gebhart/patrepeval huggingface dataset:
HIV classification using coalescent theory (2008)

Algorithms for subtype classification and breakpoint detection of HIV-I sequences are based on a classification system of HIV-l. Hence, their quality highly depend on this system. Due to the history of creation of the current HIV-I nomenclature, the current one contains inconsistencies like: The phylogenetic distance between the subtype B and D is remarkably small compared with other pairs of subtypes. In fact, it is more like the distance of a pair of subsubtypes Robertson et al. (2000); Subtypes E and I do not exist any more since they were discovered to be composed of recombinants Robertson et al. (2000); It is currently discussed whether -- instead of CRF02 being a recombinant of subtype A and G -- subtype G should be designated as a circulating recombination form (CRF) nd CRF02 as a subtype Abecasis et al. (2007); There are 8 complete and over 400 partial HIV genomes in the LANL-database which belong neither to a subtype nor to a CRF (denoted by U). Moreover, the current classification system is somehow arbitrary like all complex classification systems that were created manually. To this end, it is desirable to deduce the classification system of HIV systematically by an algorithm. Of course, this problem is not restricted to HIV, but applies to all fast mutating and recombining viruses. Our work addresses the simpler subproblem to score classifications of given input sequences of some virus species (classification denotes a partition of the input sequences in several subtypes and CRFs). To this end, we reconstruct ancestral recombination graphs (ARG) of the input sequences under restrictions determined by the given classification. These restritions are imposed in order to ensure that the reconstructed ARGs do not contradict the classification under consideration. Then, we find the ARG with maximal probability by means of Markov Chain Monte Carlo methods. The probability of the most probable ARG is interpreted as a score for the classification. To our knowledge, this particular problem was not addressed up to now. The software package Lamarc Kuhner et al. (2000) allows for sampling ARGs, but it assumes that recombination events only involve one breakpoint. However, in HIV recombinants usually have more than one breakpoint. Moreover, Lamarc does not perform an explicit breakpoint detection, but tries to find them by chance. Although this approach is suitable for most situations, it will not lead to satisfying results in case of highly recombining viruses with multiple breakpoints.
Adaptive Tuned Mass Damper based on Pre-stressable Leaf-springs (2007)

Lightweight bridges exhibit a high live load to dead load ratio. Thus, their resonance frequencies depend on the current loading state and can vary in quite a broad range. This behavior is a real challenge in vibration mitigation of such structures controlled by tuned mass dampers (TMDs), since the performance of single passive TMDs degrades significantly if the resonance frequency of a structure differs even slightly from design frequency. This study proposes an adaptive TMD, which continuously adapts its natural frequency to the current resonance frequency of the structure. The concept is based on pre-stressable leaf-springs that are controlled by piezoceramic stack actuators. Experiments performed on a first prototype show that the TMD is continuously tunable in a broad frequency range.
Isolation of Megaritolactones and Other Bioactive Metabolites from ‘Megaritiki’ Table Olives and Debittering Water (2014)

'Megaritiki' is an olive cultivar widely used in Greece for the production of low polyphenol olive oil and table olives. To investigate possible metabolic differentiation in comparison with other varieties, the composition of 'Megaritiki' olive fruits and wastewaters from the debittering procedure was studied. Moreover, the recovery of bioactive metabolites from wastewater using adsorption resin was studied to exploit this byproduct. Metabolites in fruits and wastewaters were monitored using NMR spectroscopy. The major constituents of wastewater were hydroxytyrosol-4-O-glucoside, 11-methyl-oleoside, hydroxytyrosol, and tyrosol but not oleuropein. Furthermore, wastewater afforded rengyoxide and rengyoside B, which are for the first time isolated from olives. The final edible olives, besides hydroxytyrosol and tyrosol, contained rengyoxide and cleroindicin C, which are the first isolated from the species, haleridone for the first time isolated from edible olives, and four metabolites, which are the first reported as natural products, megaritodilactone, megaritolactonic acid, methyl ester of megaritolactonic acid B, and megaritolactonol.
Frequency of atrial tachyarrhythmias following transcatheter closure of patent foramen ovale. (2006)

