Miracle-dz/UniFAR-FTUs huggingface dataset:
Development and validation of flow cytometric measurement for parasitaemia using autofluorescence and YOYO-1 in rodent malaria

SUMMARY An automated flow cytometric (FCM) detection method has been developed and validated with a simple diagnostic procedure in parasitized erythrocytes of Plasmodium berghei-infected rats using the nucleic acid-binding fluorescent dye YOYO-1. High levels of reticulocytes were detected during the course of the infection, ranging from 1·2–51·2%, but any RNA potentially confounding the assay could be removed by digestion with RNAse. The cell counts of uninfected, infected, and nucleated cells occurred with high precision. The cells were divided into different populations according to their physical or chemical properties but various factors within the assay such as cell fixation, RNA digestion, and compensation required optimization. In this study, FCM greatly simplified and accelerated parasite detection, with a mean precision of 4·4%, specificity of 98·9% and accuracy of 101·3%. The detection and quantitation limits in the assay were 0·024% and 0·074% parasitaemia, respectively. Overall, the parasite counts by FCM measurement correlated highly (r2=0·954–0·988) with the parasitaemia measured by light microscopical analysis when animals treated with suppressive, clearance, and curative doses of novel antimalarial drugs were examined. The lower levels of parasitaemia (30%) detected by microscopy compared to FCM may be related to a number of schizonts externally attached to the erythrocyte membranes that normally would not be included in microscopy counting. Lower sampling error and reliable identification of rodent erythrocyte parasites based on the principles of FCM have replaced the traditional blood smear in our laboratory.
Gene expression signature for recurrence in stage III colorectal cancers

Colorectal cancer patients with lymph node metastases (stage III) show poorer prognosis than those without. Predicting development of recurrence may guide the need for intensive follow‐up and/or adjuvant chemotherapy in such patients. The authors' objective was to identify a set of discriminating genes that could predict recurrence in stage III colorectal cancer.
Molecular Characterization of Animal Fasciola spp. Isolates from Kermanshah, Western Iran

Background: We evaluated the genetic diversity of samples identified morphologically as Fasciola spp. from sheep, cattle and goat from Kermanshah Province, western Iran using PCR-RFLP method. Methods: We used PCR-RFLP analysis of ribosomal ITS1 fragment using RsaI restriction enzyme to investigate the genetic characteristics of Fasciola species obtained from different hosts (16 sheep, 28 cattle, 4 goats). The species of Fasciola were confirmed by sequencing the 700 bp region of ribosomal ITS1 gene. Results: In Kermanshah, F. hepatica was present in 96% of the samples, F. gigantica was found only in two cattle sample. No hybrid forms were detected in the present study. Conclusion: Our results contribute to clarify the dark spots of Fasciola genotyping in different parts of Iran.
A metabolic limit on the ability to make up for lost time in endurance events.

It has been repeatedly demonstrated that the tolerable duration (t) of high-intensity cycling is well characterized as a hyperbolic function of power (P) with an asymptote that has been termed the "fatigue threshold" and with a curvature constant. This hyperbolic P-t relationship has also been confirmed in running and swimming, when speed (V) is used instead of P; that is, (V - V(F)). t = D', where V(F) is the V at the fatigue threshold, and D' is the curvature constant. Therefore, we theoretically analyzed herein the consequences of an athlete performing the initial part of an endurance event at a V different from the constant rate that would allow the performance time to be determined by the hyperbolic V-t relationship. We considered not only the V-t constraints that limit the athlete's ability to make up the time lost by too slow an early pace but also the consequences of a more rapid early pace. Our analysis demonstrates that both the V(F) and D' parameters of the athlete's V-t curve play an important role in the pace allocation strategy of the athlete. That is, 1) when the running V during any part of the whole running distance is below V(F), the athlete can never attain the goal of achieving the time equivalent to that of running the entire race at constant maximal V (i.e., that determined by one's own best V-t curve); and 2) the "endurance parameter ratio" D'/V(F) is especially important in determining the flexibility of the race pace that the athlete was able to choose intentionally.
DiPerF: an automated distributed performance testing framework

