gebhart/patrepeval huggingface dataset:
The mutational constraint spectrum quantified from variation in 141,456 humans (2020)

Genetic variants that inactivate protein-coding genes are a powerful source of information about the phenotypic consequences of gene disruption: genes that are crucial for the function of an organism will be depleted of such variants in natural populations, whereas non-essential genes will tolerate their accumulation. However, predicted loss-of-function variants are enriched for annotation errors, and tend to be found at extremely low frequencies, so their analysis requires careful variant annotation and very large sample sizes<sup>1</sup>. Here we describe the aggregation of 125,748 exomes and 15,708 genomes from human sequencing studies into the Genome Aggregation Database (gnomAD). We identify 443,769 high-confidence predicted loss-of-function variants in this cohort after filtering for artefacts caused by sequencing and annotation errors. Using an improved model of human mutation rates, we classify human protein-coding genes along a spectrum that represents tolerance to inactivation, validate this classification using data from model organisms and engineered human cells, and show that it can be used to improve the power of gene discovery for both common and rare diseases.
Studies on Enterovirus in Patients with Chronic Fatigue Syndrome (1994)

A large study on 121 patients with the chronic fatigue syndrome (CFS) that examined muscle biopsy samples for enterovirus by means of polymerase chain reaction analysis was carried out. The results were compared with those obtained from 101 muscle biopsy specimens from patients with a variety of other neuromuscular disorders (OND), including neurogenic atrophies, dystrophies, and mitochondrial, metabolic, and endocrine myopathies. Thirty-two (26.4%) of the biopsy specimens from the group of patients with CFS were positive, compared with 20 (19.8%) from the group of patients with OND, a difference that was not significant. This finding is in contrast to those of our previous smaller study in which significantly more patients with CFS than control subjects (53% [32 of 60] vs. 15% [6 of 41]) had enterovirus RNA sequences in their muscle. It was concluded that it is unlikely that persistent enterovirus infection plays a pathogenetic role in CFS, although an effect in initiating the disease process cannot be excluded.
Primary Cytotoxicity against the Envelope Glycoprotein of Human Immunodeficiency Virus-It Evidence for Antibody-Dependent Cellular Cytotoxicity In Vivo (1990)

Fresh peripheral blood mononuclear cells from human immunodeficiency virus-1 (HIV-1) seropositive donors can lyse target cells expressing the envelope glycoprotein in vitro. In most cases, this antigen-specific lysis is not mediated by T lymphocytes. Lymphoblastoid cell lines infected with recombinant vaccinia viruses expressing different forms of the envelope protein of HIV-1 were used as target cells in chromium-release assays of primary cytotoxic effector cells and of antibody-dependent cellular cytotoxicity (ADCC). By depleting effector cells of CD16+ lymphocytes, or by blocking target cell lysis with an anti-human IgG serum, primary env-specific lysis was found to be due to ADCC, the effector cells being armed in vivo with specific, cytophilic antibodies. This phenomenon is dependent on cell surface expression of the envelope protein and is directed against both gp120 and gp41. Human HIV-1 antibody-positive sera are able to mediate ADCC against HIV-infected CD4+ T lymphocytes, suggesting a possible role of ADCC in the natural infection.
Mapping and analysis of phosphorylation sites: a quick guide for cell biologists (2013)

A mechanistic understanding of signaling networks requires identification and analysis of phosphorylation sites. Mass spectrometry offers a rapid and highly sensitive approach to mapping phosphorylation sites. However, mass spectrometry has significant limitations that must be considered when planning to carry out phosphorylation-site mapping. Here we provide an overview of key information that should be taken into consideration before beginning phosphorylation-site analysis, as well as a step-by-step guide for carrying out successful experiments.
Detection of viable<i>Escherichia coli</i>O157:H7 by ethidium monoazide real-time PCR (2009)

The EMA real-time PCR has the potential to be a highly sensitive quantitative detection technique to assess the contamination of viable E. coli O157:H7 in ground beef and other meat or food products.
Opportunities and challenges for gut microbiome studies in the Indian population (2013)

