Simultaneous control of DNA and RNA processing efficiency using a nucleic acid calibration set.

PCR-based detection techniques enables reliable and sensitive nucleic acid target detection. However, quantitative determination methods often fail to control for the efficiency of nucleic acid extraction, reverse transcription, and PCR amplification. This problem is even more prominent when working with clinical samples due to target sequence loss during nucleic acid processing or the co-purification of PCR inhibitors (1,2). Handling processes are often assumed to approach 100% efficiency in the laboratory, even if practical experience shows that this efficiency can be much lower. This inability to ensure accuracy can lead to significant error in uncalibrated DNA sample quantitation. The additional need for reverse transcription of RNA may further increase the quantitative error rate, as yet another enzymatic process is involved. Nucleic acid controls have been developed based upon known sequences to calibrate either DNA or RNA handling; DNA calibrators have been used to control for the amplification of target sequences using realtime PCR methods (3–8), while RNA calibrators have been developed to test reverse transcription and amplification efficiencies (9–11). A nonpathogenic viral particle carrying a sequence for use as an external positive control of extraction and amplification has also been described (12). Unfortunately, most of the established processing controls are only suitable for limited applications (i.e., either DNA or RNA detection). Cross-contamination of biological samples or minute detection from natural sources reveals the need for completely synthetic sequences, with no homology to sequences in the nucleic acid databases. It is, therefore, beneficial to design an internal, synthetic calibration system that can control for both DNA and RNA processing steps in a single tube. This set includes both RNA and DNA targets with identical primer binding sites and, thus, primer binding efficiency, but easily distinguishable sequence characteristics, allowing for simultaneous detection, quantitation, and calibration of nucleic acid processing efficiency. A 150-bp randomly generated nucleic acid sequence was developed for use as a short control (SC). A GCrich 75-bp sequence was inserted in the middle of the 150-bp sequence to generate a 225-bp sequence, long control (LC). Besides size, the two sequences were designed to have easily distinguishable probe binding sites with a predicted product melting temperature difference of 4°C. Calibrator sequences have been published as GenBank® accession nos. EF143258 (DNA control, LC) and EF143257 (RNA control, SC). Simultaneous control of DNA and RNA processing efficiency using a nucleic acid calibration se

The Rapid Identification of Anoplophora chinensis (Coleoptera: Cerambycidae) From Adult, Larval, and Frass Samples Using TaqMan Probe Assay

A molecular diagnostic method using TaqMan probe qPCR is presented for the identification of Anoplophora chinensis (Förster) (Coleoptera: Cerambycidae) from whole body insects (adults and larvae) and frass samples stored under different conditions. The results showed a perfect amplification of DNA from all samples; the repeatability and reproducibility of the protocol were very good, with standard deviations of inter-run and intrarun variability less than or equal to 0.5. The assay allowed to discern all A. chinensis samples from those of the other non-target wood-borer species, with 100% correspondence to the homologous sequences. No amplification or cross reactions were observed with A. glabripennis (Motschulsky) (Coleoptera: Cerambycidae), which is the most related species among those tested. The protocol was validated by an internal blind panel test which showed a good correspondence between the results obtained by different operators in the same lab. The analytical sensitivity for the lab frass with the Probe qPCR, namely the lowest amount of A. chinensis DNA that can be detected (LoD), was 0.64 pg/μl with a Cq of 34.87. The use of indirect evidence for the identification of a pest is an important feature of the method, which could be crucial to detect the presence of wood-boring insects. This diagnostic tool can help prevent the introduction of A. chinensis into new environments or delimit existing outbreak areas thanks to indirect frass diagnosis

Economic and socio-political determinants of de facto monetary institutions and inflationary outcomes

In this paper we estimate a model where inflation, a measure of de facto central bank independence and an index of de facto exchange rate regime are simultaneously determined by a set of economic, political and institutional variables. De facto central bank independence is hampered by socio-political turbulence and benefits from the balance of powers between the executive and the parliament. Inflation is explained by de facto central bank independence, by the level and volatility of public expenditure and by the de facto exchange rate regime. Openness (real and financial) affects inflation through the exchange rate regime channel. Success in controlling inflation, in turn is crucial to sustain central bank independence and exchange rate stability

Unveiling the Interplay between the GASP Jellyfish Galaxy JO194 and Its Environment with Chandra