The study population included 71 patients [31 (44%) men, aged 54 +/- 14 years] with PFO, diagnosed by transesophageal echocardiography (TEE), and greater than or equal to 1 cryptogenic stroke (n = 70) or orthodoxia (n = 1). Patients underwent transcatheter closure of PFO using a 28 mm (n = 53) or a 33 mm (n = 18) CardioSEAL closure device (n = 67) or an Amplatzer occluder (n = 4). Five (7%) patients presented with newly diagnosed (n = 4) or recurrent (n = 1) episodes of AT (3 atrial fibrillation and 2 typical atrial flutter) within 1 to 480 days following the procedure, with an average time to onset of 175 +/- 221 days. ATs were more frequent in those who received a 33 mm device than those who received a 28 mm device [4/18 (22%) vs. 1/53 (2%); p < 0.05]. Patients with ATs showed a trend toward a larger left atrium only on apical view (6.5 +/- 1.4 cm vs. 5.1 +/- 0.9 cm; p = 0.05). However, the difference in left atrial size on parasternal view and right atrial size between the 2 groups was not statistically significant (4.5 +/- 1.1 cm vs. 3.7 +/- 0.8 cm and 5.9 +/- 2.4 cm vs. 4.6 +/- 0.7 cm). Conclusion. Compared to the age-matched population, sustained ATs appear to be relatively common following transcatheter closure of PFO. In our series, they seemed to occur more frequently in patients who received larger devices.
A Countermeasure Method Using Poisonous Data Against Poisoning Attacks on IoT Machine Learning (2021)

In the modern world, several areas of our lives can be improved, in the form of diverse additional dimensions, in terms of quality, by machine learning. When building machine learning models, open data are often used. Although this trend is on the rise, the monetary losses since the attacks on machine learning models are also rising. Preparation is, thus, believed to be indispensable in terms of embarking upon machine learning. In this field of endeavor, machine learning models may be compromised in various ways, including poisoning attacks. Assaults of this nature involve the incorporation of injurious data into the training data rendering the models to be substantively less accurate. The circumstances of every individual case will determine the degree to which the impairment due to such intrusions can lead to extensive disruption. A modus operandi is proffered in this research as a safeguard for machine learning models in the face of the poisoning menace, envisaging a milieu in which machine learning models make use of data that emanate from numerous sources. The information in question will be presented as training data, and the diversity of sources will constitute a barrier to poisoning attacks in such circumstances. Every source is evaluated separately, with the weight of each data component assessed in terms of its ability to affect the precision of the machine learning model. An appraisal is also conducted on the basis of the theoretical effect of the use of corrupt data as from each source. The extent to which the subgroup of data in question can undermine overall accuracy depends on the estimated data removal rate associated with each of the sources described above. The exclusion of such isolated data based on this figure ensures that the standard data will not be tainted. To evaluate the efficacy of our suggested preventive measure, we evaluated it in comparison with the well-known standard techniques to assess the degree to which the model was providing accurate conclusions in the wake of the change. It was demonstrated during this test that when the innovative mode of appraisal was applied, in circumstances in which 17% of the training data are corrupt, the degree of precision offered by the model is 89%, in contrast to the figure of 83% acquired through the traditional technique. The corrective technique suggested by us thus boosted the resilience of the model against harmful intrusion.
Computed SAR and thermal elevation in a 0.25-mm 2-D model of the human eye and head in response to an implanted retinal stimulator. I. Models and methods (2003)

