Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of epidermal growth factor receptor mutation in lung cancer by droplet digital polymerase chain reaction

Background Two types of epidermal growth factor receptor (EGFR) mutations in exon 19 and exon 21 (ex19del and L858R) are prevalent in lung cancer patients and sensitive to targeted EGFR inhibition. A resistance mutation in exon 20 (T790M) has been found to accompany drug treatment when patients relapse. These three mutations are valuable companion diagnostic biomarkers for guiding personalized treatment. Quantitative polymerase chain reaction (qPCR)-based methods have been widely used in the clinic by physicians to guide treatment decisions. The aim of this study was to evaluate the technical and clinical sensitivity and specificity of the droplet digital polymerase chain reaction (ddPCR) method in detecting the three EGFR mutations in patients with lung cancer. Methods Genomic DNA from H1975 and PC-9 cells, as well as 92 normal human blood specimens, was used to determine the technical sensitivity and specificity of the ddPCR assays. Genomic DNA of formalin-fixed, paraffin-embedded specimens from 78 Chinese patients with lung adenocarcinoma were assayed using both qPCR and ddPCR. Results The three ddPCR assays had a limit of detection of 0.02% and a wide dynamic range from 1 to 20,000 copies measurement. The L858R and ex19del assays had a 0% background level in the technical and clinical settings. The T790M assay appeared to have a 0.03% technical background. The ddPCR assays were robust for correct determination of EGFR mutation status in patients, and the dynamic range appeared to be better than qPCR methods. The ddPCR assay for T790M could detect patient samples that the qPCR method failed to detect. About 49% of this patient cohort had EGFR mutations (L858R, 15.4%; ex19del, 29.5%; T790M, 6.4%). Two patients with the ex19del mutation also had a naïve T790M mutation. Conclusion These data suggest that the ddPCR method could be useful in the personalized treatment of patients with lung cancer.
The change of definitions in a multidisciplinary landscape: the case of human embryo and pre-embryo identification

In contemporary knowledge landscapes, interdisciplinary communication is crucial. In many cases, the interaction among experts of different fields is challenging, especially with regard to controversial definitions at the intersection of law, science, and bioethics. We analyze the legal definitions of the term “embryo” as the result of legal, ethical, as well as scientific implications, at the intertwining of social changes and scientific advancements. We show how embryo is a complex word, which may be interpreted in different ways. Taking into account the latest research advances on early stage embryo development, we focus on the delicate roles of law in balancing differing claims of scientific investigation and bio-ethic concerns. We conclude that sensitive ethical definitions are the synthesis of often competing interests among different disciplines. Moreover, human feelings toward controversial biology innovations should be taken into account.
IN VIVO DERMAL ABSORPTION AND SUB-ACUTE TOXICITY STUDIES OF ESSENTIAL OIL FROM BLUMEA ERIANTHA DC

Objective: The present investigation describes in vivo dermal absorption and sub acute dermal toxicity (28 days) study of essential oil from Blumea eriantha DC (Compositae). Methods: The essential oil was extracted by hydrodistillation using Clevenger type apparatus. The dermal absorption studies were conducted in rabbits at dose of 15% (v/v) while sub acute toxicity was carried out in adult Holtzman rats at doses of 3%, 9% and 15% (v/v). The in vivo dermal absorption of essential oil was examined by means of Head space GC MS. Results: The in vivo dermal absorption did not show presence of any essential oil component in the rabbit plasma samples. Further the sub acute treatment with essential oil did not show significant differences in the body weight, food consumption, hematological and biochemical parameters examined in both female and male groups. Necropsy and histopathological examination did not reveal any treatment related changes in treated groups. However, during the first week of study skin irritation was observed only in animals treated with high dose (15%) of essential oil which receded with time. Conclusion: These findings suggest that the sub-acute dermal application of the Blumea eriantha DC essential oil in rats did not reveal any significant toxic effects at 9%. However skin irritation observed in high dose (15%) group indicating possible toxicity of essential oil. Therefore caution should be exercised in the application of essential oil especially at high dose (15%) and above.
Characterization of genetic variation among accessions of Aegilops tauschii

