Miracle-dz/UniFAR-FTUs huggingface dataset:
Diagnostic Methods of Helicobacter pylori Infection for Epidemiological Studies: Critical Importance of Indirect Test Validation

Among the methods developed to detect H. pylori infection, determining the gold standard remains debatable, especially for epidemiological studies. Due to the decreasing sensitivity of direct diagnostic tests (histopathology and/or immunohistochemistry [IHC], rapid urease test [RUT], and culture), several indirect tests, including antibody-based tests (serology and urine test), urea breath test (UBT), and stool antigen test (SAT) have been developed to diagnose H. pylori infection. Among the indirect tests, UBT and SAT became the best methods to determine active infection. While antibody-based tests, especially serology, are widely available and relatively sensitive, their specificity is low. Guidelines indicated that no single test can be considered as the gold standard for the diagnosis of H. pylori infection and that one should consider the method's advantages and disadvantages. Based on four epidemiological studies, culture and RUT present a sensitivity of 74.2–90.8% and 83.3–86.9% and a specificity of 97.7–98.8% and 95.1–97.2%, respectively, when using IHC as a gold standard. The sensitivity of serology is quite high, but that of the urine test was lower compared with that of the other methods. Thus, indirect test validation is important although some commercial kits propose universal cut-off values.
Dating the Age of the SIV Lineages That Gave Rise to HIV-1 and HIV-2

Great strides have been made in understanding the evolutionary history of simian immunodeficiency virus (SIV) and the zoonoses that gave rise to HIV-1 and HIV-2. What remains unknown is how long these SIVs had been circulating in non-human primates before the transmissions to humans. Here, we use relaxed molecular clock dating techniques to estimate the time of most recent common ancestor for the SIVs infecting chimpanzees and sooty mangabeys, the reservoirs of HIV-1 and HIV-2, respectively. The date of the most recent common ancestor of SIV in chimpanzees is estimated to be 1492 (1266–1685), and the date in sooty mangabeys is estimated to be 1809 (1729–1875). Notably, we demonstrate that SIV sequences sampled from sooty mangabeys possess sufficient clock-like signal to calibrate a molecular clock; despite the differences in host biology and viral dynamics, the rate of evolution of SIV in sooty mangabeys is indistinguishable from that of its human counterpart, HIV-2. We also estimate the ages of the HIV-2 human-to-human transmissible lineages and provide the first age estimate for HIV-1 group N at 1963 (1948–1977). Comparisons between the SIV most recent common ancestor dates and those of the HIV lineages suggest a difference on the order of only hundreds of years. Our results suggest either that SIV is a surprisingly young lentiviral lineage or that SIV and, perhaps, HIV dating estimates are seriously compromised by unaccounted-for biases.
Eradication of bacterial persisters with antibiotic-generated hydroxyl radicals

During Mycobacterium tuberculosis infection, a population of bacteria likely becomes refractory to antibiotic killing in the absence of genotypic resistance, making treatment challenging. We describe an in vitro model capable of yielding a phenotypically antibiotic-tolerant subpopulation of cells, often called persisters, within populations of Mycobacterium smegmatis and M. tuberculosis. We find that persisters are distinct from the larger antibiotic-susceptible population, as a small drop in dissolved oxygen (DO) saturation (20%) allows for their survival in the face of bactericidal antibiotics. In contrast, if high levels of DO are maintained, all cells succumb, sterilizing the culture. With increasing evidence that bactericidal antibiotics induce cell death through the production of reactive oxygen species (ROS), we hypothesized that the drop in DO decreases the concentration of ROS, thereby facilitating persister survival, and maintenance of high DO yields sufficient ROS to kill persisters. Consistent with this hypothesis, the hydroxyl-radical scavenger thiourea, when added to M. smegmatis cultures maintained at high DO levels, rescues the persister population. Conversely, the antibiotic clofazimine, which increases ROS via an NADH-dependent redox cycling pathway, successfully eradicates the persister population. Recent work suggests that environmentally induced antibiotic tolerance of bulk populations may result from enhanced antioxidant capabilities. We now show that the small persister subpopulation within a larger antibiotic-susceptible population also shows differential susceptibility to antibiotic-induced hydroxyl radicals. Furthermore, we show that stimulating ROS production can eradicate persisters, thus providing a potential strategy to managing persistent infections.
Outbreak of Type C Botulism in Birds and Mammals in the Emilia Romagna Region, Northern Italy