The gut microbiome is a complex ecosystem that affects the development, immunological responses and nutritional status of the host. Efforts are being made to unravel the complex interaction between the gut microbiome and host to have a greater understanding about its role in human health. Colonization of the gut by microbes begins at birth, but the succession and composition of the microbial community depends on a number of factors including, but not limited to, the age, diet, genetic composition, gender, geographic location, and health status of an individual. Therefore, inclusion of diverse human subjects in the study of the gut microbiome is indispensable. However, conducting such studies in India presents unique opportunities and challenges. The vast diversity in human genetic composition, dietary habits, and geographic distribution that exists in the Indian population adds to the complexity in understanding the gut microbiome. Gut microbiome-related studies from other parts of the world have reported a possible association of diseases such as obesity and diabetes with the human gut microbiome. In contrast, an in-depth assessment of risk factors associated with altered gut microbiome in such diseases in the Indian population is lacking. Studies including the Indian population may give insights into the association of the gut microbiome with various factors and diseases that may not be possible from studies on western populations. This review briefly discusses the significance of the gut microbiome on human health and the present status of gut microbiome studies in the Indian population. In addition, this review will highlight the unique opportunities and challenges for gut microbiome studies in the Indian population.
Codec System Design for Continuous Color Barcode Symbols (2008)

To address the limits of capacity and the disadvantages of motional scanning capability of traditional two-dimensional barcodes, a novel 3-D continuous barcode (3-D CoBe) is proposed. It adds color as a third dimension based on our previous research on 2-D continuous barcodes (2-D CoBe). The novel 3-D CoBe is called 2-D continuous color barcode (CCB) as well. Furthermore, we implemented a codec system including an encoding sub-system and a decoding sub-system for a target application. In the codec system, CCB is generated and printed on papers by an encoding software sub-system, in addition to being recognized and decoded by a hand-held device with a decoding sub-system in real-time. It is verified that the codec system for CCB is practical and effective.
Etna: A Fault-tolerant Algorithm for Atomic Mutable DHT Data (2005)

This paper presents Etna, an algorithm for atomic reads and writes of replicated data stored in a distributed hash table. Etna correctly handles dynamically changing sets of replica hosts, and is optimized for reads, writes, and reconfiguration, in that order. Etna maintains a series of replica configurations as nodes in the system change, using new sets of replicas from the pool supplied by the distributed hash table system. It uses the Paxos protocol to ensure consensus on the members of each new configuration. For simplicity and performance, Etna serializes all reads and writes through a primary during the lifetime of each configuration. As a result, Etna completes read and write operations in only a single round from the primary. Experiments in an environment with high network delays show that Etna’s read latency is determined by round-trip delay in the underlying network, while write and reconfiguration latency is determined by the transmission time required to send data to each replica. Etna’s write latency is about the same as that of a non-atomic replicating DHT, and Etna’s read latency is about twice that of a non-atomic DHT due to Etna assembling a quorum for every read. 1
Sound absorption and compression properties of perpendicular-laid nonwovens (2018)

This study presents an investigation into the sound absorption behavior and compression properties of perpendicular-laid nonwovens. Seven types of perpendicular-laid nonwovens produced by vibrating and rotating perpendicular lappers were selected. Nonwovens with varying thickness and areal density were prepared by the heat-pressing method to investigate the effect of structural parameters such as thickness and areal density on sound absorption ability. Measurements of sound absorption properties were carried out with a Brüel and Kjær measuring instrument. The effect of manufacturing techniques on sound absorption performance and compression properties was investigated. The effect of porosity on sound absorption ability was studied. The influence of density and fiber orientation angle on compression properties was analyzed. The results show that samples prepared by vibrating perpendicular lapper exhibit better compression properties, whereas there is no significant influence of two manufacturing techniques on sound absorption performance. The increase of areal density results in improvement in the sound absorption ability. The increase of thickness can improve the sound absorption coefficient in the low-frequency range, but decrease of the coefficient occurred in the high-frequency range. A quadratic relationship between porosity and sound absorption ability has been found. The results also show that compressional resistance has a strong relation with density – the correlation coefficient is 0.95, indicating that the compressional resistance is directly proportional to the density of perpendicular-laid nonwovens. The results indicate that the perpendicular-laid nonwovens with higher initial fiber orientation angle have better compression properties.
La relación médico-paciente. Algunos factores asociados que la afectan (2007)

