gebhart/patrepeval huggingface dataset:
The Small Subunit rRNA Modification Database (2004)

The Small Subunit rRNA Modification Database provides a listing of reported post-transcriptionally modified nucleosides and sequence sites in small subunit rRNAs from bacteria, archaea and eukarya. Data are compiled from reports of full or partial rRNA sequences, including RNase T1 oligonucleotide catalogs reported in earlier literature in studies of phylogenetic relatedness. Options for data presentation include full sequence maps, some of which have been assembled by database curators with the aid of contemporary gene sequence data, and tabular forms organized by source organism or chemical identity of the modification. A total of 32 rRNA sequence alignments are provided, annotated with sites of modification and chemical identities of modifications if known, with provision for scrolling full sequences or user-dictated subsequences for comparative viewing for organisms of interest. The database can be accessed through the World Wide Web at http://medlib.med.utah.edu/SSUmods.
A process-oriented data model for fuzzy spatial objects (1999)

I owe much to Prof
Non-Parametric Approach of Video Capsule Endoscope Localization Using Suboptimal Method of Position Bounded CWCL (2017)

For proper diagnosis, location of the wireless video capsule endoscope is required to be known by the physicians. In this paper, we propose an algorithm of localizing the capsule using path loss-based calibrated weighted centroid localization (CWCL). The main challenge in path loss-based localization is the highly randomness of measured path loss due to shadow fading and multi-path propagation effects of human body channel. To address the randomness in the measured path loss, we propose two methods of path loss estimation using Gaussian weighted average filter and the multiple input multiple output diversity scheme. Then, we calculate the weight of the sensor receiver position using the estimated path loss. Finally, the position of the capsule is estimated using position-bounded CWCL. We propose a realistic suboptimal method of estimating the calibration coefficient and also compute the optimal value of coefficient to set the benchmark. Additionally, we propose two boundary conditions on the estimated positions to improve the localization accuracy. We simulate our proposed algorithms using MATLAB to validate the accuracy and observe significant improvements without any prior knowledge of channel parameters. The proposed algorithms improve the accuracy up to 5.14-mm root mean square error and outperform the existing literature.
Adipocytes affect castration‐resistant prostate cancer cells to develop the resistance to cytotoxic action of NK cells with alterations of PD‐L1/NKG2D ligand levels in tumor cells (2018)

Blocking the adipocyte effect by inhibiting the IL-6/leptin-JAK/Stat3 signaling axis may enhance NK cell mediated immunity to CRPC cells and this strategy may help to develop future therapeutics to treat obese PCa patients.
What is the function of neuroglobin? (2009)

For a long time, haemoglobin and myoglobin had been assumed to represent the only globin types of vertebrates. In 2000, however, we discovered a third globin type by mining the genome sequence data. Based on a preferential expression in the nervous system, this globin is referred to as neuroglobin. Despite nine years of research, its function is still uncertain and a number of hypotheses have been put forward. Neuroglobin enhances cell viability under hypoxia and under various types of oxidative stress in transgenic systems, but does not appear to be strongly upregulated in response to stress. A close phylogenetic relationship with invertebrate nerve globins and its positive correlation with the oxidative metabolism and mitochondria suggest a role in O(2) supply. In vitro studies and cell culture experiments imply that neuroglobin may detoxify reactive oxygen or nitric oxide. Still other studies propose neuroglobin as being part of a signalling chain that transmits the redox state of the cell or that inhibits apoptosis. Although some functions are more probable than others, we conclude that it is still too early to definitively decide what may be the physiological role(s) of neuroglobin in vertebrates. Nevertheless, there is no doubt that neuroglobin has an essential, conserved function and is beneficial to neurons.
Assessing the Geographic Representativity of Farm Accountancy Data (2013)