X-ray studies of jellyfish galaxies opened a window into the physics of the interplay between the intracluster medium (ICM) and interstellar medium (ISM). In this paper, we present the study of an archival Chandra observation of the GASP jellyfish galaxy JO194. We observe X-ray emission extending from the stellar disk to the unwinding spiral arms with an average temperature of kT = 0.79 ± 0.03 keV. To investigate the origin of the X-ray emission, we compare the observed X-ray luminosities with those expected from the star formation rates (SFRs) obtained from Hα emission. We estimate an X-ray luminosity excess of a factor ∼2–4 with respect to the SF; therefore, we conclude that SF is not the main event responsible for the extended X-ray emission of JO194. The metallicity in the spiral arms (Z = 0.24+0.19 Z ) is consistent with that of the ICM around JO194 -0.12 (Z = 0.35 ± 0.07); thus, we suggest that ICM radiative cooling dominates the X-ray emission of the arms. We speculate that the X-ray plasma results from the ISM–ICM interplay, although the nature of this interplay is still mostly unknown. Finally, we observe that the X-ray properties of JO194 are consistent with those of two other GASP galaxies with different stellar mass, phase-space conditions in their hosting clusters, and local ICM conditions. We suggest that the conditions required to induce extended X-ray emission in jellyfish galaxies are established at the beginning of the stripping, and they can persist on long timescales so that galaxies in different clusters and evolutionary stages can present a similar extended X-ray emission

Effects of prophylactic drug therapies and anti-calcitonin peptide-related monoclonal antibodies on subjective sleep quality: An Italian multicenter study

Objective/background: sleep alterations strongly influence migraine severity. Prophylactic therapies have a major impact on migraine frequency and associated symptoms. The study purpose was to compare the impact of oral drug therapies or gene-related anti-calcitonin monoclonal antibodies (anti-CGRP mAbs) on sleep alterations. We also evaluated which drug therapies are more effective on sleep quality and the different impact on migraine frequency and life quality. Patients/methods: this is a multicenter, prospective study conducted in three specialized headache centers (Marche Polytechnic University, Ancona; University of Palermo, Palermo; Fondazione Policlinico Campus Bio-Medico, Rome). At baseline, we assigned migraine patients to preventive therapy with first-line drugs or anti-CGRP mAbs. The Pittsburgh Sleep Quality Index (PSQI) and Migraine Disability Assessment (MIDAS) scales were administered. After three months, we re-evaluated the patients with the same scales. Results: 214 patients were enrolled. Any prophylaxis was significantly associated with a reduction in PSQI score (mean difference 1.841; 95%CI:1.413-2.269; p < 0.0001), most significantly in the anti-CGRP mAb group (mean difference 1.49; 95%CI:2.617-0.366; p = 0.010). Anti-CGRP mAbs resulted in significant improvement in migraine severity and MIDAS scores. Among oral therapies, calcium antagonists and antidepressants were the most effective in reducing PSQI score between T0 and T1 (p = 0.042; p = 0.049; p < 0.0001, respectively). Conclusions: anti-CGRP mAbs revitalized the management of migraine with stable and well-documented efficacy. Our data also suggest that anti-CGRP mAbs result in a positive effect on sleep quality, with a significant improvement in PSQI scores. Knowing the relevant impact of sleep disruption on migraine severity, these data could help for the management of migraine patients

Chikungunya Outbreak in the Republic of the Congo, 2019—Epidemiological, Virological and Entomological Findings of a South-North Multidisciplinary Taskforce Investigation

The Republic of Congo (RoC) declared a chikungunya (CHIK) outbreak on 9 February 2019. We conducted a ONE-Human-Animal HEALTH epidemiological, virological and entomological investigation. Methods: We collected national surveillance and epidemiological data. CHIK diagnosis was based on RT-PCR and CHIKV-specific antibodies. Full CHIKV genome sequences were obtained by Sanger and MinION approaches and Bayesian tree phylogenetic analysis was performed. Mosquito larvae and 215 adult mosquitoes were collected in different villages of Kouilou and Pointe-Noire districts and estimates of Aedes (Ae.) mosquitos’ CHIKV-infectious bites obtained. We found two new CHIKV sequences of the East/Central/South African (ECSA) lineage, clustering with the recent enzootic sub-clade 2, showing the A226V mutation. The RoC 2019 CHIKV strain has two novel mutations, E2-T126M and E2-H351N. Phylogenetic suggests a common origin from 2016 Angola strain, from which it diverged around 1989 (95% HPD 1985–1994). The infectious bite pattern was similar for 2017, 2018 and early 2019. One Ae. albopictus pool was RT-PCR positive. The 2019 RoC CHIKV strain seems to be recently introduced or be endemic in sylvatic cycle. Distinct from the contemporary Indian CHIKV isolates and in contrast to the original Central-African strains (transmitted by Ae. aegypti), it carries the A226V mutation, indicating an independent adaptive mutation in response to vector replacement (Ae. albopictus vs Ae. aegypti)