The application of AFLPs, and SSRs to examine genetic relationships in the 54 accessions of Aegilops tauschii from 5 countries was investigated. A total of 256 (234 polymorphic) and 224 (219 polymorphic) bands were detected using 17 primer combinations of AFLP and 24 well distributed, mapped SSR markers, respectively. The UPGMA cluster plots separated the 54 accessions into three major groups based on their AFLP fragment similarities, and into five major groups based on their SSR genotypic similarities. Correlation between both genetics similarity matrices was poor. Both of molecular techniques did not group accessions strictly according to their geographical origins. These different marker systems should provide different levels of information which is important in management of germplasm resources.
A Computational Model of the Self-Teaching Hypothesis Based on the Dual-Route Cascaded Model of Reading

The self-teaching hypothesis describes how children progress toward skilled sight-word reading. It proposes that children do this via phonological recoding with assistance from contextual cues, to identify the target pronunciation for a novel letter string, and in so doing create an opportunity to self-teach new orthographic knowledge. We present a new computational implementation of self-teaching within the dual-route cascaded (DRC) model of reading aloud, and we explore how decoding and contextual cues can work together to enable accurate self-teaching under a variety of circumstances. The new model (ST-DRC) uses DRC's sublexical route and the interactivity between the lexical and sublexical routes to simulate phonological recoding. Known spoken words are activated in response to novel printed words, triggering an opportunity for orthographic learning, which is the basis for skilled sight-word reading. ST-DRC also includes new computational mechanisms for simulating how contextual information aids word identification, and it demonstrates how partial decoding and ambiguous context interact to achieve irregular-word learning. Beyond modeling orthographic learning and self-teaching, ST-DRC's performance suggests new avenues for empirical research on how difficult word classes such as homographs and potentiophones are learned.
A review on electrically conductive polypropylene and polyethylene

Conductive plastics are new generation functional materials with potential application in electronics, space and aviation industries. Polypropylene (PP) and polyethylene (PE) being most common, widely available and cheapest thermoplastic, if made conductive, can be revolutionary in the field of engineering thermoplastics. The article deals with the fabrication of electrically conductive PP and PE for electromagnetic interference/radio frequency (EMI/RF) shielding applications and protection against electrostatic discharge (ESD). It reviews different fillers used by researchers to fabricate conductive PP and PE, several factors that affect the electrical conductivity of thermoplastic composites and various processing methods that can be adopted to prepare such composites. It exhaustively covers the preparation of such conductive composites, the processing methods involved therein, and the electrical properties of the end material. Emphasis has been given to comprehend the percolation threshold and means to reduce the latter in order to achieve high electrical conductivity in PP- and PE-based composites at relatively low filler loading. POLYM. COMPOS. , 35:900–914, 2014. © 2013 Society of Plastics Engineers
A non-invasive, quantitative study of broadband spectral responses in human visual cortex

