Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Phenotypic Markers for Selection and Identification of Candida dubliniensis

ABSTRACT Candida dubliniensis is often associated with C. albicans in cultures. Easy-to-perform selective isolation procedures for these closely related species do not exist. Therefore, we evaluated previously described discriminatory phenotypic markers forC. dubliniensis. A total of 150 oral rinses from human immunodeficiency virus (HIV)-infected patients were cultured on CHROMagar Candida. Dark green colonies described as being indicative ofC. dubliniensis and other green colonies, 170 in total, were isolated. Chlamydospore formation, intracellular β-d-glucosidase activity, ability to grow at 42°C, carbohydrate assimilation pattern obtained by the API ID 32C, and Fourier transform infrared (FT-IR) spectroscopy were used for phenotypic characterization. Sequencing of the 5′ end of the nuclear large-subunit (26S) ribosomal DNA gene was used for definitive species identification for C. dubliniensis. C. dubliniensis was found in 34% of yeast-colonized HIV-infected patients. The color of the colonies on CHROMagar Candida proved to be insufficient for selecting C. dubliniensis, since only 30 of 53 provenC. dubliniensis isolates showed a dark green color in primary cultures. The described typical chlamydospore formation can give only some indication of C. dubliniensis. The assimilation pattern proved to be insufficient to discriminate C. dubliniensis from C. albicans. All C. dubliniensis strains showed no or highly restricted growth at 42°C and a lack of β-d-glucosidase activity. Unfortunately, atypical C. albicans strains can also exhibit these phenotypic traits. FT-IR spectroscopy combined with hierarchical clustering proved to be as reliable as genotyping for discriminating the two species.
Performance Pay and Prior Learning: Evidence from a Retail Chain

We report the results of two field experiments in a retail chain and show that the effectiveness of performance pay crucially hinges on prior job experience. Introducing sales-based performance pay first for district managers and later for store managers, we find negligible average treatment effects. From surveys and interviews, we develop a formal model demonstrating that the effect of performance pay decreases with experience and may even vanish in the limit. We provide empirical evidence in line with this hypothesis—for instance, finding positive treatment effects (only) in stores with low job experience. This paper was accepted by Yan Chen, decision analysis.
Multilingualism and fMRI: Longitudinal Study of Second Language Acquisition

BOLD fMRI is often used for the study of human language. However, there are still very few attempts to conduct longitudinal fMRI studies in the study of language acquisition by measuring auditory comprehension and reading. The following paper is the first in a series concerning a unique longitudinal study devoted to the analysis of bi- and multilingual subjects who are: (1) already proficient in at least two languages; or (2) are acquiring Russian as a second/third language. The focus of the current analysis is to present data from the auditory sections of a set of three scans acquired from April, 2011 through April, 2012 on a five-person subject pool who are learning Russian during the study. All subjects were scanned using the same protocol for auditory comprehension on the same General Electric LX 3T Signa scanner in Duke University Hospital. Using a multivariate analysis of covariance (MANCOVA) for statistical analysis, proficiency measurements are shown to correlate significantly with scan results in the Russian conditions over time. The importance of both the left and right hemispheres in language processing is discussed. Special attention is devoted to the importance of contextualizing imaging data with corresponding behavioral and empirical testing data using a multivariate analysis of variance. This is the only study to date that includes: (1) longitudinal fMRI data with subject-based proficiency and behavioral data acquired in the same time frame; and (2) statistical modeling that demonstrates the importance of covariate language proficiency data for understanding imaging results of language acquisition.
Molecular systematics and evolution of the aphid family Lachnidae.

