Miracle-dz/UniFAR-FTUs huggingface dataset:
Antiurolithiatic Potential of Neeri against Calcium-Oxalate Stones by Crystallization Inhibition, Free Radicals Scavenging, and NRK-52E Cell Protection from Oxalate Injury

Background: Neeri is a well-established polyherbal formulation prescribed for renal stones by the physicians but has not been experimentally evaluated for its antiurolithiatic potential using cell-lines. Objective: This study is aimed to scientifically substantiate the antiurolithiatic effect of Neeri extract (NRE) through calcium oxalate (CaOx) crystallization inhibition, scavenging of free radicals, and protection of renal tubular epithelial NRK-52E cells from oxalate-induced injury. Materials and Methods: The crystallization inhibition was studied by turbidimetric assay while the free radical scavenging potential was determined for superoxide and nitric oxide (NO) radicals. The cytoprotective effect against oxalate-induced injury was assessed by estimating lactate dehydrogenase (LDH) leakage and determining cell viability using 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. Results: NRE significantly inhibited the CaOx crystallization in a concentration-dependent manner and also scavenged superoxide (IC50 302.88 μ g/ml) and NO (IC50 300.45 μ g/ml) free radicals. It did not show any significant cytotoxicity for NRK-52E cells till the highest dose (500 μ g/ml) and found to be safe. When NRK-52E cells, injured by exposing to oxalate crystals for 24 h, were treated with NRE, it appreciably prevented the cell injury in a dose-dependent manner. It significantly decreased the elevated LDH leakage toward normal range and improved renal cell viability (82.37% ± 0.87%), hence, prevented growth and retention of crystals. Conclusion: The experimental findings concluded that Neeri is a potent antiurolithiatic formulation that inhibited CaOx crystallization and prevented tubular retention of crystals by protecting the renal cells against oxalate-induced injury as well as reducing the oxidative stress by scavenging free radicals. Abbreviations used: Ac: Absorbance of control, At: Absorbance of test, ANOVA: Analysis of variance, CaOx: Calcium oxalate, DMEM: Dulbecco's Modified Eagle's Medium, DMSO: Dimethyl sulfoxide, EDTA: Ethylenediaminetetraacetic acid, FBS: Fetal bovine serum, INT: Iodonitrotetrazolium, LDH: Lactate dehydrogenase, M: Molar, ml: Milliliter, mM: Millimolar, MTT: 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, NAD: Nicotinamide adenine dinucleotide, NADPH: Nicotinamide adenine dinucleotide phosphate, NBT: Nitro blue tetrazolium, nm: Nanometer, NO: Nitric oxide, NRE: Neeri extract, PMS: Phenazine methosulfate, ROS: Reactive oxygen species, Sc: Slope of the graph of control, SEM: Standard error of mean, Si: Slope of the graph with inhibitor, U/I: International unit, μg: Microgram, μl: Microliter.
Evidence for a 20 Parsec Disk at the Nucleus of Centaurus A

We report Hubble Space Telescope NICMOS observations of the central region of NGC 5128 at 2.2 μm and in Paα. The continuum images show extended emission typical of an elliptical galaxy and a strong unresolved central source we identify as the nucleus of the galaxy. Its position is consistent with ground-based IR and radio data, and with the peak of reddening found with the first wide field planetary camera. In Paα, we detect a prominent elongated structure, centered on the nucleus, extended by ≃2''at a position angle of ≃33°, and with a major to minor axis ratio of ~2. We interpret this as an inclined, ~40 pc diameter, thin nuclear disk of ionized gas rather than a jet-gas cloud interaction. We do see several weaker Paα features, some of which may be circumnuclear gas clouds shocked by the X-ray/radio jet. The disk is one of the smallest ever observed at the nucleus of an active galactic nucleus (AGN). It is not perpendicular to the jet but is consistent with being oriented along the major axis of the bulge. If it represents the warped outer portion of an accretion disk around a black hole, we conclude that even on the scale of a few parsecs, the disk is dominated by the galaxy gravitational potential and is not directly related to the symmetry axis of the AGN.
Delay-sensitive flooding based on expected path quality in low duty-cycled wireless sensor networks

