Miracle-dz/UniFAR-FTUs huggingface dataset:
A Rapid Phenotypic Assay for Detection of Acyclovir-Resistant Varicella-Zoster Virus with Mutations in the Thymidine Kinase Open Reading Frame

ABSTRACT Susceptibility assays by cell culture methods are time-consuming and are particularly difficult to perform with varicella-zoster virus (VZV). To overcome this limitation, we have adapted a functional test of the viral thymidine kinase (TK) in TK-deficient (tdkmutant) bacteria to detect ACV-resistant VZV in clinical samples. After PCR amplification, the complete viral TK open reading frame (ORF) is purified from PCR primers, digested with two restriction enzymes, and ligated in an oriented fashion into a bacterial expression vector. The ligation products are then used to transform tdk mutant bacteria. After transformation, an aliquot of the bacteria is plated onto a plate with minimal medium containing (i) ampicillin to select for plasmids carrying the viral TK ORF and (ii) isopropyl β-d-thiogalactopyranoside (IPTG) to induce its expression. An identical aliquot of bacteria is also plated onto a medium containing, in addition to the components described above, 5-fluorodeoxyuridine (FUdR). Compared to the number of transformants on FUdR-free medium, the number of colonies carrying TK derived from susceptible strains was reduced by 86%, on average, in the presence of FUdR. In contrast, the number of transformants carrying TK from resistant strains with a mutant TK were reduced by only 4%, on average, on FUdR-containing plates. We have assessed the validity of this assay with cell culture isolates and several clinical samples including two cerebrospinal fluid samples from which no virus could be isolated. This colony reduction assay allowed the correct identification of the TK phenotype of each VZV isolate tested and can be completed within 3 days of receipt of the sample.
Follicular Thyroid Carcinoma Presenting as Bilateral Cheek Masses

Mandibular metastasis of thyroid carcinoma is extremely rare. We present the case of a 46-year-old woman who had bilateral huge cheek masses that had grown rapidly over several years. Intra-oral mucosal tissue biopsy and imaging work-up including computed tomography scan and magnetic resonance imaging were performed and the initial diagnosis was presumed to be central giant cell granuloma. Incidentally detected thyroid lesions were studied with ultra-sonography guided fine needle aspiration and diagnosed as simple benign nodules. Due to continuous oral bleeding and the locally destructive feature of the lesions, we decided to excise the mass surgically. To avoid functional deficit, a stepwise approach was performed: Firstly, the larger left mass was excised and the mandible was reconstructed with a fibular free flap. The final pathologic diagnosis was follicular thyroid cancer. Postoperative I-131 thyroid scan and whole body positron-emissions-tomography were performed. Right side mass was revealed as a thyroid malignancy. Multiple bony metastases were detected. Since further radioactive iodine therapy was required, additional total thyroidectomy and right side mandibulectomy with fibular free flap reconstruction was performed. The patient also underwent high dose radioactive iodine therapy and palliative extra-beam radiotherapy for the metastatic lumbar lesion. Follicular thyroid carcinoma should be considered as a differential diagnosis for mandibular mass lesions.
Activity of Polymerase Proteins of Vaccine and Wild-Type Measles Virus Strains in a Minigenome Replication Assay

ABSTRACT The relative activities of five measles virus (MV) polymerase (L) proteins were compared in an intracellular, plasmid-based replication assay. When coexpressed with N and P proteins from an attenuated strain, L proteins from two attenuated viruses directed the production of up to eight times more reporter protein from an MV minigenome than the three wild-type L proteins. Northern blot analysis demonstrated that the differences in reporter protein production correlated with mRNA transcription levels. Increased activity of polymerases from attenuated viruses equally affected mRNA transcription and minigenome replication. The higher level of transcription may be a consequence of increased template availability or may be an independent effect of the elevated activity of the attenuated polymerases. Coexpression of wild-type L proteins with homologous N and P proteins did not affect the activity of the wild-type polymerases, indicating that the differential activity was a function of the L proteins alone. Use of a minigenome that incorporated two nucleotide changes found in the genomic leader of the three wild-type viruses did not raise the activity of the wild-type L proteins. These data demonstrate that increased polymerase activity differentiates attenuated from wild-type viruses and suggest that functions involved in RNA synthesis contribute to the attenuated phenotype of MV vaccine strains.
The critical role of the boreal summer mean state in the development of the IOD