Retinitis pigmentosa and age-related macular degeneration lead to blindness through progressive loss of retinal photoreceptors. Attempts are under way to construct a visual prosthesis to recover a limited sense of vision for these patients with the aid of implantable electronic devices. The function of these microchips is to provide electrical stimulation to existing viable retinal tissues - living ganglion and bipolar cells - using an array of on-chip stimulus circuits, while the dominant mechanism for power and data communication for these implanted devices has been wireless inductive telemetry using coils. This paper describes methods and models used to estimate the heating induced in the human eye and surrounding head tissues subject to the operation of this retinal prosthesis. A two-dimensional 0.25-mm high-resolution human head model has been developed with the aid of a new semiautomatic graphical segmentation algorithm. Finite-difference-based numerical methods for both electromagnetic and thermal modeling have been used to determine the influence of the specific absorption rate (associated with 2-MHz inductive coupling to the implant) and of stimulator integrated circuit (IC) power on tissue heating under different operational conditions and different hypothesis on choroidal blood flow and properties of the complex implanted circuitry. Results, provided in Part II of this paper, show that temperature increases of approximately 0.6 and 0.4/spl deg/C are induced in the midvitreous of the human eye in the absence and presence of choroidal blood flow, respectively, for a 60-electrode retinal prosthesis chip. Correspondent temperature rises of approximately 0.19 and 0.004/spl deg/C on the retina are obtained for these cases. Comparison with in vivo experimental measurements on intraocular heating in dog eyes shows good agreement.
Precision Chemistry for Precision Medicine (2015)

ADVERTISEMENT RETURN TO ISSUEPREVFirst ReactionsNEXTPrecision Chemistry for Precision MedicineGeorge M. ChurchView Author Information Department of Genetics, Harvard Medical School, Harvard University, Boston, Massachusetts 02115, United StatesE-mail: [email protected]Cite this: ACS Cent. Sci. 2015, 1, 1, 11–13Publication Date (Web):March 23, 2015Publication History Published online23 March 2015Published inissue 25 March 2015https://pubs.acs.org/doi/10.1021/acscentsci.5b00088https://doi.org/10.1021/acscentsci.5b00088newsACS PublicationsCopyright © 2015 American Chemical Society. This publication is licensed under these Terms of Use. Request reuse permissions This publication is Open Access under the license indicated. Learn MoreArticle Views5316Altmetric-Citations4LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (1 MB) Get e-AlertscloseSUBJECTS:Cancer,Genetics,Genomics,Pharmaceuticals,Physiology Get e-Alerts
Rapid Parametric Human Modeling in 3D Garment Simulation (2018)

Abstract To realize 3D garment simulation online and show the wearing effect of different body types, a method for rapid parametric human modeling is proposed in this article. The parameterization consists of two phases. In the first phase, the characteristic parameters of the sample model are extracted according to the different types of feature information. In the second phase, the deformation is realized by combining the axial deformation method and the radial weight. Thus, according to contrasts between the input measurement and the sample sizes, parametric human modeling is realized by deformation of the sample model. In the deformation stage, the axis curve is simplified to the straight-line segment in the axis deformation method, reducing the calculation. Comparative analysis and the results of experiments demonstrate that the better performance can be achieved at a higher speed, and this method realizes real-time parametric human modeling.
Step‐by‐Step Synthesis of Monodisperse Methacrylamidoalkyl Oligolactates (2006)

Abstract Summary: This paper describes the facile step‐by‐step synthesis to graft lactic acid or lactoyl lactate onto primary as well as secondary alcohol derivatives of methacrylamides via esterification. Elongation of the chains is achieved by repeating the coupling reactions with either hydroxyl‐protected monolactate or hydroxyl‐protected dilactate, followed by mild deprotection using tetrabutylammonium fluoride. This versatile synthesis route generates, on a multi‐gram scale, monodisperse oligolactates of predetermined lengths with functional end groups. The products can be used, for example, as building blocks for biodegradable polymeric materials. The synthesis of monodisperse oligo(lactic acids) with methacrylamide end groups and a predefined number of lactic acid units. magnified image The synthesis of monodisperse oligo(lactic acids) with methacrylamide end groups and a predefined number of lactic acid units.
Coupling effects in dense arrays of 3D optical metamaterials (2018)

