Miracle-dz/UniFAR-FTUs huggingface dataset:
Escherichia coli Serotype O55:H7 Diversity Supports Parallel Acquisition of Bacteriophage at Shiga Toxin Phage Insertion Sites during Evolution of the O157:H7 Lineage

ABSTRACT Enteropathogenic Escherichia coli (EPEC) continues to be a leading cause of mortality and morbidity in children around the world. Two EPEC genomes have been fully sequenced: those of EPEC O127:H6 strain E2348/69 (United Kingdom, 1969) and EPEC O55:H7 strain CB9615 (Germany, 2003). The O55:H7 serotype is a recent precursor to the virulent enterohemorrhagic E. coli O157:H7. To explore the diversity of O55:H7 and better understand the clonal evolution of O157:H7, we fully sequenced EPEC O55:H7 strain RM12579 (California, 1974), which was collected 1 year before the first U.S. isolate of O157:H7 was identified in California. Phage-related sequences accounted for nearly all differences between the two O55:H7 strains. Additionally, O55:H7 and O157:H7 strains were tested for the presence and insertion sites of Shiga toxin gene (stx)-containing bacteriophages. Analysis of non-phage-associated genes supported core elements of previous O157:H7 stepwise evolutionary models, whereas phage composition and insertion analyses suggested a key refinement. Specifically, the placement and presence of lambda-like bacteriophages (including those containing stx) should not be considered stable evolutionary markers or be required in placing O55:H7 and O157:H7 strains within the stepwise evolutionary models. Additionally, we suggest that a 10.9-kb region (block 172) previously believed unique to O55:H7 strains can be used to identify early O157:H7 strains. Finally, we defined two subsets of O55:H7 strains that share an as-yet-unobserved or extinct common ancestor with O157:H7 strains. Exploration of O55:H7 diversity improved our understanding of the evolution of E. coli O157:H7 and suggested a key revision to accommodate existing and future configurations of stx-containing bacteriophages into current models.
Complete Genome Sequence of Bacillus subtilis BSn5, an Endophytic Bacterium of Amorphophallus konjac with Antimicrobial Activity for the Plant Pathogen Erwinia carotovora subsp. carotovora

ABSTRACT Here, we present the complete genome sequence of Bacillus subtilis strain BSn5, isolated from Amorphophallus konjac calli tissue and showing strong inhibitory activity to Erwinia carotovora subsp. carotovora, which causes Amorphophallus soft rot disease and affects the industry development of this organism.
Evaluation of the traditional way of euthanasia of farmed foxes from an animal welfare point of view.

the aim of the study was to evaluate at what point consciousness is lost and brain activity ceases in electrically stunned blue foxes (Alopex lagopus), and to establish whether or not there is any return to consciousness after stunning before death. the study was conducted on 15 female blue foxes. all animals were sedated with an intramuscular injection of medetomidine. the results showed that the animals were unconscious immediately after stunning as documented by the absence of all reflexes. the EEG recording showed a status epilepticus pattern in all foxes immediately after stunning, and in none of the animals was a return to normal brain pattern observed. such a generalised status epilepticus is connected with state of total unconsciousness and ultimately leads to brain death. all the foxes in our experiment had respiratory arrest and heart fibrillation after stunning. the heart changes were irreversible in all cases and most probably contributed heavily to the death of the brain after stunning, as the fibrillating heart is not able to provide the necessary blood flow to the brain and other organs. this leads to failure of multiple organ systems and inevitable death. rapid disappearance of the BaEr after stunning indicates brainstem affection and death. magnetic resonance imaging examination and histopathological examination of the brain revealed no severe changes to the brains of any of the foxes, indicating that stunning mainly affects the function of the brain without distorting the anatomy of the brain. in conclusion, electrical stunning produces an immediate and irreversible state of unconsciousness and therefore is a humane way of euthanasia of farmed foxes.
Sources of Abnormal EEG Activity in the Presence of Brain Lesions

In routine clinical EEG, a common origin is assumed for delta and theta rhythms produced by brain lesions. In previous papers, we have provided some experimental support, based on High Resolution qEEG and dipole fitting in the frequency domain, for the hypothesis that delta and theta spectral power have independent origins related to lesion and edema respectively. This paper describes the results obtained with Frequency Domain VARETA (FD-VARETA) in a group of 13 patients with cortical space-occupying lesions, in order to: 1) Test the accuracy of FD-VARETA for the localization of brain lesions, and 2) To provide further support for the independent origin of delta and theta components. FD VARETA is a distributed inverse solution, constrained by the Montreal Neurological Institute probabilistic atlas that estimates the spectra of EEG sources. In all patients, logarithmic transformed source spectra were compared with age-matched normative values, defining the Z source spectrum. Maximum Z values were found in 10 patients within the delta band (1.56 to 3.12 Hz); the spatial extent of these sources in the atlas corresponded with the location of the tumors in the CT. In 2 patients with small metastases and large volumes of edema and in a patient showing only edema, maximum Z values were found between 4.29 and 5.12 Hz. The spatial extent of the sources at these frequencies was within the volume of the edema in the CT. These results provided strong support to the hypothesis that both delta and theta abnormal EEG activities are the counterparts of two different pathophysiological processes.
Sequence and Annotation of Rickettsia sibirica sibirica Genome