Flooding in low duty-cycled wireless sensor networks suffers from a large transmission delay because a sender has to wait until a receiver becomes active to forward a packet. With the presence of unreliable radio links, the delay performance is even more severely degraded. In this article, we aim to reduce the flooding delay in low duty-cycled wireless sensor networks in relation to link unreliability. The key idea is to build a delay-sensitive flooding tree in which a node receives packet through the shortest path in terms of the total expected number of transmissions. In addition, the algorithm allows multiple senders to send through links outside of the tree if they can provide earlier expected delivery time. To give priorities to potential senders, we employ an energy-balancing mechanism which dynamically distributes the sending role among them. The mechanism not only makes sure senders start to acquire the channel at different times to prevent collisions but also lets them alternatively take turns based on residual energy, in order to lengthen network lifetime. Compared with the best known schemes, the proposed algorithm achieves up to 8% improvement in terms of flooding delay, energy consumption, and network lifetime.
AutoVFlow: Autonomous Virtualization for Wide-Area OpenFlow Networks

It is expected that clean-slate network designs will be implemented for wide-area network applications. Multi-tenancy in OpenFlow networks is an effective method to supporting a clean-slate network design, because the cost-effectiveness is improved by the sharing of substrate networks. To guarantee the programmability of OpenFlow for tenants, a complete flow space (i.e., header values of the data packets) virtualization is necessary. Wide-area substrate networks typically have multiple administrators. We therefore need to implement a flow space virtualization over multiple administration networks. In existing techniques, a third party is solely responsible for managing the mapping of header values for flow space virtualization for substrate network administrators and tenants, despite the severity of a third party failure. In this paper, we propose an AutoVFlow mechanism that allows flow space virtualization in a wide-area networks without the need for a third party. Substrate network administrators implement a flow space virtualization autonomously. They are responsible for virtualizing a flow space involving switches in their own substrate networks. Using a prototype of AutoVFlow, we measured the virtualization overhead, the results of which show a negligible amount of overhead.
Symbolic dynamics based method for rigorous study of the existence of short cycles for chaotic systems

It is shown that the problem of existence of periodic orbits can be studied rigorously by means of a symbolic dynamics approach combined with interval methods. Symbolic dynamics is used to find approximate initial positions of periodic points and interval operators are used to prove the existence of periodic orbits in a neighborhood of the computer generated solution. As an example the Lorenz system is studied. All 2536 periodic orbits of the Poincaré map with the period n ≤ 14 are found.
Analytical model for analysis of cache behavior during cholesky factorization and its variants

In this paper, we apply several transformations to Cholesky factorization and describe a new transformation called dynamic loop reversal which can increase temporal and spatial locality. We also describe a probabilistic analytical model of the cache behavior during the standard and recursive Cholesky factorization and use it for studying effects of these transformations. Automatic methods for predicting the cache behavior have been described in the literature, but they are inaccurate in case of recursive calls, since they do not take into account the interactions between subroutines. Our model is more accurate, since it takes most of the interactions, namely on the last level of recursion, into account. We have evaluated the accuracy of the model by measurements on a cache monitor. The comparisons of the numbers of measured cache misses and the numbers of cache misses estimated by the model indicate that the accuracy of the model is within the range on units of percents.
Do standardised patients lose their confidence in primary medical care? Personal experiences of standardised patients with GPs.