We present DiPerF, a distributed performance-testing framework, aimed at simplifying and automating service performance evaluation. DiPerF coordinates a pool of machines that test a target service, collects and aggregates performance metrics, and generates performance statistics. The aggregate data collected provide information on service throughput, on service fairness' when serving multiple clients concurrently, and on the impact of network latency on service performance. Furthermore, using this data, it is possible to build predictive models that estimate a service performance given the service load. We have tested DiPerF on 100+machines on two testbeds, Grid3 and PlanetLab, and explored the performance of job submission services (pre-WS GRAM and WS GRAM) included with Globus Toolkit/spl reg/ 3.2.
Transitions at the mesoscale: morphological changes in thin solid films and magnetic filaments

One of the most striking features of Physics studying the behavior of Nature is that it covers an impressively wide range of sizes and energy scales. These ranges are continuously expanding as new knowledge is acquired and new technologies are developed. However, all the physical theories devised so far have a limited coverage, losing all its meaning or predictive power beyond certain limits which are in some cases quite narrow in front of the vast realm of the known and observable phenomena. The applicability of the di? erent physical theories establishes partial scale domains which may overlap to di? erent extents. The overlap regions between domains, called frontiers, are particularly interesting areas for scienti? c study. Therefore, the scienti? c and technical progress not only broadens the full range of lengths and speeds of physical phenomena under study, but also involves research of new physical phenomena at the frontiers between di? erent domains de? ned by well-established theories.
IP-based seamless handover scheme using ANDSF in an untrusted environment

In an Inter-WLAN-System, when an UE needs to hand over to an untrusted network, e.g., M, from its serving network, e.g., N, how to choose M and the best base station under M currently is a problem yet to be completely solved, no matter whether M and N belong to the same alliance group or not and no matter whether M and N are homogeneous or heterogeneous networks. In fact, 3GPP recommended ANDSF to solve this problem when N is a 3GPP network and M is a non-3GPP system or vice versa, i.e., when they are heterogeneous networks. Also, when selecting M, current approach neither considers the entire characteristics of mobile users, nor having significant discovery and selection policies to show the states of M, thus often leading UE to select an inappropriate M and/or a base station B in M. It results in the fact that after handover, UE may sometimes find that Radio Signal Strength Indicator (RSSI) of B is not strong, and even UE cannot connect itself to B since B's load is high. That means when M and N do not belong to the same alliance, the problem will be more serious. It also means that if we want to solve the mentioned problem in such an environment, the functions of ANDSF need to be enhanced. Therefore, in this paper, we first design an enhanced ANDSF, named E-ANDSF, which increases ANDSF with a Multiple Parameters Decision Making (MPDM) ranking scheme based on Proxy Mobile IPv6 (PMIPv6) protocol to provide PMAG in N with sufficient information, with which UE can hand over to an appropriate base station. We also propose an improved IP-based handover approach, called IP-based Handover Scheme assisted by E-ANDSF Function (IHEADs for short), which assists UE to hand over to an appropriate target base station by accessing the information provided by E-ANDSF.
Vibrissa Sensation in Superior Colliculus: Wide-Field Sensitivity and State-Dependent Cortical Feedback

Rodents use their vibrissae (whiskers) to sense and navigate the environment. A main target of this sensory information is the superior colliculus in the midbrain, which rats can use to detect meaningful whisker stimuli in behavioral contexts. Here, we used field potential, single-unit, and intracellular recordings to show that, although cells in the intermediate layers of the superior colliculus respond relatively effectively to single whiskers, the cells respond much more robustly to simultaneous, or nearly simultaneous, wide-field (multiwhisker) stimuli. The enhanced multiwhisker response is temporally stereotyped, consisting of two short latency peaks caused by convergent trigeminal synaptic inputs and cortical feedback, respectively. The cells are highly sensitive to the degree of temporal dispersion and contact order of multiwhisker stimuli, which makes them excellent detectors of initial multiwhisker contact. In addition, their output is most robust during quiescent states because of the dependence of cortical feedback on forebrain activation, and this may serve as an alerting signal to drive orienting responses.
Spinal Arteriovenous Metameric Syndrome: Clinical Manifestations and Endovascular Management

