Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome Sequence of the Deep-Rooted Yersinia pestis Strain Angola Reveals New Insights into the Evolution and Pangenome of the Plague Bacterium

ABSTRACT To gain insights into the origin and genome evolution of the plague bacterium Yersinia pestis, we have sequenced the deep-rooted strain Angola, a virulent Pestoides isolate. Its ancient nature makes this atypical isolate of particular importance in understanding the evolution of plague pathogenicity. Its chromosome features a unique genetic make-up intermediate between modern Y. pestis isolates and its evolutionary ancestor, Y. pseudotuberculosis. Our genotypic and phenotypic analyses led us to conclude that Angola belongs to one of the most ancient Y. pestis lineages thus far sequenced. The mobilome carries the first reported chimeric plasmid combining the two species-specific virulence plasmids. Genomic findings were validated in virulence assays demonstrating that its pathogenic potential is distinct from modern Y. pestis isolates. Human infection with this particular isolate would not be diagnosed by the standard clinical tests, as Angola lacks the plasmid-borne capsule, and a possible emergence of this genotype raises major public health concerns. To assess the genomic plasticity in Y. pestis, we investigated the global gene reservoir and estimated the pangenome at 4,844 unique protein-coding genes. As shown by the genomic analysis of this evolutionary key isolate, we found that the genomic plasticity within Y. pestis clearly was not as limited as previously thought, which is strengthened by the detection of the largest number of isolate-specific single-nucleotide polymorphisms (SNPs) currently reported in the species. This study identified numerous novel genetic signatures, some of which seem to be intimately associated with plague virulence. These markers are valuable in the development of a robust typing system critical for forensic, diagnostic, and epidemiological studies.
Silence models in weighted finite-state transducers

We investigate the effects of different silence modelling strategies in Weighted Finite-State Transducers for Automatic Speech Recognition. We show that the choice of silence models, and the way they are included in the transducer, can have a significant effect on the size of the resulting transducer; we present a means to prevent particularly large silence overheads. Our conclusions include that context-free silence modelling fits well with transducer based grammars, whereas modelling silence as a monophone and a context has larger overheads.
ROLE OF CEREBRAL GANGLIA IN REGULATION OF OXYGEN CONSUMPTION OF FRESHWATER BIVALVE MOLLUSC, INDONAIA CAERULEUS (PRASHAD, 1918) FROM GODAVARI RIVER DURING SUMMER

The adult bivalve mollusc, Indonaia caeruleus of 50-53 mm shell length and 6.853-8.275g body weight were subjected to (a) control (normal) (b) removal of both the cerebral ganglia, (c) injection of their cerebral ganglionic extract to intact control as well as (d) injection of ice-cold distilled water and absolute alcohol (1:1) to normal control and (e) injection of this extract to ganglia removal bivalves for 10 days. The rate of oxygen consumption in bivalves from all four groups (including control) was measured on 2 nd , 5 th and 10 th day. The study revealed that, the rate of oxygen consumption was significantly increased in cerebral ganglia removed, as well as cerebral ganglionic extract injected to ablated group on 2 nd , 5 th and 10 th day compared to control. The rate also showed significant increase in injection of extract to normal control on 2 nd day. The rate of oxygen consumption showed more increase in cerebral ganglia ablated group than extract injected one on 5th and 10th day. The results are discussed in the light
Named Entity Discovery Using Comparable News Articles

In this paper we describe a way to discover Named Entities by using the distribution of words in news articles. Named Entity recognition is an important task for today's natural language applications, but it still suffers from data sparseness. We used an observation that a Named Entity is likely to appear synchronously in several news articles, whereas a common noun is less likely. Exploiting this characteristic, we successfully obtained rare Named Entities with 90% accuracy just by comparing time series distributions of a word in two newspapers. Although the achieved recall is not sufficient yet, we believe that this method can be used to strengthen the lexical knowledge of a Named Entity tagger.
Isolation of a series of novel variants of murine mammary tumor viruses with broadened host ranges