The environment affects agriculture, via soils, weather, etc. and agriculture affects the environment locally at farm level and via its impact on climate change. Locating agriculture within its spatial environment is thus important for farmers and policy makers. Within the EU countries collect detailed farm data to understand the technical and financial performance of farms; the Farm Accountancy Data Network. However, knowledge of the spatial-environmental context of these farms is reported at gross scale. In this paper, Irish farm accounting data is geo-referenced using address matching to a national address database. An analysis of the geographic distribution of the survey farms, illustrated through a novel 2D ranked pair plot of the coordinates, compared to the national distribution of farms shows a trend in the location of survey farms that leads to a statistical difference in the climatic variables associated with the farm. The farms in the survey have significantly higher accumulated solar radiation values than the national average. As a result, the survey may not be representative spatially of the pattern of environment x farm system. This could have important considerations when using FADN data in modelling climate change impacts on agri-economic performance.
A new stability and time-delay tolerance analysis approach for Networked Control Systems (2010)

The key feature of Networked Control Systems (NCSs) is that the information is exchanged through a network among control system components. So the network induced time delay is inevitable in NCSs. The time delay, either constant (up to jitter) or random, may degrade the performance of control systems and even destabilize the systems if the systems are designed without considering the effects of the time delays properly. Once the structure of a NCS is confirmed, it is essential to identify what the maximum time delay is allowed for maintaining the system stability which, in turn, is also associated with the process of controller design. Some studies have been reported in estimation of the maximum time-delay allowed for maintaining system stability. However, most of the reported methods are normally over complicated for practical applications. A new finite difference approach is proposed in this paper for estimating the maximum time-delay tolerance, which has a simple structure and is easy to apply.
The Amplitude Reduction Factor in EXAFS (1997)

This paper was published as Journal de Physique IV, 1997, 7 (C2), pp. 151-152. It is available from http://jp4.journaldephysique.org/index.php?option=article&access=doi&doi=10.1051/jp4/1997146. Doi: 10.1051/jp4/1997146
The interplay between virus infection and the cellular RNA interference machinery (2006)

RNA interference (RNAi) plays a pivotal role in the regulation of gene expression to control cell development and differentiation. In plants, insects and nematodes RNAi also functions as an innate defence response against viruses. Similarly, there is accumulating evidence that RNAi functions as an antiviral defence mechanism in mammalian cells. Viruses have evolved highly sophisticated mechanisms for interacting with the host cell machinery, and recent evidence indicates that this also involves RNAi pathways. The cellular RNAi machinery can inhibit virus replication, but viruses may also exploit the RNAi machinery for their own replication. In addition, viruses can encode proteins or RNA molecules that suppress existing RNAi pathways or trigger the silencing of specific host genes. Besides the natural interplay between RNAi and viruses, induced RNAi provides an attractive therapy approach for the fight against human pathogenic viruses. Here, we summarize the latest news on virus-RNAi interactions and RNAi based antiviral therapy.
Pruritus Ani (2016)

Pruritus ani is a common condition with many different potential causes. Because of this, it can be difficult to treat. It is important to identify and eliminate any inciting factors, which are often unintentional consequences of the patient's attempts to alleviate symptoms. If no reversible cause is found, simple measures with diet modification and perianal hygiene are tried before using topical medications or procedures.
Very Slow Activity Fluctuations in Monkey Visual Cortex: Implications for Functional Brain Imaging (2003)

We examined fluctuations in band-limited power (BLP) of local field potential (LFP) signals recorded from multiple electrodes in visual cortex of the monkey during different behavioral states. We asked whether such signals demonstrated coherent fluctuations over time-scales of seconds and minutes, and would thus serve as good candidates for direct comparison with data obtained from functional magnetic resonance imaging (fMRI). We obtained the following results. (i) The BLP of the local field displayed fluctuations at many time-scales, with particularly large amplitude at very low frequencies (<0.1 Hz). (ii) These fluctuations exhibited high coherence between electrode pairs, particularly for BLP signals derived from the gamma frequency range. (iii) Coherence in the BLP, unlike that in the raw LFP, did not fall off sharply as a function of cortical distance. (iv) The structure and coherence of BLP changes were highly similar under distinctly different behavioral states. These results demonstrate the existence of widespread coherent activity fluctuations in the brain of the awake monkey over very long time-scales. We propose that such signals may make a significant contribution to the high variability observed in the time course of physiological signals, including those measured with functional imaging techniques. The results are discussed in the context of combined fMRI/electrophysiological recordings.
Antimicrobial Susceptibilities of Diverse <i>Bacillus anthracis</i> Isolates (2002)