BACKGROUND AND PURPOSE: SAMS is a rare form of SCAVM. We discuss the clinical presentation, endovascular management, and outcome of this disease in our series. MATERIALS AND METHODS: Retrospective review was performed in patients with SCAVM and SAMS who underwent angiography with intent to treat at our institution from 1980 to 2010. RESULTS: One hundred forty-eight SCAVMs were identified, and 28 (19%) of these were SAMS. Of these 28 patients, 24 had nidus-type AVMs and 4 had fistulas. SAMS were more prevalent in females (71% versus 48%), and also presented earlier than non-SAMS SCAVMs. Intradural hemorrhage (SAH or hematomyelia) was the most common presentation and more common than in non-SAMS lesions. Twenty-six patients underwent embolization of the intradural lesion in 50 sessions. Thirteen patients underwent treatment of intradural aneurysms in 16 sessions. Six patients underwent embolization of extradural lesions in 16 sessions. Twenty-three patients had an average of 94 months of clinical follow-up (3–309 months) after the first treatment, during which 5 patients had hemorrhages. Angiographic follow-up was performed in 20 patients at an average of 85 months (range, 3–309 months), which showed new development or enlargement of an aneurysm in 5 patients. This type of angiographic progression was more common in patients with SAMS. CONCLUSIONS: SAMS most commonly presents with hemorrhage from the SCAVM. Endovascular embolization can be performed safely with good functional outcome, though most patients clinically deteriorate in the long term. Periodic angiographic follow-up with intent to perform preventive target embolization is important to control the disease.
Characterization of the Sucrose Phosphate Phosphatase (SPP) Isoforms from Arabidopsis thaliana and Role of the S6PPc Domain in Dimerization

Sucrose-phosphate phosphatase (SPP) catalyses the final step in the sucrose biosynthesis pathway. Arabidopsis thaliana genome codifies four SPP isoforms. In this study, the four Arabidopsis thaliana genes coding for SPP isoforms have been cloned, expressed in Escherichia coli and the kinetic and regulatory properties of the purified enzymes analysed. SPP2 is the isoform showing the highest activity, with SPP3b and SPP3a showing lower activity levels. No activity was detected for SPP1. We propose that this lack of activity is probably due to the absence of an essential amino acid participating in catalysis and/or in the binding of the substrate, sucrose-6-phosphate (Suc6P). The expression patterns of Arabidopsis SPP genes indicate that SPP2 and SPP3b are the main isoforms expressed in different tissues and organs, although the non-catalytic SPP1 is the main isoform expressed in roots. Thus, SPP1 could have acquired new unknown functions. We also show that the three catalytically active SPPs from Arabidopsis are dimers. By generating a chimeric SPP composed of the monomeric cyanobacterial SPP fused to the higher plant non-catalytic S6PPc domain (from SPP2), we show that the S6PPc domain is responsible for SPP dimerization. This is the first experimental study on the functionality and gene expression pattern of all the SPPs from a single plant species.
Forecasting State Tax Revenue : A Bayesian Vector Autoregression Approach

This paper compares alternative time-series models to forecast state tax revenues. Forecast accuracy is compared to a benchmark random walk forecast. Quarterly data for California is used to forecast total tax revenue along with its three largest components, sales, income, and corporate tax revenue. For oneand four-quarter-ahead forecasts from 2004 to 2009, Bayesian vector autoregressions generally forecast best based on root mean squared errors compared to standard vector autoregressions or a random walk model. Similar to the macroeconomic forecasting experience, Bayesian vector autoregressions should be consider as a useful and cost effective revenue forecasting model for state governments. *This paper was written while on sabbatical leave during the Fall 2009 semester. The author thanks the College of Business and Economics for financial support. I thank Shirley Svorny for helpful comments.
Personality Traits of Patients With Multiple Sclerosis and Their Relationship With Clinical Characteristics

Abstract Few studies have investigated personality characteristics in people with multiple sclerosis (MS), and little is known about the relationship between personality and clinical characteristics in these patients. We aimed to investigate the personality traits of MS patients and their relationship with clinical characteristics. The study population consisted of 74 MS patients and age-matched, sex-matched, and education level–matched healthy controls. All participants were instructed to complete the self-administered 240-item Temperament and Character Inventory and the Beck Depression Inventory. The MS patients exhibited higher harm avoidance (HA) and lower self-directedness scores than the control group, although these differences disappeared after controlling for depression. Duration of the disease was positively correlated with HA and negatively correlated with novelty-seeking scores. Expanded Disability Status Scale scores were negatively correlated with reward dependence. Our results suggest a possible relationship between personality characteristics and the stage of the disease or the degree of damage in MS patients.
Local injection of stem cell factor (SCF) improves myocardial homing of systemically delivered c-kit + bone marrow-derived stem cells.