We have previously isolated mouse mammary tumor virus (MMTV) host range variants by serial virus passage in feline cells. These variants productively infect cells of a broad range of species but replicate most efficiently in feline cells. We report here the isolation of a series of novel MMTV host range variants that have the ability to replicate with high efficiency in murine, rat, canine and human cells, respectively; these variants were isolated by serial virus passage in cells of each respective species. These new variants, furthermore, all retained their ability to efficiently replicate in feline cells, and each exhibited unique host range properties. The novel MMTV variants obtained from murine, rat, feline, canine, and human cells showed no overt evidence of recombination with endogenous type‐C viruses in that they retained their antigenic reactivities in group‐specific radioimmunoassays for MMTV polypeptides, and were unreactive for type‐C virus proteins when tested by radioimmunoassays and DNA polymerase assays. These novel MMTV host range variants now broaden the spectrum of studies that can be undertaken involving MMTV replication and the initiation and promotion of virus‐mediated mammary cell transformation.
Both alpha- and beta-subunits contribute to the agonist sensitivity of neuronal nicotinic acetylcholine receptors

A family of genes has been identified that encodes subunits of nicotinic acetylcholine receptors (nAChRs) and is expressed in the nervous system. Functional neuronal nAChRs can be expressed in Xenopus oocytes by injection of RNA encoding 1 of 2 different beta-subunits (beta 2, beta 4) in pairwise combination with RNA encoding 1 of 3 different alpha-subunits (alpha 2, alpha 3, alpha 4). We examined the sensitivity of these 6 different alpha- beta-subunit combinations to the nicotinic agonists ACh, nicotine, cytisine, and 1,1-dimethyl-4- phenylpiperazinium (DMPP). Each subunit combination displayed a distinct pattern of sensitivity to these 4 agonists. The alpha 2 beta 2 combination was 5-fold more sensitive to nicotine than to acetylcholine, while the alpha 3 beta 2 combination was 17-fold less sensitive to nicotine than to ACh, and the alpha 3 beta 4 combination was equally sensitive to both nicotine and ACh. nAChRs composed of alpha 2, alpha 3, or alpha 4 in combination with beta 2 were 14–100- fold less sensitive to cytisine than to ACh. In contrast, nAChRs composed of alpha 2, alpha 3, or alpha 4 in combination with beta 4 were 3–17-fold more sensitive to cytisine than to ACh. The alpha 2 beta 2, alpha 3 beta 2, and alpha 3 beta 4 combinations were each equally sensitive to DMPP and ACh, while the alpha 2 beta 4, alpha 4 beta 2, and alpha 4 beta 4 combinations were 4–24-fold less sensitive to DMPP than to ACh. We also demonstrated that these differences are neither a consequence of variation in the relative amounts of RNA injected nor an artifact of oocyte expression. The oocyte system can accurately express ligand-gated ion channels because mouse muscle nAChRs expressed in oocytes display pharmacological properties similar to those reported for these receptors expressed on BC3H-1 cells. We conclude that both the alpha- and the beta-subunits contribute to the pharmacological characteristics of neuronal nAChRs.
Recent Trend Toward Decrease in the Incidence of Childhood Type 2 Diabetes in Tokyo

We previously reported that the annual incidences of children with type 2 diabetes as detected by urine glucose screening at school in Tokyo during 1981–1995 were significantly higher than the incidence in 1974–1980 (1). We evaluated recent changes in the annual incidence of childhood type 2 diabetes in Tokyo. The results were analyzed using Fisher’s exact probability test. From 1974 to 2004, a total of 9,242,259 school students were tested for glucosuria to detect diabetes. A total of 236 children were diagnosed as having type 2 diabetes through this screening program. Overall, 83.9% …
Test generation and minimization with "basic" statecharts

Model-based testing as a black-box testing technique has grown in importance. The models used represent the relevant features of the system under consideration (SUC), and can also be used as a basis for generating test case sets. In this work we introduce a novel representation of state-charts which subsumes common features of different state-chart variants. Based on this model and well-defined test criteria, efficient algorithms are introduced for generating test case sets. Those test case sets are minimized to cover both the model of SUC and its inversion, i.e., the complementary model.
Body Condition and the Adrenal Stress Response in Captive American Kestrel Juveniles