Currently, non-invasive methods for studying the human brain do not routinely and reliably measure spike-rate-dependent signals, independent of responses such as hemodynamic coupling (fMRI) and subthreshold neuronal synchrony (oscillations and event-related potentials). In contrast, invasive methods—microelectrode recordings and electrocorticography (ECoG)—have recently measured broadband power elevation in field potentials (~50–200 Hz) as a proxy for locally averaged spike rates. Here, we sought to detect and quantify stimulus-related broadband responses using magnetoencephalography (MEG). Extracranial measurements like MEG and EEG have multiple global noise sources and relatively low signal-to-noise ratios; moreover high frequency artifacts from eye movements can be confounded with stimulus design and mistaken for signals originating from brain activity. For these reasons, we developed an automated denoising technique that helps reveal the broadband signal of interest. Subjects viewed 12-Hz contrast-reversing patterns in the left, right, or bilateral visual field. Sensor time series were separated into evoked (12-Hz amplitude) and broadband components (60–150 Hz). In all subjects, denoised broadband responses were reliably measured in sensors over occipital cortex, even in trials without microsaccades. The broadband pattern was stimulus-dependent, with greater power contralateral to the stimulus. Because we obtain reliable broadband estimates with short experiments (~20 minutes), and with sufficient signal-to-noise to distinguish responses to different stimuli, we conclude that MEG broadband signals, denoised with our method, offer a practical, non-invasive means for characterizing spike-rate-dependent neural activity for addressing scientific questions about human brain function.
Culturing substrates in fl uence the morphological , mechanical and biochemical features of lung adenocarcinoma cells cultured in 2 D or 3 D

Alternative models such as three-dimensional (3D) cell cultures represent a distinct milestone towards capturing the realities of cancer biology in vitro and reduce animal experimentation in the preclinical stage of drug discovery. Significant work remains to be done to understand how substrates used in in vitro alternatives influence cancer cells phenotype and drug efficacy responses, so that to accurately link such models to specific in vivo
Improving Document Classification Using Ontologies

This paper proposes a new objective metric called SEMCON to enrich existing concepts in domain ontologies for describing and organizing multimedia documents. The SEMCON model exploits the document contextually and semantically. The preprocessing module collects a document and partitions that into several passages. Then a morpho-syntatic analysis is performed on the partitioned passages and a list of nouns as part-of-speech (POS) is extracted. An observation matrix based on statistical features is then computed followed by computing the contextual score. The semantics is then incorporated by computing a semantic similarity score between two terms term (noun) that is extracted from a document and term that already exists in the ontology as a concept. Eventually, an overall objective score is computed by adding contextual score with semantic score. Subjective experiments are conducted to evaluate the performance of the SEMCON model. The model is compared with state-of-the-art tf*idf and χ (Chi square) using F1 measure. The experimental results show that SEMCON achieved an improved accuracy of 10.64% over the tf*idf and 13.04% over the χ.
A technique for fabricating abutment replica with hot melt adhesive material to minimize residual cement in implant restoration: a case report

Removal of excess cement is important to prevent biological complication in cementation of implant restoration with subgingival margin. It can be difficult to completely remove excess cement. Several techniques have been introduced to minimize excess cement using abutment replica. In this case report, a simple method for making abutment replica with hot melt adhesive material in dental office was described. This technique is simple and effective because it can be used for pre-fabricated or custom abutment without additional laboratory procedure. In addition, it can minimize excess cement after cementation of implant restoration.
The Phonologic Deficit in Adolescence and Adult Life

Developmental dyslexia is defined as an unexpected difficulty in reading in adults and children who otherwise possess the intelligence and motivation considered necessary for accurate and fluent reading and who also have had reasonable reading instruction. Dyslexia (or specific reading disability) is the most common and most carefully studied of the learning disabilities, affecting 80 percent of all individuals identified as learning disabled. This article reviews recent advances in the neurobiology of dyslexia and their implications for adults with dyslexia; it provides an update to a previous article we wrote for Focus on Basics. continued on page 3
Two new schemes for classifying propagating cracks in human tooth structure.

