Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid Identification of Candida Species with Species-Specific DNA Probes

ABSTRACT Rapid identification of Candida species has become more important because of an increase in infections caused by species other than Candida albicans, including species innately resistant to azole antifungal drugs. We previously developed a PCR assay with an enzyme immunoassay (EIA) format to detect amplicons from the five most common Candida species by using universal fungal primers and species-specific probes directed to the ITS2 region of the gene for rRNA. We designed probes to detect seven additional Candidaspecies (C. guilliermondii, C. kefyr,C. lambica, C. lusitaniae,C. pelliculosa, C. rugosa, andC. zeylanoides) included in the API 20C sugar assimilation panel, five probes for species not identified by API 20C (C. haemulonii, C. norvegica,C. norvegensis, C. utilis, andC. viswanathii), and a probe for the newly described species C. dubliniensis, creating a panel of 18Candida species probes. The PCR-EIA correctly identified multiple strains of each species tested, including five identified asC. albicans by the currently available API 20C database but determined to be C. dubliniensis by genotypic and nonroutine phenotypic characteristics. Species identification time was reduced from a mean of 3.5 days by conventional identification methods to 7 h by the PCR-EIA. This method is simple, rapid, and feasible for identifying Candida species in clinical laboratories that utilize molecular identification techniques and provides a novel method to differentiate the new species, C. dubliniensis, from C. albicans.
Asymptotic-preserving schemes for multiscale physical problems

We present the asymptotic transitions from microscopic to macroscopic physics, their computational challenges and the asymptotic-preserving (AP) strategies to compute multiscale physical problems efficiently. Specifically, we will first study the asymptotic transition from quantum to classical mechanics, from classical mechanics to kinetic theory, and then from kinetic theory to hydrodynamics. We then review some representative AP schemes that mimic these asymptotic transitions at the discrete level, and hence can be used crossing scales and, in particular, capture the macroscopic behaviour without resolving the microscopic physical scale numerically.
Practice Effects and Amyloid Deposition: Preliminary Data on a Method for Enriching Samples in Clinical Trials

Clinical trials in Alzheimer disease are moving toward prevention studies in prodromal individuals with amyloid burden. However, methods are needed to identify individuals expected to be amyloid positive for these studies to be feasible and cost-effective. The current study sought to determine whether short-term practice effects on cognitive tests can identify those with notable uptake on amyloid imaging. Twenty-five, nondemented older adults (15 cognitively intact, 10 with mild cognitive impairment) underwent amyloid imaging through 18F-flutemetamol and 2 cognitive testing sessions across 1 week to determine practice effects on a visual memory test. Results indicated that, whereas 18F-flutemetamol uptake showed little association with baseline performance on a visual memory test (r=−0.04, P=0.85), it was significantly correlated with practice effects across 1 week on that same memory measure (r=−0.45, P=0.02), with greater uptake being associated with lower practice effects. The odds ratio of notable 18F-flutemetamol uptake was 5 times higher in individuals with low practice effects compared with high practice effects. Although these preliminary results need to be replicated in larger samples, short-term practice effects on cognitive tests may provide an affordable screening method to identify individuals who are amyloid positive, which could enrich samples for preventative clinical trials in Alzheimer disease.
Clinicopathologic characteristics and treatment outcome of the addition of rituximab to chemotherapy for CD 5-positive in comparison with CD 5-negative diffuse large B-cell lymphoma

Clinicopathologic characteristics and treatment outcome of the addition of rituximab to chemotherapy for CD5-positive in comparison with CD5-negative diffuse large B-cell lymphoma N. Niitsu*, M. Okamoto, J.-i. Tamaru, T. Yoshino, N. Nakamura, S. Nakamura, K. Ohshima, H. Nakamine & M. Hirano Department of Hematology, Comprehensive Cancer Center, International Medical Center, Saitama Medical University, Saitama; Adult Lymphoma Treatment Study Group, Nagoya, Japan
Finite Control Set Model Predictive Current Control for Grid-Connected Voltage-Source Converters With LCL Filters: A Study Based on Different State Feedbacks