The aphid family Lachnidae (c. 320 spp.)-sister-group to the economically devastating family Aphididae (c. 3300 spp.)-encompasses a diverse array of associations with hostplants and attendant hymenopterans and of life histories, including potentially long-term parthenogenesis. Most-parsimonious phylogenetic trees were inferred from partial (905-coding-bp) sequences of elongation factor 1alpha (EF-1alpha) and complete (675-bp) sequences of cytochrome oxidase 2 (CO2). The EF-1alpha, CO2, and combined analyses did not conflict with each other. Most tribes and infratribal relationships were robustly supported; intertribal relationships were mostly unresolved in the separate analysis and only weakly supported in the combined analysis. Both genes indicated a close relationship between the genera Nippolachnus and Tuberolachnus, both of which include species with the unusual habit of feeding along the midrib of leaves of Eriobotrya and which are here referred to the tribe Tuberolachnini Mamontova. A sister-group relationship between Tuberolachnini and the putatively ancient asexual tribe Tramini is supported. The combined analysis provides support (albeit weak) for the hypothesis that conifer-feeding is ancestral in Lachninae, which in turn implies that conifer-feeding may be a homologous and uninterrupted habit across disparate families of aphidoids (e.g., Adelgidae, Mindaridae, Drepanosiphidae, and Lachnidae).
Identification and quantitative analysis of physalin D and its metabolites in rat urine and feces by liquid chromatography with triple quadrupole time-of-flight mass spectrometry.

Physalin D is known to show extensive bioactivities. However, no excretion study has elucidated the excretion of physalin D and its metabolites. This study investigates the excretion of physalin D and its metabolites in rats. Metabolites in rat urine and feces were separated and identified by liquid chromatography with triple quadrupole time-of-flight mass spectrometry. Furthermore, a validated high-performance liquid chromatography with tandem mass spectrometry method was developed to quantify physalin D, physalin D glucuronide, and physalin D sulfate in rat feces and urine after the intragastric administration of physalin D. The analyte showed good linearity over a wide concentration range (r > 0.995), and the lower limit of quantification was 0.0532 μg/mL and 0.226 μg/g for urine and feces, respectively. Nine metabolites, including five phase I and four phase II metabolites, were identified and clarified after dosing in vivo. Only 4.0% of the gavaged dose, including physalin D and its phase II metabolites, was excreted in urine, whereas 10.8% was found in feces in the unchanged form. The results indicate that the extensive and rapid metabolism may be the main factors leading to the short half-life of physalin D. These results can provide a basis for further studies on the structural modification and pharmacology of physalin D.
Evaluation of analgesic and anti‐inflammatory activities of Nectandra megapotamica (Lauraceae) in mice and rats

The bioactivity‐guided phytochemical investigation of the crude hydralcoholic extract of Nectandra megapotamica was carried out using the abdominal constriction test in mice, which led to the isolation of three active compounds: α‐asarone (1), galgravin (2) and veraguensin (3). The crude extract (EBCA, 300 mg kg−1) and isolated compounds 1, 2, and 3, at different doses, were evaluated using the acetic acid‐induced abdominal constriction test in mice, carrageenan‐induced paw oedema in rats, and hot plate tests in rats. The EBCA showed a significant effect in the abdominal constriction and hot plate tests, but did not show activity in the rat paw oedema assay. All isolated compounds displayed activity in the abdominal constriction test, but only compound 1 was active in the hot plate test. Compounds 2 and 3 displayed activity in the anti‐inflammatory assay. It was suggested that the analgesic effects obtained for EBCA could be due mainly to the presence of its major compound, α‐asarone (1).
Role of tumor necrosis factor receptor 2 (TNFR2) in colonic epithelial hyperplasia and chronic intestinal inflammation in mice.

BACKGROUND & AIMS Tumor necrosis factor (TNF) induces multiple effects including cell proliferation and death by ligation with TNF receptor type II (TNFR2). We studied the role of TNFR2 in chronic inflammation-induced colonic epithelial alteration. METHODS TNFR2 expression in colonic epithelial cells (CECs) was assessed by ribonuclease protection assay (RPA) and immunohistochemistry (IHC) in patients with inflammatory bowel disease (IBD) and murine colitis models. TNFR2 expression was also analyzed using COLO205 cells. The role of TNFR2 in colonic epithelial homeostasis was examined by generating interleukin 6-deficient TCR alpha KO (alpha IL-6DKO) or TNFR2-deficient TCR alpha (alpha TNFR2DKO) mice. RESULTS TNFR2 expression was up-regulated in CEC in both human ulcerative colitis and Crohn's disease. In vitro studies showed that TNFR2 expression was up-regulated by a cooperative effect of key proinflammatory cytokines. By RPA, the increased expression of TNFR2 was detectable in TCR alpha KO mice with colitis compared with TCR alpha KO mice without colitis or wild-type mice. In alpha IL-6DKO mice, TNFR2 expression, proliferation, and nuclear factor kappa B activation of CECs were markedly reduced compared with TCR alpha KO mice. alpha TNFR2 mice also showed significantly less colonic epithelial proliferation compared with TCR alpha KO mice. CONCLUSIONS Expression of TNFR2 is consistently increased on CECs in both murine colitis models as well as patients with IBD. TNFR2 may play an important role in colonic inflammation-associated alteration in the intestinal epithelium.
Avian influenza, non‐tariff measures and the poultry exports of China†