: Currently, the dental profession has no comprehensive classification method or scheme to identify the many types of propagating cracks in human tooth structure. This article presents two new and practical classification systems that encompass numerous types of cracks. The first is the more simplified--the Surface and Position Classification System. The second and more comprehensive system is the Directional Crack Propagation System.
Functional Characterization of the Cleavage Specificity of the Sapovirus Chymotrypsin-Like Protease

ABSTRACT Sapovirus is a positive-stranded RNA virus with a translational strategy based on processing of a polyprotein precursor by a chymotrypsin-like protease. So far, the molecular mechanisms regulating cleavage specificity of the viral protease are poorly understood. In this study, the catalytic activities and substrate specificities of the predicted forms of the viral protease, the 3C-like protease (NS6) and the 3CD-like protease-polymerase (NS6-7), were examined in vitro. The purified NS6 and NS6-7 were able to cleave synthetic peptides (15 to 17 residues) displaying the cleavage sites of the sapovirus polyprotein, both NS6 and NS6-7 proteins being active forms of the viral protease. High-performance liquid chromatography and subsequent mass spectrometry analysis of digested products showed a specific trans cleavage of peptides bearing Gln-Gly, Gln-Ala, Glu-Gly, Glu-Pro, or Glu-Lys at the scissile bond. In contrast, peptides bearing Glu-Ala or Gln-Asp at the scissile bond (NS4-NS5 and NS5-NS6, or NS6-NS7 junctions, respectively) were resistant to trans cleavage by NS6 or NS6-7 proteins, whereas cis cleavage of the Glu-Ala scissile bond of the NS5-NS6 junction was evidenced. Interestingly, the presence of a Phe at position P4 overruled the resistance to trans cleavage of the Glu-Ala junction (NS5-NS6), whereas substitutions at the P1 and P2′ positions altered the cleavage efficiency. The differential cleavage observed is supported by a model of the substrate-binding site of the sapovirus protease, indicating that the P4, P1, and P2′ positions in the substrate modulate the cleavage specificity and efficiency of the sapovirus chymotrypsin-like protease.
Bayesian Analysis Using a Simple Likelihood Model Outperforms Parsimony for Estimation of Phylogeny from Discrete Morphological Data

Despite the introduction of likelihood-based methods for estimating phylogenetic trees from phenotypic data, parsimony remains the most widely-used optimality criterion for building trees from discrete morphological data. However, it has been known for decades that there are regions of solution space in which parsimony is a poor estimator of tree topology. Numerous software implementations of likelihood-based models for the estimation of phylogeny from discrete morphological data exist, especially for the Mk model of discrete character evolution. Here we explore the efficacy of Bayesian estimation of phylogeny, using the Mk model, under conditions that are commonly encountered in paleontological studies. Using simulated data, we describe the relative performances of parsimony and the Mk model under a range of realistic conditions that include common scenarios of missing data and rate heterogeneity.
Factors Affecting Patient Portal Use Among Low-Income Pregnant Women: Mixed-Methods Pilot Study

Background Patient portals offer patients personalized and secure Web access to their medical information and enable patients to manage their health care online. However, there is a lack of information about patient acceptance and use of patient portals among low-income pregnant women. Objective This formative research aims to assess the potential of a patient portal, MyChart, for improving prenatal health care and pregnancy outcomes, and identify the barriers and facilitators of MyChart use among low-income pregnant women. Methods A mixed-methods study was conducted with a convenience sample of 18 low-income pregnant women comprising low- and high-risk patients enrolled in a prenatal clinic in eastern North Carolina. MyChart use, patient demographics, and pregnancy information were collected by reviewing electronic medical charts. Health literacy was measured. Reported use and attitudes toward MyChart were collected using a semi-structured interview. Results Although 39% (7/18) of participants interviewed signed up for MyChart, only 22% (4/18) of them became active users. Another 33% (6/18) had never heard of MyChart or was unsure of how to access it. Users primarily accessed test results and appointment schedules. The main facilitating factors for patient portal use were information and motivation from health care providers and concerns about pregnancy due to a history of miscarriage. Reported barriers were lack of educational resources, lack of care provider encouragement, and technical difficulties possibly exacerbated by low health literacy. Participants also suggested improvements for MyChart, especially the provision of discussion-based support for pregnant women. Conclusions The one-time verbal introduction of MyChart does not meet current patients’ needs. Data reveal the need for more consistent patient education and support programs, tailored to patients’ previous pregnancy histories. The clinic also needs to facilitate better provider-patient communication about the importance of MyChart use.
Electronic Communications of the EASST Volume 45 ( 2011 ) Proceedings of the Fourth International Workshop on Formal Methods for Interactive Systems ( FMIS 2011 ) Formal Modeling and Analysis for Interactive Hybrid Systems