Boreal summer is a critical season for the rapid development of the Indian Ocean Dipole (IOD). In this study, three factors related to the boreal summer mean state are proposed to be important for the rapid development of the IOD, by strengthening the equatorial zonal wind anomaly and thus the dynamic Bjerknes feedback. Firstly, as part of the Indo‐Pacific warm pool, the high mean SST in the southeastern tropical Indian Ocean (SEIO) acts as an essential prerequisite for the development of anomalous convection. Secondly, the maximum of the suppressed precipitation in response to a cold SST anomaly (SSTA) in the SEIO, shifts northward towards the equator because the mean precipitation is equatorially trapped in boreal summer. Thirdly, the monsoonal easterly shear in boreal summer promotes an enhanced, more equatorially symmetric low‐level Rossby wave response to a prescribed equatorially asymmetric heating over the SEIO. The above three processes promote a greater equatorial zonal wind response and thus a greater Bjerknes feedback, as well as a greater IOD development during boreal summer.
A Small Motor Cortex Lesion Abolished Ocular Dominance Plasticity in the Adult Mouse Primary Visual Cortex and Impaired Experience-Dependent Visual Improvements

It was previously shown that a small lesion in the primary somatosensory cortex (S1) prevented both cortical plasticity and sensory learning in the adult mouse visual system: While 3-month-old control mice continued to show ocular dominance (OD) plasticity in their primary visual cortex (V1) after monocular deprivation (MD), age-matched mice with a small photothrombotically induced (PT) stroke lesion in S1, positioned at least 1 mm anterior to the anterior border of V1, no longer expressed OD-plasticity. In addition, in the S1-lesioned mice, neither the experience-dependent increase of the spatial frequency threshold (“visual acuity”) nor of the contrast threshold (“contrast sensitivity”) of the optomotor reflex through the open eye was present. To assess whether these plasticity impairments can also occur if a lesion is placed more distant from V1, we tested the effect of a PT-lesion in the secondary motor cortex (M2). We observed that mice with a small M2-lesion restricted to the superficial cortical layers no longer expressed an OD-shift towards the open eye after 7 days of MD in V1 of the lesioned hemisphere. Consistent with previous findings about the consequences of an S1-lesion, OD-plasticity in V1 of the nonlesioned hemisphere of the M2-lesioned mice was still present. In addition, the experience-dependent improvements of both visual acuity and contrast sensitivity of the open eye were severely reduced. In contrast, sham-lesioned mice displayed both an OD-shift and improvements of visual capabilities of their open eye. To summarize, our data indicate that even a very small lesion restricted to the superficial cortical layers and more than 3mm anterior to the anterior border of V1 compromised V1-plasticity and impaired learning-induced visual improvements in adult mice. Thus both plasticity phenomena cannot only depend on modality-specific and local nerve cell networks but are clearly influenced by long-range interactions even from distant brain regions.
Perceptual conditions affecting ease of association.

Four experiments replicated Asch's findings in 1969 that perceiving two terms in a unitary relationship facilitates their association. In Exp. I and II, pronouncing a CV-C pair as a monosyllable produced high associative recall of the terminal C to the CV cue, while pronouncing the CV-C as two separate terms caused relatively low associative recall. The result held for both intentional and incidental learning conditions. In Exp. Ill and IV, 5s were to associate a color patch to each of IS geometric figures. Association was high when the figure was the same color as the color patch, low when the figure was a different color than the color patch, and intermediate when the figure was an uncolored, black-onwhite outline. Asch (1969) has emphasized the importance of the relationship between perception and memory. In particular, the perceptual relation between pairs of elements may be expected to substantially influence the ease of associating the pairs. Some earlier pertinent data (Asch, 1962) compared the learning of associations between color responses and geometric figures when these were presented in various perceptual relations. The shape and the color could be shown during the study trial in a "constitutive" or "unitary" relationship in which the shape appears to be composed of the colored material. A solidly colored figure on a white background or a colored-outline contour on a white background exemplify constitutive relationships. Alternatively, the shape-color relationship could be nonunitary, as when the figure was a blackoutline contour on a colored background or beside a colored patch. The experimental task was to learn to associate color
Stochastic Problems in the Simulation of Labor Supply