Abstract Over a 7-day period beginning 8 August 2011, a large number of wild birds of several species were found dead or with neurologic clinical signs along the shore of Crostolo stream, in the Emilia Romagna region, Italy. Twenty-eight Mallards (Anas platyrhynchos), two Hooded Crows (Corvus corone cornix), and three coypus (Myocastor coypus) were found moribund on the Crostolo stream bank, collected, and sent to Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Reggio Emilia Section. The cause of mortality was determined to be Clostridium botulinum type C toxin. The toxin was identified by a mouse bioassay for botulinum toxins and confirmed in bird sera and blowfly larvae (Lucilia caesar) collected from the stomachs of birds.
Experimental Evaluation of an Industrial Application Layer Protocol Over Wireless Systems

Several recent studies have addressed the suitability of current wireless technologies for industrial communications which, frequently, are requested to cope with severe timing constraints. Most of the analysis that have lately appeared in the literature have focused on the performance offered by the lower layers of the communication stack. However, in order to obtain a complete picture, it is important to analyze how this gets coupled with the features of higher layer protocols typically employed by industrial communication applications. In this paper, we investigate the performance obtained by an application layer protocol, derived from those currently employed by wired fieldbuses, running over COTS devices based on two popular wireless communication standards, namely, IEEE 802.15. 4 and IEEE 802.11. In particular, we present a mapping of the application service elements onto the services offered by the mentioned wireless systems and discuss some possible design choices. A prototype of the application layer protocol is then implemented for each considered wireless technology and the performance figures evaluated by means of experimental measurements.
Towards a classification of static electrovacuum spacetimes containing an asymptotically flat spacelike hypersurface with compact interior

We show that static electrovacuum black hole spacetimes containing an asymptotically flat spacelike hypersurface with compact interior and with both degenerate and non-degenerate components of the event horizon do not exist, under the supplementary hypothesis that all degenerate components of the event horizon have charges of the same sign. This extends previous uniqueness theorems of Simon and Masood-ul-Alam (where only non-degenerate horizons were allowed) and Heusler (where only degenerate horizons were allowed).
Stereolithographically fabricated aluminum nitride microchannel substrates for integrated power electronics cooling

The presence of multiple thermally resistive layers in power electronics packages diminishes the enhanced convective benefit of high-performance microchannel cold plates. One improvement reported here is the development of stereolithographically defined aluminum nitride (AlN) microchannel integrated coldplates as substrates for power electronics packages. High-resolution fabrication of green ceramic parts using a standard stereolithography machine has been enabled by the development of photosensitive ceramic materials. Complex microchannel integrated AlN substrates with simplified fluid connections have been produced with 2-3 mm channel height and channel width down to 200 mum. This structure bypasses the majority of the traditional thermal stack, bringing the coolant closer to the heat source. The substrates were packaged and tested with 4 mm Silicon Carbide pin diodes as heat sources at pressure drops from < 1 kPa up to 70 kPa (10 psi) and power levels exceeding 80 W (500 W/cm2). Measured total thermal stack resistivity on best performing devices was about 0.1 K-cm2/W at 70 kPa (-10 psi) and 0.14 K-cm2/W at 5 kPa (-0.7 psi). Paths for further performance improvement, broadening of fabrication possibilities, and transition to real-world systems are briefly discussed.
A predictive model of short cervix at 20–24 weeks using first‐trimester cervical length measurement and maternal history

