Miracle-dz/UniFAR-FTUs huggingface dataset:
The evolution of a conjugative plasmid and its ability to increase bacterial fitness

Conjugative plasmids are extra-chromosomal DNA elements that are capable of horizontal transmission and are found in many natural isolated bacteria. Although plasmids may carry beneficial genes to their bacterial host, they may also cause a fitness cost. In this work, we studied the evolution of the R1 plasmid and we found that, in spite of the R1 plasmid conferring an initial cost to its host, after 420 generations the cost disappeared in all five independent evolution experiments. In fact, in two of these five experiments evolved conjugative plasmids actually conferred a fitness advantage to their hosts. Furthermore, the relative fitness of the ancestral clone bearing one of the evolved plasmids is significantly higher than both the plasmid-free ancestral cells and the evolved cells carrying the evolved plasmid. Given that the R1 plasmid may spread among different species of enterobacteria, we wondered what the effect of the evolved plasmid would be inside Salmonella enterica cells. We found that the evolved plasmid is also able to dramatically increase the relative fitness of these cells. Our results suggest that even if general usage of antibiotics is halted, conjugative plasmids that have been selected with antibiotics in previous years can still persist among bacterial populations or even invade new strains.
Subclinical atrial fibrillation and the risk of stroke.

BACKGROUND One quarter of strokes are of unknown cause, and subclinical atrial fibrillation may be a common etiologic factor. Pacemakers can detect subclinical episodes of rapid atrial rate, which correlate with electrocardiographically documented atrial fibrillation. We evaluated whether subclinical episodes of rapid atrial rate detected by implanted devices were associated with an increased risk of ischemic stroke in patients who did not have other evidence of atrial fibrillation. METHODS We enrolled 2580 patients, 65 years of age or older, with hypertension and no history of atrial fibrillation, in whom a pacemaker or defibrillator had recently been implanted. We monitored the patients for 3 months to detect subclinical atrial tachyarrhythmias (episodes of atrial rate >190 beats per minute for more than 6 minutes) and followed them for a mean of 2.5 years for the primary outcome of ischemic stroke or systemic embolism. Patients with pacemakers were randomly assigned to receive or not to receive continuous atrial overdrive pacing. RESULTS By 3 months, subclinical atrial tachyarrhythmias detected by implanted devices had occurred in 261 patients (10.1%). Subclinical atrial tachyarrhythmias were associated with an increased risk of clinical atrial fibrillation (hazard ratio, 5.56; 95% confidence interval [CI], 3.78 to 8.17; P<0.001) and of ischemic stroke or systemic embolism (hazard ratio, 2.49; 95% CI, 1.28 to 4.85; P=0.007). Of 51 patients who had a primary outcome event, 11 had had subclinical atrial tachyarrhythmias detected by 3 months, and none had had clinical atrial fibrillation by 3 months. The population attributable risk of stroke or systemic embolism associated with subclinical atrial tachyarrhythmias was 13%. Subclinical atrial tachyarrhythmias remained predictive of the primary outcome after adjustment for predictors of stroke (hazard ratio, 2.50; 95% CI, 1.28 to 4.89; P=0.008). Continuous atrial overdrive pacing did not prevent atrial fibrillation. CONCLUSIONS Subclinical atrial tachyarrhythmias, without clinical atrial fibrillation, occurred frequently in patients with pacemakers and were associated with a significantly increased risk of ischemic stroke or systemic embolism. (Funded by St. Jude Medical; ASSERT ClinicalTrials.gov number, NCT00256152.).
Territoire, gouvernance et intelligence territoriale

Depuis quelques annees, les politiques ont change de visage et ce, dans tous les pays de l’Union Europeenne. Territoire, partenariat, gouvernance multi-niveaux, intelligence territoriale, sont des notions qui tendent a s’imposer. Dans cet expose, nous essayons d’analyser ces concepts et en quoi ils repondent en fait a des mutations qui se developpent actuellement. Ces changements ne sont pas seulement conceptuels, ils repondent en realite a des mutations ideologiques du role de l’Etat dans un nouvel ordre social. Partant de nos travaux au sein de l’Observatoire Local de l’Emploi de l’Universite de Huelva, nous nous interrogeons sur l’abandon progressif de la responsabilite de l’Etat dans les politiques publiques, plus specifiquement dans les politiques d’inclusion sociale, et sur ses possibles dangers.
Safety of Intraperitoneal Injection of Adipose Tissue‐Derived Autologous Mesenchymal Stem Cells in Cats

