Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessment of canine distemper virus infection in vaccinated and unvaccinated dogs

Canine distemper is the most prevalent viral disease of dogs, which has high mortality rate. Vaccination of dogs against canine distemper is the only measure to control the disease. The aim of the present study was to find out the effect of commercial live attenuated vaccines in the control of distemper and the importance of the annual vaccination against distemper based on the occurrence of infection. One hundred and sixty conjunctival samples, collected from dogs with clinical symptoms suggestive of canine distemper, were screened by Dot-Enzyme Linked Immunosorbent Assay (DotELISA) for the presence of canine distemper virus. The application of Dot-ELISA in screening the samples was validated using Indirect Immunofluorescence assay as the standard technique. Out of the 160 samples tested by Dot-ELISA, 112 (70%) were positive for canine distemper. The results of Dot-ELISA used for epidemiological study based on sex, age and vaccination status showed that dogs of both the sexes and 1-5 years of age were more susceptible to Canine distemper virus infection and there is a lack of regular annual vaccination of dogs which results in the high incidence of distemper in dogs of 1-5 years of age. The present study suggests that vaccination followed by regular annual boosters against distemper would effectively protect the dogs from the disease.
Ca flux, contractility, and excitation-contraction coupling in hypertrophic rat ventricular myocytes.

Left ventricular hypertrophy (∼40%) was induced in rats by banding of the abdominal aorta. After 16 wk, ventricular homogenates were prepared for biochemical measurements and ventricular myocytes were isolated for functional studies. In myocytes, the effects of banding on intracellular Ca handling, contraction, and excitation-contraction (E-C) coupling were determined using indo 1 fluorescence and whole cell voltage clamp. After steady-state field or voltage-clamp stimulation to load the sarcoplasmic reticulum (SR), SR Ca content assessed by caffeine-induced Ca transients was the same in sham and banded groups. Despite this, cell shortening amplitudes were significantly depressed in the banded group, suggesting altered contractile properties. In banded rats, the SR Ca-adenosinetriphosphatase (Ca-ATPase) mRNA level was reduced, as was homogenate thapsigargin-sensitive SR Ca-ATPase, but cytosolic free Ca concentration ([Ca]i) decline attributed to SR Ca-ATPase activity in intact cells was not slowed. Banding also reduced Na/Ca exchange mRNA level but did not affect either Na-dependent sarcolemmal45Ca transport in homogenate or the rate of [Ca]idecline in intact cells attributed to Na/Ca exchange (during caffeine-induced contractures). Banding also did not change the rate of [Ca]i decline mediated by the combined function of the mitochondrial Ca uptake and sarcolemmal Ca-ATPase in intact cells. Ca current ( I Ca) density and voltage dependence were the same in sham and banded groups. Ryanodine receptor mRNA, protein content, and ryanodine affinity were also unchanged in the banded group. At 1 mM extracellular Ca concentration ([Ca]o), banding did not affect E-C coupling efficacy in intact cells under voltage clamp (i.e., same contraction for given I Ca and SR Ca load). However, when [Ca]o was reduced to 0.5 mM, the efficacy of E-C coupling was greatly depressed in the banded group (even though I Ca and SR Ca content were matched). In summary, unloaded myocyte contraction was depressed in these hypertrophic hearts, but Ca transport was little altered, at 1 mM [Ca]o. However, reduction of [Ca]o to 0.5 mM appears to unmask a depressed fractional SR Ca release in response to a given I Ca trigger and SR Ca load.
Prioritizing Manual Test Cases in Traditional and Rapid Release Environments