An effective strategy for discovering certain kinds of automation surprise and other problems in interactive systems is to build models of the participating (automated and human) agents and then explore all reachable states of the composed system looking for divergences between mental states and those of the automation. Various kinds of model checking provide ways to automate this approach when the agents can be modeled as discrete automata. But when some of the agents are continuous dynamical systems (e.g., airplanes), the composed model is a hybrid (i.e., mixed continuous and discrete) system and these are notoriously hard to analyze. We describe an approach for very abstract modeling of hybrid systems using relational approximations and their automated analysis using infinite bounded model checking supported by an SMT solver. When counterexamples are found, we describe how additional constraints can be supplied to direct counterexamples toward plausible scenarios that can be confirmed in high-fidelity simulation. The approach is illustrated though application to a known (and now corrected) human-automation interaction problem in Airbus aircraft.
Comparative Study of Functional Nasal Reconstruction Using Structural Reinforcement

Importance Nasal reconstruction after Mohs surgery is a unique challenge in that it must satisfy both functional and aesthetic goals. Despite some advocacy in the literature for using structural reinforcement to achieve both functional and aesthetic outcomes in soft-tissue reconstruction, no study has validated this claim by comparing reconstruction with and without structural support. Objective To evaluate the effectiveness of and need for structural reinforcement when reconstructing the nasal alar and sidewall subunits. Design, Setting, and Participants This study was a retrospective review of the medical records of 190 patients 18 years or older who underwent nasal reconstruction after Mohs surgery in a tertiary care academic center between January 1, 2013, and August 31, 2015. Data on each patient included demographics, comorbidities, smoking status, details of the lesion, size of defect, subunits involved, and reconstructive technique. Patients were divided into 2 cohorts composed of those who had reconstruction with structural reinforcement (ie, cartilage grafting or suspension suture) and those with only soft-tissue reconstruction. Patients with nasal obstruction from the functional collapse of the reconstructed area and no history of nasal obstruction were included (n = 38). Patients who had a follow-up of less than 2 months, no alar or sidewall involvement, nasal obstruction secondary to turbinate hypertrophy, septal deflection or other nonstructural causes, and incomplete documentation for analysis were excluded (n = 102). Main Outcomes and Measures Rates of postoperative nasal obstruction secondary to nasal sidewall collapse and need for revision surgery. Results Of the 38 patients who met the inclusion criteria, 22 were men and 16 were women with a mean (range) age of 64.5 (35-92) years. Twenty-three patients (61%) underwent reconstruction by a facial plastic surgeon and 15 (39%) by 2 dermatologic surgeons. Three (8%) underwent reconstruction without reinforcement and experienced postoperative nasal obstruction. The mean size of reconstructed defects that resulted in nasal valve collapse was 2.1 cm in diameter (range, 1.2-2.6 cm). Defect size was associated with incidence of postoperative nasal obstruction. For defects greater than 1.2 cm in diameter, patients reconstructed without reinforcement had a statistically significant increase of nasal obstruction secondary to functional nasal collapse compared with patients reconstructed with reinforcement (3 of 14 [21%] vs 0 of 17; 95% CI, 0.005-0.358; P = .04). Conclusions and Relevance Nasal defects greater than 1.2 cm in diameter and involving the alar and sidewalls were associated with lower incidence of postoperative nasal obstruction when a structural reinforcement technique was used in reconstruction. The findings of this study support the structural reinforcement of the nasal functional subunits during Mohs reconstructive surgery to achieve optimal outcomes. Level of Evidence 3.