We examined the adrenal response to handling stress of birds in different body conditions. In order to affect the birds' body condition, young (73‐d old) female American kestrels (Falco sparverius) were maintained for 6 wk on one of three diets: a control diet (fed ad lib.) and two calorically restricted diets. To invoke a stress response, we removed birds from their cages and took repeated blood samples over the course of an hour. All birds responded to handling stress with an increase in plasma corticosterone, but control birds (in good body condition) showed a more rapid increase to maximum corticoste‐rone levels, followed by a decrease. Both groups of food‐restricted birds had a slower rate of increase to maximum corticosterone levels and then maintained high corticosterone levels through 60 min. These results suggest that birds in good physical condition respond more quickly to stressors and adapt physiologically to stressful situations more rapidly than do birds in poor physical condition. This difference may reflect the ability of birds in good condition to mobilize fat for energy, while birds in poor condition must mobilize protein (i.e., muscle).
On‐line Identification and Quantification of Mean Shifts in Bivariate Processes using a Neural Network‐based Approach

Many statistical process control (SPC) problems are multivariate in nature because the quality of a given process or product is determined by several interrelated variables. Various multivariate control charts (e.g. Hotelling's $T^2$, multivariate cumulative sum and multivariate exponentially weighted moving average charts) have been designed for detecting mean shifts. However, the main shortcoming of such charts is that they can detect an unusual event but do not directly provide the information required by a practitioner to determine which variable or group of variables has caused the out‐of‐control signal. In addition, these charts cannot provide more detailed shift information, for example the shift magnitude, which would be very useful for quality practitioners to search the assignable causes that give rise to the out‐of‐control situation. This work proposes a neural network‐based model that can identify and quantify the mean shifts in bivariate processes on‐line. The performance evaluation performed by the simulation demonstrates that the proposed model outperforms the conventional multivariate control schemes in terms of average run length, and can accurately estimate the magnitude of the shift of each of the shifted variables in a real‐time mode. Extensive simulation is also carried out to examine the effects of correlation on the performance of the proposed model. A numerical example is presented to illustrate the usage of the proposed model. Although a mean shift identification and quantification tool for bivariate SPC is the particular application presented here, the proposed neural network‐based methodology can be applied to multivariate SPC in general. Copyright © 2006 John Wiley & Sons, Ltd.
Stability analysis of FAST TCP using PI transfer function

A new approach for the stability analysis of FAST TCP system is used for the investigation of one special kind of dynamical systems. This approach is based on results from the stability theory, optimal control theory, and variational methods. The optimal control approach allows us to obtain sufficient algebraic stability conditions for FAST TCP system. The way to obtain necessary and sufficient conditions for stability of systems with parameter r is shown in this paper. This method leads, in some cases, to algebraic necessity and sufficient conditions of absolute stability. Furthermore, case results illustrate the validity of parameter r for the stability of FAST TCP.
Probabilistic Models of Quake II Player Movement

Probabilistic models have proven an effective means for reasoning in the face of uncertainty. We are interested in applying these probabilistic methods to computer games. We build Markov models of Quake II maps and use them to analyze and predict player movements. We show these models provide decent prediction in the short term, but grow worse when trying to predict further into the future. We further analyze the difficulty of predicting behavior over longer time periods, and use the KL-divergence metric to indicate the differences in
Threshold Selection for Unsupervised Detection, With an Application to Microphone Arrays

Detection is usually done by comparing some criterion to a threshold. It is often desirable to keep a performance metric such as false alarm rate constant across conditions. Using training data to select the threshold may lead to suboptimal results on test data recorded in different conditions. This paper investigates unsupervised approaches, where no training data is used. A probabilistic model is fitted on the test data using the EM algorithm, and the threshold value is selected based on the model. The proposed approach (1) does not use training data, (2) uses the test data itself to compensate for simplifications inherent to the model, and (3) permits the use of more complex models in a straightforward manner. On a microphone array speech detection task, the proposed unsupervised approach achieves similar or better results than the "training" approach. The methodology is general and may be applied to other contexts than microphone arrays, and other performance metrics than FAR
Restoration of Arbitrarily Warped Historical Document Images Using Flow Lines