This paper focuses on the direct impact of avian influenza outbreaks and the impact of the consequent non‐tariff measures (NTMs) on the international poultry trade. Using monthly export data from China and its 122 poultry importing countries, a random‐effect gravity model has been adopted. Emphasising the agri‐food trade in a global value chain context, the research analysis distinguishes between ‘agri‐food goods’ (mostly uncooked poultry products) and ‘processed goods’ (mostly cooked poultry products). The results show that domestic avian influenza outbreaks have a significant negative impact on a country's poultry imports compared with such outbreaks in exporting countries. Moreover, NTMs induced by avian influenza reduce the uncooked poultry trade but temporarily increase the cooked poultry trade. However, with a time‐lag, the cooked poultry trade may soon face increasing NTMs. The results also imply that developing countries that attempt to export agri‐food products to developed countries should increase and enhance processed food production.
The Performance of Mechanical Earnings Forecasts

We analyze three different mechanical models to forecast earnings and compare their forecasts with those of analysts. Moreover, we evaluate implied cost of capital (ICC) estimates that are based on these forecasts. With our analyses we answer three open questions in the literature. 1) Do model forecasts or analysts’ forecasts perform better? 2) Are ICCs derived from analysts’ forecasts more reliable than ICCs based on model forecasts? And 3) does higher forecast performance also translate into more reliable ICCs? First, we find that analysts’ forecasts are even more accurate than the most accurate model forecasts. However, second, we find that model-based ICCs are always more reliable than analyst-based ICCs. Moreover, model-based ICCs are particularly reliable for a sample of firms for which no analysts’ forecasts are available. While the lack of reliability of analyst-based ICCs seems to indicate a missing link between forecast performance and ICC reliability, in fact, third, we find that ceteris paribus higher forecast performance translates into more reliable ICCs, that is, within one earnings definition the most accurate forecasts also yield the most reliable ICCs.
Pancreatic D-Cell Recognition of D-Glucose: Studies with D-Glucose, D-Glyceraldehyde, Dihydroxyacetone, D-Mannoheptulose, D-Fructose, D-Galactose, and D-Ribose

To investigate how the D-cell recognizes the glucose stimulus, the hormone response to (1) glucose, (2) the trioses glyceraldehyde and dihydroxyacetone, (3) the metabolic blocker, mannoheptulose, and (4) the lowor nonmetabolized sugars galactose, fructose, or ribose were studied using the isolated dog pancreas. We found (1) a sigmoidal relationship between extracellular glucose concentrations and the somatostatin release. The threshold concentration was around 5 mM and the largest increase in somatostatin release occurs between 5 and-10 mM of glucose. (2) Glyceraldehyde at concentrations ranging between 1.25 and 5 mM stimulated the release of somatostatin, whereas the higher concentrations of 10 and 20 mM were suppressive. Dihydroxyacetone (11 mM), also initiated somatostatin release in the absence of glucose. Both of the trioses stimulated B- and inhibited A-cell secretion. (3) Mannoheptulose (5 mM) attenuated somatostatin and insulin secretion to 8.3 mM glucose, while it augmented glucagon output. In contrast, mannoheptulose (5 mM) did not affect D-, A-, or B-cell responses to glyceraldehyde (5 mM) in the absence of glucose. (4) The somatostatin, insulin, and glucagon release remained unchanged when 8.3 mM of either galactose, fructose, or ribose was added. The results suggest that the initiation of glucose-mediated D- as well as Aand B-cell responses depends on the metabolism of the sugar.
Dynamic observation of polypide in semen and blood of rabbits infected with Toxoplasma tachyzoites

