An Optimal Algorithm for the Maximum-Density Segment Problem

We address a fundamental problem arising from analysis of biomolecular sequences. The input consists of two numbers $w_{\min}$ and $w_{\max}$ and a sequence $S$ of $n$ number pairs $(a_i,w_i)$ with $w_i>0$. Let {\em segment} $S(i,j)$ of $S$ be the consecutive subsequence of $S$ between indices $i$ and $j$. The {\em density} of $S(i,j)$ is $d(i,j)=(a_i+a_{i+1}+...+a_j)/(w_i+w_{i+1}+...+w_j)$. The {\em maximum-density segment problem} is to find a maximum-density segment over all segments $S(i,j)$ with $w_{\min}\leq w_i+w_{i+1}+...+w_j \leq w_{\max}$. The best previously known algorithm for the problem, due to Goldwasser, Kao, and Lu, runs in $O(n\log(w_{\max}-w_{\min}+1))$ time. In the present paper, we solve the problem in O(n) time. Our approach bypasses the complicated {\em right-skew decomposition}, introduced by Lin, Jiang, and Chao. As a result, our algorithm has the capability to process the input sequence in an online manner, which is an important feature for dealing with genome-scale sequences. Moreover, for a type of input sequences $S$ representable in $O(m)$ space, we show how to exploit the sparsity of $S$ and solve the maximum-density segment problem for $S$ in $O(m)$ time.Comment: 15 pages, 12 figures, an early version of this paper was presented at 11th Annual European Symposium on Algorithms (ESA 2003), Budapest, Hungary, September 15-20, 200

Full counting statistics and phase diagram of a dissipative Rydberg gas

Ultra-cold gases excited to strongly interacting Rydberg states are a promising system for quantum simulations of many-body systems. For off-resonant excitation of such systems in the dissipative regime, highly correlated many-body states exhibiting, among other characteristics, intermittency and multi-modal counting distributions are expected to be created. So far, experiments with Rydberg atoms have been carried out in the resonant, non-dissipative regime. Here we realize a dissipative gas of rubidium Rydberg atoms and measure its full counting statistics for both resonant and off-resonant excitation. We find strongly bimodal counting distributions in the off-resonant regime that are compatible with intermittency due to the coexistence of dynamical phases. Moreover, we measure the phase diagram of the system and find good agreement with recent theoretical predictions. Our results pave the way towards detailed studies of many-body effects in Rydberg gases.Comment: 12 pages, 5 figure

Effect of precursor solution dark incubation on gold nanorods morphology

Abstract Gold nanorods were synthesized in an aqueous solution of hexadecyltrimethylammonium bromide via a combination of chemical reduction and UV photoirradiation. Gold ligand complexes, present in the stock solution, are initially reduced, by ascorbic acid as mild reducing agent. The gold ions nucleation and colloid growth proceeds then by subsequent UV irradiation of the so-obtained precursor solution. We present a systematic study of the effect of incubation of the precursor solution on the dispersion state and aspect ratio of the produced nanorods. Incubation of the precursor solution allows the synthesis of higher aspect ratio nanorods with narrower size distribution compared to those obtained without incubation. We propose a mechanism for the gold nanorods formation including two stages, a nucleation and a diffusive growth. This allows us to explain the synthesis improvement as a consequence of the increase in the size of the gold ligand complexes aggregates, leading to a decrease of the nanorods growth rate

Targeted rapid amplification of cDNA ends (T-RACE)—an improved RACE reaction through degradation of non-target sequences

Amplification of the 5′ ends of cDNA, although simple in theory, can often be difficult to achieve. We describe a novel method for the specific amplification of cDNA ends. An oligo-dT adapter incorporating a dUTP-containing PCR primer primes first-strand cDNA synthesis incorporating dUTP. Using the Cap finder approach, another distinct dUTP containing adapter is added to the 3′ end of the newly synthesized cDNA. Second-strand synthesis incorporating dUTP is achieved by PCR, using dUTP-containing primers complimentary to the adapter sequences incorporated in the cDNA ends. The double-stranded cDNA-containing dUTP serves as a universal template for the specific amplification of the 3′ or 5′ end of any gene. To amplify the ends of cDNA, asymmetric PCR is performed using a single gene-specific primer and standard dNTPs. The asymmetric PCR product is purified and non-target transcripts containing dUTP degraded by Uracil DNA glycosylase, leaving only those transcripts produced during the asymmetric PCR. Subsequent PCR using a nested gene-specific primer and the 3′ or 5′ T-RACE primer results in specific amplification of cDNA ends. This method can be used to specifically amplify the 3′ and 5′ ends of numerous cDNAs from a single cDNA synthesis reaction