AIMS Recent studies have shown that stem cell therapy may alleviate the detrimental effects of myocardial infarction. Yet, most of these reports observed only modest effects on cardiac function, suggesting that there still is need for improvement before widespread clinical use. One potential approach would be to increase migration of stem cells to the heart. We therefore tested whether local administration of stem cell factor (SCF) improves myocardial homing of intravenously infused lin-/c-kit+ stem cells after myocardial infarction. METHODS AND RESULTS Myocardial infarction was induced in mice via ligation of the left anterior descending artery and 2.5 microg of SCF were injected into the peri-infarct zone. Sham-operated mice and animals with intramyocardial injection of phosphate-buffered saline (PBS) served as controls. Twenty-four hours after myocardial infarction, lin-/c-kit+ stem cells were separated from murine bone marrow by magnetic cell sorting, labelled with the green fluorescent cell tracker CFDA or 111 Indium, and subsequently 750 000 labelled cells were systemically infused via the tail vein. Another 24 or 72 h later, respectively (i.e. 48 and 96 h after myocardial infarction), hearts were removed and analysed for myocardial homing of stem cells. Green fluorescent stem cells were exclusively detected in the peri-infarct zone of animals having prior SCF treatment. Radioactive measurements revealed that an intramyocardial SCF injection significantly amplified myocardial homing of lin-/c-kit+ stem cells compared to animals with PBS injections (3.58 +/- 0.53 vs. 2.28 +/- 0.23 cpm/mg/10(6)cpm, +60%, P < 0.05) and sham-operated mice without myocardial infarction (3.58 +/- 0.53 vs. 1.95 +/- 0.22 cpm/mg/10(6)cpm, +85%, P < 0.01). Similar results were obtained 72 h after stem cell injection. CONCLUSION We demonstrate that intramyocardial administration of SCF sustainably directs more lin-/c-kit+ stem cells to the heart. Future studies will have to show whether higher levels of myocardial SCF (i.e. by virus-mediated gene transfer) can further improve homing of systemically delivered c-kit+ stem cells and thus favourably influence cardiac remodelling following myocardial infarction.
Expression of collagen I, smooth muscle alpha-actin, and vimentin during the healing of alkali-burned and lacerated corneas.

PURPOSES Alkali-burned corneas can seldom heal properly to restore corneal transparency. To provide a better understanding of this devastating corneal injury, we compared the expression of collagen I, smooth muscle alpha-actin (alpha-SMA), and vimentin in lacerated and alkali-burned rabbit corneas. METHODS A radiolabeled cDNA probe of alpha 1(I) chain was used in slot-blot hybridization to determine the levels of alpha 1(I) mRNA in alkali-burned corneas. In situ hybridization was used to identify the cell types that express the alpha 1(I) chain. Antibodies against collagen I, alpha-SMA, and vimentin were used in immunohistochemical studies to determine the tissue distribution of collagen I and to identify cells expressing alpha-SMA and vimentin. RESULTS The levels of alpha 1(I) mRNA in alkali-burned corneas increased steadily after the alkali burn and reached a plateau within 2 weeks. One day after alkali burn, specific in situ hybridization signals were detected in stromal cells immediately surrounding the edge of the corneal injury. As the healing proceeded, the fibroblastic cells migrated into the injured stroma, and they showed positive reactions by in situ hybridization and by immunostaining with anti-collagen I probes. In alkali-burned corneas, retrocorneal membranes were formed 1 week after injury. This fibrillar membrane was stained by anti-collagen I antibody, and the fibroblastic cells in the membrane were hybridized by the 3H-labeled alpha 1(I) cDNA probe. No retrocorneal membrane was formed in the lacerated corneas, even after the injured corneas were allowed to heal for 3 weeks. The epithelial cells in the epithelial plug of lacerated corneas were positive by in situ hybridization, whereas the epithelial cells in the regenerated epithelium of alkali-burned cornea was not. Antibodies against alpha-SMA reacted with the migrating fibroblastic cells but did not react with epithelial cells or endothelial cells in the injured corneas. Anti-vimentin antibody reacted with fibroblastic cells, endothelial cells, and keratocytes in normal and injured corneas, and with the basal epithelial cells of injured corneas. CONCLUSIONS During wound healing, the keratocytes that migrate to injured stroma transform into myofibroblasts. These myofibroblasts express high levels of alpha 1(I) mRNA, alpha-SMA, and vimentin. The healing of alkali-burned corneas differ from that of lacerated corneas in that the retrocorneal membranes are formed in the former but not in the latter. In addition, the epithelial cells of alkali-burned corneas lack alpha 1(I) mRNA, whereas it is found in the epithelium of lacerated corneas. These differences may result from the persistence of inflammatory cells in the alkali-burned corneas.
Radiation hybrid mapping of three candidate genes for bovine neuronal ceroid lipofuscinosis: CLN3, CLN5 and CLN6