Toxoplasma gondii (T。 gondii ) 是细胞内部的寄生于的原生动物之一并且可以在损害的胎儿或免疫引起严重医药复杂并发症个人。 当时， T.gondii 在尖锐舞台期间作为 tachyzoite 存在作为 bradyzoite 在在人的房间的长期的阶段期间。 改进疾病的预防，诊断，和治疗的理解，探索分发和变化和 T 的另外的生物特征是重要的。 在主人的 gondii。 trophozoite 在主人的口水，血或尿被发现了。 一些研究在血或在尿建议了传播抗体和 toxoplasma 传播抗原(TCA ) 的动态变化。 T。 因为它仅仅是在尺寸的几测微计，因此，大多数研究被执行，在织物或血的 gondii 不能完全在显微镜下面被数由老鼠接种或免疫学方法的品质上。 量的荧光灯的聚合酶链反应(QF-PCR ) 和它的申请在主人为 polypide 的动态观察提起了可能性。 在这研究，血和精液从感染 toxoplasma tachyzoites 和 T 的雄的兔子模型被收集。 gondii 被检测由 QF-PCRquantitatively。
Urban driven phenotypic changes: empirical observations and theoretical implications for eco-evolutionary feedback

Emerging evidence that cities drive micro-evolution raises the question of whether rapid urbanization of Earth might impact ecosystems by causing systemic changes in functional traits that regulate urban ecosystems' productivity and stability. Intraspecific trait variation—variation in organisms' morphological, physiological or behavioural characteristics stemming from genetic variability and phenotypic plasticity—has significant implications for ecological functions such as nutrient cycling and primary productivity. While it is well established that changes in ecological conditions can drive evolutionary change in species' traits that, in turn, can alter ecosystem function, an understanding of the reciprocal and simultaneous processes associated with such interactions is only beginning to emerge. In urban settings, the potential for rapid trait change may be exacerbated by multiple selection pressures operating simultaneously. This paper reviews evidence on mechanisms linking urban development patterns to rapid phenotypic changes, and differentiates phenotypic changes for which there is evidence of micro-evolution versus phenotypic changes which may represent plasticity. Studying how humans mediate phenotypic trait changes through urbanization could shed light on fundamental concepts in ecological and evolutionary theory. It can also contribute to our understanding of eco-evolutionary feedback and provide insights for maintaining ecosystem function over the long term. This article is part of the themed issue ‘Human influences on evolution, and the ecological and societal consequences’.
Evaluation of two different resonance frequency devices to detect implant stability: a clinical trial.

BACKGROUND Resonance frequency analysis (RFA) provides a non-invasive assessment of implant stability. The established RFA device uses electronic technology, whereas a recently developed device uses magnetic technology. The goal of this clinical trial was to evaluate the ability of the magnetic RFA device to detect changes in stability during early healing following implant placement and to determine whether the implant stability quotient (ISQ) values obtained correlated with those made with the electronic device. METHODS RFA assessments were performed using electronic- and magnetic-based devices on 34 non-submerged titanium dental implants in 17 patients. Each patient received two implants in the posterior maxilla or mandible. Implant stability was measured at placement and weekly until week 6, when implants received provisional crowns, and at 12 weeks, when definitive crowns were cemented. During each visit, measurements were taken three times and averaged to obtain a single representative ISQ for each device. RESULTS At placement, the mean ISQ obtained with the electronic device was 61.9 (95% confidence interval [CI], 59.4 to 64.3); it increased to 63.2 (95% CI, 61.2 to 65.2) at 12 weeks. With the magnetic device, the mean ISQs were 70.6 (95% CI, 68.4 to 72.8) and 75.9 (95% CI, 74.2 to 77.7), respectively. Both devices indicated a pattern of decreased mean stability from 1 to 3 weeks post-placement, small fluctuations in mean ISQ from 3 to 6 weeks, and significantly increased mean stability from 6 to 12 weeks. For the complete set of implant measures across all weeks, the paired electronic and magnetic ISQ values correlated significantly (r = 0.52; P <0.001). CONCLUSIONS This study demonstrates that changes in implant stability measured with the newer magnetic device correlate well with those found with the electronic device. Both devices confirmed the initial decreases in implant stability that occur following placement and identified an increase in stability during the first 6 weeks of functional loading.
Binding of YY1 to a site overlapping a weak TATA box is essential for transcription from the uteroglobin promoter in endometrial cells

