Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Multiplex Tandem Real-Time PCR for Detection of Cryptosporidium spp., Dientamoeba fragilis, Entamoeba histolytica, and Giardia intestinalis in Clinical Stool Samples

ABSTRACT The aim of this study was to describe the first development and evaluation of a multiplex tandem PCR (MT-PCR) assay for the detection and identification of 4 common pathogenic protozoan parasites, Cryptosporidium spp. , Dientamoeba fragilis, Entamoeba histolytica, and Giardia intestinalis, from human clinical samples. A total of 472 fecal samples submitted to the Department of Microbiology at St. Vincent's Hospital were included in the study. The MT-PCR assay was compared to four real-time PCR (RT-PCR) assays and microscopy by a traditional modified iron hematoxylin stain. The MT-PCR detected 28 G. intestinalis, 26 D. fragilis, 11 E. histolytica, and 9 Cryptosporidium sp. isolates. Detection and identification of the fecal protozoa by MT-PCR demonstrated 100% correlation with the RT-PCR results, and compared to RT-PCR, MT-PCR exhibited 100% sensitivity and specificity, while traditional microscopy of stained fixed fecal smears exhibited sensitivities and specificities of 56% and 100% for Cryptosporidium spp. , 38% and 99% for D. fragilis, 47% and 97% for E. histolytica, and 50% and 100% for G. intestinalis. No cross-reactivity was detected in 100 stool samples containing various other bacterial, viral, and protozoan species. The MT-PCR assay was able to provide rapid, sensitive, and specific simultaneous detection and identification of the four most important diarrhea-causing protozoan parasites that infect humans. This study also highlights the lack of sensitivity demonstrated by microscopy, and thus, molecular methods such as MT-PCR must be considered the diagnostic methods of choice for enteric protozoan parasites.
SuperDARN Electrostatic Potential Function Estimation of Field-Aligned Currents

Magnetic field-aligned currents (FACs) flow between the Earth’s ionosphere and magnetosphere. The connection afforded by FACs means that magnetospheric dynamics may be discerned in ground-based observations of the ionosphere, observations such as the ionospheric plasma velocity measurements made by the Super Dual Auroral Radar Network (SuperDARN). Signatures of FACs are present in the radar data as vorticity in the ionospheric plasma flow. In this thesis, a new method of estimating FACs on a hemispheric scale from ground-based radar observations is presented. The method produces maps of estimated FAC density divided by height-integrated ionospheric Pedersen conductivity through direct calculation from electrostatic potential (voltage) functions that are generated from SuperDARN plasma velocity measurements. Comparisons of the maps to FAC estimates obtained from groundand satellite-based observations using established methods show good qualitative agreement. A short case study of a geomagnetic event that occurred between the evening of 31 May 2013 and the morning of 1 June 2013 is presented to demonstrate the utility of the new potential function-based method. Future applications of the new method are suggested, such as to multi-instrument studies including SuperDARN. The new method is especially useful in that it is easily automated, easily adaptable to new SuperDARN data analysis software, and provides hemisphere-scale FAC maps with the oneor two-minute cadence of the underlying SuperDARN potential functions.
Compression and injection molding techniques for natural fiber composites

Abstract: The forming of a natural fiber composite part, particularly when it involves intricate geometries, is often one of most difficult challenges faced by manufacturers. The intrinsic properties of natural fibers, such as the hygroscopicity and heat sensitivity, further complicate this process. This chapter outlines the challenges faced during compression and injection molding, which are two of the most frequently used techniques for forming natural fiber composites. Several emerging technologies – such as micro-braiding, long fiber pellet and textile insert molding – that are tailored for natural fiber composite forming will be introduced. A strategy to enhance the thermal resistance of natural fibers so that they can be incorporated into high temperature engineering thermoplastics is also discussed.
Electric Field Induced Fluorescence Modulation of Single Molecules in PMMA Based on Electron Transfer

We present a method to modulate the fluorescence of non-polar single squaraine-derived rotaxanes molecules embedded in a polar poly(methyl methacrylate) (PMMA) matrix under an external electric field. The electron transfer between single molecules and the electron acceptors in a PMMA matrix contributes to the diverse responses of fluorescence intensities to the electric field. The observed instantaneous and non-instantaneous electric field dependence of single-molecule fluorescence reflects the redistribution of electron acceptors in PMMA induced by electronic polarization and orientation polarization of polar polymer chains in an electric field.
Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon

Single nucleotide polymorphisms (SNPs) are a class of genetic markers that are well suited to a broad range of research and management applications. Although advances in genotyping chemistries and analysis methods continue to increase the potential advantages of using SNPs to address molecular ecological questions, the scarcity of available DNA sequence data for most species has limited marker development. As the number and diversity of species being targeted for large‐scale sequencing has increased, so has the potential for using sequence from sister taxa for marker development in species of interest. We evaluated the use of Oncorhynchus mykiss and Salmo salar sequence data to identify SNPs in three other species (Oncorhynchus tshawytscha, Oncorhynchus nerka and Oncorhynchus keta). Primers designed based on O. mykiss and S. salar alignments were more successful than primers designed based on Oncorhynchus‐only alignments for sequencing target species, presumably due to the much larger number of potential targets available from the former alignments and possibly greater sequence conservation in those targets. In sequencing ∼89 kb we observed a frequency of 4.30 × 10−3 SNPs per base pair. Approximately half (53/101) of the subsequently designed validation assays resulted in high‐throughput SNP genotyping markers. We speculate that this relatively low conversion rate may reflect the duplicated nature of the salmon genome. Our results suggest that a large number of SNPs could be developed for Pacific salmon using sequence data from other species. While the costs of DNA sequencing are still significant, these must be compared to the costs of using other marker classes for a given application.
10-GHz All-Optical Gate Based on a III–V/SOI Microdisk

We demonstrate an ultrafast and low-power all-optical gate in pump-probe configuration based on free-carrier- induced refractive index modulation in a 5-μm radius InP-InGaAsP microdisk heterogeneously integrated onto a silicon-on-insulator waveguide circuit. High-speed gating is obtained by extracting the carriers from the microdisk active layer by applying a reverse bias. Measured transient responses show that this gate is capable of working up to 20 GHz.
Transcriptional activation by EBV nuclear antigen 1 is essential for the expression of EBV's transforming genes

EBV is a paradigm for human tumor viruses because, although it infects most people benignly, it also can cause a variety of cancers. Both in vivo and in vitro, EBV infects B lymphocytes in G0, induces them to become blasts, and can maintain their proliferation in cell culture or in vivo as tumors. How EBV succeeds in these contrasting cellular environments in expressing its genes that control the host has not been explained. We have genetically dissected the EBV nuclear antigen 1 (EBNA1) gene that is required for replication of the viral genome, to elucidate its possible role in the transcription of viral genes. Strikingly, EBNA1 is essential to drive transcription of EBV's transforming genes after infection of primary B lymphocytes.
Influence of the femoral head size on early postoperative gait restoration after total hip arthroplasty.

BACKGROUND We investigated the effects of using large-diameter femoral heads in total hip prostheses on early postoperative gait restoration in patients undergoing total hip arthroplasty (THA). METHODS We collected data for 19 primary THAs using 28-mm metal-on-polyethylene heads (conventional group) and for 12 THAs (BHR group) using metal-on-metal femoral heads with an average size of 45 mm (range, 40 - 49 mm). All patients had unilateral femoral head avascular necrosis. All patients underwent Harris Hip Scores evaluation and gait analysis with the IDEEA device at the same 3 time points which were before surgery and then at 1 month and again at 3 months after surgery, and the parameters measured were walking speed, stride length (SL), single limb support (SLS), cycle duration (CD), and swing power (SP). Harris Hip Scores and gait analysis parameters for both groups were compared. RESULTS Intraclass comparison indicated that Harris Hip Scores, speed scores, and gait parameter measures in both groups improved significantly with the passage of time; Interclass comparison showed no significance between Harris(1m postop) - Harris(preop) and Harris(3m postop) - Harris(preop) in both groups. The speed in the BHR group at 1 month and at 3 months after surgery was significantly higher than that of conventional group. At 1 month after surgery, each mean for SL(normal) - SL(affected), (SLS(normal) - SLS(affected))/CD, and SP(normal) - SP(affected) in the BHR group was significantly lower than that for the conventional group. At 3 months after surgery, the differences between means for both groups for SL(normal) - SL(affected), (SLS(normal) - SLS(affected))/CD, and SP(normal) - SP(affected) were not significant, but the mean of SP(normal) - SP(affected) in the BHR group was significantly lower than that in the conventional group. CONCLUSIONS Our data suggest that large-diameter femoral heads in THA provide better early gait restoration than conventional-size femoral heads.
The Application and Mechanism of Action of Ribavirin in Therapy of Hepatitis C

Ribavirin has been used as an antiviral agent for several decades. Although it has activity against numerous viruses, its major use clinically has been in the treatment of respiratory syncytial virus in paediatric patients and chronic HCV infection in both children and adults. This review highlights the clinical application and mechanism of action of ribavirin and discusses the future role of ribavirin in treatment of HCV where there are intense research efforts to improve therapy.
Vinorelbine and cisplatin (CIVIC regimen) for the treatment of metastatic breast carcinoma after failure of anthracycline‐ and/or paclitaxel‐containing regimens

