Miracle-dz/UniFAR-FTUs huggingface dataset:
Antiprimer quenching-based real-time PCR and its application to the analysis of clinical cancer samples.

BACKGROUND Nucleic acid amplification plays an increasingly important role in genetic analysis of clinical samples, medical diagnostics, and drug discovery. We present a novel quantitative PCR technology that combines the advantages of existing methods and allows versatile and flexible nucleic acid target quantification in clinical samples of widely different origin and quality. METHODS We modified one of the 2 PCR primers by use of an oligonucleotide "tail" fluorescently labeled at the 5' end. An oligonucleotide complementary to this tail, carrying a 3' quenching molecule (antiprimer), was included in the reaction along with 2 primers. After primer extension, the reaction temperature was lowered such that the antiprimer hybridizes and quenches the fluorescence of the free primer but not the fluorescence of the double-stranded PCR product. The latter provides real-time fluorescent product quantification. This antiprimer-based quantitative real-time PCR method (aQRT-PCR) was used to amplify and quantify minute amounts of input DNA for genes important to cancer. RESULTS Simplex and multiplex aQRT-PCR demonstrated linear correlation (r(2) >0.995) down to a DNA input equivalent to 20 cells. Multiplex aQRT-PCR reliably identified the HER-2 gene in microdissected breast cancer samples; in formalin-fixed, paraffin-embedded specimens; and in plasma circulating DNA from cancer patients. Adaptation to multiplex single-nucleotide polymorphism detection via allele-specific aQRT-PCR allowed correct identification of apolipoprotein B polymorphisms in 51 of 51 human specimens. CONCLUSION The simplicity, versatility, reliability, and low cost of aQRT-PCR make it suitable for genetic analysis of clinical specimens.
Comparison of Portal Venous and Delayed Phases of Gadolinium-Enhanced Magnetic Resonance Imaging Study of Cirrhotic Liver for the Detection of Contrast Washout of Hypervascular Hepatocellular Carcinoma

Objective: To retrospectively compare portal venous phase (PVP) and delayed phase (DP) for the detection of tumor washout at gadobenate dimeglumine-enhanced liver magnetic resonance imaging (MRI) in cirrhotic patients with hypervascular hepatocellular carcinoma (HCC). Methods: Thirty-three patients with 55 HCCs underwent 1.5-T MRI by means of fat-suppressed T1-weighted sequence obtained before and after gadobenate dimeglumine administration, during early and late arterial phases, PVP (70 seconds), and DP (180 seconds). Detection rates of contrast washout of hypervascular HCCs and tumor-to-liver contrast on PVP and DP were measured and compared. Results: Among 54 hypervascular HCCs, washout was present in 24 (44%) of 54 tumors on PVP and in 44 (82%) of 54 on DP (P < 0.001). In 20 (37%) of 54 tumors, washout was deemed present only on DP. Delayed phase images yielded significantly higher mean tumor-to-liver contrast absolute values compared with PVP images (−24.5 [56.1] vs −9.3 [52.6], P = 0.001). Conclusions: Delayed phase is superior to PVP for the washout detection of hypervascular HCC at gadobenate dimeglumine-enhanced MRI of cirrhotic liver.
Adaptive time delay estimation algorithm for indoor near‐field electromagnetic ranging

The near‐field electromagnetic ranging technology exploits the near‐field behavior of radio signals to measure distance in indoor real‐time location system. In this paper, we propose a new adaptive time‐delay estimation algorithm based on maximum correntropy criterion (MCC) and received signal strength indication (RSSI), abbreviated as RSSIMCC. The proposed RSSIMCC algorithm estimates the time delay between the electric and magnetic components of low‐frequency signals in the near field instead of detecting the phase difference. An inaccurate time‐delay estimation value obtained according to the RSSI is used as the initial time delay of adaptive time‐delay estimator, which is not far from the true time delay and can improve the convergence speed. Through the analysis of simulation and experiment results, we conclude that the proposed RSSIMCC algorithm can estimate the time delay with small steady‐state error in near‐field electromagnetic ranging application. Then the time delay estimated by RSSIMCC algorithm can be exploited based on the near‐field behavior of radio signals for ranging in an indoor environment. Copyright © 2016 John Wiley & Sons, Ltd.
Yes/no reversals as neurobehavioral sequela: a disorder of language, praxis, or inhibitory control?