Background Chronic inflammatory diseases are common in cats and mesenchymal stem cells (MSC) are a promising therapeutic approach for management of these disorders. The purpose of this study was to evaluate the safety of intraperitoneal injection of MSC in cats. Hypothesis Intrapertioneal injection of autologous MSC in cats is safe. Animals Ten healthy adult purpose‐bred cats. Methods Mesenchymal stem cells were isolated from subcutaneous adipose tissue collected during ovariohysterectomy and characterized for expression of CD90, CD105 and CD44 and trilineage differentiation. Three weeks postoperatively a complete blood count, serum chemistry profile, urinalysis, and abdominal ultrasound were performed. Five cats then received 1 × 106 of autologous MSC/kg of body weight intraperitoneally with ultrasound guidance; 5 additional cats were sham injected. Cats were monitored for 6 weeks with daily physical examinations and weekly clinicopathological evaluations. Abdominal ultrasonography was repeated at weeks 1 and 5 after injection. Results Serious adverse effects were not observed in any MSC‐injected cat. Two animals developed transient lethargy and decreased activity. Jejunal lymph node size was increased in MSC‐injected cats compared to controls at weeks 1 (1.38 ± 0.25 versus 0.88 ± 0.25 cm2; P = .036) and 5 (1.75 ± 0.82 versus 0.79 ± 0.12 cm2; P = .047). A hyperechoic renal segmental cortical lesion was observed in 1 MSC‐injected cat. Conclusions and Clinical Relevance Intraperitoneal MSC injection was well tolerated with only mild, self‐limiting adverse effects being observed in 2 cats. This route provides a safe means of administration for cell‐based treatment in cats.
Analysis of the current-voltage characteristics of Silicon on Ferroelectric Insulator Field Effect Transistor (SOF-FET)

This paper presents the current-voltage (I-V) characteristic of our proposed Silicon-on-Ferroelectric Insulator Field Effect Transistor (SOF-FET). The proposed SOF-FET is based on the concept of silicon-on-insulator (SOI) device technology and it utilizes a negative capacitance that can be achieved by inserting a layer of ferroelectric insulator inside the bulk silicon substrate of the device. The negative capacitance (NC) effect can provide an internal signal boosting that leads to steeper subthreshold slope, which is the prime requirement for ultra-low-power circuit operation. Here we have analyzed the impacts of channel doping profile on the behavior of the proposed SOF-FET. The major focus of this paper is the investigation of the current-voltage (I-V) characteristics of the proposed SOF-FET. Here the (I-V) characteristics of both the subthreshold and the saturation regions of the proposed device have been derived.
Composition of Model-based Test Coverage Criteria

In this paper, we discuss adjustable coverage criteria and their combinations in model-based testing. We formalize coverage criteria and specify test goals using OCL. Then, we propose a set of functions which describe the test generation process in a generic way. Each coverage criterion is mapped to a set of test goals. Based on this set of functions, we propose a generic framework enabling flexible integration of various test generators and unified treatment of test coverage criteria.
Experimental Study of the Safety of Pancreas Cryosurgery: The Comparison of 2 Different Techniques of Cryosurgery

Objectives: To test the feasibility of cryosurgery for pancreatic carcinoma and to observe the consequence of cryosurgery by 2 different techniques. Methods: Twelve healthy pigs underwent laparotomy, during which, chop amputation of common bile duct and duodenum were performed, meanwhile other intra-abdominal organs with the pancreas were isolated. Two different techniques of cryosurgery were performed on the pancreas. Group A (n = 6) accepted the mild hypothermic cryosurgery with liquid nitrogen superficial refrigeration, and group B (n = 6) were performed with the deep hypothermic cryosurgery at −170°C with LCS2000 cryogenic surgical system. All the animals' digestive tract was reconstructed with cholecystojejunostomy and gastroenterostomy, respectively. Results: Acute necrotizing pancreatitis occurred on all animals in group A, of which 5 of the 6 died within 1 week, whereas only 1 of the 6 reported a 4-week survival. All animals in group B survived during the observation, in which only a transient increment and a gradual correction of pancreatic amylase level were recorded. Small pancreatic pseudocyst occurred in 1 case. Conclusions: Mild hypothermic cryosurgery with liquid nitrogen superficial refrigeration might lead to pancreatic injury and induce acute pancreatitis, yet deep hypothermic cryosurgery with adequate time showed a promising effect in destroying pancreatic tissue and preventing acute pancreatitis.
A MICROMACHINED GEOMETRIC MOIRÉ INTERFEROMETRIC FLOATING-ELEMENT SHEAR STRESS SENSOR

