Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of the updated Vitek yeast identification data base

Using 398 isolates of yeasts and yeastlike fungi comprising 9 genera and 26 species, as well as the hyphomycete Geotrichum candidum and the achlorophyllous alga Prototheca wickerhamii, we compared the API 20C yeast identification system with the modified Vitek yeast identification system with an expanded data base. We found 11 discrepancies between the two systems: five (1.3%) of the isolates (Blastoschizomyces capitatus, 1; Candida albicans, 1; Hansenula anomala, 1; Rhodotorula minuta, 2) had biocodes not included in the expanded Vitek data base, and six (1.5%) of the isolates (Candida lusitaniae, 1; Candida parapsilosis, 1; Cryptococcus uniguttulatus, 1; H. anomala, 1; Torulopsis candida, 2) were misidentified by the Vitek system. Overall, the efficacy of the Vitek system compares favorably with that of the API 20C in the identification of clinically important yeasts.
Expression of myelin proteolipid and basic protein mRNAS in cultured cells

Studies were undertaken to investigate the regulation of myelin‐specific mRNA expression in cultured cells. Three experimental systems were investigated: primary oligodendrocytes grown as enriched cell populations, primary oligodendrocytes grown in the presence of chick spinal cord neurons, and C6 cells. cDNA probes specific for the myelin proteolipid mRNA and the myelin basic protein mRNA were used to quantitate proteolipid and myelin basic protein mRNA levels in cells under different experimental conditions. C6 cells expressed less than 0.2% of the proteolipid mRNA that was expressed in primary oligodendrocytes. Primary oligodendrocytes expressed the myelin‐specific mRNAs for at least 104 days in culture, and the level of these mRNAs in cultures was elevated fourfold by coculturing rat oligodendrocytes with chick spinal cord neurons.
Progressive obesity alters the steroidogenic response to ovulatory stimulation and increases the abundance of mRNAs stored in the ovulated oocyte

Obese women who are able to attain pregnancy are at increased risk for early‐pregnancy loss due, in part, to reduced oocyte quality. We and others have demonstrated that female Lethal Yellow (LY) mice and female C57BL/6 mice fed a high fat diet (B6‐HFD) exhibit phenotypes consistent with human obesity. These studies also showed that zygotes collected from LY and B6‐HFD females have reduced developmental competence. The current hypothesis is that LY and B6‐HFD females exhibit an abnormal response to gonadotropin stimulation compared to C57BL/6 controls fed normal rodent chow (B6‐ND), resulting in the ovulation of oocytes with an altered molecular phenotype which may contribute to its reduced developmental competence. To test this hypothesis, age‐matched B6‐ND, B6‐HFD, and LY females were stimulated with exogenous gonadotropins, then circulating hormone levels and the phenotypes of ovulated oocytes were analyzed. There was no difference in ovulation rate or in the percentage of morphologically abnormal oocytes collected from the oviduct of any females. Progesterone and progesterone/estradiol ratios, however, were increased in B6‐HFD and LY compared to B6‐ND females 16 hr post‐human chorionic gonadotropin treatment. The transcript abundance of several candidate oocyte genes was also increased in B6‐HFD‐ and LY‐derived oocytes compared to B6‐ND‐derived oocytes. These data suggest that increased insulin and leptin levels of obese females elevated circulating progesterone concentrations, altered transcriptional activity during oocyte growth, and/or impaired mechanisms of RNA translation and degradation during oocyte maturation. These changes in mRNA abundance likely contribute to reduced oocyte quality and the subsequent poor embryogenesis associated with obesity. Mol. Reprod. Dev. 81: 735–747, 2014. © 2014 Wiley Periodicals, Inc.
Impact of donor-specific antibodies on results of liver transplantation