El medico y el equipo de salud son sometidos a cambios en su habitual forma de actuar; por otra parte, el paciente ha modificado su condicion, -merced a lo accesible del conocimiento-, tiene ahora un mayor nivel cultural y conoce mejor sus derechos como ciudadano y como consumidor. Hoy en dia, el binomio medico-paciente suele ser mas complejo, a menudo un nuevo integrante se suma, el que esta representado por los sistemas publicos o privados de salud y, por otra parte, la transformacion del paciente en derechohabiente o usuario. Ello induce a que la relacion se vea interferida y se convierta en una relacion medico-institucion-paciente, medico-administracion-paciente o medico-norma-paciente. Como se vislumbra en este breve analisis reflexivo, la relacion clasicamente binomial entre medico-paciente, ubicados frente a frente en la privacidad de un consultorio, y generada con el unico objetivo de recuperar la salud del enfermo, ha cambiado radicalmente y evoluciona de manera constante
Medical Treatment of Aortic Stenosis (2016)

Untreated, severe, symptomatic aortic stenosis is associated with a dismal prognosis. The only treatment shown to improve survival is aortic valve replacement; however, before symptoms occur, aortic stenosis is preceded by a silent, latent phase characterized by a slow progression at the molecular, cellular, and tissue levels. In theory, specific medical therapy should halt aortic stenosis progression, reduce its hemodynamic repercussions on left ventricular function and remodeling, and improve clinical outcomes. In the present report, we performed a systematic review of studies focusing on the medical treatment of patients with aortic stenosis. Lipid-lowering therapy, antihypertensive drugs, and anticalcific therapy have been the main drug classes studied in this setting and are reviewed in depth. A critical appraisal of the preclinical and clinical evidence is provided, and future research avenues are presented.
Tutorial and Survey Paper Power Minimization in IC Design: Principles and Applications (1996)

Low power has emerged as a principal theme in today’s electronics industry. The need for low power has caused a major paradigm shift in which power dissipation is as important as performance and area. This article presents an in-depth survey of CAD methodologies and techniques for designing low power digital CMOS circuits and systems and describes the many issues facing designers at architectural, logical, and physical levels of design abstraction. It reviews some of the techniques and tools that have been proposed to overcome these difficulties and outlines the future challenges that must be met to design low power, high performance systems.
Recent results from R&D on superconductors at CRPP (2003)

Prototype conductors for the ITER magnets have been tested extensively in the SULTAN facility at CRPP in the last decade. The in-depth characterization of the high current carrying conductors provided a valuable feedback in the design, with performance optimization and cost reduction. From the transient stability results on full size, short length conductor samples, the temperature margin required to withstand the plasma disruption has been found to be much smaller than originally assumed. A comparison between two specially designed sub-size conductors (the SeCRETS experiment) showed that the copper fraction in the superconducting Nb3Sn composite can be reduced without affecting the stability, leading to a substantial reduction of the overall amount of superconducting composite to be procured for the ITER magnets. The ac loss measurements carried out over a broad range of ac field frequency, brought evidence of two regimes of losses, complementing the test results of the ITER model coils and indicating that the correct eddy currents loss to be retained in the design for plasma disruption and initiation is much smaller than the value extrapolated from the slow charge of the model coils. The impact of the coolant speed on the stability behaviour of NbTi and Nb3Sn cable-in-conduit has been observed both in transient field and dc experiments, leading to the conclusion that the assumption of a constant value for the heat exchange coefficient is inadequate in the design criteria.
Based on Artificial Neural Networks for voice recognition word segment (2011)