Test case prioritization is one of the most practically useful activities in testing, specially for large scale systems. The goal is ranking the existing test cases in a way that they detect faults as soon as possible, so that any partial execution of the test suite detects maximum number of defects for the given budget. Test prioritization becomes even more important when the test execution is time consuming, e.g., manual system tests vs. automated unit tests. Most existing test case prioritization techniques are based on code coverage, which requires access to source code. However, manual testing is mainly done in a black- box manner (manual testers do not have access to the source code). Therefore, in this paper, we first examine the existing test case prioritization techniques and modify them to be applicable on manual black-box system testing. We specifically study a coverage- based, a diversity-based, and a risk driven approach for test case prioritization. Our empirical study on four older releases of Mozilla Firefox shows that none of the techniques are strongly dominating the others in all releases. However, when we study nine more recent releases of Firefox, where the development has been moved from a traditional to a more agile and rapid release environment, we see a very signifiant difference (on average 65% effectiveness improvement) between the risk-driven approach and its alternatives. Our conclusion, based on one case study of 13 releases of an industrial system, is that test suites in rapid release environments, potentially, can be very effectively prioritized for execution, based on their historical riskiness; whereas the same conclusions do not hold in the traditional software development environments.
FACIES, ENVIRONMENTS, AND FOSSIL PRESERVATION IN THE BARSTOW FORMATION, MOJAVE DESERT, CALIFORNIA

Abstract: Continental deposits of the middle Miocene Barstow Formation formed in an extensional basin of the Mojave region. Mammalian faunas of the type section in the Mud Hills, California, are the basis for defining the Barstovian North American Land Mammal Age. Prior mapping, lithostratigraphy, geochronology, and fossil collecting have established a structural, chronostratigraphic, and biostratigraphic framework for the Barstow Formation. Here, we analyze the sedimentary facies of the lithostratigraphic sequence, infer the major depositional environments, and assess controls on fossil preservation in relation to major facies. We recognize six major facies associations that represent alluvial fans, shallow or seasonal lakes, and channels and floodplains. The transition from older, fan-dominated to younger, floodplain-dominated environments reflects changes in tectonics, accommodation, drainage, and depositional settings during the formation and filling of the basin. Fossil-mammal concentrations are common in four facies associations. Body fossils are abundant in two facies associations that represent well-drained floodplains and spring-fed wetlands. Fossil concentrations are moderately abundant in facies associations that represent floodplains and channel deposits, and fossils are rare in facies associations that represent alluvial fans and lake margins. The highest frequency of fossil localities occurs in the facies associations representing both suitable life habitats and high preservation potential for terrestrial mammals.
piRNAs Are Associated with Diverse Transgenerational Effects on Gene and Transposon Expression in a Hybrid Dysgenic Syndrome of D. virilis

Sexual reproduction allows transposable elements (TEs) to proliferate, leading to rapid divergence between populations and species. A significant outcome of divergence in the TE landscape is evident in hybrid dysgenic syndromes, a strong form of genomic incompatibility that can arise when (TE) family abundance differs between two parents. When TEs inherited from the father are absent in the mother's genome, TEs can become activated in the progeny, causing germline damage and sterility. Studies in Drosophila indicate that dysgenesis can occur when TEs inherited paternally are not matched with a pool of corresponding TE silencing PIWI-interacting RNAs (piRNAs) provisioned by the female germline. Using the D. virilis syndrome of hybrid dysgenesis as a model, we characterize the effects that divergence in TE profile between parents has on offspring. Overall, we show that divergence in the TE landscape is associated with persisting differences in germline TE expression when comparing genetically identical females of reciprocal crosses and these differences are transmitted to the next generation. Moreover, chronic and persisting TE expression coincides with increased levels of genic piRNAs associated with reduced gene expression. Combined with these effects, we further demonstrate that gene expression is idiosyncratically influenced by differences in the genic piRNA profile of the parents that arise though polymorphic TE insertions. Overall, these results support a model in which early germline events in dysgenesis establish a chronic, stable state of both TE and gene expression in the germline that is maintained through adulthood and transmitted to the next generation. This work demonstrates that divergence in the TE profile is associated with diverse piRNA-mediated transgenerational effects on gene expression within populations.
Low-dimensional representations for the simulation and control of complex dynamics