ABSTRACT Rickettsia sibirica sibirica is the causative agent of Siberian or North Asian tick typhus, a tick-borne rickettsiosis known to exist in Siberia and eastern China. Here we present the draft genome of Rickettsia sibirica sibirica strain BJ-90 isolated from Dermacentor sinicus ticks collected in Beijing, China.
Consensus-based sparse signal reconstruction algorithm for wireless sensor networks

This article presents a distributed Bayesian reconstruction algorithm for wireless sensor networks to reconstruct the sparse signals based on variational sparse Bayesian learning and consensus filter. The proposed approach is able to address wireless sensor network applications for a fusion-center-free scenario. In the proposed approach, each node calculates the local information quantities using local measurement matrix and measurements. A consensus filter is then used to diffuse the local information quantities to other nodes and approximate the global information at each node. Then, the signals are reconstructed by variational approximation with resultant global information. Simulation results demonstrate that the proposed distributed approach converges to their centralized counterpart and has good recovery performance.
The Aeromonas hydrophila wb*O34 Gene Cluster: Genetics and Temperature Regulation

ABSTRACT The Aeromonas hydrophila wb*O34 gene cluster of strain AH-3 (serotype O34) was cloned and sequenced. This cluster contains genes necessary for the production of O34-antigen lipopolysaccharide (LPS) in A. hydrophila. We determined, using either mutation or sequence homology, roles for the majority of genes in the cluster by using the chemical O34-antigen LPS structure obtained for strain AH-3. The O34-antigen LPS export system has been shown to be a Wzy-dependent pathway typical of heteropolysaccharide pathways. Furthermore, the production of A. hydrophila O34-antigen LPS in Escherichia coli K-12 strains is dependent on incorporation of the Gne enzyme (UDP-N-acetylgalactosamine 4-epimerase) necessary for the formation of UDP-galactosamine in these strains. By using rapid amplification of cDNA ends we were able to identify a transcription start site upstream of the terminal wzz gene, which showed differential transcription depending on the growth temperature of the strain. The Wzz protein is able to regulate the O34-antigen LPS chain length. The differential expression of this protein at different temperatures, which was substantially greater at 20°C than at 37°C, explains the previously observed differential production of O34-antigen LPS and its correlation with the virulence of A. hydrophila serotype O34 strains.
Randomized geographic-based routing with nearly guaranteed delivery for three-dimensional ad hoc network

Several routing algorithms have been proposed for efficient routing in mobile ad hoc networks, most of them consider mobile nodes embedded in two-dimensional environments. However, in reality, these networks are embedded in three-dimensional environments. Usually, two-dimensional routing algorithms have several assumptions that are not valid for three-dimensional spaces. In this article, we propose four different randomized geographic-based routing algorithms that have the following properties: (1) nearly guaranteed delivery rate, by using randomize route to overcome local minimum problems; (2) low overhead, by extracting a virtual backbone of the network and then conducting the routing algorithms over the extracted backbone to decrease the search space; (3) low path dilation, by hybridizing the new algorithms with progress-based routing which have very low path dilation; and (4) works in three-dimensional environment. The first algorithm 3DRanDom chooses the next neighbor randomly from a dominating set of the network (extracted locally). The second algorithm 3DRanDomProb extracts a dominating set and sends to one of the resulted neighbors randomly with more probability for the nodes closer to the destination. The third algorithm G_3DRanDomProb tries to progress as much as possible to the destination, if the progress is not possible, the algorithm switches to 3DRanDomProb. The fourth algorithm G_3DRanDomProb_G uses progress-based routing as much as possible, then it switches to 3DRanDomProb until it overcomes the local minimum problem and then goes back to progress-based routing. We show experimentally that these hybrid randomized routing algorithms on three-dimensional mobile ad hoc networks can achieve nearly guaranteed delivery while discovering routes significantly closer in length to the shortest path and with low overhead.
Effect of Waveform on Tactile Perception by Electrovibration Displayed on Touch Screens