Historical documents frequently suffer from arbitrary geometric distortions (warping and folds) due to storage conditions, use and to, some extent, the printing process of the time. In addition, page curl can be prominent due to the scanning technique used. Such distortions adversely affect OCR and print-on-demand quality. Previous approaches to geometric restoration either focus only on the correction of page curl or require supplementary information obtained by additional scanning hardware -- not practical for existing scans. This paper presents a new approach to detect and restore arbitrary warping and folds, in addition to page curl. Warped text lines and the smooth deformation between them are precisely modelled as primary and secondary flow lines that are then restored to their original linear shape. Preliminary, but representative, experimental results, in comparison to a leading page curl removal method and an industry-standard commercial system, demonstrate the effectiveness of the proposed method.
Spondylodiscitis due to Bacteroides fragilis: Two cases and review

Non-iatrogenic spondylodiscitis caused by anaerobic bacteria remains exceptional. We describe 2 cases of spondylodiscitis with epidural abscess due to Bacteroides fragilis, 1 after colonoscopy with biopsy and 1 in a cirrhotic patient. The clinical and imaging findings were not discriminant relative to other pyogenic spondylodiscitis. One should consider B. fragilis when treating a spondylodiscitis with epidural abscess, especially in patients with a possibly digestive portal of entry.
ViePEP - A BPMS for Elastic Processes

In today's IT industry resource-intensive tasks are playing an increasing role in business processes. By the emergence of Cloud computing it is nowadays possible to deploy such tasks onto computing resources leased in an on-demand fashion from Cloud providers. This enabled the realization of so-called Elastic Processes (EPs). These are able to dynamically adjust their used resources in order to meet varying workloads. Till now, traditional Business Process Management Systems (BPMSs) do not consider the needs of Elastic Processes such as monitoring the current system load, reasoning about optimally utilized resources, in order to ensure given Quality of Service constraints while executing required actions such as starting, stopping servers or moving services from one server to an other. This paper focuses on our current work on ViePEP, a research BPMS for the Cloud capable of handling the aforementioned requirements of EPs.
ENHANCEMENT OF SATURATION BOILING OF PF-5060 DIELECTRIC LIQUID ON MICROPOROUS SURFACES

This research experimentally investigated microporous Copper (MPC) surfaces for enhancing nucleate boiling and increasing the Critical Heat Flux (CHF) of PF-5060 dielectric liquid and the potential application of the results to immersion cooling of high power computer chips. MPC surfaces of different thicknesses (80—230 \uf06dm), fabricated using conventional electrochemical deposition at high current density, have different morphology and microstructure. The PF-5060 liquid is chemically inert, environmentally friendly, and has low enough saturation temperature (~ 54oC at 0.10 MPa). This helps maintain the chip junctions temperature below that recommended by the chip manufacturer (85-120 oC, depending on the application). '
Expression of aminopeptidase-n (CD 13) in normal tissues and malignant neoplasms of epithelial and lymphoid origin.

AIMS--To provide a detailed knowledge of the distribution of the CD13 molecule, also known as the protease aminopeptidase-N, on both normal tissues and malignant neoplasms of epithelial and lymphoid origin. METHODS--CD13 antigen was examined by immunocytochemistry, using a recently produced antibody (VS5E) alongside a commercially available anti-CD13 monoclonal antibody. The VS5E recognising CD13 was produced by immunising a doxorubicin resistant breast cancer cell line (MCF-7-ADr). A striking feature of this antibody was that it stained the doxorubicin resistant cells but not the parental cell line. Both antibodies were tested on a broad range of normal tissues and three common types of epithelial malignancy (colon n = 28, lung n = 30, breast n = 35), and 12 cases of Hodgkin's and 52 of non-Hodgkin's lymphomas. RESULTS--CD13 was expressed on many tissue and cell types outside the haematopoietic system. In particular it was present on breast epithelium and in 20% (seven of 35) of breast carcinomas, but absent in normal and neoplastic colonic and bronchial tissues and lymphomas. CONCLUSIONS--This study provides not only detailed information about the expression of the CD13 antigen, but also raises the important possibility that CD13 expression may correlate with drug resistance in breast carcinomas.
Critical Blood Pressure Threshold Dependence of Hypertensive Injury and Repair in a Malignant Nephrosclerosis Model