This study identifies a linguistic phenomenon suggestive of damage to fronto‐subcortical circuitry. Our objective was to determine the occurrence and neuroradiological/neurobehavioral correlates of yes/no reversals in corticobasal degeneration (CBD), and document occurrence of reversals in other neurological conditions. In a prospective study, we evaluated 34 CBD patients using a neuropsychologic battery and magnetic resonance imaging. Patients were subdivided into two groups: those with (n = 11) and without (n = 23) yes/no reversals. In a retrospective study conducted during the period of 1991–2001, we identified 33 patients for whom yes/no reversals occurred to compare correlates with prospective study findings. In the prospective study, 11 patients (32.3%) had yes/no reversals. Significant between‐group differences were found in scores of lexical fluency (P = 0.02) and prehension (P = 0.03). Prehension scores correlated with facial praxis (P < 0.0001) and upper limb praxis scores (P < 0.0001) in the yes/no reversal group only. In the retrospective study, nine CBD patients and 24 non‐CBD patients had yes/no reversals, with damage to fronto‐subcortical areas present in all patients. Results suggest an association with deficits in mental flexibility and inhibitory control. High within‐group correlations of lexical fluency and prehension with praxis scores suggest a relationship of yes/no reversals with multiple factors.
Use of Bacteriocin Producing Lactococcus lactis subsp. lactis LABW4 to Prevent Listeria monocytogenes Induced Spoilage of Meat

A bacteriocin producing strain of Lactococcus lactis subsp. lactis LABW4 was isolated from naturally fermented milk product which exhibited strong antibacterial activity against Listeria monocytogenes MTCC657, a food spoilage psychrophilic organism. Both cell free and heat killed supernatants of LABW4 were effective to produce zones of inhibition against L. monocytogenes in vitro. The antibacterial metabolite(s) of LABW4 showed strong cidal effect on the growth of L. monocytogenes. Meat samples, mixed with heat killed supernatant of LABW4 when inoculated with Listeria, remain fresh up to 25 days in refrigerated condition whereas spoilage started immediately after 24 hours of inoculation for control sets. Enhancement of Lactate dehydrogenase of L. monocytogenes upon treatment with LABW4 cell free supernatant suggested its lytic mode of action. Cell lysis or degradations were also supported by scanning electron micrograph of treated cells.
Hydroxychloroquine sulfate treatment is associated with later onset of systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is a clinically diverse, complex autoimmune disease which may present with coincident onset of many criteria or slow, gradual symptom accrual. Early intervention has been postulated to delay or prevent the development of more serious sequelae. One option for treatment in this setting is hydroxychloroquine. Using 130 US military personnel who later met ACR SLE criteria, a retrospective study of onset, development and progression of SLE with and without pre-classification hydroxychloroquine (n = 26) use was performed. Patients treated with hydroxychloroquine prior to diagnosis had a longer (Wilcoxon signed rank test, P = 0.018) time between the onset of the first clinical symptom and SLE classification (median: 1.08 versus 0.29 years). Patients treated with prednisone before diagnosis also more slowly satisfied the classification criteria (Wilcoxon signed rank test, P = 0.011). The difference in median times between patients who received NSAIDs before diagnosis, as opposed to those who did not, was not different (P = 0.19). Patients treated with hydroxychloroquine also had a lower rate of autoantibody accumulation and a decreased number of autoantibody specificities at and after diagnosis. These findings are consistent with early hydroxychloroquine use being associated with delayed SLE onset. A prospective, blinded trial testing the capacity of hydroxychloroquine to delay or prevent SLE in high risk populations is warranted. Lupus (2007) 16, 401—409.
Towards verification-based development of in-vehicle safety critical software: a case study

The ever increasing software complexity in the safety critical automotive domain induces new challenges in ensuring a fault-free system design. In this paper we propose a novel approach using Analytical Software Design (ASD). The ASD toolsuite provides means to develop software that is robust by construction. We show the integration of the ASD approach in the commonly used development workflow using Matlab/Simulink by means of a case study.
Speciation and inversions: chimps and humans.