A test of 25 genetically diverse isolates of Bacillus anthracis was conducted to determine their susceptibility to seven clinically relevant antimicrobial agents. Etest strips (AB BIODISK, Solna, Sweden) were used to measure the MICs for the isolates. Using the National Committee for Clinical Laboratory Standards MIC breakpoints for staphylococci, three isolates were found to be resistant to penicillin and five were found to be resistant to cefuroxime. The penicillin-resistant isolates were negative for beta-lactamase production. Continued surveillance of B. anthracis field isolates is recommended to monitor antimicrobial susceptibility.
RoF cell-cluster architecture in WDM/TDM hybrid-PON for train communication system (2008)

When today?s commuters in the train want to access broadband multimedia services. However, the classical solutions such as WLAN and UMTS are not sufficient to provide a high bandwidth to train users. In this paper, we discuss the RoF cell-cluster architecture in WDM/TDM hybrid-PON for train users. Also, we propose RoF cell-cluster architecture concept that can reduce the optical switching times and enlarge the coverage length of service.
Fisheye Keyboard: Whole Keyboard Displayed on Small Device (2014)

In this article, we propose a soft keyboard with interaction inspired by research on visualisation information. Our goal is to find a compromise between readability and usability on a whole character layout for an Ultra mobile PC. The proposed interactions allow to display all keys on a small screen while making pointing easier for the user by expanding any given key as a function of its distance from the stylus.
Role of Radiotherapy in the Treatment of Renal Cell Cancer: Updated and Critical Review (2017)

In the coming years, new studies will be published to confirm and increase the indications for use of RT.
Heat Transfer Performances and Exergetic Optimization for Solar Heat Receiver (2011)

Solar energy is one kind of important resource for clean and renewable energy, and is widely investigated in many fields. In order to increase the operating temperature and thermodynamic efficiency, concentrated solar radiation is widely used to heat the working fluid in solar thermal power system (Trieb & Nitsch, 1998) and other industrial engineerings (Klein et al., 2007; Ali et al., 2008). Concentrated solar radiation (Kalogirou, 2004) can be collected by the parabolic trough collector, parabolic dish reflector, heliostat field, etc. The concentrated energy flux has been studied in kinds of solar energy system. Moustafa et al. (1995) measured the solar flux density distribution on a plane receiver due to a flat heliostat. Estrada et al. (2007) proposed a calorimeter to measure the concentrated solar power produced by a point focus solar concentrator. Solar thermal power system based on trough, dish or heliostat field is a very promising and challenging technology for its high operating temperature and thermodynamic efficiency. In solar thermal power plant (Odeh et al., 2003), the heat transfer medium in solar heat receiver is heated by concentrated solar radiation to some high temperature, and then it can be used to operate kinds of heat engine and generate electricity. As a result, the heat receiver (Ortega et al., 2008) is the key problem for the photo-thermal transformation, and the heat transfer performance of solar heat receiver is the hotspot for solar energy research. The basic types of heat receiver in concentrated solar thermal system mainly include heat pipe receiver (Fujiwara et al., 1990), parabolic trough solar receiver (Gong et al., 2010), cavity receiver (Wu et al., 2010), and multistage solar receiver (Taragan, 1999), etc. The dynamical and thermal characteristics of solar heat receiver have been investigated in much literature (Cui et al., 2008; Grena, 2010). In general, the heat losses from solar receiver mainly include three contributions: radiation heat loss, convective heat loss, and conduction heat loss. The radiation heat loss (Melchior et al., 2008; Li et al., 2010) is mainly dependent upon the receiver structure, wall temperature, and emissivity/absorptivity of the receiver walls, while the convective heat loss (Clausing, 1981) is mainly determined by the receiver structure, wall temperature, and wind velocity. The heat conduction loss (Zavoico, 2001) exists in cavity receiver through the insulation wall, and it can be ignored in many solar heat receivers.
Entomology and pest management (1989)