This paper presents different state feedback approaches of finite control set model predictive control (FCS-MPC) applied to a grid-connected voltage-source converter (VSC) with an LCL filter. Besides converter-side current feedback, two multivariable control approaches and line-side current control are introduced and compared based on theoretical and experimental evaluation. As the LCL filter introduces an additional resonance frequency to the system, the use of different active damping (AD) methods in combination with FCS-MPC is discussed. Furthermore, practical control implementation issues are discussed. The presented methods reveal the great potential, high dynamic performance, and flexibility of FCS-MPC, enabling multivariable control as well as both reduced switching losses and low harmonic current distortion at the same time. Eventually, the feasibility of the theoretical control concepts is shown in a laboratory environment.
Proteome map of normal rat retina and comparison with the proteome of diabetic rat retina: New insight in the pathogenesis of diabetic retinopathy

We have employed proteomics to establish a proteome map of the normal rat retina. This baseline map was then used for comparison with the early diabetic rat retinal proteome. Diabetic rat retinae were obtained from Dark Agouti rats after 10 wk of streptozotocin‐induced hyperglycaemia. Extracted proteins from normal and diabetic rat retinae were separated and compared using 2‐DE. A total of 145 protein spots were identified in the normal rat retina using MALDI‐MS and database matching. LC‐coupled ESI‐MS increased the repertoire of identified proteins by 23 from 145 to 168. Comparison with early diabetic rat retinae revealed 24 proteins unique to the diabetic gels, and 37 proteins absent from diabetic gels. Uniquely expressed proteins identified included the HSPs 70.1A and 8, and platelet activating factor. There were eight spots with increased expression and 27 with decreased expression on diabetic gels. Beta catenin, phosducin and aldehyde reductase were increased in expression in diabetes whilst succinyl coA ligase and dihydropyrimidase‐related protein were decreased. Identification of such changes in protein expression has given new insights and a more comprehensive understanding of the pathogenesis of diabetic retinopathy, widening the scope of potential avenues for new therapies for this common cause of blindness.
‘Simply forgot’ is the most frequently stated reason for missed doses of HAART irrespective of degree of adherence

Previous studies have reported that forgetfulness is the most frequently mentioned reason for missed doses among patients on highly active antiretroviral therapy (HAART). However, no previous study has compared the reasons given by highly nonadherent patients with the reasons given by patients with better adherence. The objective of this study was to examine further patients' self‐reported reasons for missing doses of HAART and to compare the reasons given by patients with lower adherence with those given by patients with higher adherence.
Assessment of cardiovascular reflexes: influence of posture and period of preceding rest.

The aim of the present study was to investigate the effects of a pretest redistribution of blood volume and of a change in the neurohumoral condition on the blood pressure (BP) and heart rate (HR) responses to three commonly used cardiovascular reflex tests: standing up, forced breathing, and the Valsalva maneuver in 10 healthy male subjects. Base-line conditions were altered by changing posture and the duration of rest preceding the test stimulus. A continuous recording of finger BP was obtained noninvasively by a Finapres. The main observations from this study are with respect to standing up: lengthening the period of preceding rest from 1 to 20 min enlarges the initial BP (systolic/diastolic) decrease (from 8 +/- 10/9 +/- 4 to 27 +/- 8/19 +/- 4 mmHg, P less than 0.01) and the subsequent BP overshoot (from 17 +/- 10/12 +/- 7 to 31 +/- 10/18 +/- 7 mmHg, P less than 0.05); to forced breathing: inspiratory-expiratory changes in BP but not in HR are larger in the upright posture (P less than 0.05); and to the Valsalva maneuver: change in posture from supine to standing increases the phase II BP decrease (from 18 +/- 12/8 +/- 6 to 45 +/- 16/21 +/- 9 mmHg), phase IV systolic BP overshoot (from 26 +/- 16 to 71 +/- 17 mmHg), delta HRmax (from 30 +/- 10 to 47 +/- 12 beats/min), and the Valsalva ratio (HRmax/HRmin), from 2.0 +/- 0.3 to 2.6 +/- 0.7, all significant at P less than 0.01. (ABSTRACT TRUNCATED AT 250 WORDS)
Targeted microbubble mediated sonoporation of endothelial cells in vivo