A pilot study of a new chemotherapy, the CIVIC regimen, was performed in 58 patients with metastatic breast carcinoma previously treated with chemotherapy with or without hormonal therapy (n = 41). Cisplatin, 20 mg/m2/day, was given (Days 1‐5) every 21 days during a 1‐hour intravenous (i.v.) infusion, and vinorelbine (VNB) was delivered at a dose of 6 mg i.v. bolus followed by VNB, 6 mg/m2/day, in continuous i.v. infusion (Days 1‐5) every 21 days.
New Vibrio species associated to molluscan microbiota: a review

The genus Vibrio consists of more than 100 species grouped in 14 clades that are widely distributed in aquatic environments such as estuarine, coastal waters, and sediments. A large number of species of this genus are associated with marine organisms like fish, molluscs and crustaceans, in commensal or pathogenic relations. In the last decade, more than 50 new species have been described in the genus Vibrio, due to the introduction of new molecular techniques in bacterial taxonomy, such as multilocus sequence analysis or fluorescent amplified fragment length polymorphism. On the other hand, the increasing number of environmental studies has contributed to improve the knowledge about the family Vibrionaceae and its phylogeny. Vibrio crassostreae, V. breoganii, V. celticus are some of the new Vibrio species described as forming part of the molluscan microbiota. Some of them have been associated with mortalities of different molluscan species, seriously affecting their culture and causing high losses in hatcheries as well as in natural beds. For other species, ecological importance has been demonstrated being highly abundant in different marine habitats and geographical regions. The present work provides an updated overview of the recently characterized Vibrio species isolated from molluscs. In addition, their pathogenic potential and/or environmental importance is discussed.
Assessment of cardiovascular regulation through irreversibility analysis of heart period variability: a 24 hours Holter study in healthy and chronic heart failure populations

We propose an approach based on time reversibility analysis to characterize the cardiovascular regulation and its nonlinearities as derived from 24 hours Holter recordings of heart period variability in a healthy population (n=12, age: median=43 years, range=34–55 years) and in a pathological group of age-matched chronic heart failure (CHF) patients (n=13, primarily in NYHA class II, age: median=37 years, range=33–56 years, ejection fraction: median=25%, range=13–30%). Two indices capable of detecting nonlinear irreversible dynamics according to different strategies of phase-space reconstruction (i.e. a fixed two-dimensional phase-space reconstruction and an optimal selection of the embedding dimension, respectively) are tested and compared with a more traditional nonlinear index based on local nonlinear prediction. Results showed that nonlinear dynamics owing to time irreversibility at short time scales are significantly present during daytime in healthy subjects, more frequently present in the CHF population and less frequently during night-time in both groups, thus suggesting their link with a dominant sympathetic regulation and/or with a vagal withdrawal. On the contrary, nonlinear dynamics owing to time irreversibility at longer, dominant time scales were insignificantly present in both groups. During daytime in the healthy population, irreversibility was mostly due to the presence of asymmetric patterns characterized by bradycardic runs shorter than tachycardic ones. Nonlinear dynamics produced by mechanisms different from those inducing temporal irreversibility were significantly detectable in both groups and more frequently during night-time. The present study proposes a method to distinguish different types of nonlinearities and assess their contribution over different temporal scales. Results confirm the usefulness of this method even when applied in uncontrolled experimental conditions such as those during 24 hours Holter recordings.
Advances in Brief Expression of CD 44 Variant Proteins in Human Colorectal Cancer Is Related to Tumor Progression 1

Specific ( '1)44 variant glycoproteins are overexpressed at particular stages of colorectal tumor progression. Some variants of the C 1)44 glycoprotein without exon v6 sequences appear at the earliest stage of tumorigenesis, i.e., in early adenomas. Expression of variants containing exon v6 sequences is largely restricted to the advanced stages of tumor develop ment and in addition is more prevalent and intense in metastatic (Dukes C/D) than in nonmetastatic (Dukes A/B) carcinomas. The observation that CD44 variants containing a protein domain of CD44 that confers full metastatic potential to rat carcinoma and sarcoma cell lines is increasingly expressed during colorectal tumor progression indicates that this domain may have an important role in tumor progression and metastasis in hu mans. Information on v6 expression, which can be obtained by routine immunohistochemistry, may prove of important prognostic value, particu larly in carcinomas (Dukes A and B) that have not yet given rise to detectable mÃ©tastases.
Orchestrating change: An artistic representation of software evolution

Several visualization tools have been proposed to highlight interesting software evolution phenomena. These tools help practitioners to navigate large and complex software systems, and also support researchers in studying software evolution. However, little work has explored the use of sound in the context of software evolution. In this paper, we propose the use of musical interpretation to support exploration of software evolution data. In order to generate music inspired by software evolution, we use parameter-based sonification, i.e., a mapping of dataset characteristics to sound. Our approach yields musical scores that can be played synthetically or by a symphony orchestra. In designing our approach, we address three challenges: (1) the generated music must be aesthetically pleasing, (2) the generated music must accurately reflect the changes that have occurred, and (3) a small group of musicians must be able to impersonate a large development team. We assess the feasibility of our approach using historical data from Eclipse, which yields promising results.
Price-aware real-time ride-sharing at scale: an auction-based approach