Most patients with essential hypertension do not exhibit substantial renal damage. Renal autoregulation by preventing glomerular transmission of systemic pressures has been postulated to mediate this resistance. Conversely, malignant nephrosclerosis (MN) has been postulated to develop when severe hypertension exceeds a critical ceiling. If the concept is valid, even modest blood pressure (BP) reductions to below this threshold regardless of antihypertensive class (1) should prevent MN and (2) lead to the healing of the already developed MN lesions. Both predicates were tested using BP radiotelemetry in the stroke-prone spontaneously hypertensive rats receiving 1% NaCl as drinking fluid for 4 weeks. Severe hypertension (final 2 weeks average systolic BP, >200 mm Hg) and MN (histological damage score 36±5; n=27) developed in the untreated stroke-prone spontaneously hypertensive rats but were prevented by all antihypertensive classes (enalapril [n=15], amlodipine [n=13], or a hydralazine/hydrochlorothiazide combination [n=15]) if the final 2-week systolic BP remained <190 mm Hg. More impressively, modest systolic BP reductions to 160 to 180 mm Hg (hydralazine/hydrochlorothiazide regimen) initiated at ≈4 weeks in additional untreated rats after MN had already developed (injury score 35±4 in the right kidney removed before therapy) led to a striking resolution of the vascular and glomerular MN injury over 2 to 3 weeks (post-therapy left kidney injury score 9±2, P<0.0001; n=27). Proteinuria also declined rapidly from 122±9.5 mg/24 hours before therapy to 20.5±3.6 mg 1 week later. These data clearly demonstrate the barotrauma-mediated pathogenesis of MN and the striking capacity for spontaneous and rapid repair of hypertensive kidney damage if new injury is prevented.
Lagrangian Structures in Very High-Frequency Radar Data and Optimal Pollution Timing

Very High-frequency (VHF) radar technology produces detailed surface velocity maps near the surface of coastal waters. The use of measured velocity data in environmental prediction, however, has remained unexplored. In this paper, we uncover a striking flow structure in coastal radar observations along the coast of Florida. This structure governs the spread of organic contaminants or passive drifters released in the area. We compute the Lyapunov exponents of the VHF radar data to determine optimal release windows in which contaminants are advected efficiently away from the coast and we show that a VHF radar-based pollution release scheme using the hidden flow structure reduces the effect of industrial pollution in the coastal environment.
Metformin is not just an antihyperglycaemic drug but also has protective effects on the vascular endothelium

Metformin, a synthetic dimethyl biguanide, has been in clinical use for over 55 years, and today is considered the first‐choice drug for the treatment of type 2 diabetes used by an estimated 125 million people worldwide. Metformin is orally effective, not metabolized, excreted unchanged by the kidney, relatively free of side effects and well tolerated by the majority of patients. Of importance is that the United Kingdom Prospective Diabetes Study 20‐year study of type 2 diabetics, completed in 1998, compared patients treated with insulin, sulfonylureas and metformin and concluded that metformin provided vascular protective actions. Cardiovascular disease is the primary basis for the high morbidity and mortality that is associated with diabetes and that metformin proved to be protective resulted in a dramatic increase in its use. The vascular protective actions of metformin are thought to be secondary to the antihyperglycaemic effects of metformin that are mediated via activation of AMP kinase and subsequent inhibition of hepatic gluconeogenesis, fatty acid oxidation as well as an insulin sensitizing action in striated muscle and adipose tissue. As reflected by a number of clinical studies, patients treated with metformin also have improvement in endothelial function as measured by the use of plethysmography and measurement of flow‐mediated vasodilatation. These data as well as data from animal studies are supportive that metformin has a direct protective action on the vascular endothelium. In this review article, we discuss the pharmacology of metformin and critique the literature as to its cellular sites and mechanism(s) of action.