Ultrasound contrast agents as drug-delivery systems are an emerging field. Recently, we reported that targeted microbubbles are able to sonoporate endothelial cells in vitro. In this study, we investigated whether targeted microbubbles can also induce sonoporation of endothelial cells in vivo, thereby making it possible to combine molecular imaging and drug delivery. Live chicken embryos were chosen as the in vivo model. αvß3-targeted microbubbles attached to the vessel wall of the chicken embryo were insonified at 1 MHz at 150 kPa (1 × 10 000 cycles) and at 200 kPa (1 × 1000 cycles) peak negative acoustic pressure. Sonoporation was studied by intravital microscopy using the model drug propidium iodide (PI). Endothelial cell PI uptake was observed in 48% of microbubble-vessel-wall complexes at 150 kPa (n = 140) and in 33% at 200 kPa (n = 140). Efficiency of PI uptake depended on the local targeted microbubble concentration and increased up to 80% for clusters of 10 to 16 targeted microbubbles. Ultrasound or targeted microbubbles alone did not induce PI uptake. This intravital microscopy study reveals that sonoporation can be visualized and induced in vivo using targeted microbubbles.
A phosphopantetheinyl transferase that is essential for mitochondrial fatty acid biosynthesis.

In this study we report the molecular genetic characterization of the Arabidopsis mitochondrial phosphopantetheinyl transferase (mtPPT), which catalyzes the phosphopantetheinylation and thus activation of mitochondrial acyl carrier protein (mtACP) of mitochondrial fatty acid synthase (mtFAS). This catalytic capability of the purified mtPPT protein (encoded by AT3G11470) was directly demonstrated in an in vitro assay that phosphopantetheinylated mature Arabidopsis apo-mtACP isoforms. The mitochondrial localization of the AT3G11470-encoded proteins was validated by the ability of their N-terminal 80-residue leader sequence to guide a chimeric GFP protein to this organelle. A T-DNA-tagged null mutant mtppt-1 allele shows an embryo-lethal phenotype, illustrating a crucial role of mtPPT for embryogenesis. Arabidopsis RNAi transgenic lines with reduced mtPPT expression display typical phenotypes associated with a deficiency in the mtFAS system, namely miniaturized plant morphology, slow growth, reduced lipoylation of mitochondrial proteins, and the hyperaccumulation of photorespiratory intermediates, glycine and glycolate. These morphological and metabolic alterations are reversed when these plants are grown in a non-photorespiratory condition (i.e. 1% CO2 atmosphere), demonstrating that they are a consequence of a deficiency in photorespiration due to the reduced lipoylation of the photorespiratory glycine decarboxylase.
Use of formal Methods in Medical Decision Making

Apparent low usage of formal decision techniques by general clinicians has raised questions about dissemination methods and about the techniques' perceived usefulness. Two literature searches examined whether use of formal decision techniques among clinicians had indeed failed to increase from the 1970s to the 1980s. A general MEDLINE search for the period 1983-87 relative to 1973-77 indicated that usage of formal decision techniques had more than doubled. This increase, however, was due to increased coverage of formal decision techniques in specialist methods journals. A manual search of seven major clinical journals and a MEDLINE search restricted to the clinical journals of the manual search disclosed no increase in overall usage for the same time periods. MEDLINE detected only a small subset of the actual instances of formal method usage found by the manual search. Individual medical subspecialties were found to utilize different formal decision techniques to different degrees. The authors suggest interventions that may increase the usage of formal decision techniques among general clinicians. Key words: decision analysis; decision automation; decision trees; Bayes'theorem; sensitivity analysis; ROC analysis; formal modeling. (Med Decis Making 1992;12:298-306)
Adverse events and infections in patients with rheumatoid arthritis treated with conventional drugs or biologic agents: a real world study.