Purpose of reviewTo critically examine the recent literature evaluating the importance of HLA donor-specific antibody (DSA) impact on liver transplant and simultaneous liver–kidney transplant (SLKT) outcomes. Recent findingsMany preformed DSAs, especially of low mean fluorescence intensity (MFI), are absorbed by the liver at transplant. However, patients with post-liver transplant DSA, especially of higher MFI, are at increased risk of acute and chronic rejection. C4d staining, when positive, may be helpful but lacks sensitivity especially in formalin tissue. SLKT recipients may need close follow-up when class II DSA is found, as the liver protects the kidney from hyperacute rejection, but can still cause early renal antibody-mediated rejection, liver allograft rejection, and impair patient, liver allograft, and renal allograft survival. SummarySome DSAs are relevant in liver transplant and can lead to acute and chronic allograft rejection. However, before clinical practice patterns can change we must create unified diagnostic criteria, define the pathologic potential of different DSAs, and improve the specificity of current testing.
Detection of the Plasmodium falciparumAntigen Histidine-Rich Protein 2 in Blood of Pregnant Women: Implications for Diagnosing Placental Malaria

ABSTRACT Pregnant women have an increased susceptibility to infection byPlasmodium falciparum. Parasites may be present in the placenta yet not detectable in peripheral blood smears by routine light microscopy. In order to determine how frequently misdiagnosis occurs, peripheral blood and placental samples were collected from 1,077 Cameroonian women at the time of giving birth and examined for the presence of malarial parasites by using light microscopy. Results showed that 20.1% of the women who had placental malaria were peripheral blood smear negative. Thus, malarial infection was not detected by microscopic examination of peripheral blood smears from approximately one out of five malaria-infected women. Since P. falciparum parasites secrete histidine-rich protein 2 (HRP-2), we sought to determine if detecting HRP-2 in either peripheral plasma or whole blood might be used to diagnose the presence of parasites “hidden” in the placenta. Samples of peripheral plasma from 127 women with different levels of placental malarial infection were assayed by HRP-2-specific enzyme-linked immunosorbent assay. HRP-2 was detected in 88% of the women with placental malaria who tested negative by blood smear. Additionally, whole blood was obtained from 181 women and tested for HRP-2 with a rapid, chromatographic strip test (ICT). The ICT test accurately detected malarial infection in 89.1% ofP. falciparum-infected women. Furthermore, 94% of women with malaria were accurately diagnosed by using a combination of microscopy and the ICT test. Thus, detection of HRP-2 in conjunction with microscopy should improve diagnosis of malaria in pregnant women.
Family Benefits and Poverty: The Case of Russia

25 years have passed since the beginning of market reforms in Russia. Like other post-soviet countries, in the early 1990s Russia faced a period of sharp decline in real household incomes. Then a gradual growth of population well-being began. However, income inequality was deep throughout this time. The poverty headcount is still over 10% on average and differs a lot among territories and socio-demographic groups. Russian poverty has certain specifics: there is a high risk of poverty for young working families with children. This paper analyses the effectiveness of family benefits from various perspectives. We consider their impact on the poverty of families with children, using the concepts of absolute, relative and subjective poverty. The study is based on pooled and panel household data from the Russia Longitudinal Monitoring Survey – Higher School of Economics (RLMS HSE), 2003-2015. We model the influence of child benefits on the probability of being poor and estimate various econometric models. Other controlled factors influencing recipient household risk of poverty include the type of settlement, family structure, education and employment. The results are robust and show the negative influence of family benefits on household risk for absolute and relative poverty. However, the subjective perception of poverty is positively correlated with benefits. The study also shows leakage and significant gaps in coverage in the system of family benefits. Overall, the study reveals the low effectiveness of family benefits in Russia and indicates a need for improved targeting.
Pedestrian Gap Acceptance Logit Model in Unsignalized Crosswalks Conflict Zone