Modern work in labor supply attempts to account for nonlinear budget sets created by government tax and transfer programs. Progressive taxation leads to nonlinear convex budget sets while the earned income credit, social security contributions, AFDC, and the proposed NIT plans all lead to nonlinear, nonconvex budget sets. Where nonlinear budget sets occur, the expected value of the random variable, labor supply, can no longer be calculated by simply 'plugging in' the estimated coefficients. Properties of the stochastic terms which arise from the residual or from a stochastic preference structure need to be accounted for. This paper considers both analytical approaches and Monte Carlo approaches to the problem. We attempt to find accurate and low cost computational techniques which would permit extensive use of simulation methodology. Large samples are typically included in such simulations which makes computational techniques an important consideration. But these large samples may also lead to simplifications in computational techniques because of the averaging process used in calculation of simulation results. This paper investigates the tradeoffs available between computational accuracy and cost in simulation exercises over large samples.
Soil microbial community variation correlates most strongly with plant species identity, followed by soil chemistry, spatial location and plant genus

Soil ecologists have debated the relative importance of dispersal limitation ("everything" is not "everywhere") and ecological factors in determining the structure of soil microbial communities. The relative explanatory power of spatial and ecological factors, including plant species identity and even plant relatedness, for different fractions of the soil microbial community (i.e. bacterial and fungal communities) are poorly understood. We sampled field soils in a northern California field site, and find that soil microbial community variation correlates most strongly with plant species identity, followed by soil chemistry, spatial location and plant genus.
Effective superpotentials via Konishi anomaly

We use Ward identities derived from the generalized Konishi anomaly in order to compute effective superpotentials for SU(N), SO(N) and Sp(N) supersymmetric gauge theories coupled to matter in various representations. In particular we focus on cubic and quartic tree level superpotentials. With this technique higher order corrections to the perturbative part of the effective superpotential can be easily evaluated.
Time Varying Correlations between Stock and Bond Returns - Evidence from Russia

The purpose of this study is to look at the relationship between stock market and bond market of Russia for the period of July 1994 to Dec. 2007. We attempt to examine whether the correlations between two classes of assets are time varying by using multivariate conditional volatility models. We start our investigation by applying Bollerslev (1990) Constant conditional correlation model to test whether varying correlations are statistically significant then we use DCC-GARCH (1, 1) model proposed by Engle (2002) to analyze the dynamics of conditional correlations between the two assets. Finally, to investigate the asymmetries in conditional variances, covariances, and correlations, we adopt an asymmetric version of the Dynamic Conditional Correlation (ADCC) model proposed by Engle et al. (2006). Our empirical results do not support the assumption of constant conditional correlation and we found clear evidence of time varying correlations between Russian stocks and bond market. Our results offers a batter understanding for the dynamics of the correlations between stocks and bonds in an emerging market setting which is obviously very valuable for the portfolio managers, international investors, risk analysts and financial researchers as well as for the policy implications.
Grabbing attention without knowing: Automatic capture of attention by subliminal spatial cues

The present study shows that an abrupt onset cue that is not consciously perceived can cause attentional facilitation followed by inhibition at the cued location. The observation of this classic biphasic effect of facilitation followed by inhibition of return (IOR) suggests that the subliminal cue captured attention in a purely exogenous way. Since IOR is not observed following endogenous shifts of spatial attention, but is observed following exogenous, stimulus-driven shifts of spatial attention, it is unlikely that top-down control settings or other non-attentional effects played a role. The current findings are interpreted in terms of a neurobiological model of visual awareness.
Clinical observations on associations between the UGT1A1 genotype and severe toxicity of irinotecan.