Most work in computer simulation has focused on off-line algorithms where each step can take arbitrarily long to compute. This thesis focuses instead on interactive simulations that run in real-time. Besides running quickly, such simulations must allow interaction, remain stable under unexpected user input, and remain "correct" (in some sense) for unbounded periods of time. Further, biomechanical simulation requires near-instantaneous planning without simulating the future. These requirements motivate the development of fundamentally new simulation algorithms. This thesis approaches the interactive simulation problem by developing new, low-dimensional representations of the phenomena being simulated. These representations perform several functions at once. First, they can correlate many degrees of freedom of the underlying phenomenon, allowing us to represent the system with fewer variables. Second, the reduction is constructed so as to allow rapid simulation or control. Finally, the representations allow us to express correctness constraints. Three examples of such simulations are presented, covering fluids, crowds, and human animation. The fluid model enables large, real-time, detailed flows with continuous user interaction, and can handle moving objects immersed in the flow. The crowd model is based on a fluid-like continuum representation, and naturally exhibits emergent phenomena that have been observed in real crowds. Finally, the human model can automatically compute near-optimal human animations using a low-dimensional basis representation of the planning space.
Adaptive Content-Aware Scaling for Improved Video Streaming

Streaming video applications on the Internet generally have very high bandwidth requirements and yet are often unresponsive to network congestion. In order to avoid congestion collapse and improve video quality, these applications need to respond to congestion in the network by deploying mechanisms to reduce their bandwidth requirements under conditions of heavy load. In reducing bandwidth, video with high motion will look better if all the frames are kept but the frames have low quality, while video with low motion will look better if some frames are dropped but the remaining frames have high quality. Unfortunately current video applications scale to fit the available bandwidth without regard to the video content. In this thesis, we present an adaptive content-aware scaling mechanism that reduces the bandwidth occupied by an application by either dropping frames (temporal scaling) or by reducing the quality of the frames transmitted (quality scaling). We have designed a streaming video client and server with the server capable of quantifying the amount of motion in an MPEG stream and scaling each scene either temporally or by quality as appropriate, maximizing the appearance of each video stream. We have evaluated the impact of content-aware scaling by conducting a user study wherein the subjects rated the quality of video clips that were first scaled temporally and then by quality in order to establish the optimal mechanism for scaling a particular stream. We find that content-aware scaling can improve video quality by as much as 50%. We have also evaluated the practical impact of adaptively scaling the video stream by conducting a user study for longer video clips with varying amounts of motion and available bandwidth. We find that for such clips also the improvement in perceptual quality on account of adaptive content-aware scaling is as high as 30%
Pre-B cell to macrophage transdifferentiation without significant promoter DNA methylation changes

Transcription factor-induced lineage reprogramming or transdifferentiation experiments are essential for understanding the plasticity of differentiated cells. These experiments helped to define the specific role of transcription factors in conferring cell identity and played a key role in the development of the regenerative medicine field. We here investigated the acquisition of DNA methylation changes during C/EBPα-induced pre-B cell to macrophage transdifferentiation. Unexpectedly, cell lineage conversion occurred without significant changes in DNA methylation not only in key B cell- and macrophage-specific genes but also throughout the entire set of genes differentially methylated between the two parental cell types. In contrast, active and repressive histone modification marks changed according to the expression levels of these genes. We also demonstrated that C/EBPα and RNA Pol II are associated with the methylated promoters of macrophage-specific genes in reprogrammed macrophages without inducing methylation changes. Our findings not only provide insights about the extent and hierarchy of epigenetic events in pre-B cell to macrophage transdifferentiation but also show an important difference to reprogramming towards pluripotency where promoter DNA demethylation plays a pivotal role.
Raft Formation by the Red Imported Fire Ant, Solenopsis invicta