Electroactive biofilms: new means for electrochemistry

This work demonstrates that electrochemical reactions can be catalysed by the natural biofilms that form on electrode surfaces dipping into drinking water or compost. In drinking water, oxygen reduction was monitored with stainless steel ultra-microelectrodes under constant potential electrolysis at )0.30 V/SCE for 13 days. 16 independent experiments were conducted in drinking water, either pure or with the addition of acetate or dextrose. In most cases, the current increased and reached 1.5–9.5 times the initial current. The current increase was attributed to biofilm forming on the electrode in a similar way to that has been observed in seawater. Epifluorescence microscopy showed that the bacteria size and the biofilm morphology depended on the nutrients added, but no quantitative correlation between biofilm morphology and current was established. In compost, the oxidation process was investigated using a titanium based electrode under constant polarisation in the range 0.10–0.70 V/SCE. It was demonstrated that the indigenous micro-organisms were responsible for the current increase observed after a few days, up to 60 mA m)2. Adding 10 mM acetate to the compost amplified the current density to 145 mA m)2 at 0.50 V/SCE. The study suggests that many natural environments, other than marine sediments, waste waters and seawaters that have been predominantly investigated until now, may be able to produce electrochemically active biofilm

Multi-photon, multi-mode polarization entanglement in parametric down-conversion

We study the quantum properties of the polarization of the light produced in type II spontaneous parametric down-conversion in the framework of a multi-mode model valid in any gain regime. We show that the the microscopic polarization entanglement of photon pairs survives in the high gain regime (multi-photon regime), in the form of nonclassical correlation of all the Stokes operators describing polarization degrees of freedom

From Uterus to Brain: An Update on Epidemiology, Clinical Features, and Treatment of Brain Metastases From Gestational Trophoblastic Neoplasia

In this review, we provide the state of the art about brain metastases (BMs) from gestational trophoblastic neoplasia (GTN), a rare condition. Data concerning the epidemiology, clinical presentation, innovations in therapeutic modalities, and outcomes of GTN BMs are comprehensively presented with particular attention to the role of radiotherapy, neurosurgery, and the most recent chemotherapy regimens. Good response rates have been achieved thanks to multi-agent chemotherapy, but brain involvement by GTNs entails significant risks for patients’ health since sudden and extensive intracranial hemorrhages are possible. Moreover, despite the evolution of treatment protocols, a small proportion of these patients ultimately develops a resistant disease. To tackle this unmet clinical need, immunotherapy has been recently proposed. The role of this novel option for this subset of patients as well as the achieved results so far are also discussed

Strongly correlated excitation of a quasi-1D Rydberg gas

Rydberg excitation dynamics of a 87-Rb cold atom cloud is investigated in an effective one-dimensional geometry. We measure the excitation dynamics and the full counting statistics for resonant and off-resonant excitation to the 70S state. While for a resonant laser excitation the counting distributions have a strong sub-Poissonian character, we find strongly bimodal counting distributions in the off-resonant regime. The n-th central moments, up to n = 4, of the counting distributions are derived from the measured counting distributions

Multi-boson effects and the normalization of the two-pion correlation function

The two-pion correlation function can be defined as a ratio of either the measured momentum distributions or the normalized momentum space probabilities. We show that the first alternative avoids certain ambiguities since then the normalization of the two-pion correlator contains important information on the multiplicity distribution of the event ensemble which is lost in the second alternative. We illustrate this explicitly for specific classes of event ensembles.Comment: 6 pages, three figures,submit to PR

Serum KL-6 could represent a reliable indicator of unfavourable outcome in patients with COVID-19 pneumonia

KL-6 is a sialoglycoprotein antigen which proved elevated in the serum of patients with different interstitial lung diseases, especially in those with a poorer outcome. Given that interstitial pneumonia is the most common presentation of SARS-CoV2 infection, we evaluated the prognostic role of KL-6 in patients with COVID-19 pneumonia. Patients with COVID-19 pneumonia were prospectively enrolled. Blood samples were collected at the time of enrolment (TOE) and on day 7 (T1). Serum KL-6 concentrations were measured by chemiluminescence enzyme immunoassay using a KL-6 antibody kit (LUMIPULSE G1200, Fujirebio) and the cut-off value was set at > 1000 U/mL. Fifteen out of 34 enrolled patients (44.1%) died. Patients with unfavourable outcome showed significantly lower P/F ratio and higher IL-6 values and plasmatic concentrations of KL-6 at TOE compared with those who survived (median KL-6: 1188 U/mL vs. 260 U/mL, p 1000 U/mL resulted independently associated with death (aOR: 11.29, p 1000 U/mL resulted independently associated with death and showed good accuracy in predicting a poorer outcome. KL-6 may thus represent a quick, inexpensive, and sensitive parameter to stratify the risk of severe respiratory failure and death