‘Quot homines, tot sententiae. ’ Terenz (195–159 ACE), Roman poet There is a great variation among GPs, concerning performance, behaviour, consultation strategies, diagnostic and treatment procedures, and this variation is considered as an indicator for poor quality of the service.1–6 But variation can also be regarded as an advantage, mainly because patients can choose the GP who suits their personal needs or preferences best. This applies especially to healthcare systems without a list system, as in Germany, where patients can move from one GP to another practically as often as they want to. A doctor, for example, who has a dominating way of communicating, attracts patients who prefer a doctor who tells them frankly what they have to do. Other patients prefer doctors with a more patient-centred communication style. Due to these differences patients may have the advantage of a better choice. But what do patients actually think of this variation? A research project on inter-doctor variation in German general practice offered the opportunity to examine this question in an additional evaluation. In the project, in which the inter-doctor variation on managing headaches was examined, university students were trained to play a standardised role of a patient with an acute headache (methods and results published elsewhere). 7 In the additional study presented here, we wanted to find out about the personal views of these ‘actors’ and whether their experience changed their view on the primary healthcare service. For this purpose a focus group discussion was chosen. This does not generate universally valid results but it was seen as an adequate tool to elicit the experiences of the actors and to explore differences in opinions as well as define consensus.8 ### Sample In September 2002 the focus group discussion was conducted with four of the six students who participated as …
An oligomeric form of simian virus 40 large T-antigen is immunologically related to the cellular tumor antigen p53

The cellular tumor antigen p53 is bound to the simian virus 40 (SV40) large T-antigen in SV40-infected and -transformed cells. As a result, p53 can in general be immunoprecipitated by either monoclonal or polyclonal antibodies that react with large T-antigen. Despite extensive immunological characterization of both these antigens, they have not previously been found to share any antigenic determinants. We have isolated several monoclonal antibodies that bind to the human p53 protein (K. Leppard and L. V. Crawford, EMBO J. 2:1457-1464, 1983) and show here that antibody PAb1104 has distinct, intrinsic activities towards both p53 and SV40 large T-antigen. Only a subset of T-antigen is bound by PAb1104. This subset is an oligomeric form of T-antigen, as judged by its sedimentation velocity in sucrose. In contrast, all of the detectable p53 carries the PAb1104-reactive determinant. The detection of a chance cross-reactivity between two antigens that are already well characterized and which associate with one another in vivo is highly unlikely. It is possible therefore that the element of structural similarity between large T and p53 that is implied by our results has some genuine functional significance.
Evidence for Inbreeding Depression and Pre-Copulatory, but Not Post Copulatory Inbreeding Avoidance in the Cabbage Beetle Colaphellus bowringi

Inbreeding is known to have adverse effects on fitness-related traits in a range of insect species. A series of theoretical and experimental studies have suggested that polyandrous insects could avoid the cost of inbreeding via pre-copulatory mate choice and/or post-copulatory mechanisms. We looked for evidence of pre-copulatory inbreeding avoidance using female mate preference trials, in which females were given the choice of mating with either of two males, a sibling and a non-sibling. We also tested for evidence of post-copulatory inbreeding avoidance by conducting double mating experiments, in which four sibling females were mated with two males sequentially, either two siblings, two non-siblings or a sibling and a non-sibling in either order. We identified substantial inbreeding depression: offspring of females mated to full siblings had lower hatching success, slower development time from egg to adult, lower survival of larval and pupal stages, and lower adult body mass than the offspring of females mated to non-sibling males. We also found evidence of pre-copulatory inbreeding avoidance, as females preferred to mate with non-sibling males. However, we did not find any evidence of post-copulatory inbreeding avoidance: egg hatching success of females mating to both sibling and non-sibling males were consistent with sperm being used without bias in relation to mate relatedness. Our results suggest that this cabbage beetle has evolved a pre-copulatory mechanism to avoid matings between close relative, but that polyandry is apparently not an inbreeding avoidance mechanism in C. bowringi.
On condition of reaching a high level of consensus when new decision makers join