Colorectal Cancer Stage at Diagnosis Before vs During the COVID-19 Pandemic in Italy

IMPORTANCE Delays in screening programs and the reluctance of patients to seek medical attention because of the outbreak of SARS-CoV-2 could be associated with the risk of more advanced colorectal cancers at diagnosis. OBJECTIVE To evaluate whether the SARS-CoV-2 pandemic was associated with more advanced oncologic stage and change in clinical presentation for patients with colorectal cancer. DESIGN, SETTING, AND PARTICIPANTS This retrospective, multicenter cohort study included all 17 938 adult patients who underwent surgery for colorectal cancer from March 1, 2020, to December 31, 2021 (pandemic period), and from January 1, 2018, to February 29, 2020 (prepandemic period), in 81 participating centers in Italy, including tertiary centers and community hospitals. Follow-up was 30 days from surgery. EXPOSURES Any type of surgical procedure for colorectal cancer, including explorative surgery, palliative procedures, and atypical or segmental resections. MAIN OUTCOMES AND MEASURES The primary outcome was advanced stage of colorectal cancer at diagnosis. Secondary outcomes were distant metastasis, T4 stage, aggressive biology (defined as cancer with at least 1 of the following characteristics: signet ring cells, mucinous tumor, budding, lymphovascular invasion, perineural invasion, and lymphangitis), stenotic lesion, emergency surgery, and palliative surgery. The independent association between the pandemic period and the outcomes was assessed using multivariate random-effects logistic regression, with hospital as the cluster variable. RESULTS A total of 17 938 patients (10 007 men [55.8%]; mean [SD] age, 70.6 [12.2] years) underwent surgery for colorectal cancer: 7796 (43.5%) during the pandemic period and 10 142 (56.5%) during the prepandemic period. Logistic regression indicated that the pandemic period was significantly associated with an increased rate of advanced-stage colorectal cancer (odds ratio [OR], 1.07; 95%CI, 1.01-1.13; P = .03), aggressive biology (OR, 1.32; 95%CI, 1.15-1.53; P < .001), and stenotic lesions (OR, 1.15; 95%CI, 1.01-1.31; P = .03). CONCLUSIONS AND RELEVANCE This cohort study suggests a significant association between the SARS-CoV-2 pandemic and the risk of a more advanced oncologic stage at diagnosis among patients undergoing surgery for colorectal cancer and might indicate a potential reduction of survival for these patients

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2

The Sardinia Radio Telescope . From a technological project to a radio observatory

Context. The Sardinia Radio Telescope (SRT) is the new 64 m dish operated by the Italian National Institute for Astrophysics (INAF). Its active surface, comprised of 1008 separate aluminium panels supported by electromechanical actuators, will allow us to observe at frequencies of up to 116 GHz. At the moment, three receivers, one per focal position, have been installed and tested: a 7-beam K-band receiver, a mono-feed C-band receiver, and a coaxial dual-feed L/P band receiver. The SRT was officially opened in September 2013, upon completion of its technical commissioning phase. In this paper, we provide an overview of the main science drivers for the SRT, describe the main outcomes from the scientific commissioning of the telescope, and discuss a set of observations demonstrating the scientific capabilities of the SRT. Aims: The scientific commissioning phase, carried out in the 2012-2015 period, proceeded in stages following the implementation and/or fine-tuning of advanced subsystems such as the active surface, the derotator, new releases of the acquisition software, etc. One of the main objectives of scientific commissioning was the identification of deficiencies in the instrumentation and/or in the telescope subsystems for further optimization. As a result, the overall telescope performance has been significantly improved. Methods: As part of the scientific commissioning activities, different observing modes were tested and validated, and the first astronomical observations were carried out to demonstrate the science capabilities of the SRT. In addition, we developed astronomer-oriented software tools to support future observers on site. In the following, we refer to the overall scientific commissioning and software development activities as astronomical validation. Results: The astronomical validation activities were prioritized based on technical readiness and scientific impact. The highest priority was to make the SRT available for joint observations as part of European networks. As a result, the SRT started to participate (in shared-risk mode) in European VLBI Network (EVN) and Large European Array for Pulsars (LEAP) observing sessions in early 2014. The validation of single-dish operations for the suite of SRT first light receivers and backends continued in the following year, and was concluded with the first call for shared-risk early-science observations issued at the end of 2015. As discussed in the paper, the SRT capabilities were tested (and optimized when possible) for several different observing modes: imaging, spectroscopy, pulsar timing, and transients