This paper presents the development of a floating-element shear stress sensor that permits the direct measurement of skin friction based on geometric Moire interferometry. The sensor was fabricated using an aligned waferbond/thin-back process producing optical gratings on the backside of a floating element and on the top surface of the support wafer. Experimental characterization indicates a static sensitivity of 0.26 µm/Pa, a resonant frequency of 1.7 kHz, and a noise floor of 6.2 mPa/√Hz.
Comparison of sirolimus-eluting vs. bare-metal stents for the treatment of infrapopliteal obstructions.

BACKGROUND Drug-eluting stents have been shown to be very effective in the treatment of coronary artery disease. In this independent, single-centre registry we assess the safety and efficacy of the sirolimus-eluting stent versus bare-metal balloon expandable stent for symptomatic infrapopliteal obstructions. METHODS AND RESULTS A total of 60 consecutive patients with infrapopliteal arterial obstructions were treated by stent implantation into the tibial and peroneal arteries and the data was entered into a prospective registry. All patients were treated with balloon-expandable coronary stents with a stent length of 33 mm and a nominal diameter of 3.5 mm. Enrolment was limited to patients treatable with a single stent. 30 patients (56.7% male, mean age 71.4 years, 83.3% diabetics) received a sirolimus-eluting balloon-expandable stent. 30 patients (63.3% male, mean age 73.0 years, 76.6% diabetics) were treated with uncoated bare-metal stents. At follow-up, the cumulative rates of Major Adverse Events were 10.0% vs. 46.6%. The rates of major amputation, bypass surgery or Target Lesion Revascularisation (TLR) were all zero for the sirolimus group compared with 10.0%, 0% and 23.3% in the bare metal stent group. There were 7 deaths (sirolimus =3, bare metal =7). Angiographic follow-up comparing sirolimus vs. bare metal revealed stent occlusion 0% vs. 17.4%, restenosis >50% of 0% vs. 39.1% (p 0.0007) and mean degree of in-stent restenosis of 1.8+/-4.8% vs. 53+/-40.9% (p <0.0001) respectively. CONCLUSION In this registry sirolimus-eluting stents were shown to be safe and effective in the treatment of focal infrapopliteal obstructions.
Mechanical filtering for narrow-band hearing in the weta

SUMMARY This paper constitutes a major attempt to associate tympanic deflections with the mechanoreceptor organ location in an acoustic insect. The New Zealand tree weta (Hemideina thoracica) has tympanal ears located on each of the prothoracic tibiae. The tympana exhibit a sclerotized oval plate, membranous processes bulging out from the tibial cuticle and many loosely suspended ripples. We used microscanning laser Doppler vibrometry to determine how such a tympanal membrane vibrates in response to sound and whether the sclerotized region plays a role in hearing. The tympanum displays a single resonance at the calling frequency of the male, an unusual example of an insect tympana acting as a narrow bandpass filter. Both tympana resonate in phase with the stimulus and with each other. Histological sections show that the tympanal area is divided into two distinct regions, as in other ensiferans. An oval plate lies in the middle of a thickened region and is surrounded by a transparent and uniformly thin region. It is hinged dorsally to the tympanal rim and thus resembles the model of a ‘hinged flap’. The thickened region appears to act as a damping mass on the oscillation of the thin region, and vibration displacement is reduced in this area. The thinner area vibrates with higher amplitude, inducing mechanical pressure on the dorsal area adjacent to the crista acustica. We present a new model showing how the thickened region might confer a mechanical gain onto the activation of the crista acustica sensory neurons during the sound-induced oscillations.
A revised annotation and comparative analysis of Helicobacter pylori genomes.