Three-dimensional (3D) metafilms composed of periodic arrays containing single and multiple micrometer-scale vertical split ring resonators per unit cell were fabricated using membrane projection lithography. In contrast to planar and stacked planar structures such as cut wire pairs and fishnet structures, these 3D metafilms have a thickness t ~&lambda;<sub>d</sub>/4, allowing for classical thin film effects in the long wavelength limit. The infrared specular far-field scattering response was measured for metafilms containing one and two resonators per unit cell, and compared to numerical simulations. Excellent agreement in the frequency region below the onset of diffractive scattering was obtained. The metafilms demonstrate strong bi-anisotropic polarization dependence. Further, we show that for 3D metafilms, just as in solids, complex unit cells with multiple atoms (inclusions) per unit cell possess a richer set of excitation mechanisms. The highlight of these new coupling mechanisms is the excitation of the 3D analog to the 2D cut-wire-pair magnetic response.
A Venture to Discover the Treatment of Coronavirus Disease 2019 (COVID 19): SARS-CoV-2 (2020)

In December 31, 2019, hospitals pronounced a cluster of instances with pneumonia of unknown motive in Wuhan, Hubei, China, attracting brilliant interest nationally and worldwide.The pandemic of coronavirus disease 2019 precipitated by means of the SARS-CoV-2 offers an unheard of venture to discover superb capsules for treatment.Given the speedy tempo of scientific discovery and medical statistics generated by means of the massive quantity of human beings unexpectedly contaminated by using SARS-CoV-2, clinicians want correct proof involving nice clinical remedies for this infection.This paper analysis the literature on all on hand records about the Treatments of COVID-19.Treatments, together with Antibodies, Vaccines, antiviral agents, convalescent plasma transfusion, corticosteroids, chloroquine and hydroxychloroquine, are mentioned in this article.
Fast Li+ Conduction Mechanism and Interfacial Chemistry of a NASICON/Polymer Composite Electrolyte (2020)

The unclear Li<sup>+</sup> local environment and Li<sup>+</sup> conduction mechanism in solid polymer electrolytes, especially in a ceramic/polymer composite electrolyte, hinder the design and development of a new composite electrolyte. Moreover, both the low room-temperature Li<sup>+</sup> conductivity and large interfacial resistance with a metallic lithium anode of a polymer membrane limit its application below a relatively high temperature. Here we have identified the Li<sup>+</sup> distribution and Li<sup>+</sup> transport mechanism in a composite polymer electrolyte by investigating a new solid poly(ethylene oxide) (PEO)-based NASICON-LiZr<sub>2</sub>(PO<sub>4</sub>)<sub>3</sub> composite with <sup>7</sup>Li relaxation time and <sup>6</sup>Li → <sup>7</sup>Li trace-exchange NMR measurements. The Li<sup>+</sup> population of the two local environments in the composite electrolytes depends on the Li-salt concentration and the amount of ceramic filler. A composite electrolyte with a [EO]/[Li<sup>+</sup>] ratio <i>n</i> = 10 and 25 wt % LZP filler has a high Li<sup>+</sup> conductivity of 1.2 × 10<sup>-4</sup> S cm<sup>-1</sup> at 30 °C and a low activation energy owing to the additional Li<sup>+</sup> in the mobile A2 environment. Moreover, an in situ formed solid electrolyte interphase layer from the reaction between LiZr<sub>2</sub>(PO<sub>4</sub>)<sub>3</sub> and a metallic lithium anode stabilized the Li/composite-electrolyte interface and reduced the interfacial resistance, which provided a symmetric Li/Li cell and all-solid-state Li/LiFePO<sub>4</sub> and Li/LiNi<sub>0.8</sub>Co<sub>0.1</sub>Mn<sub>0.1</sub>O<sub>2</sub> cells a good cycling performance at 40 °C.
Bilayer Hydrogel With Autologous Stem Cells Derived From Debrided Human Burn Skin for Improved Skin Regeneration (2013)

