic regimens. In addition, given the reduction in levels of virus-specific immune responses, it would seem prudent to consider enhancing these responses using vaccine strategies prior to the withdrawal of antiviral therapy.
Role of Graphene Oxide Liquid Crystals in Hydrothermal Reduction and Supercapacitor Performance (2016)

The formation of liquid crystal (LC) phases in graphene oxide (GO) aqueous solution is utilized to develop high-performance supercapacitors. To investigate the effect of LC formation on the properties of subsequently reduced GO (rGO), we compare films prepared through blade-coating of viscous LC-GO solution and ultrasonic spray-coating of diluted GO aqueous dispersion. After hydrothermal reduction under identical conditions, the films show different morphology, oxygen content, and specific capacitance. Trapped water in the LC GO film plays a role in preventing restacking of sheets and facilitating the removal of oxygenated groups during the reduction process. In device architectures with either liquid or polymer electrolyte, the specific capacitance of the blade-coated film is twice as high as that of the spray-coated one. For a blade-coated film with mass loading of 0.115 mg/cm(2), the specific capacitance reaches 286 F/g in aqueous electrolyte and 263 F/g in gelled electrolyte, respectively. This study suggests a route to pilot-scale production of high-performance graphene supercapacitors through blade-coated LC-GO films.