A new set of models has resurrected a role for chromosomal inversions in the formation of new species. Traditional models, which are generally considered to be unlikely in most cases, had imagined that inversions might aid speciation by directly causing low hybrid fitness. In contrast, the newer models focus on the effect that inversions have on local recombination rates. A test of these models found a strikingly high rate of amino-acid substitution within regions where humans and chimpanzees differ by inversions, suggesting perhaps that our ancestral species underwent a divergence process in which gene flow and inversions played a key role. However, it remains uncertain whether this interesting finding is actually consistent with the proposed model.
of Nebraska - Lincoln of Nebraska - Lincoln When Portfolios Become Part of the Grading Process: A Case When Portfolios Become Part of the Grading Process: A Case Study in a Junior High Setting Study in a Junior High Setting

it is stated. I want to use the benchmarks and the standard as a way of setting different levels of meeting the standard. What I would like to do is have the clarity of the rubric I have been using for their writing-I thought about bringing the students in on this process, yet I'm not really sure about this at the present time-one of those good old comfort issues. (Meeting notes, 1111 1/96) but this was lacking in some respects. curricula allow freedom I need. There too many recipes rather than a conceptual framework. When I look at the standards, I see components that need to make up my curriculum. I can hang my scope and se- quence onto something. [The standard] provides a common language. I can talk to my peers about the standards. It is important that as colleagues we are in agreement regarding the meaning of the standards if we are to use them as a common language.
Effects of Magnesium Supplementation in a Porcine Model of Myocardial Ischemia and Reperfusion

We tested the hypothesis that acute, intravenous (i.v.) magnesium (Mg2+) supplementation would protect against myocardial stunning in an in situ swine model of regional ischemia and reperfusion and that a concomitant inhibitory effect on platelet aggregation would be elicited. An open-chest model was used, with transient occlusion of the left anterior descending coronary artery (LAD) for 8 min. Regional contractile function was assessed by measuring wall thickening fraction with epicardial Doppler crystals. One control group (n = 6) and two treatment groups were studied: group I (n = 6) received 750 mg MgSO4 before occlusion; group II (n = 6) received 1 g MgSO4 after the occlusion. Both protocols produced significant hypermagnesemia. In group I, platelet aggregation was measured before and after Mg2+ treatment using platelet-rich plasma (PRP) and various agonists (ADP 5 and 10 mM and collagen 1 mg/ml). As compared with controls, both treatment groups experienced significantly less postischemic dysfunction, with systolic function returning more quickly to baseline. Furthermore, platelet aggregation was significantly decreased immediately after Mg2+ infusion. Inhibition of platelet aggregation induced by Mg2+ treatment occurs concomitantly with significant amelioration of postischemic myocardial dysfunction.
Deletion Mapping in Squamous Cell Carcinomas of the Esophagus Narrows a Region Containing a Putative Tumor Suppressor Gene to about 200 Kilobases on Distal Chromosome 9 ql

We previously reported definition of a region containing a putative tumor suppressor gene for csophageal squamous cell carcinoma within an ~4-cM genomic segment at 9q31-q32. We have investigated this region further using six new microsatellite markers isolated from yeast artificial chromosome clones covering the deleted region and have narrowly de fined the commonly deleted region to a segment between two loci, KM9.I and D9SI77. On the basis of the contig map of cosmid and yeast artificial chromosome clones, we estimate the physical size of the region of interest to be about 200 kh. Because the distal 9q region also has been implicated as the site of a tumor suppressor gene(s) related to squamous cell carci nomas of other tissues, our map provides useful information for attempts to identify a common gene for carcinomas of this cell type.
Epigenetic Regulation, Somatic Homologous Recombination, and Abscisic Acid Signaling Are Influenced by DNA Polymerase ϵ Mutation in Arabidopsis[W][OA]