BACKGROUND Severe toxicity is commonly observed in cancer patients receiving irinotecan (CPT-11). UDP glucuronosyltransferase1A1 (UGT1A1) catalyzes the glucuronidation of the active metabolite SN-38 but the relationship between UGT1A1 and severe toxicity remains unclear. Our study aimed to assess this point to guide clinical use of CPT-11. MATERIALS AND METHODS 89 cancer patients with advanced disease received CPT-11-based chemotherapy for at least two cycles. Toxicity, including GI and hematologic toxicity was recorded in detail and UGT1A1 variants were genotyped. Regression analysis was used to analyse relationships between these variables and tumor response. RESULTS The prevalence of grade III-IV diarrhea was 10.1%, this being more common in patients with the TA 6/7 genotype (5 of 22 patients, 22.7%) (p<0.05). The prevalence of grade III-IV neutropenia was 13.4%and also highest in patients with the TA 6/7 genotype (4 of 22 patients; 18.2%) but without significance (p>0.05). The retreatment total bilirubin levels were significantly higher in TA6/7 patients (mean, 12.75μmol/L) with compared to TA6/6 (mean, 9.92 μmol/L) with p<0.05. CONCLUSIONS Our study support the conclusion that patients with a UGT1A1*28 allele (s) will suffer an increased risk of severe irinotecan-induced diarrhea, whether with mid-or low-dosage. However, the UGT1A1*28 allele (s) did not increase severe neutropenia. Higher serum total bilirubin is an indication that patients UGT1A1 genotype is not wild-type, with significance for clinic usage of CPT-11.
Anterior Segment Tomography with the Cirrus Optical Coherence Tomography

Optical coherence tomography (OCT) is an optical acquisition method to examine biological tissues. In recent years, OCT has become an important imaging technology used in diagnosing and following macular pathologies. Further development enabled application of optical coherence tomography in evaluation of the integrity of the nerve fiber layer, optic nerve cupping, anterior chamber angle, or corneal topography. In this manuscript we overview the use of OCT in the clinical practice to enable corneal, iris, ciliary body, and angle evaluation and diagnostics.
Purchasing Power Parity in the Case of Romania: Evidence from Structural Breaks

Purchasing Power Parity has most likely been one of the most investigated issues of the last decades within economic literature. The results from such studies are not consistent and not only important for policy makers and economists but also extremely important for policy implications in international finance. Purchasing Power Parity states the exchange rate between two countries should reflect the relative purchasing power of these two countries. This study tests the validity of the purchasing power parity hypothesis in Romania with employing Zivot–Andrews unit root test by taking structural break into account. We use annual data from 1991 to 2012 and the results show that purchasing power parity does not hold in Romania.
Unification of step bunching phenomena on vicinal surfaces

We unify step bunching (SB) instabilities occurring under various conditions on crystal surfaces below roughening. We show that when attachment-detachment of atoms at step edges is the rate-limiting process, the SB of interacting, concentric circular steps is equivalent to the commonly observed SB of interacting straight steps under deposition, desorption, or drift. We derive a continuum Lagrangian partial differential equation, which is used to study the onset of instabilities for circular steps. These findings place on a common ground SB instabilities from numerical simulations for circular steps and experimental observations of straight steps.
Book Review: How Welfare States Shape the Democratic Public: Policy Feedback, Participation, Voting and Attitudes

This crucial volume significantly advances the study of policy feedbacks. With contributions from many subfields and methodological approaches, it offers both sophisticated theorizing and new empirical examples that show how policies make politics in a variety of ways. Innovative research designs provide more convincing inference than ever. And the normative questions engaged about welfare performance, evaluation, participation, and accountability could not be more important or timely in this era of austerity and discord over the future of welfare states. ’
Total Factor Productivity, Social Infrastructure, and Output Per Worker: A Cross-Country Analysis