OBJECTIVES Treatment of rheumatoid arthritis (RA) with disease-modifying anti-rheumatic drugs (DMARDs), either synthetic (sDMARDs) or biologic agents (bDMARDs) has significantly improved disease outcome. However, the impact of therapy-related adverse events (AEs), mild, moderate or serious, on disease outcome is under debate. The purpose of the study was to test the hypothesis that AEs, including infections, are rather common in patients receiving bDMARDs than in those receiving sDMARDs. METHODS Analysis of the medical records of patients followed in a single outpatient clinic was performed. In total, 1403 adults (295 men, 1108 women) were included in the analysis (969 treated with sDMARDs only, 434 with bDMARDs). All AEs and infections were recorded and their severity was graded according to international criteria. Incident rates were calculated and Kaplan-Meier plots as well as Cox proportional-hazards models were performed to examine the association of treatment groups with the risk of any AE. RESULTS The risk of any AE, irrespective of severity, was significantly higher in patients with bDMARDs with the adjusted hazard ratio being 1.98 (95% CI: 1.64 to 2.39). Patients in the biologic group treated initially with infliximab or adalimumab had a higher risk of AE compared to patients receiving etanercept or other biologic agents. Among patients treated with methotrexate, those receiving a dose below 10 mg had a higher risk of any AE when compared to those receiving higher doses. CONCLUSIONS The risk of any AE among RA patients treated with bDMARDs was significantly higher compared to those treated with sDMARDs.
The duration of zidovudine benefit in persons with asymptomatic HIV infection. Prolonged evaluation of protocol 019 of the AIDS Clinical Trials Group.

OBJECTIVE To determine the durability of zidovudine-induced delay in clinical progression of asymptomatic human immunodeficiency virus (HIV) disease and to assess the relationship between this effect and the entry CD4+ cell count. DESIGN AND INTERVENTIONS Extended follow-up data from subjects participating in protocol 019 of the AIDS [acquired immunodeficiency syndrome] Clinical Trials Group were examined. Subjects were offered a total daily dose of 500 mg of open-label zidovudine after the unblinding of the original randomized trial in 1989. Original treatment groups included placebo, 500 mg of zidovudine, or 1500 mg of zidovudine daily in divided doses. Three distinct analyses were conducted to assess the duration of zidovudine's effect on progression to AIDS or death: (1) analysis of all follow-up information from all subjects, (2) analysis of all subjects but with follow-up of original placebo-assigned subjects censored at the time open-label zidovudine was initiated, and (3) analysis of the effect of initiating zidovudine in subjects initially assigned to receive placebo. SETTING University-based and university-affiliated AIDS research clinics participating in AIDS Clinical Trials Group protocol 019. PATIENTS A total of 1565 asymptomatic HIV-infected subjects with entry CD4+ cell counts less than 0.50 x 10(9)/L (500/microL). MAIN OUTCOME MEASURE Time to progression to AIDS or death. RESULTS During follow-up of up to 4.5 years (mean, 2.6 years), 232 subjects progressed to AIDS or died. In each of the three analyses described herein, zidovudine was associated with a significant (P = .008, .004, .007) decrease in the risk of such progression. However, each of these analyses also indicated a decreasing placebo:zidovudine relative risk with duration of use (P = .002, .08, .04), suggesting a nonpermanent effect. The duration of benefit appeared to be related to entry CD4+ cell count, with greater benefit in those with higher counts at entry. No significant differences in survival were found between those originally randomized to zidovudine or placebo. CONCLUSIONS Zidovudine at 500 mg/d caused a significant delay in progression to AIDS or death, but its earlier use in asymptomatic disease was not associated with an additional prolongation of survival compared with delayed initiation. The delay in progression diminished over time especially in subjects with entry CD4+ cell counts less than 0.30 x 10(9)/L (300/microL). Treatment strategies that alter drug regimens before the loss of zidovudine benefit should be explored.
Risk factors for cutaneous malignant melanoma in a northern italian population

The relationship between cutaneous malignant melanoma (CMM) and the colour of skin, hair and eyes, the extent of sun exposure and reaction to it, education, and the occurrence of skin neoplasms in patients and their families was evaluated in a case‐control study of 103 cases of CMM and 205 control subjects hospitalized for acute conditions other than malignant or hormonal disease. A significantly higher risk was associated with fair skin as compared to dark/medium skin (RR = 4.0; 95% CI: 1.5‐10.5) and positive family history for CMM (RR = 8.1; 95% CI: 1.0‐200.9). CMM seemed to occur more frequently, but not significantly so, in individuals with brown or blond hair, higher education and clinically diagnosed dysplastic naevi. Outdoor occupation and heavy sun exposure in the last 20 years seemed to increase the risk of CMM in sunexposed sites but to be negatively associated with CMM in normally unexposed sites.
A Driving Simulator Study on Adaptive Cruise Control Failure