Based on abscisic acid (ABA) inhibition of seed germination and seedling growth assays, we isolated an ABA overly sensitive mutant (abo4-1) caused by a mutation in the Arabidopsis thaliana POL2a/TILTED1(TIL1) gene encoding a catalytic subunit of DNA polymerase ϵ. The dominant, ABA-insensitive abi1-1 or abi2-1 mutations suppressed the ABA hypersensitivity of the abo4-1 mutant. The abo4/til1 mutation reactivated the expression of the silenced Athila retrotransposon transcriptional silent information (TSI) and the silenced 35S-NPTII in the ros1 mutant and increased the frequency of somatic homologous recombination (HR) ∼60-fold. ABA upregulated the expression of TSI and increased HR in both the wild type and abo4-1. MEIOTIC RECOMBINATION11 and GAMMA RESPONSE1, both of which are required for HR and double-strand DNA break repair, are expressed at higher levels in abo4-1 and are enhanced by ABA, while KU70 was suppressed by ABA. abo4-1 mutant plants are sensitive to UV-B and methyl methanesulfonate and show constitutive expression of the G2/M-specific cyclin CycB1;1 in meristems. The abo4-1 plants were early flowering with lower expression of FLOWER LOCUS C and higher expression of FLOWER LOCUS T and changed histone modifications in the two loci. Our results suggest that ABO4/POL2a/TIL1 is involved in maintaining epigenetic states, HR, and ABA signaling in Arabidopsis.
Anatomical and functional overlap within the insula and anterior cingulate cortex during interoception and phobic symptom provocation

The anterior insula and the dorsal anterior cingulate cortex (ACC) are regarded as key brain structures associated with the integration of perceived phobic characteristics of external stimuli and the perception of ones own body responses that leads to emotional feelings. To test to what extent the activity in these two brain structures anatomically and functionally overlap during phobic reactions and interoception, we submitted the same group of phobic participants (n = 29; either spider or blood‐injection‐injury (BII) phobics) and controls (n = 17) to both type of experimental paradigms. Results showed that there was a clear anatomical overlap in the Blood Oxygen Level‐Dependent (BOLD) responses within the anterior insula and ACC elicited during phobic symptom provocation and during interoceptive awareness. The activity within these two brain structures also showed to be correlated in the spider phobia group, but not in the BII phobic participants. Our results seem to support the idea that the activity within these two brain areas would be associated with the integration of perceived stimuli characteristics and bodily responses that lead to what we label as “fear. ” However, that seems not to be the case in BII phobia, where more research is needed in order to clarify to what extent that could be associated with the idiosyncratic physiological response that these patients present in front of phobic stimuli (i.e., drop in heart rate and blood pressure). Hum Brain Mapp, 2013. © 2011 Wiley Periodicals, Inc.
Gas-grain chemical models of star-forming molecular clouds as constrained by ISO and SWAS observations

We have investigated the gaseous and solid state molecular composition of dense interstellar material that periodically experiences processing in the shock waves associated with ongoing star formation. Our motivation is to confront these models with the stringent abundance constraints on CO2 ,H 2 Oa nd O 2, in both gas and solid phases, that have been set by ISO and SWAS. We also compare our results with the chemical composition of dark molecular clouds as determined by ground-based telescopes. Beginning with the simplest possible model needed to study molecular cloud gas-grain chemistry, we only include additional processes where they are clearly required to satisfy one or more of the ISO-SWAS constraints. When CO, N2 and atoms of N, C and S are eciently desorbed from grains, a chemical quasi-steady-state develops after about one million years. We nd that accretion of CO2 and H2O cannot explain the (CO2=H2O)ice ISO observations; as with previous models, accretion and reaction of oxygen atoms are necessary although a high O atom abundance can still be derived from the CO that remains in the gas. The observational constraints on solid and gaseous molecular oxygen are both met in this model. However, we nd that we cannot explain the lowest H2O abundances seen by SWAS or the highest atomic carbon abundances found in molecular clouds; additional chemical processes are required and possible candidates are given. One prediction of models of this type is that there should be some regions of molecular clouds which contain high gas phase abundances of H2O, O2 and NO. A further consequence, we nd, is that interstellar grain mantles could be rich in NH2OH and NO2. The search for these regions, as well as NH2OH and NO2 in ices and in hot cores, is an important further test of this scenario. The model can give good agreement with observations of simple molecules in dark molecular clouds such as TMC-1 and L134N. Despite the fact that S atoms are assumed to be continously desorbed from grain surfaces, we nd that the sulphur chemistry independently experiences an \accretion catastrophe". The S-bearing molecular abundances cease to lie within the observed range after about 3 10 6 years and this indicates that there may be at least two ecient surface desorption mechanisms operating in dark clouds { one quasi-continous and the other operating more sporadically on this time-scale. We suggest that mantle removal on short time-scales is mediated by clump dynamics, and by the eects of star formation on longer time-scales. The applicability of this type of dynamical-chemical model for molecular cloud evolution is discussed and comparison is made with other models of dark cloud chemistry.
Morphological analyzer and generator for Tamil Language