To develop a model for the prediction of short cervix ( ≤ 15 mm) at 20–24 weeks by combining maternal history and transvaginal ultrasonographic measurement of cervical length at 11–14 weeks. To explore the value of an additional ultrasound examination of the cervix at about 17 weeks.
Contourlet-1.3 texture image retrieval system

Contourlet transform has better performance in directional information representation than wavelet transform and has been studied by many researchers in retrieval systems and has been shown that it is superior to wavelet ones at retrieval rate. In order to improve the retrieval rate further, an anti-aliasing contourlet-1.3 transform based texture image retrieval system was proposed in this paper. In the system, the contourlet transform was constructed by anti-aliasing critical subsampled Laplacian pyramid cascaded by critical subsampled directional filter banks, sub-bands energy and standard deviations in contourlet domain are cascaded to form feature vectors, and the similarity metric is Canberra distance. Experimental results show that contourlet-1.3 transform based image retrieval system is superior to those of the original contourlet transform, nun-subsampled contourlet system and contourlet-2.3 under the same system structure with almost same length of feature vectors, retrieval time and memory needed; and anti-aliasing contourlet decomposition structure parameter can make significant effects on retrieval rates, especially scale number.
Strain measurements on porous concrete samples for triaxial compression and extension tests under very high confinement

This article presents the production of strain measurements on porous concrete samples for use in triaxial compression and extension tests with a very high lateral confining pressure. When a massive concrete structure is subjected to severe loadings (e.g. rock falls, near-field detonations, and ballistic impacts), the material undergoes triaxial loading at a high confining pressure. To reproduce high levels of stress with well-controlled loading paths, static tests are carried out on concrete using a high-capacity triaxial press, called GIGA. This press allows the testing of concrete specimens (7 cm in diameter and 14 or 15.5 cm long) for levels of confining pressure ranging up to 850 MPa and axial stresses of up to 2.35 GPa. The porous characteristic of the material together with the high confining pressure require both developing a material protection device and building strain gauge-based instrumentation of unprecedented design for such confining pressures. In addition, the effect of pressure and other sources of error on strain and stress measurements are identified herein thanks to tests performed on model materials. This study shows that the effect of pressure on strain gauge measurements is negligible, whereas this same effect proves significant in the axial displacement measurement by means of a linear variable differential transformer (LVDT) sensor and must be taken into account therefore during the data processing phase. This article will present the initial results of triaxial compression tests conducted at high confining pressure on both dry and saturated concrete samples instrumented with gauges. It will also provide results of a triaxial extension test conducted at high confinement on dry concrete: a unique step in characterizing the triaxial behaviour of concrete. Moreover, it will be demonstrated that simultaneous axial strain measurements using gauges and the LVDT sensor serve to evaluate strain homogeneity of the sample tested at high confinement.
No room to breathe: the importance of lung hyperinflation in COPD

Patients with chronic obstructive pulmonary disease (COPD) are progressively limited in their ability to undertake normal everyday activities by a combination of exertional dyspnoea and peripheral muscle weakness. COPD is characterised by expiratory flow limitation, resulting in air trapping and lung hyperinflation. Hyperinflation increases acutely under conditions such as exercise or exacerbations, with an accompanying sharp increase in the intensity of dyspnoea to distressing and intolerable levels. Air trapping, causing increased lung hyperinflation, can be present even in milder COPD during everyday activities. The resulting activity-related dyspnoea leads to a vicious spiral of activity avoidance, physical deconditioning, and reduced quality of life, and has implications for the early development of comorbidities such as cardiovascular disease. Various strategies exist to reduce hyperinflation, notably long-acting bronchodilator treatment (via reduction in flow limitation and improved lung emptying) and an exercise programme (via decreased respiratory rate, reducing ventilatory demand), or their combination. Optimal bronchodilation can reduce exertional dyspnoea and increase a patient's ability to exercise, and improves the chance of successful outcome of a pulmonary rehabilitation programme. There should be a lower threshold for initiating treatments appropriate to the stage of the disease, such as long-acting bronchodilators and an exercise programme for patients with mild-to-moderate disease who experience persistent dyspnoea.
Precoding-Based Network Alignment for Three Unicast Sessions