Huge amounts of genomic information are currently being generated. Therefore, biologists require structured, exhaustive and comparative databases. The PyloriGene database (http://genolist.pasteur.fr/PyloriGene) was developed to respond to these needs, by integrating and connecting the information generated during the sequencing of two distinct strains of Helicobacter pylori. This led to the need for a general annotation consensus, as the physical and functional annotations of the two strains differed significantly in some cases. A revised functional classification system was created to accommodate the existing data and to make it possible to classify coding sequences (CDS) into several functional categories to harmonize CDS classification. The annotation of the two complete genomes was revised in the light of new data, allowing us to reduce the percentage of hypothetical proteins from approximately 40 to 33%. This resulted in the reassignment of functions for 108 CDS (approximately 7% of all CDS). Interestingly, the functions of only approximately 13% of CDS (222 out of 1658 CDS) were annotated as a result of work done directly on H.pylori genes. Finally, comparison of the two published genomes revealed a significant amount of size variation between corresponding (orthologous) CDS. Most of these size variations were due to natural polymorphisms, although other sources of variation were identified, such as pseudogenes, new genes potentially regulated by slipped-strand mispairing mechanism, or frame-shifts. 113 of these differences were due to different start codon assignments, a common problem when constructing physical annotations.
Tackling antimicrobial resistance

Bacteria resistant to antibiotic therapy are becoming much more common and this has led to mounting concern in the UK and worldwide.1–4 Many pathogens are now 'multiresistant', that is, they are resistant to several classes of antimicrobial drug. Infection with such organisms may be particularly difficult to treat. In this article, we briefly discuss how resistance and multiresistance occur. We consider some of the important pathogens involved and the problems they pose in hospitals and the community. We discuss strategies for slowing the accumulation of antibiotic resistance and the implications for doctors treating patients with common infections.
How does landscape structure influence catchment transit time across different geomorphic provinces?

Despite an increasing number of empirical investigations of catchment transit times (TTs), virtually all are based on individual catchments and there are few attempts to synthesize understanding across different geographical regions. Uniquely, this paper examines data from 55 catchments in five geomorphic provinces in northern temperate regions (Scotland, United States of America and Sweden). The objective is to understand how the role of catchment topography as a control on the TTs differs in contrasting geographical settings. Catchment inverse transit time proxies (ITTPs) were inferred by a simple metric of isotopic tracer damping, using the ratio of standard deviation of δ18O in streamwater to the standard deviation of δ18O in precipitation. Quantitative landscape analysis was undertaken to characterize the catchments according to hydrologically relevant topographic indices that could be readily determined from a digital terrain model (DTM). The nature of topographic controls on transit times varied markedly in different geomorphic regions. In steeper montane regions, there are stronger gravitational influences on hydraulic gradients and TTs tend to be lower in the steepest catchments. In provinces where terrain is more subdued, direct topographic control weakened; in particular, where flatter areas with less permeable soils give rise to overland flow and lower TTs. The steeper slopes within this flatter terrain appear to have a greater coverage of freely draining soils, which increase sub‐surface flow, therefore increasing TTs. Quantitative landscape analysis proved a useful tool for inter‐catchment comparison. However, the critical influence of sub‐surface permeability and connectivity may limit the transferability of predictive tools of hydrological function based on topographic parameters alone. Copyright © 2009 John Wiley & Sons, Ltd.
Spatial and temporal analysis of the distribution of hantavirus pulmonary syndrome in Buenos Aires Province, and its relation to rodent distribution, agricultural and demographic variables

We studied the spatial and temporal distribution of Hantavirus Pulmonary Syndrome (HPS) cases from 1998 to 2001 in the Buenos Aires Province, Argentina. HPS is a severe viral disease whose natural reservoir are rodents of the subfamily Sigmodontinae (Muridae) and which occurs in many countries of South and North America. We considered two spatial arrangements: cells of 18.5 × 18.5 km2; and departments, the political subdivisions of the province, as spatial units. We tested the departure from a Poisson distribution of the number of cases per cell and per month with the Variance/Mean index, while the interaction between spatial and temporal clustering was tested by means of the Knox and Mantel tests. We constructed probability maps in which the HPS rates per department were considered Poisson variates according to population, area and the product of population and area. We analysed the relation between rodent distribution, environmental and demographic variables and HPS cases conducting preliminary univariate analysis from which we selected variables to enter in general linearized models. We found that both the spatial and temporal distribution of cases is strongly aggregated. The spatiotemporal interaction appears to be related to a strong seasonality and the existence of particular ecological conditions rather than epidemic transmission of the disease. The main explanatory variables for the distribution of HPS cases among the departments of the Buenos Aires Province were human population, the distribution of the rodent Oxymycterus rufus and evapotranspiration. The last two variables are probably indicators of favourable ecological conditions for the reservoirs, which encompass other variables not taken into account in this study.
Towards an Elastographic Atlas of Brain Anatomy