Speech recognition is to study so that the machine can accurately hear the voice of the contents of people's problems, that is, accurate identification of words. Since the 90's it has been the focus of speech recognition has shifted to large vocabulary, continuous speech, speaker-up, man-machine voice communication has become a research focus. Use one kinds of arithmetic to study speech recognition: Dynamic Time Warping (DTW). Build a basic test platform of speech recognition using DTW.
Smart automotive lighting for vehicle safety (2013)

It is believed that vehicle-to-vehicle (V2V) communications and accurate positioning with sub-meter error could bring vehicle safety to a different level. However, to this date it is still unclear whether the envisioned V2V standard, dedicated short-range communications, can become available in commercially available vehicle products, while widely available consumergrade GPS receivers do not provide the required accuracy for many safety applications. In this article, combining visible light communications and visible light positioning, we propose the use of smart automotive lighting in vehicle safety systems. These lights would be able to provide the functions of illumination and signaling, reliable communications, and accurate positioning in a single solution. The proposed solution has low complexity, and is shown to be scalable in high vehicle density and fast topology changing scenarios. In this article, we also present several design guidelines for such a system, based on the results of our analytic and empirical studies. Finally, evaluation of our prototype provides evidence that the system can indeed detect potential risks in advance and provide early warnings to the driver in real-world scenarios, lowering the probability of traffic accidents.
Hiding under the Carpet: A New Strategy for Cloaking (2008)

A new type of cloak is discussed: one that gives all cloaked objects the appearance of a flat conducting sheet. It has the advantage that none of the parameters of the cloak is singular and can in fact be made isotropic. It makes broadband cloaking in the optical frequencies one step closer.
Guest Editorial Low-Dose CT: What Has Been Done, and What Challenges Remain? (2017)

The introduction of computed tomography (CT) in 1972 was among the most significant development in medical imaging since the discovery of X-rays in 1895. In addition, the innovation of computationally reconstructing tomographic images from projection data significantly influenced the development of other medical imaging modalities, such as magnetic resonance imaging and single photon and positron emission tomography. With the advent of helical and multi-detector-row CT (MDCT) scanners in the 1990s and 2000s along with innovations in cone-beam CT (CBCT) in many forms, CT gained unmatched speed and adaptability for volumetric imaging, leading to widespread use for diagnostic imaging, emergency examination, image-guided interventions, treatment planning, and monitoring of therapeutic response.
Studies on the chemical constituents of rutaceous plants. LV. The development of a versatile method for the synthesis of antitumor-active benzo(c)phenanthridine alkaloids. 5. A new method for quaternization of the benzo(c)phenanthridine nucleus. (1984)

A versatile method of synthesis of the quaternary benzo [c] phenanthridine alkaloid (1), having a tertiary benzo [c] phenanthridine skeleton, from the norbase (3) is described. Treatment of the norbase (3) with sodium borohydride in formic or in acetic acid gave the N-methyl-(5) or the N-ethyl-(7) dihydrobase, respectively, in good yield. The N-methyldihydrobase (5) could also be prepared by treatment of the norbase (3) with sodium borohydride and dimethyl sulfate in hexamethylphosphoric triamide. The dihydrobases (5 and 7) were readily convertible to the corresponding quaternary benzo [c] phenanthridine alkaloids by oxidation with Jones reagent or with 2, 3-dichloro-5, 6-dicyano-1, 4-benzoquinone (DDQ) in good yields. In addition, we found that the air-oxidation of the carbanions derived from the ψ-cyanides (11) of the quaternary bases (1) gave the corresponding oxybases (10) in excellent yields.
Photovoltaic properties of CVD amorphous silicon (1982)