We consider the problem of network coding across three unicast sessions over a directed acyclic graph, where the sender and receiver of each unicast session are both connected to the network via a single edge of unit capacity. We consider a network model in which the middle of the network can only perform random linear network coding, and restrict our approaches to precoding-based linear schemes, where the senders use precoding matrices to encode source symbols. We adapt a precoding-based interference alignment technique, originally developed for the wireless interference channel, to construct a precoding-based linear scheme, which we refer to as precoding-based network alignment scheme (PBNA). A primary difference between this setting and the wireless interference channel is that the network topology can introduce dependencies among the elements of the transfer matrix, which we refer to as coupling relations, and can potentially affect the achievable rate of PBNA. We identify all these coupling relations and interpret them in terms of network topology. We then present polynomial-time algorithms to check the presence of these coupling relations in a particular network. Finally, we show that, depending on the coupling relations present in the network, the optimal symmetric rate achieved by precoding-based linear scheme can take only three possible values, all of which can be achieved by PBNA.
Machine Learning Markets

Prediction markets show considerable promise for developing flexible mechanisms for machine learning. Here, machine learning markets for multivariate systems are defined, and a utility-based framework is established for their analysis. This differs from the usual approach of defining static betting functions. It is shown that such markets can implement model combination methods used in machine learning, such as product of expert and mixture of expert approaches as equilibrium pricing models, by varying agent utility functions. They can also implement models composed of local potentials, and message passing methods. Prediction markets also allow for more flexible combinations, by combining multiple different utility functions. Conversely, the market mechanisms implement inference in the relevant probabilistic models. This means that market mechanism can be utilized for implementing parallelized model building and inference for probabilistic modelling.
Prevalence and Direct Economic Losses from Bovine Tuberculosis in Makurdi, Nigeria

A retrospective study was conducted to investigate the prevalence of bovine tuberculosis and direct economic losses (DEL) from tuberculosis in cattle slaughtered in Makurdi abattoirs from 2008 to 2012, using abattoir records obtained from the Ministry of Agriculture and Natural Resources. Out of 61654 cattle slaughtered during the study period 1172 (1.90%) were positive for tuberculosis lesions. The annual prevalence of bovine tuberculosis ranges from 0.90% in 2008 to 4.04% in 2012. There was significant (P < 0.05) difference in annual prevalence of bovine tuberculosis. It was also observed that there was no seasonal difference in the prevalence of bovine tuberculosis. A total of 1935 affected organs by BTB weighing 3046.50 kg, amounting to 2.91 × 106 Naira (1.82 × 104 USD), were condemned within the study period. Seasonal variation in organ condemnation due to bovine tuberculosis was significantly different (Mann-Whitney U statistics = 774 × 103, P = 0.034). It was concluded that bovine tuberculosis is prevalent in Makurdi and accounts for heavy economic losses due to condemnation of edible organs.
Yeast Mon2p is a highly conserved protein that functions in the cytoplasm-to-vacuole transport pathway and is required for Golgi homeostasis

Although the small Arf-like GTPases Arl1-3 are highly conserved eukaryotic proteins, they remain relatively poorly characterized. The yeast and mammalian Arl1 proteins bind to the Golgi complex, where they recruit specific structural proteins such as Golgins. Yeast Arl1p directly interacts with Mon2p/Ysl2p, a protein that displays some sequence homology to the large Sec7 guanine exchange factors (GEFs) of Arf1. Mon2p also binds the putative aminophospholipid translocase (APT) Neo1p, which performs essential function(s) in membrane trafficking. Our detailed analysis reveals that Mon2p contains six distinct amino acid regions (A to F) that are conserved in several other uncharacterized homologs in higher eukaryotes. As the conserved A, E and F domains are unique to these homologues, they represent the signature of a new protein family. To investigate the role of these domains, we made a series of N- and C-terminal deletions of Mon2p. Although fluorescence and biochemical studies showed that the B and C domains (also present in the large Sec7 GEFs) predominantly mediate interaction with Golgi/endosomal membranes, growth complementation studies revealed that the C-terminal F domain is essential for the activity of Mon2p, indicating that Mon2p might also function independently of Arl1p. We provide evidence that Mon2p is required for efficient recycling from endosomes to the late Golgi. Intriguingly, although transport of CPY to the vacuole was nearly normal in the Δmon2 strain, we found the constitutive delivery of Aminopeptidase 1 from the cytosol to the vacuole to be almost completely blocked. Finally, we show that Mon2p exhibits genetic and physical interactions with Dop1p, a protein with a putative function in cell polarity. We propose that Mon2p is a scaffold protein with novel conserved domains, and is involved in multiple aspects of endomembrane trafficking.
Multi-product inventory planning with downward substitution, stochastic demand and setup costs