Morphological analysis is an essential component in Natural Language Processing (NLP) applications ranging from spell checker to machine translation. When performing a morphological analysis it leads to segmentation of a word into morphemes, combined with an analysis of the attachments of these morphemes. In English language the complexity of the formation of words is not much higher compared with Indic languages. Hence, Tamil language too does have its complexities when building up a NLP application. The morphemes in the language, the rules how these morphemes are connected and the changes occur when they attach together are the important factors that need to be considered when building up a Morphological Analyzer for any language. Our “Morphological Analyzer and Generator for Tamil Language” will be generating the word forms of a stem/ root, given a particular context and at the same time, a surface form in Tamil language should get analyzed into its proper context. This model tries to cover only the nouns and verbs in the Tamil language. This paper illustrates how the lexicon and the orthographic rules of Tamil language have been written as regular expressions using only finite state operations and how this approach has been implemented to develop a morphological analyzer/generator. This model is built using the Xerox toolkit, which uses “Two-level Morphology”, and almost 2000 noun stems and 96 verb stems have been incorporated into the network. A noun stem now produces about 40 different forms and a verb stem produces up to 240 forms. We have also defined our own transliteration scheme for this purpose.
An empirical investigation of single‐objective and multiobjective evolutionary algorithms for developer's assignment to bugs

In this paper, the modeling of developers’ assignment to bugs (DAB) is studied. The problem is modeled both as a single objective (minimize bug fix time) and as a bi‐objective (minimize bug fix time and cost) combinatorial optimization problem. Two models of developer assignment are considered where in the first model a single developer is assigned per bug (single developer model), while in the second model a single developer is assigned for each competency area of a bug (individual competency model). The latter model is proposed in this paper. For the single developer model, GA@DAB, an existing genetic algorithm‐based approach, is extended to support precedence among bugs. For the individual competency model of DAB, one genetic algorithm‐based approach (Competence@DAB) and one nondominated sorting genetic algorithm II‐based approach (CompetenceMulti2@DAB ) are proposed to generate solutions minimizing time and minimizing both time and cost, respectively. The performance of the proposed approaches was evaluated for 2040 bugs of 19 open‐source milestone projects from the Eclipse platform. Our results and analysis show that the proposed individual competency model is far better than the single developer model, with average bug fix time reduction of 39.7% across all projects. Copyright © 2016 John Wiley & Sons, Ltd.
Blockade of glucocorticoid receptors rapidly restores hippocampal CA1 synaptic plasticity after exposure to chronic stress

Prolonged exposure to stressful events has been reported to inhibit the ability of hippocampal synapses to increase their synaptic efficacy. Here we tested if these effects could be prevented by blocking activation of glucocorticoid receptors during the last 4 days of the stress paradigm. In order to address this question, animals were exposed to 21 days of variable and inescapable stressors. Handled animals served as controls. During the last 4 days of the stress regime, animals were treated with the glucocorticoid receptor antagonist RU486. We found that 1 day after the last stressor, synaptic plasticity in the CA1 area of hippocampal slices is impaired in chronically stressed animals. Importantly, treating chronically stressed animals with RU486 for 4 days completely prevented this decrease in synaptic potentiation; RU486 treatment of handled controls did not affect potentiation. Treating hippocampal slices from control animals with high levels of corticosterone also impaired synaptic plasticity; this effect was similar for untreated and RU486‐treated animals. Treating slices from chronically stressed animals with corticosterone did not further decrease synaptic plasticity. These data indicate that 4 days blockade of the glucocorticoid receptor, during a stress regime, is sufficient to fully restore synaptic plasticity.