The objective of this study was to demonstrate that stem cells isolated from discarded skin obtained after debridement can be used with collagen and fibrin-based scaffolds to develop a tissue-engineered vascularized dermal equivalent. Discarded tissue samples were collected from severely burned patients undergoing wound debridement. Stem cells were isolated from the adipose tissue layer and their growth and immunophenotype characterized. To develop a skin equivalent, debrided skin adipose stem cells (dsASCs) were added to a collagen-polyethylene glycol (PEG) fibrin-based bilayer hydrogel and analyzed in vitro. The effect of the bilayered hydrogels on wound healing was demonstrated using an excision wound model in athymic rats. The dsASCs isolated from all samples were CD90, CD105, and stromal cell surface protein-1 positive, similar to adipose stem cells isolated from normal human lipoaspirates. Within the bilayer hydrogels, dsASCs proliferated and differentiated, maintained a spindle-shaped morphology in collagen, and developed a tubular microvascular network in the PEGylated fibrin. Rat excision wounds treated with bilayer hydrogels showed less wound contraction and exhibited better dermal matrix deposition and epithelial margin progression than controls. Stem cells can be isolated from the adipose layer of burned skin obtained during debridement. When dsASCs are incorporated within collagen-PEGylated fibrin bilayer hydrogels, they develop stromal and vascular phenotypes through matrix-directed differentiation without use of growth factors. Preliminary in vivo studies indicate that dsASC-bilayer hydrogels contribute significantly to wound healing and provide support for their use as a vascularized dermal substitute for skin regeneration to treat large surface area burns.
Saving Private Randomness in One-Way Functions and Pseudorandom Generators. (2007)

Can a one-way function f on n input bits be used with fewer than n bits while retaining comparable hardness of inversion? We show that the answer to this fundamental question is negative, if one is limited black-box reductions. Instead, we ask whether one can save on secret random bits at the expense of more public random bits. Using a shorter secret input is highly desirable, not only because it saves resources, but also because it can yield tighter reductions from higher-level primitives to one-way functions. Our first main result shows that if the number of output elements of f is at most 2 k, then a simple construction using pairwiseindependent hash functions results in a new one-way function that uses only k secret bits. We also demonstrate that it is not the knowledge of security of f, but rather of its structure, that enables the savings: a black-box reduction cannot, for a general f, reduce the secret-input length, even given the knowledge that security of f is only 2 −k; nor can a black-box reduction use fewer than k secret input bits when f has 2 k distinct outputs. Our second main result is an application of the public-randomness approach: we show a construction of a pseudorandom generator based on any regular one-way function with output range of known size 2 k. The construction requires a seed of only 2n + O(k log k) bits (as opposed to O(n log n) in previous constructions); the savings come from the reusability of public randomness. The secret part of the seed is of length only k (as opposed to n in previous constructions), less than the length of the one-way function input.
Assessment of a deep-learning system for fracture detection in musculoskeletal radiographs (2020)

Missed fractures are the most common diagnostic error in emergency departments and can lead to treatment delays and long-term disability. Here we show through a multi-site study that a deep-learning system can accurately identify fractures throughout the adult musculoskeletal system. This approach may have the potential to reduce future diagnostic errors in radiograph interpretation.
Amino‐functionalized polystyrene nanoparticles activate the NLRP3 inflammasome in human macrophages (2013)

Nanoparticles are increasingly used in different biological and biomedical applications. However, their impact on cell functions is not well understood. Here we demonstrate that aminofunctionalized polystyrene nanoparticles (PS‐NH 2 ) of ~100 nm but not carboxy‐functionalized (PS‐COOH) or non‐functionalized (PS) particles of the same size induce NLRP3 inflammasome activation and subsequent release of IL‐1β by human macrophages. PS‐NH 2 were found to induce time‐dependent lysosomal destabilization followed by release of lysosomal enzymes, which trigger mitochondrial damage and increased formation of reactive oxygen species (ROS). Accumulation of mitochondria‐derived ROS causes oxidation of thioredoxin and its dissociation from the thioredoxin‐interacting protein (TXNIP). Liberated TXNIP forms a complex with the inflammasome, which promotes recruitment and activation of caspase‐1 followed by processing of pro‐IL‐1β to IL‐ 1β. Treatment of macrophages with the ROS scavenger N ‐acetyl‐ L ‐cysteine abolishes both, the caspase‐1 activation and the subsequent release of IL‐1β. Using an in vitro knockdown approach, we showed that PS‐NH 2 but not PS‐COOH or PS induce activation of specifically the NLRP3 inflammasome. Thus, aminofunctionalized nanoparticles may induce proinflammatory activation of human macrophages, an effect that can be antagonized by radical scavengers. Supported by the DFG.