Abstract The raft behavior of the invasive red imported fire ant, Solenopsis invicta Buren (Hymenoptera: Formicidae), has been documented for over a century. However, no rigorous tests have been performed elucidating the structure, limits, and important characteristics of this behavior. Rafting makes S. invicta competitive in both native and foreign environments. Further understanding of this behavior will provide critical advancement to the comprehension of this ant's global invasion ecology. Though speculations exist, no one has looked at the movements of individuals within the raft formation, the longevity of rafts, raft success rate, or the importance of different life stages and varying types of adults to raft formation. Furthermore, bubble use has been extensively studied in arthropods, but it has never been documented in social insects. The use of bubbles as a means of floatation has never before been noted in raft formation. This study shows that ants trapped under water escape by lifting themselves to the air-water interface through the use of bubbles collected from submerged substrate. The presence of larvae was noted to increase colony survival and maximize raft longevity due in part their ability to hold bubbles under hydrophobic setae.
Ovarian cancer death reduction for women at high risk: Workload implications for gynaecology services

Summary Ovarian cancer spreads early, presents late and is difficult to cure. Reducing death rates from ovarian malignancy has focussed on the unaffected females of families with a high chance of a mutant gene such as BRCA1 and BRCA2. We set up a familial ovarian cancer service in a district general hospital in the UK, serving a population of 330,000. The clinical genetics team acted as gatekeepers to the service. Risk assessment, ultrasound and biochemical screening and prophylactic oophorectomy were discussed. Gene testing was offered when appropriate. This study reviews the levels of activity for the first 8 years of the service. In all, 153 women were referred, of whom 34 (16%) did not have significant clinical histories. Of the 114 who fulfilled the UKFOCSS criteria for family history and age, four were quickly found to be gene mutation negative and 20 (17%) declined intervention. A total of 29 (25%) chose prophylactic oophorectomy and 61 (54%) chose ultrasound screening.
Drug-Eluting Stent Update 2007: Part III: Technique and Unapproved/Unsettled Indications (Left Main, Bifurcations, Chronic Total Occlusions, Small Vessels and Long Lesions, Saphenous Vein Grafts, Acute Myocardial Infarctions, and Multivessel Disease)

Randomized trials have largely demonstrated that percutaneous coronary intervention (PCI) with sirolimus-eluting (SES) and paclitaxel-eluting stents (PES) results in a significant reduction in the occurrence of angiographic restenosis and revascularization compared with bare metal stents (BMS). 1–4 The benefit of drug-eluting stents (DES) also has been confirmed in “real-world” scenarios. In this setting, when the analysis was focused on high-risk patient and lesion subgroups, a benefit still existed despite the presence of restenosis.5–7 These expanded indications do not yet cover many other types of complex lesions for which only registries or randomized trials, not yet published, are available so far (Tables 1 through 7⇓⇓⇓⇓⇓⇓). This topic is discussed in detail in this review. An important clarification is that the lack of proof is most probably due to the difficulty in performing randomized trials in high-risk groups using BMS as controls. It will be no surprise to find that the field in which DES perform best compared with BMS is likely to be complex lesions and patients8 (Figure 1). View this table: TABLE 1. DES in Unprotected Left Main Stenosis View this table: TABLE 2. DES in Bifurcation Lesions View this table: TABLE 3. DES in Chronic Total Occlusions View this table: TABLE 4. DES in Small-Vessel Disease and Long Lesions View this table: TABLE 5. DES in SVGs View this table: TABLE 6. DES in Acute MI View this table: TABLE 7. DES in Multivessel Disease Figure 1. Lesion complexity and stent performance in the BMS and DES eras. Adapted from Edelman et al.8 Current American Heart Association/American College of Cardiology (AHA/ACC) and European Society of Cardiology (ESC) guidelines consider the presence of a stenosis in the unprotected left main coronary artery (LMCA) a class IIa or IIb indication, respectively, for PCI if coronary artery bypass grafting (CABG) is not a viable option.9,10 Moreover, according to the AHA/ACC 2005 guidelines, in …
Effect of black tea on histological and immunohistochemical changes in pancreatic tissues of normal and streptozotocin‐induced diabetic mice (Mus musculus)