– The consensus opinion helps with the achievement of fairness of the decision process, especially when the new decision makers (DMs) are added into the group decision making (GDM). This paper aims to show by constructing consensus models that when some conditions are met, the consensus level does not decrease even when new DMs are invited to join the GDM (new opinions are added to the GDM). , – This paper first constructs a deviation which is the difference between each two individual opinions. The smaller these differences are, the higher consensus degree (level) of the group. Then, a consensus optimization model based on individual differences (IDCO) is constructed by minimizing the aggregated deviations. Lastly, based on the optimization model, the condition of reaching a high level of consensus when new DMs are added into the GDM is discussed. , – The discussion on the properties of the IDCO indicates that once the consensus with all DMs reaching an acceptable level, the consensus deviation degree decreases as the number of DMs increases when certain conditions are met, and the consensus level does not decrease even when new DMs join the GDM. , – Practically, high-level consensus needs to be reached no matter how difficult it is when the new opinions are added into the GDM. To see how this end could be achieved, this paper takes the fuzzy preference relations as particular instances to investigate the conditions of consensus under which new DMs (opinions) are added into the GDM. The rather holistic analysis leads us to such a conclusion that the authors can replace this particular kind of preference, as used in the discussion, in many other cases by, for instance, multiplicative preference relation, linguistic preference relation, etc.
A Deathly Dnase Activity for Dicer

Altogether , these results converge to a model where TPP1 in vivo, similarly to the in vitro findings, binds to telomeres and connects them to telomerase, and this activity may evolve different shelterin subcomplex rearrangements. Other proteins binding to the single-stranded region of telomeres also may be involved in modulation of telomerase activity. For instance, an additional OB-fold-containing protein, related to an RPA large subunit, was found to be associated with a highly processive form of telomerase in the ciliate Tetrahymena thermophila (Min and Collins, 2009). Similarly , a novel protein factor, CTC1, was described recently at telomeres (Miyake et al., 2009; Surovtseva et al., 2009). This single-stranded binding protein found in plants and humans shares sequence similarities with Cdc13 and possesses functions in telomere protection. However, it remains to be examined whether it is also involved in telomerase-dependent telomere length homeostasis. The question to answer now is how TPP1 coordinates both end protection and telomerase recruitment, and how this duality is eventually regulated as a function of telomere length in normal somatic cells. Likewise, how is this balance eventually altered in cancer cells? Indeed, if TPP1-POT1 is required for protection, are all telomeres bound to it? Do TPP1-containing complexes invariably serve both roles at all bound telo-meres? Future experiments in the field will certainly shed new lights on this aspect of the increasingly complex and dynamic world of chromosome ends. Recently reporting in Science, Nakagawa et al. describe an unexpected role for Dicer in chromosome fragmentation during apoptosis in C. elegans. They find that cleavage of DCR-1 by the caspase CED-3 redirects its regulatory activity, by destroying its dsRNase activity while activating an intrinsic DNase activity. RNase III enzymes are a widely distributed family of double stranded RNA (dsRNA)-specific ribonucleases. Since the discovery of E. coli RNase III in the 1960s, the functions of this protein family in ribosomal RNA biogenesis and mRNA decay or regulation have been well studied in bacteria and yeast (MacRae and Doudna, 2007). Importance of their homologs in higher eukaryotes was recognized only in the last decade. In particular, Dicer-family RNase III enzymes are central to the biogenesis of Argo-naute-associated small regulatory RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs). Because miRNAs play important roles in diverse biological settings, Dicer genes are essential for many aspects of development and physiology. The cell death pathway has critical connections with the miRNA pathway, since many …
Cardioembolic Stroke: Clinical Features, Specific Cardiac Disorders and Prognosis

This article provides the reader with an overview and up-date of clinical features, specific cardiac disorders and prognosis of cardioembolic stroke. Cardioembolic stroke accounts for 14-30% of ischemic strokes and, in general, is a severe condition; patients with cardioembolic infarction are prone to early and long-term stroke recurrence, although recurrences may be preventable by appropriate treatment during the acute phase and strict control at follow-up. Certain clinical features are suggestive of cardioembolic infarction, including sudden onset to maximal deficit, decreased level of consciousness at onset, Wernicke’s aphasia or global aphasia without hemiparesis, a Valsalva manoeuvre at the time of stroke onset, and co-occurrence of cerebral and systemic emboli. Lacunar clinical presentations, a lacunar infarct and especially multiple lacunar infarcts, make cardioembolic origin unlikely. The more common high risk cardioembolic conditions are atrial fibrillation, recent myocardial infarction, mechanical prosthetic valve, dilated myocardiopathy, and mitral rheumatic stenosis. Transthoracic and transesophageal echocardiogram can disclose structural heart diseases. Paroxysmal atrial dysrhyhtmia can be detected by Holter monitoring. In-hospital mortality in cardioembolic stroke (27.3%, in our series) is the highest as compared with other subtypes of cerebral infarction. In our experience, in-hospital mortality in patients with early embolic recurrence (within the first 7 days) was 77%. Patients with alcohol abuse, hypertension, valvular heart disease, nausea and vomiting, and previous cerebral infarction are at increased risk of early recurrent systemic embolization. Secondary prevention with anticoagulants should be started immediately if possible in patients at high risk for recurrent cardioembolic stroke in which contraindications, such as falls, poor compliance, uncontrolled epilepsy or gastrointestinal bleeding are absent.
GLIPR-2 Overexpression in HK-2 Cells Promotes Cell EMT and Migration through ERK1/2 Activation

