Potential impact of a microarray-based nucleic acid assay for rapid detection of gram-negative bacteria and resistance markers in positive blood cultures

We evaluated the Verigene Gram-negative blood culture (BC-GN) test, a microarray that detects Gram-negative bacteria and several resistance genes. A total of 102 positive blood cultures were tested, and the BC-GN test correctly identified 97.9% of the isolates within its panel. Resistance genes (CTX-M, KPC, VIM, and OXA genes) were detected in 29.8% of the isolates, with positive predictive values of 95.8% (95% confidence interval [CI], 87.7% to 98.9%) in Enterobacteriaceae and 100% (95% CI, 75.9% to 100%) in Pseudomonas aeruginosa and negative predictive values of 100% (95% CI, 93.9% to 100%) and 78.6% (95% CI, 51.0% to 93.6%), respectively

Dual-domain reporter approach for multiplex identification of major SARS-CoV-2 variants of concern in a microarray-based assay

: Since the emergence of the COVID-19 pandemic in December 2019, the SARS-CoV-2 virus continues to evolve into many variants emerging around the world. To enable regular surveillance and timely adjustments in public health interventions, it is of the utmost importance to accurately monitor and track the distribution of variants as rapidly as possible. Genome sequencing is the gold standard for monitoring the evolution of the virus, but it is not cost-effective, rapid and easily accessible. We have developed a microarray-based assay that can distinguish known viral variants present in clinical samples by simultaneously detecting mutations in the Spike protein gene. In this method, the viral nucleic acid, extracted from nasopharyngeal swabs, after RT-PCR, hybridizes in solution with specific dual-domain oligonucleotide reporters. The domains complementary to the Spike protein gene sequence encompassing the mutation form hybrids in solution that are directed by the second domain ("barcode" domain) at specific locations on coated silicon chips. The method utilizes characteristic fluorescence signatures to unequivocally differentiate, in a single assay, different known SARS-CoV-2 variants. In the nasopharyngeal swabs of patients, this multiplex system was able to genotype the variants which have caused waves of infections worldwide, reported by the WHO as being of concern (VOCs), namely Alpha, Beta, Gamma, Delta and Omicron variants

Random walks on randomly evolving graphs

A random walk is a basic stochastic process on graphs and a key primitive in the design of distributed algorithms. One of the most important features of random walks is that, under mild conditions, they converge to a stationary distribution in time that is at most polynomial in the size of the graph. This fundamental property, however, only holds if the graph does not change over time; on the other hand, many distributed networks are inherently dynamic, and their topology is subjected to potentially drastic changes. In this work we study the mixing (i.e., convergence) properties of random walks on graphs subjected to random changes over time. Specifically, we consider the edge-Markovian random graph model: for each edge slot, there is a two-state Markov chain with transition probabilities p (add a non-existing edge) and q (remove an existing edge). We derive several positive and negative results that depend on both the density of the graph and the speed by which the graph changes

Zero-variance principle for Monte Carlo algorithms

We present a general approach to greatly increase at little cost the efficiency of Monte Carlo algorithms. To each observable to be computed we associate a renormalized observable (improved estimator) having the same average but a different variance. By writing down the zero-variance condition a fundamental equation determining the optimal choice for the renormalized observable is derived (zero-variance principle for each observable separately). We show, with several examples including classical and quantum Monte Carlo calculations, that the method can be very powerful.Comment: 9 pages, Latex, to appear in Phys. Rev. Let

Hamiltonian dynamics of homopolymer chain models

The Hamiltonian dynamics of chains of nonlinearly coupled particles is numerically investigated in two and three dimensions. Simple, off-lattice homopolymer models are used to represent the interparticle potentials. Time averages of observables numerically computed along dynamical trajectories are found to reproduce results given by the statistical mechanics of homopolymer models. The dynamical treatment, however, indicates a nontrivial transition between regimes of slow and fast phase space mixing. Such a transition is inaccessible to a statistical mechanical treatment and reflects a bimodality in the relaxation of time averages to corresponding ensemble averages. It is also found that a change in the energy dependence of the largest Lyapunov exponent indicates the theta-transition between filamentary and globular polymer configurations, clearly detecting the transition even for a finite number of particles.Comment: 11 pages, 8 figures, accepted for publication in Physical Review

Folding, Design and Determination of Interaction Potentials Using Off-Lattice Dynamics of Model Heteropolymers

We present the results of a self-consistent, unified molecular dynamics study of simple model heteropolymers in the continuum with emphasis on folding, sequence design and the determination of the interaction parameters of the effective potential between the amino acids from the knowledge of the native states of the designed sequences.Comment: 8 pages, 3 Postscript figures, uses RevTeX. Submitted to Physical Review Letter