In this study, we investigated the effect of input voltage waveform on our haptic perception of electrovibration on touch screens. Through psychophysical experiments performed with eight subjects, we first measured the detection thresholds of electrovibration stimuli generated by sinusoidal and square voltages at various fundamental frequencies. We observed that the subjects were more sensitive to stimuli generated by square wave voltage than sinusoidal one for frequencies lower than 60 Hz. Using Matlab simulations, we showed that the sensation difference of waveforms in low fundamental frequencies occurred due to the frequency-dependent electrical properties of human skin and human tactile sensitivity. To validate our simulations, we conducted a second experiment with another group of eight subjects. We first actuated the touch screen at the threshold voltages estimated in the first experiment and then measured the contact force and acceleration acting on the index fingers of the subjects moving on the screen with a constant speed. We analyzed the collected data in the frequency domain using the human vibrotactile sensitivity curve. The results suggested that Pacinian channel was the primary psychophysical channel in the detection of the electrovibration stimuli caused by all the square-wave inputs tested in this study. We also observed that the measured force and acceleration data were affected by finger speed in a complex manner suggesting that it may also affect our haptic perception accordingly.
Lower limb stiffness: Considerations for female athletes

Women demonstrate lower limb stiffness recruitment strategies, which may predispose them to greater sustainment of lower limb injuries, particularly to the anterior cruciate ligament. To positively alter such strategies in women, lower limb muscle strenght (particularly hamstrings) and tendon stiffness should be increased before performing high-intensity plyometics.
Library interoperability via inheritance

To allow Eiffel programs to run on the Java Virtual Machine we have adopted a translation scheme which addresses issues of library interoperability for the two languages. We describe an approach which permits Eiffel code to inherit Java code directly rather than adopt a more conventional external call mechanism. With this approach we can choose to access the Java code as descendants or as clients. In effect we are able to make the Java classes appear directly as Eiffel classes. In particular we can program applets in Eiffel just as a Java programmer does, inheriting directly from the applet class provided by the system and redefining appropriate routines. In addition, where Eiffel library classes are implemented with external calls provided by the Eiffel run-time, our translator is able to mix its translated code with Java implementations of the run-time functions. This ability to inherit Java code in the Eiffel source, and to use inherited versions of Eiffel run-time code on the Java side allows us to utilise both Eiffel and Java libraries in JVM-targetted Eiffel programs.
A user-centric Internet of Things platform to empower users for managing security and privacy concerns in the Internet of Energy

Current worldwide energy challenges require the synergy of multidisciplinary actions and activities affecting different stakeholders, such as governments, utility companies, and citizens. In recent years, these needs are being addressed through the integration of the Smart Grid paradigm with the so-called Internet of Things, in order to make energy decisions aware of data from devices that are physically deployed on a smart city. However, to address such concerns, many of the scenarios from this resulting ecosystem, require huge amounts of data in order to make efficient and effective decisions about energy distribution and saving. In this sense, the application of proper security mechanisms to allow the selective disclosure of information to the intended parties is crucial to guarantee that users’ privacy is not harmed. In this work, we propose the application of specific attribute-based access control technologies to protect the energy data that are outsourced from different devices. This integration is part of the ongoing work within MiMurcia Smart City project, which is intended to provide an integral platform to build a more sustainable and efficient city.
Why not just switch on the light?: light and its versatile applications in the field of nanomedicine

Abstract Over the last decade, the emerging field of nanomedicine has undergone rapid progresses. Different internal and external stimuli like pH, temperature, radiation, ultrasound or light have been introduced to expand the diagnostic and therapeutic options of various applications within the field. This review focuses on the novel application of light in the field of nanomedicine as a mechanism to control drug delivery, release and biochemical and genetic functionality at the target. The field of functional nanomaterials for medicine, and in particular of light responsive nanocarriers, polymers and biomolecules offer new therapeutic options but also requires substantial further research to render this approach broadly applicable in clinical practice.
Predictive values of metabolic syndrome in children

Metabolic syndrome is a clinical term encompassing risk factors (obesity, insulin resistance, dyslipidemia and hypertension), which yield an increased risk for the development of diabetes mellitus type 2 and cardiovascular disorders in adolescence. Two sets of criteria for diagnosing metabolic syndrome were applied, the criteria for adults, specifically adapted for children, and the criteria defined by the International Diabetes Federation (IDF). A reliability analysis was conducted; sensitivity (SE), specificity (SP), positive predictive value (PPV) and negative predictive value (NPV) of applying certain criteria of both definitions of metabolic syndrome. Metabolic syndrome in adolescents was diagnosed much more frequently using the specific criteria (41%) in comparison to the IDF criteria (22%). Using the specific criteria for children and adolescents, it was established that the HDL cholesterol was the most specific and had the largest PPV. Using the IDF criteria for diagnosing metabolic syndrome, the reliability analysis established that the highest PPV was recorded with the elevated level of triglycerides. The specific criteria have been found to be more efficient in diagnosing metabolic syndrome in adolescents. The highest predictive value was displayed by dyslipidemic disorders, hypertriglyceridemia and hypo HDL cholesterolemia.
Rifampin Resistance rpoB Alleles or Multicopy Thioredoxin/Thioredoxin Reductase Suppresses the Lethality of Disruption of the Global Stress Regulator spx in Staphylococcus aureus