The epithelial-to-mesenchymal transition (EMT) of tubular epithelial cells in the adult kidney is one of the key events in renal interstitial fibrosis. Glioma pathogenesis related-2 (GLIPR-2) has been shown to be up-regulated in proximal tubular cells (PTCs) in the fibrotic kidney. However, the biological function of GLIPR-2 remains unknown. In this study, we found that GLIPR-2 expression is elevated in the kidney tissue samples of patients with diabetic nephropathy (DN). Human proximal renal tubular epithelial cells (HK-2 cells) were transfected with pcDNA3.0-GLIPR-2 and selected with G418. To identify the biological function of GLIPR-2, an epithelial-to-mesenchymal transition (EMT) PCR array analysis was performed, and genes that had statistically significantly altered expression levels with more than a two-fold difference compared with the pcDNA3.0-transfected HK-2 cells were considered. Key elements of the EMT process, such as E-cadherin and vimentin, were transcriptionally activated in the pcDNA3.0-GLIPR-2-transfected sublines. In addition, α-SMA gene expression, which is a marker of myofibroblasts, increased in the pcDNA3.0-GLIPR-2-transfected HK-2 cells. The cell migration assay demonstrated that the transfection of HK-2 with GLIPR-2 promoted cell migration following an EMT. Additionally, consistent with the effects of increased EGFR expression levels, we found that the activation of extracellular signal-regulated kinases 1 and 2 (ERK1/2) was highly elevated in the pcDNA3.0-GLIPR-2-transfected group. Our study demonstrates that GLIPR-2 overexpression in HK-2 cells can potentiate EMT-like processes in this cell type through the ERK1/2 signaling pathway. GLIPR-2 may be responsible for the development of renal fibrosis by increasing the accumulation of interstitial fibroblasts.
Next-generation sequencing: from basic research to diagnostics.

BACKGROUND For the past 30 years, the Sanger method has been the dominant approach and gold standard for DNA sequencing. The commercial launch of the first massively parallel pyrosequencing platform in 2005 ushered in the new era of high-throughput genomic analysis now referred to as next-generation sequencing (NGS). CONTENT This review describes fundamental principles of commercially available NGS platforms. Although the platforms differ in their engineering configurations and sequencing chemistries, they share a technical paradigm in that sequencing of spatially separated, clonally amplified DNA templates or single DNA molecules is performed in a flow cell in a massively parallel manner. Through iterative cycles of polymerase-mediated nucleotide extensions or, in one approach, through successive oligonucleotide ligations, sequence outputs in the range of hundreds of megabases to gigabases are now obtained routinely. Highlighted in this review are the impact of NGS on basic research, bioinformatics considerations, and translation of this technology into clinical diagnostics. Also presented is a view into future technologies, including real-time single-molecule DNA sequencing and nanopore-based sequencing. SUMMARY In the relatively short time frame since 2005, NGS has fundamentally altered genomics research and allowed investigators to conduct experiments that were previously not technically feasible or affordable. The various technologies that constitute this new paradigm continue to evolve, and further improvements in technology robustness and process streamlining will pave the path for translation into clinical diagnostics.