Pedestrians are the most vulnerable road users. For evaluating and modifying pedestrian safety in unsignalized crosswalks,the first important issue is to identify and explore factors affecting the interaction behavior of pedestrians andvehicles in conflict areas. By analyzing those factors and determining how they affect road user's behavior, we canrepresent the plans and procedures to promote awareness and safety of both pedestrians and drivers. The goal of thisarticle is to study pedestrian decision making behavior in unsignalized crosswalks and to determine factors affectingthe crossing behavior in conflict areas. The supposed goal of this study was assessing how each factor can influencepedestrian-vehicle conflict behavior by means of developing logistic regression models. This work explores a varietyof factors that may impact the gap acceptance behavior of pedestrian to provide a promising decision model. Discretechoice (probit) models of the gap acceptance decision are estimated from observations of pedestrians behavior whencrossing at conflict zone.Analysis results show that variables like vehicle speed change (VSC), pedestrian distance to vehicle lane (PDV), pedestrianage (PA) and vehicle position to the start point of pedestrian (Vp) are effective in Pedestrian gap Acceptance(PGA). Modeling decision making behavior by logit models, resulted in neglected R Square of 0.882 and correctclassification of 94.9 pair wise cases. Area under ROC curve resulted in 0.98 that means the reliability of models isextracted. The results also showed that some variables like vehicle type (VT), waiting time (WT), number of pedestrianswalking in a group (PN) and Gap or Lag are not effective in decision making logit models.
Regulation of the Ras‐GTPase activating protein neurofibromin by C‐tail phosphorylation: implications for protein kinase C/Ras/extracellular signal‐regulated kinase 1/2 pathway signaling and neuronal differentiation

PKC, Ras, and ERK1/2 signaling is pivotal to differentiation along the neuronal cell lineage. One crucial protein that may play a central role in this signaling pathway is the Ras GTPase‐activating protein, neurofibromin, a PKC substrate that may exert a positive role in neuronal differentiation. In this report, we studied the dynamics of PKC/Ras/ERK pathway signaling, during differentiation of SH‐SY5Y neuroblastoma cells upon treatment with the PKC agonist, phorbol ester 12‐O‐tetradecanoyl‐phorbol‐13‐acetate (TPA). Surprisingly, we observed that, among other PKC‐dependent signaling events, TPA induced a rapid and sustained decrease of neurofibromin immunoreactivity which was not due to proteolysis. Instead, we identified a specific phosphorylation event at the C‐tail of neurofibromin. This phosphorylation was acute and correlated perfectly with the signaling dynamics of the Ras/ERK pathway. Moreover, it persisted throughout prolonged treatment and TPA‐induced differentiation of SH‐SY5Y cells, concurrently with sustained activation of ERK1/2. Most importantly, C‐tail phosphorylation of neurofibromin correlated with a shift of neurofibromin localization from the nucleus to the cytosol. We propose that PKC‐dependent, sustained C‐tail phosphorylation is a requirement for prolonged recruitment of neurofibromin from the nucleus to the cytosol in order for a fine regulation of Ras/ERK pathway activity to be achieved during differentiation.
Oxidative Stress Measures of Lipid and DNA Damage in Human Tears

Purpose We evaluate feasibility and repeatability of measures for lipid peroxidation and DNA oxidation in human tears, as well as relationships between outcome variables, and compared our findings to previously reported methods of evaluation for ocular sun exposure. Methods A total of 50 volunteers were seen for 2 visits 14 ± 2 days apart. Tear samples were collected from the inferior tear meniscus using a glass microcapillary tube. Oxidative stress biomarkers were quantified using enzyme-linked immunosorbent assay (ELISA): lipid peroxidation by measurement of hexanoyl-lysine (HEL) expression; DNA oxidation by measurement of 8-oxo-2′-deoxyguinosone (8OHdG) expression. Descriptive statistics were generated. Repeatability estimates were made using Bland-Altman plots with mean differences and 95% limits of agreement were calculated. Linear regression was conducted to evaluate relationships between measures. Results Mean (±SD) values for tear HEL and 8OHdG expression were 17368.02 (±9878.42) nmol/L and 66.13 (±19.99) ng/mL, respectively. Repeatability was found to be acceptable for both HEL and 8OHdG expression. Univariate linear regression supported tear 8OHdG expression and spring season of collection to be predictors of higher tear HEL expression; tear HEL expression was confirmed as a predictor of higher tear 8OHdG expression. Conclusions We demonstrate feasibility and repeatability of estimating previously unreported tear 8OHdG expression. Seasonal temperature variation and other factors may influence tear lipid peroxidation. Support is demonstrated to suggest lipid damage and DNA damage occur concurrently on the human ocular surface.
Capital Market and Economic Growth in Nigeria