Information Gathering in Ad-Hoc Radio Networks with Tree Topology

We study the problem of information gathering in ad-hoc radio networks without collision detection, focussing on the case when the network forms a tree, with edges directed towards the root. Initially, each node has a piece of information that we refer to as a rumor. Our goal is to design protocols that deliver all rumors to the root of the tree as quickly as possible. The protocol must complete this task within its allotted time even though the actual tree topology is unknown when the computation starts. In the deterministic case, assuming that the nodes are labeled with small integers, we give an O(n)-time protocol that uses unbounded messages, and an O(n log n)-time protocol using bounded messages, where any message can include only one rumor. We also consider fire-and-forward protocols, in which a node can only transmit its own rumor or the rumor received in the previous step. We give a deterministic fire-and- forward protocol with running time O(n^1.5), and we show that it is asymptotically optimal. We then study randomized algorithms where the nodes are not labelled. In this model, we give an O(n log n)-time protocol and we prove that this bound is asymptotically optimal

Hamiltonian dynamics of the two-dimensional lattice phi^4 model

The Hamiltonian dynamics of the classical $\phi^4$ model on a two-dimensional square lattice is investigated by means of numerical simulations. The macroscopic observables are computed as time averages. The results clearly reveal the presence of the continuous phase transition at a finite energy density and are consistent both qualitatively and quantitatively with the predictions of equilibrium statistical mechanics. The Hamiltonian microscopic dynamics also exhibits critical slowing down close to the transition. Moreover, the relationship between chaos and the phase transition is considered, and interpreted in the light of a geometrization of dynamics.Comment: REVTeX, 24 pages with 20 PostScript figure

A Human Monoclonal Antibody with Neutralizing Activity against Highly Divergent Influenza Subtypes

The interest in broad-range anti-influenza A monoclonal antibodies (mAbs) has recently been strengthened by theidentification of anti-hemagglutinin (HA) mAbs endowed with heterosubtypic neutralizing activity to be used in the designof ‘‘universal’’ prophylactic or therapeutic tools. However, the majority of the single mAbs described to date do not bindand neutralize viral isolates belonging to highly divergent subtypes clustering into the two different HA-based influenzaphylogenetic groups: the group 1 including, among others, subtypes H1, H2, H5 and H9 and the group 2 including, amongothers, H3 subtype. Here, we describe a human mAb, named PN-SIA28, capable of binding and neutralizing all testedisolates belonging to phylogenetic group 1, including H1N1, H2N2, H5N1 and H9N2 subtypes and several isolates belongingto group 2, including H3N2 isolates from the first period of the 1968 pandemic. Therefore, PN-SIA28 is capable ofneutralizing isolates belonging to subtypes responsible of all the reported pandemics, as well as other subtypes withpandemic potential. The region recognized by PN-SIA28 has been identified on the stem region of HA and includes residueshighly conserved among the different influenza subtypes. A deep characterization of PN-SIA28 features may represent auseful help in the improvement of available anti-influenza therapeutic strategies and can provide new tools for thedevelopment of universal vaccinal strategies

The SHOX gene and the short stature. Roundtable on diagnosis and treatment of short stature due to SHOX haploinsufficiency: How genetics, radiology and anthropometry can help the pediatrician in the diagnostic process padova (April 20th, 2011)

The growth of the human body depends from a complex interaction between nutritional, environmental and hormonal factors and by a large number of different genes. One of these genes, short stature homeobox (SHOX), is believed to play a major role in growth. SHOX haploinsufficiency is associated with a wide spectrum of conditions, all characterized growth failure such as Leri-Weill dyschondrosteosis , Turner syndrome, short stature with subtle auxological and radiological findings and the so called “idiopathic short stature” (short stature with no specific findings other than growth failure). The document was prepared by a multidisciplinary team (paediatric endocrinologists, paediatrician, radiologist, geneticist and epidemiologist) to focus on the investigation of children with suspected SHOX- deficiency (SHOX-D) for an early identification and a correct diagnostic work - up of this genetic disorder. On the basis of a number of screening studies, SHOX-D appears to be a relatively frequent cause of short stature. The following recommendations were suggested by our multidisciplinary team: (i) a careful family history, measurements of body proportions and detection of any dysmorphic features are important for the suspect of a genetic disorder ,(ii)the presence of any combination of the following physical findings, such as reduced arm span/ height ratio, increased sitting height/height ratio, above average BMI, Madelung deformity, cubitus valgus, short or bowed forearm, dislocation of the ulna at the elbow, or the appearance of muscular hypertrophy, should prompt the clinician to obtain a molecular analysis of the SHOX region, (iii) it is of practical importance to recognise early or mild signs of Madelung deformity on hand and wrist radiographs, (iv) growth hormone ,after stimulation test, is usually normal . However, treatment with rhGH may improve final adult height; the efficacy of treatment is similar to that observed in those treated for Turner syndrome