The aim of the present study is to evaluate the effect of hot water extract of black tea in regenerating β cells in streptozotocin‐induced diabetic mice. Light microscopic examination of pancreatic sections of streptozotocin‐induced diabetic mice showed the acinar cells to be small, shrunken, and with deteriorated β cells. The dose of streptozotocin not only altered the function of β cells but also damaged the acinar region. The changes in acinar cells were coarsening of endoplasmic reticulation suggesting alteration in their secretory function. The control pancreatic tissue showed well‐defined granulated islets and dark β cells when stained with chrome hematoxylin and phloxine. Interestingly, pancreatic sections of diabetic mice fed with black‐tea extract showed regeneration of β cells and acinar region appeared normal with increased numbers of β cells. To understand the probable mechanism of action of black‐tea extract, we analyzed inducible nitric oxide synthase (iNOS) expression by immunohistochemistry and the results showed an increased iNOS levels in streptozotocin‐induced diabetic pancreas, and such high iNOS levels were inhibited in black‐tea extract treated mice. According to histological results obtained, it can be concluded that the black‐tea extract helps in regeneration of damaged pancreas and protects pancreatic β cells by its antioxidant action against nitrosative stress in streptozotocin‐induced diabetes. Microsc. Res. Tech., 2009. © 2009 Wiley‐Liss, Inc.
Local field potential reflects perceptual suppression in monkey visual cortex

Neurophysiological and functional imaging experiments remain in apparent disagreement on the role played by the earliest stages of the visual cortex in supporting a visual percept. Here, we report electrophysiological findings that shed light on this issue. We monitored neural activity in the visual cortex of monkeys as they reported their perception of a high-contrast visual stimulus that was induced to vanish completely from perception on a subset of trials. We found that the spiking of neurons in cortical areas V1 and V2 was uncorrelated with the perceptual visibility of the target, whereas that in area V4 showed significant perception-related changes. In contrast, power changes in the lower frequency bands (particularly 9–30 Hz) of the local field potential (LFP), collected on the same trials, showed consistent and sustained perceptual modulation in all three areas. In addition, for the gamma frequency range (30–50 Hz), the responses during perceptual suppression of the target were correlated significantly with the responses to its physical removal in all areas, although the modulation magnitude was considerably higher in area V4 than in V1 and V2. These results, taken together, suggest that low-frequency LFP power in early cortical processing is more closely related to the representation of stimulus visibility than is spiking or higher frequency LFP activity.
Modulation of DNA methylation states and infant immune system by dietary supplementation with ω-3 PUFA during pregnancy in an intervention study.

BACKGROUND Early-life exposures to tobacco smoke and some dietary factors have been identified to induce epigenetic changes in genes involved in allergy and asthma development. Omega-3 (n-3) polyunsaturated fatty acid (PUFA) intake during pregnancy could modulate key cytokines and T helper (Th) cell maturation; however, little is known about the mechanism by which ω-3 PUFA could have a beneficial effect in preventing inflammatory disorders. OBJECTIVE We sought to test whether prenatal dietary supplementation with ω-3 PUFA during pregnancy may modulate epigenetic states in the infant immune system. DESIGN This study was based on a randomized intervention trial conducted in Mexican pregnant women supplemented daily with 400 mg docosahexaenoic acid (DHA) or a placebo from 18 to 22 wk of gestation to parturition. We applied quantitative profiling of DNA methylation states in Th1, Th2, Th17, and regulatory T-relevant genes as well as LINE1 repetitive elements of cord blood mononuclear cells (n = 261). RESULTS No significant difference in promoter methylation levels was shown between ω-3 PUFA-supplemented and control groups for the genes analyzed; however, ω-3 PUFA supplementation was associated with changes in methylation levels in LINE1 repetitive elements (P = 0.03) in infants of mothers who smoked during pregnancy. Furthermore, an association between the promoter methylation levels of IFNγ and IL13 was modulated by ω-3 PUFA supplementation (P = 0.06). CONCLUSIONS Our results indicate that maternal supplementation with ω-3 PUFA during pregnancy may modulate global methylation levels and the Th1/Th2 balance in infants. Therefore, the epigenetic mechanisms could provide attractive targets for prenatal modulation and prevention of inflammatory disorders and potentially other related diseases in childhood and adulthood.