Adaptive cruise control automatically adjusts vehicle speed and distance to a preceding vehicle, thus enhancing driver comfort and safety. Previous studies have shown that adaptive cruise control induces positive behavioral adaptation by drawing consistency in driving speed and headway-time regardless of driving styles. However, the studies have also shown that the drivers' reliance on the system induced negative adaptation including reduced lane keeping ability and reduced attention during driving. This study further investigated effect of negative behavioral adaptation to adaptive cruise control. Failure of adaptive cruise control was simulated using a full-scale driving simulator and driver behavior under the simulated failure was studied. Twenty drivers participated in the study to compare reaction time, distance between the cars, and eye movement. Three different driving scenarios were used: adaptive cruise control off, adaptive cruise control on and adaptive cruise control on followed by braking algorithm failure. Experiment results showed that the drivers took longer time to recognize and react to sudden speed reduction by the car ahead when driving with adaptive cruise control and even longer when adaptive cruise control failed. This indicates potential danger of negative behavioral adaptation to adaptive cruise control and requires prevention strategy such as education and public awareness
Basal omega-3 fatty acid status affects fatty acid and oxylipin responses to high-dose n3-HUFA in healthy volunteers[S]

A subject's baseline FA composition may influence the ability of dietary highly unsaturated omega-3 FAs (n3-HUFA) to change circulating profiles of esterified FAs and their oxygenated metabolites. This study evaluates the influence of basal n3-HUFA and n3-oxylipin status on the magnitude of response to n3-HUFA consumption. Blood was collected from fasting subjects (n = 30) before and after treatment (4 weeks; 11 ± 2 mg/kg/day n3-HUFA ethyl esters). Esterified FAs were quantified in erythrocytes, platelets, and plasma by GC-MS. Esterified oxylipins were quantified in plasma by LC-MS/MS. Treatment with n3-HUFAs increased n3-HUFAs and decreased n6-HUFAs in all reservoirs and increased plasma n3-oxylipins without significantly changing n6-oxylipin concentrations. As subject basal n3-HUFAs increased, treatment-associated changes decreased, and this behavior was reflected in the percentage of 20:5n3 + 22:6n3 in red blood cell membrane FAs (i.e., the omega-3 index). To maintain an omega-3 index of 8% and thus reduce cardiovascular disease risk, our analyses suggest a maintenance dose of 7 mg/kg/day n3-HUFA ethyl esters for a 70-kg individual. These results suggest that the basal n3 index may have clinical utility to establish efficacious therapeutic experimental feeding regimens and to evaluate the USDA Dietary Guidelines recommendations for n3-HUFA consumption.
Effects of Neonicotinoids and Crop Rotation for Managing Wireworms in Wheat Crops

ABSTRACT Soil-dwelling insects are severe pests in many agroecosystems. These pests have cryptic life cycles, making sampling difficult and damage hard to anticipate. The management of soil insects is therefore often based on preventative insecticides applied at planting or cultural practices. Wireworms, the subterranean larvae of click beetles (Coleoptera: Elateridae), have re-emerged as problematic pests in cereal crops in the Pacific Northwestern United States. Here, we evaluated two management strategies for wireworms in long-term field experiments: 1) treating spring wheat seed with the neonicotinoid thiamethoxam and 2) replacing continuous spring wheat with a summer fallow and winter wheat rotation. Separate experiments were conducted for two wireworm species—Limonius californicus (Mannerheim) and Limonius infuscatus (Motschulsky). In the experiment with L. californicus, spring wheat yields and economic returns increased by 24–30% with neonicotinoid treatments. In contrast, in the experiment with L. infuscatus, spring wheat yields and economic returns did not increase with neonicotinoids despite an 80% reduction in wireworms. Thus, the usefulness of seed-applied neonicotinoids differed based on the wireworm species present. In experiments with both species, we detected significantly fewer wireworms with a no-till summer fallow and winter wheat rotation compared with continuous spring wheat. This suggests that switching from continuous spring wheat to a winter wheat and summer fallow rotation may aid in wireworm management. More generally, our results show that integrated management of soildwelling pests such as wireworms may require both preventative insecticide treatments and cultural practices.