Entomology and pest management , Entomology and pest management , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
Comparison of pyrimidine and purine nucleoside secretion and nucleoside kinase expression in resident and elicited peritoneal macrophages. (1981)

Thymidine was found in culture supernatants from both normal peritoneal macrophages and macrophages elicited in vivo with LPS under conditions in which there was no detectable TK activity. Abrogation of thymidine secretion was observed only when elicited macrophages were cultured in the presence of macrophage growth factor (MGF), whereas resident macrophages continued secreting under similar conditions. Similarly, TK activity was induced with MGF only in elicited, but not in resident, macrophages; LPS added in vitro failed to render resident macrophages susceptible to stimulation by MGF. Tests for adenosine and deoxyadenosine in macrophage supernatants proved that these nucleosides were not secreted by these cells. Although AK was consistently expressed in both resident and elicited macrophages, no significant dAK levels could be detected in either cell population. In contrast to TK, both purine nucleoside kinases could not be modulated or induced with MGF. The data indicate different reactivity to MGF by resident and elicited macrophages and a difference in pyrimidine vs purine nucleoside secretion as well as nucleoside kinase expression by these cells.
Molecular imprinted polymers as synthetic receptors for the analysis of myco- and phyco-toxins (2008)

Continuous exposure to low doses of myco- and phyco-toxins poses severe risks to human health. Contemporary analytical methods have the sensitivity required for contamination detection and quantification, but direct application of these methods on real samples can be rarely performed because of matrix complexity. Thus, selective analytical methods, relying on intelligent functional materials are needed. Recent years have seen the increasing use of molecular imprinted polymers in contaminant analysis because these materials seem to be particularly suitable for applications where analyte selectivity is essential. In this review, several applications of molecular imprinted polymers in myco- and phyco-toxin contamination analysis will be discussed.
Perceived Risk, Trust, and the Politics of Nuclear Waste (1991)

The Department of Energy's program for disposing of high-level radioactive wastes has been impeded by overwhelming political opposition fueled by public perceptions of risk. Analysis of these perceptions shows them to be deeply rooted in images of fear and dread that have been present since the discovery of radioactivity. The development and use of nuclear weapons linked these images to reality and the mishandling of radioactive wastes from the nation's military weapons facilities has contributed toward creating a profound state of distrust that cannot be erased quickly or easily. Postponing the permanent repository and employing dry-cask storage of wastes on site would provide the time necessary for difficult social and political issues to be resolved.
Posterolateral microdiscectomy for cervical monoradiculopathy caused by posterolateral soft cervical disc sequestration (1990)

The controversy over whether to use a posterior or anterior approach for surgical treatment of soft cervical discs is still largely unsettled. However, although the posterior approach may be underutilized, it has distinct advantages when there are specific indications. Out of a large pool of cases, 53 patients presented with acute monoradiculopathy caused by soft cervical disc herniation. In 36 of these, the disc was sequestered (nonconfined) and was posterolateral to the disc space as seen on computerized tomography-myelography. Distinct motor weakness was a common clinical finding in all 36 cases. These patients were treated by using a 2- to 3-cm skin incision for the posterolateral microsurgical approach. The extent of the lateral facetectomy depended upon the relationship between the nerve root and the disc. All fragments were lateral to the dural sac and were sequestered through the anulus fibrosus and the posterior longitudinal ligament. Sequestrations were removed under direct microscopic vision, but the disc space was not entered. Pain relief and motor-power improvement in the affected radicular distribution were immediate in all patients. Sensory deficit and residual motor loss improved dramatically with normalization at approximately 6 months. No complications occurred and the mean hospital stay was 2 days. The follow-up period varied from 4 to 42 months with a mean of 26 months. Thus far, there have been no recurrences or other associated complications. By using strict selection criteria and a microsurgical posterolateral approach with removal of the sequestered disc fragment, excellent results with normalization of the monoradiculopathy can be obtained. The ease of this technique, low risk, minimal complications, and excellent results make it an attractive alternative to the anterior approach. The clinical presentations, specific indications, surgical technique, and clinical results are discussed; and a prototype of a small cervical self-retaining retractor is described.
Trade Union Growth Waves in Hong Kong (1998)