This study seeks to evaluate the contribution of capital market to the growth of Nigeria’s economy. To achieve this objective, an error correction model was estimated for economic growth in Nigeria, using Vector Error Correction techniques on an annual time series data spanning from 1981 to 2014. The data were subjected to Phillip Perron Unit Root Test at level and first difference. The result shows that, at one percent significance level, all the variables were stationary at first differencing. The result of the normalized cointegrated series further reveals that market capitalization rate, total value of listed securities, labor force participation rate, accumulated savings and capital formation are significant macroeconomic determinants factors of economic growth in Nigeria. It was then recommended that, for the capital market to realizes its full potentials, its environment must be enabled to promote and encourage investment opportunities for both local and international investors, since the stock market operates in a macroeconomic environment. Consequently, an improvement in the Nigerian trading system with the aim of increasing the ease with which investors can purchase and sell shares, could guarantee the stock market liquidity
FEM numerical model study of heating in magnetic nanoparticles

Electromagnetic heating of nanoparticles is complicated by the extremely short thermal relaxation time constants and difficulty of coupling sufficient power into the particles to achieve desired temperatures. Magnetic field heating by the hysteresis loop mechanism at frequencies between about 100 and 300 kHz has proven to be an effective mechanism in magnetic nanoparticles. Experiments at 2.45 GHz show that Fe3O4 magnetite nanoparticle dispersions in the range of 1012 to 1013 NP/mL also heat substantially at this frequency. An FEM numerical model study was undertaken to estimate the order of magnitude of volume power density, Qgen (W m-3) required to achieve significant heating in evenly dispersed and aggregated clusters of nanoparticles. The FEM models were computed using Comsol Multiphysics; consequently the models were confined to continuum formulations and did not include film nano-dimension heat transfer effects at the nanoparticle surface. As an example, the models indicate that for a single 36 nm diameter particle at an equivalent dispersion of 1013 NP/mL located within one control volume (1.0 x 10-19 m3) of a capillary vessel a power density in the neighborhood of 1017 (W m-3) is required to achieve a steady state particle temperature of 52°C - the total power coupled to the particle is 2.44 μW. As a uniformly distributed particle cluster moves farther from the capillary the required power density decreases markedly. Finally, the tendency for particles in vivo to cluster together at separation distances much less than those of the uniform distribution further reduces the required power density.
Comparison between Language and Music

Abstract: Similarities and differences between language and music processing are examined from an evolutionary and a cognitive perspective. Language and music cannot be considered single entities; they need to be decomposed into different component operations or levels of processing. The central question concerns one of the most important claims of the generative grammar theory, that is, the specificity of language processing: do the computations performed to process language rely on specific linguistic processes or do they rely on general cognitive principles? Evidence from brain imaging results is reviewed, noting that this field is currently in need of metanalysis of the available results to precisely evaluate this claim. A series of experiments, mainly using the event‐related brain potentials method, were conducted to compare different levels of processing in language and music. Overall, results favor language specificity when certain aspects of semantic processing in language are compared with certain aspects of melodic and harmonic processing in music. By contrast, results support the view that general cognitive principles are involved when aspects of syntactic processing in language are compared with aspects of harmonic processing in music. Moreover, analysis of the temporal structure led to similar effects in language and music. These tentative conclusions must be supported by other brain imaging results to shed further light on the spatiotemporal dynamics of the brain structure‐function relationship.
The Substitutability of Immigrant and Native Labor: Evidence at the Establishment Level