The Neuronal Ceroid Lipofuscinoses (NCLs) are a group of inherited neurodegenerative disorders that affect children and a range of different animal species (Goebel et al., 1999), including sheep (Jolly et al., 1992, 2002; Järplid and Haltia, 1993; Woods et al., 1994; Tammen et al., 2001) and cattle (Read and Bridges, 1969; Harper et al., 1988; Hafner et al., 2005). Six different human genetic variants of NCL have been characterized and the genes designated CLN1, 2, 3, 5, 6 and 8 . Together the NCLs are considered to be one of the most commonly inherited neurodegenerative disorders that affect children with a global prevalence of between 1–8 in every 100,000 live-births (Zhong, 2000). However, the functional and biochemical aspects of this group of disorders have not been fully described and no effective treatments are available at present. The molecular characterization of existing animal models will be necessary to control this disorder in the livestock industry and will assist in developing treatments for human sufferers. The candidate genes CLN3 , CLN5 and CLN6 have been mapped to facilitate linkage analysis in cattle and sheep.
Echocardiographic assessment of cardiac function in conscious and anesthetized mice.

Using a high-frequency linear transducer (15L8), we studied 1) the feasibility of performing echocardiography in nonanesthetized mice compared with mice given pentobarbital sodium (Pento) or a mixture of ketamine and xylazine and 2) the feasibility of echocardiographic evaluation of left ventricular (LV) hypertrophy, dilatation, and function in mice with two-kidney, one-clip hypertension or myocardial infarction (MI). Heart rate (HR) in awake mice was 658 ± 9 beats/min; Pento and ketamine plus xylazine reduced HR to 377 ± 11 and 293 ± 19 beats/min, respectively, associated with a significant decrease in shortening fraction (SF), ejection fraction (EF), and cardiac output (CO) and an increase in LV end-diastolic (LVEDD) and end-systolic dimensions (LVESD). Mice with 4 wk of two-kidney, one-clip hypertension had increased LV mass (15.62 ± 0.62 vs. 22.17 ± 1.79 mg) without altered LV dimensions, SF, EF, or CO. Mice studied 4 wk post-MI exhibited obvious LV dilatation and systolic dysfunction, as evidenced by increased LVEDD and LVESD and decreased SF, EF, and CO. Our findings clearly show the adverse impact of anesthesia on basal cardiac function and the difficulty in interpreting data obtained from anesthetized mice. We believe this is the first study to demonstrate the feasibility of using echocardiography to assess cardiovascular function in the nonanesthetized mouse.
On Hemangioblasts in Chicken

Hemangioblasts are bi-potential precursors for blood and endothelial cells (BCs and ECs). Existence of the hemangioblast in vivo by its strict definition, i.e. a clonal precursor giving rise to these two cell types after division, is still debated. Using a combination of mitotic figure analysis, cell labeling and long-term cell tracing, we show that, in chicken, cell division does not play a major role during the entire ventral mesoderm differentiation process after gastrulation. One eighth of cells do undergo at least one round of division, but mainly give rise to daughter cells contributing to the same lineage. Approximately 7% of the dividing cells that contribute to either the BC or EC lineage meet the criteria of true hemangioblasts, with one daughter cell becoming a BC and the other an EC. Our data suggest that hemangioblast-type generation of BC/EC occurs, but is not used as a major mechanism during early chicken development. It remains unclear, however, whether hemangioblast-like progenitor cells play a more prominent role in later development.