Cerebral viscoelastic constants can be measured in a noninvasive, image-based way by magnetic resonance elastography (MRE) for the detection of neurological disorders. However, MRE brain maps of viscoelastic constants are still limited by low spatial resolution. Here we introduce three-dimensional multifrequency MRE of the brain combined with a novel reconstruction algorithm based on a model-free multifrequency inversion for calculating spatially resolved viscoelastic parameter maps of the human brain corresponding to the dynamic range of shear oscillations between 30 and 60 Hz. Maps of two viscoelastic parameters, the magnitude and the phase angle of the complex shear modulus, |G*| and φ, were obtained and normalized to group templates of 23 healthy volunteers in the age range of 22 to 72 years. This atlas of the anatomy of brain mechanics reveals a significant contrast in the stiffness parameter |G*| between different anatomical regions such as white matter (WM; 1.252±0.260 kPa), the corpus callosum genu (CCG; 1.104±0.280 kPa), the thalamus (TH; 1.058±0.208 kPa) and the head of the caudate nucleus (HCN; 0.649±0.101 kPa). φ, which is sensitive to the lossy behavior of the tissue, was in the order of CCG (1.011±0.172), TH (1.037±0.173), CN (0.906±0.257) and WM (0.854±0.169). The proposed method provides the first normalized maps of brain viscoelasticity with anatomical details in subcortical regions and provides useful background data for clinical applications of cerebral MRE.
Exit from Hell? Reducing the Impact of Amplification DDoS Attacks

Amplification vulnerabilities in many UDP-based network protocols have been abused by miscreants to launch Distributed Denial-of-Service (DDoS) attacks that exceed hundreds of Gbps in traffic volume. However, up to now little is known about the nature of the amplification sources and about countermeasures one can take to remediate these vulnerable systems. Is there any hope in mitigating the amplification problem? In this paper, we aim to answer this question and tackle the problem from four different angles. In a first step, we monitored and classified amplification sources, showing that amplifiers have a high diversity in terms of operating systems and architectures. Based on these results, we then collaborated with the security community in a large-scale campaign to reduce the number of vulnerable NTP servers by more than 92%. To assess possible next steps of attackers, we evaluate amplification vulnerabilities in the TCP handshake and show that attackers can abuse millions of hosts to achieve 20× amplification. Lastly, we analyze the root cause for amplification attacks: networks that allow IP address spoofing. We deploy a method to identify spoofing-enabled networks from remote and reveal up to 2,692 Autonomous Systems that lack egress filtering.
Detailed structure of the top of the melt body beneath the East Pacific Rise at 9°40′N from waveform inversion of seismic reflection data

We have applied waveform inversion to multichannel seismic reflection data collected at the East Pacific Rise at 9°40'N in order to determine the precise velocity structure of the magma body causing the axial magma chamber reflection. Our analysis supports the idea of a molten sill as previously suggested from forward modeling of seismic data from this location. Our inverted solution has a 30-m-thick sill with a P wave seismic velocity of 2.6 km s -1 . Although not well constrained by the data we believe that the S wave velocity in the sill is not significantly different from 0.0 km s -1 . The low P- and S- wave velocities in the sill imply that it contains less than 30% crystals. The molten sill is underlain by a velocity gradient in which the P wave velocity increases from 2.6 to 3.5 km s -1 over a vertical distance of 50-m. The shape of our velocity-depth profile implies that accretion of material to the roof of the sill is minor compared to accretion to the floor. The underlying velocity gradient zone may represent crystal settling under gravity. We suggest that only material from the 30-m-thick layer can erupt.