The gene for rabbit uteroglobin codes for a small calcium-, steroid-, and biphenyl metabolite-binding homodimeric protein which is expressed in a variety of epithelial cell types such as Clara cells (lung) and the glandular and luminal cells of the endometrium. One important region mediating its efficient transcription in a human endometrium-derived cell line, Ishikawa, is centered around a noncanonical TATA box. Two factors, TATA core factor (TCF), expressed in cell lines derived from uteroglobin-expressing tissues, and the ubiquitously expressed TATA palindrome factor, bind to the DNA major groove at two adjacent sites within this region. Here, we report the identification of the TATA palindrome factor as the transcription/initiation factor YY1 by microsequencing of the biochemically purified factor from HeLa cells. The binding site for YY1 within the uteroglobin gene is unique in its sequence and its location overlapping a weak TATA box (TACA). Binding of YY1 was required for efficient transcription in TCF-positive Ishikawa cells, which responded only weakly to a change of TACA to TATA, although in vitro binding affinity for the TATA-box-binding protein increased by 1 order of magnitude. In contrast, in CV-1 cells, lacking TCF, binding of YY1 was not required for transcription in the context of a wild-type TACA box, whereas a change from TACA to TATA led to significantly increased reporter gene expression. DNA binding data exclude a role of YY1 in stabilizing the interaction of the TATA-box-binding protein with the uteroglobin promoter. We conclude that cell lines derived from uteroglobin-expressing tissues overcome the weak TATA box with the help of auxiliary factors, one of them being YY1.
The Active Site of Methanol Synthesis over Cu/ZnO/Al2O3 Industrial Catalysts

Mechanisms in Methanol Catalysis The industrial production of methanol from hydrogen and carbon monoxide depends on the use of copper and zinc oxide nanoparticles on alumina oxide supports. This catalyst is “structure sensitive”; its activity can vary by orders of magnitude, depending on how it is prepared. Behrens et al. (p. 893, published online 19 April; see the Perspective by Greeley) used a combination of bulk and surface-sensitive analysis and imaging methods—along with insights from density functional theory calculations—to study several catalysts, including the one similar to that used industrially. High activity depended on the presence of steps on the copper nanoparticles stabilized by defects such as stacking faults. Partial coverage of the copper nanoparticles with zinc oxide was critical for stabilizing surface intermediates such as HCO and lowering energetic barriers to the methanol product. Catalysis is favored by stepped copper nanoparticles decorated with zinc oxide, which promotes stronger intermediate binding. One of the main stumbling blocks in developing rational design strategies for heterogeneous catalysis is that the complexity of the catalysts impairs efforts to characterize their active sites. We show how to identify the crucial atomic structure motif for the industrial Cu/ZnO/Al2O3 methanol synthesis catalyst by using a combination of experimental evidence from bulk, surface-sensitive, and imaging methods collected on real high-performance catalytic systems in combination with density functional theory calculations. The active site consists of Cu steps decorated with Zn atoms, all stabilized by a series of well-defined bulk defects and surface species that need to be present jointly for the system to work.
Ethnic Variation in Site of Death of Older Adults Dually Eligible for Medicaid and Medicare

This is a retrospective study using secondary data to investigate variation in site of death by ethnicity and to determine how hospice enrollment affects site of death. Data for this study were obtained between 1996 and 2000 from linked Medi‐Cal and Medicare claims from 18 California counties participating in a state legislated effort to improve chronic care services in California. Subjects examined in this study included 38,519 decedents aged 65 and older who died between 1997 and 2000 and were dually eligible the entire year immediately before death. Demographic variables were site of death, cause of death, hospice use, and care setting in the year before death. Results revealed that blacks and Latinos were significantly more likely than whites to die at home, although being black or Asian was negatively associated with hospice use. This variation did not change when hospice use was controlled. Thus, although minorities were more likely to die at home, they were less likely to receive hospice care. Because patients dying at home without hospice care report higher rates of pain than those who have hospice care, physicians must work to ensure that minority patients understand all end‐of‐life care options, including hospice, and how these care options can be delivered in a culturally competent manner.