In this paper we consider a single period multi-product inventory problem with stochastic demand, setup cost for production, and one-way product substitution in the downward direction. We model the problem as a two-stage integer stochastic program with recourse where the first stage variables determine which products to produce and how much to produce, and the second stage variables determine how the products are allocated to satisfy the realized demand. We exploit structural properties of the model and utilize a combination of optimization techniques including network flow, dynamic programming, and simulation-based optimization to develop effective heuristics. Through a computational study, we evaluate the performance of our heuristics by comparison with the corresponding optimal solution obtained from a large scale mixed integer linear program. The computational study indicates that our solution methodology can be very effective (98.8% on average) and can handle industrial-sized problems efficiently. We also provide several new qualitative insights on issues such as the effect of demand variance and cost parameters on the optimal number of products setup, the amount produced or inventoried, and the benefits of allowing substitution.
Real-time Ultrasound-guided Central Venous Access via the Subclavian Approach

CASE HISTORY A 58-year-old man presented with an infected left hand which had been bitten by a rat six weeks earlier. He had a swollen, red, tender left hand and enlarged ipsilateral axillary lymph nodes, but remained afebrile. Laboratory investigations (ESR, white cell count) were unremarkable. Significantly, his past medical history included aortic valve replacement in 1990, subsequently complicated by a homonymous hemianopia and atrial fibrillation. As a result, he was anti-coagulated with warfarin. A transoesophageal echocardiogram was performed. This suggested bacterial endocarditis. After cardiology review, it was recommended that he be commenced on intravenous gentamicin and vancomycin for a period of six weeks. (He had a documented allergy to penicillin.) His anticoagulation was to be maintained during this time by a heparin infusion without interruption. His proposed management with longterm intravenous antibiotics was complicated by known anatomical anomalies of his thoracic vasculature resulting from major blunt thoracic trauma and corrective surgery in 1975. He was subsequently referred to the Anaesthetic Department for placement of suitable long term venous access.
Proteasome Function Is Regulated by Cyclic AMP-dependent Protein Kinase through Phosphorylation of Rpt6*

Dysregulation of the proteasome has been documented in a variety of human diseases such as Alzheimer, muscle atrophy, cataracts etc. Proteolytic activity of 26 S proteasome is ATP- and ubiquitin-dependent. O-GlcNAcylation of Rpt2, one of the AAA ATPases in the 19 S regulatory cap, shuts off the proteasome through the inhibition of ATPase activity. Thus, through control of the flux of glucose into O-GlcNAc, the function of the proteasome is coupled to glucose metabolism. In the present study we found another metabolic control of the proteasome via cAMP-dependent protein kinase (PKA). Contrary to O-Glc-NAcylation, PKA activated proteasomes both in vitro and in vivo in association with the phosphorylation at Ser120 of another AAA ATPase subunit, Rpt6. Mutation of Ser120 to Ala blocked proteasome function. The stimulatory effect of PKA and the phosphorylation of Rpt6 were reversible by protein phosphatase 1γ. Thus, hormones using the PKA system can also regulate proteasomes often in concert with glucose metabolism. This finding might lead to novel strategies for the treatment of proteasome-related diseases.