Real-time ride-sharing, which enables on-the-fly matching between riders and drivers (even en-route), is an important problem due to its environmental and societal benefits. With the emergence of many ride-sharing platforms (e.g., Uber and Lyft), the design of a scalable framework to match riders and drivers based on their various constraints while maximizing the overall profit of the platform becomes a distinguishing business strategy. A key challenge of such framework is to satisfy both types of the users in the system, e.g., reducing both riders' and drivers' travel distances. However, the majority of the existing approaches focus only on minimizing the total travel distance of drivers which is not always equivalent to shorter trips for riders. Hence, we propose a fair pricing model that simultaneously satisfies both the riders' and drivers' constraints and desires (formulated as their profiles). In particular, we introduce a distributed auction-based framework where each driver's mobile app automatically bids on every nearby request taking into account many factors such as both the driver's and the riders' profiles, their itineraries, the pricing model, and the current number of riders in the vehicle. Subsequently, the server determines the highest bidder and assigns the rider to that driver. We show that this framework is scalable and efficient, processing hundreds of tasks per second in the presence of thousands of drivers. We compare our framework with the state-of-the-art approaches in both industry and academia through experiments on New York City's taxi dataset. Our results show that our framework can simultaneously match more riders to drivers (i.e., higher service rate) by engaging the drivers more effectively. Moreover, our frame-work schedules shorter trips for riders (i.e., better service quality). Finally, as a consequence of higher service rate and shorter trips, our framework increases the overall profit of the ride-sharing platforms.
Real-time filesystems. Guaranteeing timing constraints for disk accesses in RT-Mach

Traditional real-time systems have largely avoided the use of disks due to their relative slow speeds and their unpredictability. However, many real-time applications including multimedia systems and real-time database applications benefit significantly from the use of disks to store and access real-time data. We investigate the problem of obtaining guaranteed timely access to files on a disk in a real-time system. Our study focuses on several aspects of this problem of providing a real-time filesystem. First, we consider the use of two real-time disk scheduling algorithms: earliest deadline scheduling and just-in-time scheduling, a variation of aperiodic servers for the disk. The latter algorithm is designed to improve disk throughput that can be hurt when a real-time scheduling algorithm such as EDF is applied directly. Admission control policies with practically acceptable properties of performance and usability are provided. Next, we design and implement a real-time filesystem on the RT-Mach microkernel-based system running a real-time shell. The new interface we develop is based on RT-Mach's resource reservation paradigm and provides guaranteed and timely access for multiple concurrent applications requiring disk bandwidth with different timing and volume requirements. Finally, we perform a detailed performance evaluation of the real-time filesystem including its raw performance. We show the following positive but rather surprising result: our real-time scheduling filesystem not only provides guaranteed and timely access but also does so at relatively high levels of throughput. Traditional disk scheduling algorithms offer completely unacceptable file access latencies for real-time applications and do so only at slightly higher throughput.
Vitamin C Facilitates Dopamine Neuron Differentiation in Fetal Midbrain Through TET1‐ and JMJD3‐Dependent Epigenetic Control Manner

Intracellular Vitamin C (VC) is maintained at high levels in the developing brain by the activity of sodium‐dependent VC transporter 2 (Svct2), suggesting specific VC functions in brain development. A role of VC as a cofactor for Fe(II)‐2‐oxoglutarate‐dependent dioxygenases has recently been suggested. We show that VC supplementation in neural stem cell cultures derived from embryonic midbrains greatly enhanced differentiation toward midbrain‐type dopamine (mDA) neurons, the neuronal subtype associated with Parkinson's disease. VC induced gain of 5‐hydroxymethylcytosine (5hmC) and loss of H3K27m3 in DA phenotype gene promoters, which are catalyzed by Tet1 and Jmjd3, respectively. Consequently, VC enhanced DA phenotype gene transcriptions in the progenitors by Nurr1, a transcription factor critical for mDA neuron development, to be more accessible to the gene promoters. Further mechanism studies including Tet1 and Jmjd3 knockdown/inhibition experiments revealed that both the 5hmC and H3K27m3 changes, specifically in the progenitor cells, are indispensible for the VC‐mediated mDA neuron differentiation. We finally show that in Svct2 knockout mouse embryos, mDA neuron formation in the developing midbrain decreased along with the 5hmC/H3k27m3 changes. These findings together indicate an epigenetic role of VC in midbrain DA neuron development. Stem Cells 2015;33:1320–1332