ABSTRACT Staphylococcus aureus is capable of causing a remarkable spectrum of disease, ranging from mild skin eruptions to life-threatening infections. The survival and pathogenic potential of S. aureus depend partly on its ability to sense and respond to changes in its environment. Spx is a thiol/oxidative stress sensor that interacts with the C-terminal domain of the RNA polymerase RpoA subunit, leading to changes in gene expression that help sustain viability under various conditions. Using genetic and deep-sequencing methods, we show that spx is essential in S. aureus and that a previously reported Δspx strain harbored suppressor mutations that allowed it to grow without spx. One of these mutations is a single missense mutation in rpoB (a P-to-L change at position 519 encoded by rpoB [rpoB-P519L]) that conferred high-level resistance to rifampin. This mutation alone was found to be sufficient to bypass the requirement for spx. The generation of rifampin resistance libraries led to the discovery of an additional rpoB mutation, R484H, which supported strains with the spx disruption. Other rifampin resistance mutations either failed to support the Δspx mutant or were recovered at unexpectedly low frequencies in genetic transduction experiments. The amino acid residues encoded by rpoB-P519L and -R484H map in close spatial proximity and comprise a highly conserved region of RpoB. We also discovered that multicopy expression of either trxA (encoding thioredoxin) or trxB (encoding thioredoxin reductase) supports strains with the deletion of spx. Our results reveal intriguing properties, especially of RNA polymerase, that compensate for the loss of an essential gene that is a key mediator of diverse processes in S. aureus, including redox and thiol homeostasis, antibiotic resistance, growth, and metabolism. IMPORTANCE The survival and pathogenicity of S. aureus depend on complex genetic programs. An objective for combating this insidious organism entails dissecting genetic regulatory circuits and discovering promising new targets for therapeutic intervention. In this study, we discovered that Spx, an RNA polymerase-interacting stress regulator implicated in many stress responses in S. aureus, including responses to oxidative and cell wall antibiotics, is essential. We describe two mechanisms that suppress the lethality of spx disruption. One mechanism highlights how only certain rifampin resistance-encoding alleles of RpoB confer new properties on RNA polymerase, with important mechanistic implications. We describe additional stress conditions where the loss of spx is deleterious, thereby highlighting Spx as a multifaceted regulator and attractive drug discovery target.
Genome Sequence of the Methanotrophic Alphaproteobacterium Methylocystis sp. Strain Rockwell (ATCC 49242)

ABSTRACT Methylocystis sp. strain Rockwell (ATCC 49242) is an aerobic methane-oxidizing alphaproteobacterium isolated from an aquifer in southern California. Unlike most methanotrophs in the Methylocystaceae family, this strain has a single pmo operon encoding particulate methane monooxygenase but no evidence of the genes encoding soluble methane monooxygenase. This is the first reported genome sequence of a member of the Methylocystis species of the Methylocystaceae family in the order Rhizobiales.
Early Detection of Metabolic Changes Using Microdialysis During and After Experimental Kidney Transplantation in a Porcine Model

Background: Microdialysis (MD) can detect organ-related metabolic changes before they become measurable in plasma through the biochemical parameters. This study aims to evaluate the early detection of metabolic changes during experimental kidney transplantation (KTx). Material and methods: During preparation of 8 donor kidneys, one MD catheter was inserted in the renal cortex and samples were collected. After a 6-hour cold ischemia time (CIT), kidneys were implanted in the 8 recipient pigs. Throughout the warm ischemia time (WIT) and after reperfusion, kidneys were monitored. The interstitial glucose, lactate, pyruvate, glutamate, and glycerol concentrations were evaluated. Results: A significant decline in glucose level was observed at the end of CIT. The lactate level was reduced to the minimum point of 0.35 ± 0.08 mmol/L in CIT. After reperfusion, lactate values raised significantly. During the WIT, the pyruvate level increased, continued until the end of the WIT. For glutamate, a steady increase was noted during explantation, CIT, WIT, and early reperfusion phases. The increase of glycerol value continued in the early postreperfusion, which was then followed by a sharp decline. Conclusion: MD is a fast and simple minimally invasive method for measurement of metabolic substrates in renal parenchyma during KTx. MD offers the option of detecting minor changes of interstitial glucose, lactate, pyruvate, glutamate, and glycerol in every stage of KTx. Through the use of MD, metabolic changes can be continuously monitored during the entire procedure of KTx.