Focal adhesion kinase (FAK) is considered as an attractive target for oncology. A series of F-18 labeled 5-bromo-N<sup>2</sup>-(4-(2-fluoro-pegylated (FPEG))-3,5-dimethoxyphenyl)-N<sup>4</sup>-(4-methoxyphenyl)pyrimidine-2,4-diamine derivatives were prepared and evaluated as the FAK targeted radiotracers for the early diagnoses of tumor. For the study of the FAK targeted drug molecules, this was the first attempt to develop the tumor diagnostic imaging agents on the radiopharmaceutical level. They inhibited the activity of FAK with IC<sub>50</sub> in the range of 91.4-425.7 nM, and among which the result of the [<sup>19</sup>F]2 was relatively good and had a modest IC<sub>50</sub> of 91.4 nM. The [<sup>19</sup>F]2 was also profiled in vitro against some other kinds of cancer-related kinases (including two kinds of non-receptor tyrosine kinase: PYK2 and JAK2, and three kinds of receptor tyrosine kinase: IGF-1R, EGFR and PDGFRβ). It displayed 25.2 folds selectivity against PYK2, 35.1 folds selectivity against EGFR, and more than 100 folds selectivity against IGF-1R, JAK2 and PDGFRβ. For the biodistribution in S180 bearing mice, the corresponding [<sup>18</sup>F]2 were also relatively good, with modest tumor uptake of 5.47 ± 0.19 and 5.80 ± 0.06 %ID/g at 15 and 30 min post-injection, respectively. Furthermore, its tumor/muscle, tumor/bone and tumor/blood ratio at 15 min post-injection were 3.16, 2.53 and 4.52, respectively. And its tumor/muscle, tumor/bone and tumor/blood ratio at 30 min post-injection were 3.14, 2.76 and 4.43, respectively. In addition, coronal micro-PET/CT images of a mouse bearing S180 tumor clearly confirmed that [<sup>18</sup>F]2 could be accumulated in tumor, especially at 30 min post-injection. Besides, for the [<sup>18</sup>F]2, both the biodistribution data and the micro-PET/CT imaging study showed significantly reduced uptake of the radiotracer in the tumor tissue at 30 min post-injection in mice that received PF-562,271 (one of the reported best selective FAK inhibitor which was developed by Pfitzer Inc. and inhibited the activity of FAK with IC<sub>50</sub> value of 1.5 nM) at 1 h before the injection of radiotracer. In combination with the above kinase profiling assay, it could be indicated that the uptake of [<sup>18</sup>F]2 in tumor of the mouse model was due to FAK expression, and that [<sup>18</sup>F]2 might be a kind of selectively FAK targeted tumor imaging agents. What's more, the results of the MD (molecular dynamics) simulations were in agreement with the changing trends of the interaction between the different F-19 standards and the FAK (expressed as the in vitro inhibitory abilities of enzymatic activities of FAK in this article), which was also in agreement with and had great effect on the changing trends of the uptake of the corresponding F-18 labeled tracers in tumor and some of theirs target/non-target ratios.
Low energy x-ray preionization source for discharge excited lasers (1981)

A low voltage (50 kV), low energy (3 J) x-ray preionization source has been developed specifically for avalanche discharge laser preionization. The new device uses a single stage high-voltage capacitor switched by a gradient grid hydrogen thyratron that drives a cold-cathode electron beam. Intense x-ray emission is produced by allowing the e beam to impact a high Z target foil. The entire system can operate up to 35 Hz repetition rate and produce an electron preionization density of ∼108 cm−3 in most rare-gas/halide laser gas mixtures.
Synthesis of Dityrosine Cross-Linked Peptide Dimers Using the Miyaura−Suzuki Reaction (2003)

[reaction: see text] Since peroxidase-catalyzed dityrosine formation is inefficient for peptides, we have developed alternative conditions for intermolecular dityrosine formation using the Miyaura-Suzuki reaction. A one-pot reaction is effective for cross-linking short peptides, but longer peptides inhibit the Suzuki step, mandating a traditional two-step procedure using potassium acetate for the Miyaura reaction and potassium carbonate for the Suzuki coupling. These palladium-based methods are complementary to the well-established peroxidase-catalyzed oxidative phenolic coupling of full-length proteins.