In this paper we develop and estimate a model of output per worker where total factor productivity is embedded into the model. Unlike previous research, we use the price of capital to proxy for capital intensity and the Economic Security Index developed by the ILO (2004) to capture social infrastructure. Using cross-sectional and panel regressions, we arrive at plausible and robust estimates of the key structural parameters of the model. Our results show that differences in capital intensity and educational attainment account for the bulk of cross-country variation in output per worker, leaving little residual variation. Total factor productivity accounts, at most, for a factor of 2.5 in explaining the 32-fold output gap between wealthy and poor nations.
Satellite NG2 Progenitor Cells Share Common Glutamatergic Inputs with Associated Interneurons in the Mouse Dentate Gyrus

Several studies have provided evidence that NG2-expressing (NG2+) progenitor cells are anatomically associated to neurons in gray matter areas. By analyzing the spatial distribution of NG2+ cells in the hilus of the mouse dentate gyrus, we demonstrate that NG2+ cells are indeed closely associated to interneurons. To define whether this anatomical proximity reflected a specific physiological interaction, we performed patch-clamp recordings on hilar NG2+ cells and interneurons between 3 and 21 postnatal days. We first observed that hilar NG2+ cells exhibit spontaneous glutamatergic EPSCs (sEPSCs) whose frequency and amplitude increase during the first 3 postnatal weeks. At the same time, the rise time and decay time of sEPSCs significantly decreased, suggesting that glutamatergic synapses in NG2+ cells undergo a maturation process that is reminiscent of what has been reported in neurons during the same time period. We also observed that hilar interneurons and associated NG2+ cells are similarly integrated into the local network, receiving excitatory inputs from both granule cells and CA3 pyramidal neurons. By performing pair recordings, we found that bursts of activity induced by GABAergic antagonists were strongly synchronized between both cell types and that the amplitude of these bursts was positively correlated. Finally, by applying carbachol to increase EPSC activity, we observed that closely apposed cells were more likely to exhibit synchronized EPSCs than cells separated by >200 μm. The finding that NG2+ cells are sensing patterns of activity arising in closely associated neurons suggests that NG2+ cell function is finely regulated by the local network.
Heterogeneity in Models of Electoral Choice

Heterogeneity or the presence of a variety of decision rules in a population has usually been ignored in voting research. A method for handling heterogeneous preferences using rank order data is developed and applied to a simple issue-voting model. The estimated average effect of partisanship is substantially higher when the assumption of homogeneity is relaxed, though many self-identified partisans also use ideological criteria to evaluate candidates and many independents rely on partisan criteria.
Signalling network with a bistable hysteretic switch controls developmental activation of the σF transcription factor in Bacillus subtilis

The sporulation process of the bacterium Bacillus subtilis unfolds by means of separate but co‐ordinated programmes of gene expression within two unequal cell compartments, the mother cell and the smaller forespore. σF is the first compartment‐specific transcription factor activated during this process, and it is controlled at the post‐translational level by a partner‐switching mechanism that restricts σF activity to the forespore. The crux of this mechanism lies in the ability of the anti‐sigma factor SpoIIAB (AB) to form alternative complexes either with σF, holding it in an inactive form, or with the anti‐anti‐sigma factor SpoIIAA (AA) and a nucleotide, either ATP or ADP. In the complex with AB and ATP, AA is phosphorylated on a serine residue and released, making AB available to capture σF in an inactive complex. Subsequent activation of σF requires the intervention of the SpoIIE serine phosphatase to dephosphorylate AA, which can then attack the AB–σF complex to induce the release of σF. By incorporating biochemical, biophysical and genetic data from the literature we have constructed an integrative mathematical model of this partner‐switching network. The model predicts that the self‐enhancing formation of a long‐lived complex of AA, AB and ADP transforms the network into an essentially irreversible hysteretic switch, thereby explaining the sharp, robust and irreversible activation of σF in the forespore compartment. The model also clarifies the contributions of the partly redundant mechanisms that ensure correct spatial and temporal activation of σF, reproduces the behaviour of various mutants and makes strong, testable predictions.