A key issue for understanding the impact of immigration on native labor market opportunities is the degree of substitutability between immigrants and natives. If immigrants are perfect substitutes for natives, each newly hired immigrant displaces one native. If immigrants and natives are imperfect substitutes, however, the displacement e¤ect can be smaller. In this paper, I use detailed establishment-level data from Germany to study the shortand longer-run displacement e¤ects of increased immigrant hiring by rms after the fall of the Iron Curtain in 1989. I compare employment trends at rms in the same local labor market that either hired or did not hire immigrants using both a matching approach and an instrumental variables strategy that exploits pre-existing immigrant job networks. The empirical results from both approaches show statistically signi cant but relatively modest displacement e¤ects. Over a 1-2 year horizon, hiring one additional immigrant displaces roughly 0.3 native workers. Over a longer (3-4) year horizon the displacement e¤ects are smaller, and insigni cantly different from zero. I show that these results imply an elasticity of substitution between immigrants and natives of between 10 and 15. Perhaps surprisingly, the rm level evidence is consistent with previous estimates based on local and national labor market comparisons. E-mail: rcampos@econ.berkeley. edu. Address: University of California, 508-1 Evans Hall, Berkeley, CA 94720-3880. I am extremely grateful to the Institute of Employment and Research (IAB) in Nuremberg, Germany for data access and generous nancial support. The Center of Labor Economics and the Institute of Business and Economic Research at UC Berkeley also provided nancial support. I thank David Card and Emmanuel Saez for advice and guidance during the completion of this paper. I thank comments by Eva Arceo-Gomez, Monica Deza, Daniel Egel, Patrick Kline, Enrico Moretti, Kevin Stange and Andrea Weber. All remaining errors are my own.
Disease spectrum of patients with antineutrophil cytoplasmic autoantibodies of defined specificity: distinct differences between patients with anti‐proteinase 3 and anti‐myeloperoxidase autoantibodies

Franssen C, Gans R, Kallenberg C, Hageluken C, Hoorntje S (University Hospital, Groningen; Free University Hospital, Amsterdam; and Catharina Hospital, Eindhoven; the Netherlands). Disease spectrum of patients with antineutrophil cytoplasmic autoantibodies of defined specificity: distinct differences between patients with antiproteinase 3 and antimyeloperoxidase autoantibodies. J Intern Med 1998; 244: 209–16.
Definition of Best Medical Treatment in Asymptomatic and Symptomatic Carotid Artery Stenosis

Implementation of best medical treatment (BMT) is the cornerstone of the management of patients with either asymptomatic or symptomatic carotid artery stenosis. We review the literature to define the components of BMT. Smoking cessation, maintaining a healthy body weight, moderate exercise, and a Mediterranean diet are essential lifestyle measures. Moderate alcohol consumption may also be beneficial but recommending it to patients may be hazardous if they consume too much. The importance of lifestyle measures is largely underestimated by both physicians and patients. Blood pressure and diabetes control, antiplatelet agents, and lipid-lowering treatment with statins/ezetimibe comprise the pharmacological components of BMT. Initiation of an intensive regimen of BMT is a sine qua non for patients with carotid artery stenosis whether or not they are offered or undergo an invasive revascularization procedure.
Correlation of abnormal intracranial vessel velocity, measured by transcranial Doppler ultrasonography, with abnormal conjunctival vessel velocity, measured by computer-assisted intravital microscopy, in sickle cell disease.

The Stroke Prevention Trial has confirmed that utilization of transcranial Doppler ultrasonography (TCD), which examines blood flow in large intracranial vessels, can identify children with sickle cell disease (SCD) who are at high risk of developing a premature stroke. It is not known to what extent the vasculopathy in SCD involves small vessels and whether the abnormalities, if present, correlate with large-vessel vasculopathy. Eighteen children with SCD were examined with TCD to determine middle cerebral artery (MCA) velocity and computer-assisted intravital microscopy (CAIM) to determine bulbar conjunctival vessel velocity during the same visit for vasculopathy correlation. High MCA velocity (> or = 200 cm/sec) was found by TCD in 4 patients who also showed abnormal conjunctival velocity (< 0.2 mm/sec or intermittent trickle flow) by CAIM. Three patients had conditional (> or = 170 cm/sec and < 200 cm/sec) MCA velocity: 2 showed abnormal (trickle) and 1 showed normal conjunctival velocity (1.9 mm/sec). One patient with unmeasurable MCA velocity had abnormal (trickle) conjunctival velocity. Of the remaining 10 patients who had normal MCA velocity, 2 showed abnormal (0.05 mm/sec and 0.1 mm/sec) and 8 showed normal conjunctival velocities (1.1-2.4 mm/sec). The MCA velocities correlated significantly with bulbar conjunctival flow velocities (P < or =.008, Fisher exact test). A correlation exists between MCA (large-vessel) and conjunctival (small-vessel) flow velocities. CAIM is a noninvasive quantitative technique that might contribute to the identification of SCD patients at high risk of stroke. Small-vessel vasculopathy might be an important pathological indicator and should be further explored in a large-scale study. (Blood. 2001;97:3401-3404)