The development of a trade union movement in Hong Kong, as in other industrial societies, has been an uneven process. We focus in this paper on three major growth waves -1920-26, 1946-51 and from the early 1970s to the 1990s when union formation and membership have risen substantially. We describe the strategies of organisational development pursued by Hong Kong trade unions during these three growth waves, the economic, political and social circumstances in which these choices were made, and the consequences of these choices for the movement's subsequent development. We argue that environmental variables including the nature of market economy, the voluntarist approach to labour relations of the colonial political regime, and the character of the working population have interacted with strategies of organisational development to affect the ease or difficulty of creating and sustaining union organisation. We conclude with a brief discussion of the impact on the union movement of China's resumption of sovereignty over Hong Kong and of the recent economic turmoil in the region.
<i>Gammarus</i>-Microbial Interactions: A Review (2011)

Gammarus spp. are typically classified as shredders under the functional feeding group classification. In the wild and in the laboratory, Gammarus spp. will often shred leaves, breaking them down into finer organic matter fractions. However, leaf litter is a poor quality food source (i.e., high C : N and C : P ratios) and very little leaf material is assimilated by shredders. In freshwater habitats leaf litter is colonized rapidly (within ∼1-2 weeks) by aquatic fungi and bacteria, making the leaves more palatable and nutritious to consumers. Several studies have shown that Gammarus spp. show preference for conditioned leaves over nonconditioned leaves and certain fungal species to others. Furthermore, Gammarus spp. show increased survival and growth rates when fed conditioned leaves compared to non-conditioned leaves. Thus, Gammarus spp. appear to rely on the microbial biofilm associated with leaf detritus as a source of carbon and/or essential nutrients. Also, Gammarus spp. can have both positive and negative effects on the microbial communities on which they fed, making them an important component of the microbial loop in aquatic ecosystems.
A rapid, point of care red blood cell agglutination assay for detecting antibodies against SARS-CoV-2 (2020)

Abstract The COVID-19 pandemic has brought the world to a halt, with cases observed around the globe causing significant mortality. There is an urgent need for serological tests to detect antibodies against SARS-CoV-2, which could be used to assess the prevalence of infection, as well as ascertain individuals who may be protected from future infection. Current serological tests developed for SARS-CoV-2 rely on traditional technologies such as enzyme-linked immunosorbent assays (ELISA) and lateral flow assays, which may lack scalability to meet the demand of hundreds of millions of antibody tests in the coming year. Herein, we present an alternative method of antibody testing that just depends on one protein reagent being added to patient serum/plasma or whole blood and a short five-minute assay time. A novel fusion protein was designed that binds red blood cells (RBC) via a single-chain variable fragment (scFv) against the H antigen and displays the receptor-binding domain (RBD) of SARS-CoV-2 spike protein on the surface of RBCs. Upon mixing of the fusion protein, RBD-scFv with recovered COVID-19 patient serum and RBCs, we observed agglutination of RBCs, indicating the patient developed antibodies against SARS-CoV-2 RBD. Given that the test uses methods routinely used in hospital clinical labs across the world, we anticipate the test can be rapidly deployed with only the protein reagent required at projected manufacturing cost at U.S. cents per test. We anticipate our agglutination assay may find extensive use in low-resource settings for detecting SARS-CoV-2 antibodies.